6021 Fall 2004

MASSACHUSETTS INSTITUTE OF TECHNOLOGY
Department of Electrical Engineering and Computer Science,
Department of Mechanical Engineering,
Division of Bioengineering and Environmental Health,
Harvard-MIT Division of Health Sciences and Technology
Quantitative Physiology: Cells and Tissues
2.791J/2.794J/6.021J/6.521J/BE.370J/BE.470J/HST.541J
Homework Assignment #1
Issued: September 8, 2004

Due: September 16, 2004
Reading
Lecture 2 Volume 1: 3.1-3.1.3 3.2-3.2.2
Lecture 3 Volume 1: 3.1.4-3.1.5 3.5-3.5.2.1
Lecture 4 Volume 1: 3.6-3.6.1.2 3.7-3.7.2
Announcements
Homework will consist of Exercises and Problems. Exercises are generally more conceptual and
require less number crunching. Exercises often require writing sentences to explain what you have
learned. Written solutions should be submitted for both Exercises and Problems.
Exercise 1. According to the random walk model, solute molecules move and thereby diffuse be
cause of collisions with water molecules. Solute collisions with other solute molecules are gener
ally ignored under the assumption that the water molecules vastly outnumber the solute molecules.
To get a feeling for the validity of this assumption, and to appreciate the number of particles and
spatial scales involved, consider the diffusion of potassium ions in the cytoplasm of a red blood
cell. Assume that the volume of the cell is 90 fL, and that the concentration of potassium ions in
the cytoplasm is 150 mmol/L.
Part a. Estimate the number of potassium ions in the cytoplasm of the cell.
Part b. Estimate the average distance between potassium ions in the cell.
Part c. Estimate the number of water molecules in the cytoplasm of the cell.
Part d. Estimate the average distance between water molecules in cytoplasm.
Part e. Determine the ratio of water molecules to potassium ions in cytoplasm.
Exercise 2. At a junction between two neurons, called a synapse, there is a 20 nm cleft that
separates the cell membranes. A chemical transmitter substance is released by one cell (the pre
synaptic cell), diffuses across the cleft, and arrives at the membrane of the other (post-synaptic)
cell. Assume that the diffusion coefcient of the chemical transmitter substance is D = 5
106 cm2 /s. Make a rough estimate of the delay caused by diffusion of the transmitter substance
across the cleft. What are the limitations of this estimate? Explain.
cn (x, t)
Exercise 3. The time course of one-dimensional diffusion of a solute from a point source in space
and time has the form
no
2
ex /4Dt ,
cn (x, t) =
4Dt
where no is the number of moles of solute per unit area placed at x = 0 at t = 0. c n (x, t) is
computed as a function of time for locations xa and xb , and shown in the following figure.
xb
xa
Is xa > xb or is xa < xb ? Explain.

Problem 1. A general solution to a first-order linear differential equation with constant coefficients
can be written as
n(t) = n + (n0 n )et/ .
a) Determine the slope m0 = dn/dt at t = 0 in terms of the constants n , n0 and .
b) If this slope were extended for t > 0 (i.e., if n (t) = n0 + m0 t), for what value of t will
n (t) = n ?
c) Plot n(t) and n (t) when n0 = 10, n = 10, and = 1.
Problem 2. Four solutions to the differential equation
dx(t)
+ Ax(t) + B = 0
dt
are shown in the following plot.
3
3
0
10
Part a. Find values of A and B that are consistent with curve a. Are these values unique? If not,
find a second set of constants that are consistent.
Part b. Repeat part a for curve b. Compare these results to those of part a. Explain similarities and
differences.
Part c. Repeat part a for curve c. Compare these results to those of parts a and b. Explain
similarities and differences.
Part d. Repeat part a for curve d. Determine all possible values of A and B for this case.
2
Problem 3. Assume that no mol/cm2 of sucrose (with a diffusion constant D 0.5 105 cm2 /s)
are placed in a trough of water at a point x = 0 at time t = 0. Assume that the concentration of
sucrose is a function of x and t only.
a) Show that for any xed point xp the maximum concentration occurs at time tm = x2p /2D.
b) How long does it take for the concentration to reach a maximum at x = 1 cm?
Problem 4. The following gure illustrates a cascaded system of two water tanks. Water ows out
of the rst tank and into the second at a rate r1 (t), and out of the second tank at a rate r2 (t).
r1(t)
h1(t)
h2(t)
r2(t)
The rates of ow out of the tanks are proportional to the heights of the water in the tanks: r 1 (t) =
k1 h1 (t) and r2 (t) = k2 h2 (t), where k1 and k2 are each 0.02 m2 /minute. The height of tank 1 is 1 m
and that of tank 2 is 2 m. The cross-sectional area of tank 1 is A1 = 4 m2 and that of the second
tank is A2 = 2 m2 . At time t = 0, tank 1 is full and tank 2 is empty.
a. If the height of water in tank 2 ever exceeds the height of the tank (2 m), the water will
overow. Will the water ever overow? Explain.
b. Set up a system of differential equations to determine h2 (t). Solve the equations to determine
an expression for h2 (t).
c. At what time does the water in tank 2 reach its peak? What will be the maximum height of
water ever achieved in tank 2?
d. At what time will the water stop owing out of tank 1? Explain your answer in mathematical
terms and then in physical terms.
e. If both tanks were full at t = 0, would the second tank ever overow? Explain.
Concentrations
of A and B
Problem 5. Transport by diffusion tends to move solutes from regions of high concentration to
regions of low concentration, thereby making the spatial distribution of solute more uniform. Thus
diffusion is often associated with mixing. However, diffusion can also be used to separate solutes in
a mixture. Such separation is important as a mechanism to purify mixtures of biological materials
(such as mixtures of DNA fragments) and is currently being exploited in microfabricated systems
for biological and medical analysis (which we will look at in greater detail in the Microuidics
Laboratory Project).
Assume that a mixture of two molecular species is loaded into a long and narrow channel lled
with water. Let x represent distance in the the longitudinal direction and assume that n 0 molecules
of solute A and n0 molecules of solute B are loaded into location x = 0 at time t = 0. Assume that
solutes A and B have different molecular weights and that their diffusivities are D A = 107 cm2 /s
and DB = 4 107 cm2 /s, respectively. The following gure illustrates how the two species tend
to separate as they diffuse.
x (m)
10
10
Part a. As time elapses, the number of molecules of solute A that remain in a test region within
the 10m of the starting position (i.e., 10m< x < 10m) decreases. Determine the amount of
time t0 required to get 5% of solute A to leave the test region.
Part b. At time t = t0 found in part a, determine the amount of solute B in the test region.
Part c. Determine the ratio of solute A to solute B in the test region at time t = t 0 . Explain how
diffusion has lead to a separation of solute A from solute B.
2.791J/2.794J/6.021J/6.521J/BE.370J/BE.470J/HST.541J
Reading
Lecture 5 Volume 1:
Lecture 6 Volume 1:
Lecture 7 Volume 1:
Lecture 8 Volume 1:

3.8-3.8.5
4.1-4.3.2.3 4.4-4.5.1.2
4.7-4.7.1.2
4.7.2-p.230 Fig.4.26 Fig.4.28 4.8.2-4.8.3
Exercise 1. Describe the dissolve-diffuse theory for diffusion through cellular membranes.
Exercise 2. Two time constants are involved in two-compartment diffusion through a membrane:
the steady-state time constant of the membrane (ss ) and the equilibrium time constant for the two
compartments (eq ). Without the use of equations, describe these two time constants.
Exercise 3. A solute n diffuses through a membrane that separates two compartments that have
different initial concentrations. The concentrations in the two compartments as a function of time,
can (t) and cnb (t), are shown in the following gure.
can (t)
cbn (t)
The volumes of the two compartments are Va and Vb . Is Va > Vb or is Va < Vb ? Explain.
Exercise 4. Dene osmolarity.
Exercise 5. The following three formulas for the sugar (trisaccharide) rafnose (found in sugar
beets) were proposed:
C12 H28 O14 ,
C18 H42 O21 ,
C36 H84 O42 .
De Vries (1888) used a plant cell to determine that plasmolysis occurred with a solution containing
59.4 grams of rafnose per liter of water whereas plasmolysis occurred in a solution of sucrose at a
concentration of 0.1 mol/L. Based on these measurements, de Vries determined the correct formula
for rafnose. Which formula would you choose and why would you choose it?
Problem 1. Consider diffusion through a thin membrane that separates two otherwise closed com
partments. As illustrated in Figure 1, the membrane and both compartments have cross sectional
areas A = 1 cm2 . Compartment 1 has length L1 = 50 cm, compartment 2 has length L2 = 10
c(x, t)
c1 (t)
c2 (t)
Area = 1 cm2
W = 104 cm
L1 = 50 cm
L2 = 10 cm
Figure 1: Two compartments separated by a membrane.

cm, and the membrane thickness is W = 104 cm. Assume that (1) the compartments contain
sugar solutions and that both compartments are well stirred so that the concentration of sugar in
compartment 1 can be written as c1 (t) and that in compartment 2 can be written as c2 (t); (2) the
concentration of sugar in the membrane can be written as c(x, t), where x represents distance
through the membrane; (3) the diffusivity of sugar in the membrane is D sugar = 105 cm2 /s and
the membrane:water partition coefcient km:w is 1; (4) the concentration of sugar in the membrane
has reached steady state at time t = 0 and that c1 (0) = 1 mol/L and c2 (0) = 0 mol/L.
a) Compute the ux of sugar through the membrane at time t = 0, s (0).
b) Compute the nal value of concentration of sugar in compartment 1, c 1 ().
c) Let eq characterize the amount of time required to reach equilibrium. What would happen
to eq if the diffusivity of sugar in the membrane were doubled? Explain your reasoning.
2
Problem 2. A thin membrane and a thick membrane, that are otherwise identical, are used to
separate identical solutions of volume V = 1 cm3 (Figure 2). All the membrane surfaces facing
the solutions have area A = 1 cm2 . The thin membrane has thickness ds = 104 cm; the thick
membrane has thickness dl = 1 cm. For t < 0 the aqueous solutions on both sides of the membrane
are identical and do not contain solute n. At t = 0 a small concentration of solute n is added to
the solution on side 1 of the membrane. You may assume that there is no water ow across the
membrane. The diffusion coefcient and membrane:solution partition coefcient of n in both
membranes are Dn = 105 cm2 /s and kn = 2, respectively.
Thin membrane
ds
c1n
Thick membrane
dl
c2n
c1n
c2n
n
Surface area A
Figure 2: Schematic diagrams of thin and thick membranes.

a) For each membrane, estimate the time ss that it takes for the concentration prole in the
membrane to reach its steady-state spatial distribution.
b) For each membrane, nd the time eq that it takes for the solutions on the two sides of
the membrane to come to equilibrium assuming that the spatial distribution of solute in the
membrane is the steady-state distribution.
c) Is it reasonable to assume that Ficks Law for membranes applies for the thin membrane at
each instant in time, i.e., does
n (t) = Ps (c1n (t) c2n (t)) ?
where Ps is the permeability of the thin membrane.
d) Is it reasonable to assume that Ficks Law for membranes applies for the thick membrane at
n (t) = Pl (c1n (t) c2n (t)) ?
where Pl is the permeability of the thick membrane.
Problem 3. Glucose is dripped at a constant rate R = 2mol/s into a bath that contains 10 12
identical red blood cells, as shown in the following gure.
Assume that each red blood cell has a volume VC = 25 (m)3 and a surface area AC = 80 (m)2 ,
and that neither of these changes over the time interval considered in this problem. Assume that
the volume of the bath is 1 L, and that the bath is well stirred. (You may assume that the amount
of water dripped into the bath is negligibly small.) The concentration of glucose in the bath, c b (t),
if found to increase as a function of time t, as shown in the following plot.
cb(t) (mmol/L)
5
t (s)
0
0
300
600
900
Part a. Is the following logic True or False?

The ux of glucose through each of the cell membranes cannot be constant over the
time 0 < t < 900 s, because if it were, the concentration cb (t) would be a linear
function of time.
If the truthfulness of this statement cannot be determined from the information provided, describe
what additional information is needed.
Part b. Determine the ux of glucose through the membrane of each cell at time t = 900 s.
Use our normal convention that outward ux (i.e., ux leaving the cell) is positive and inward
ux is negative. Determine the numerical value (or numerical expression) and units. If you
cannot determine the numerical value from the information provided, describe what additional
information is needed.
Part c. Determine the ux of glucose through the membrane of each cell at time t = 0 s. Use
our normal convention that outward ux (i.e., ux leaving the cell) is positive and inward ux
is negative. Determine the numerical value (or numerical expression) and units. If you cannot
determine the numerical value from the information provided, describe what additional information
is needed.
4
Problem 4. All cells are surrounded by a cell membrane. The cytoplasm of most cells contains a
variety of organelles that are also enclosed within membranes. Assume that a spherical cell with
radius R = 50m contains a spherical organelle called a vesicle, with radius r = 1m, as shown
in the following gure.
bath
spherical cell
radius R = 50 m
spherical vesicle
radius r = 1 m
Assume that the membranes surrounding the cell and vesicle are uniform lipid bilayers with iden
tical compositions and the same thickness d = 10 nm. Assume that solute X is transported across
both the cell and vesicle membrane via the dissolve and diffuse mechanism. Assume that X dis
solves equally well in the bath and in the aqueous interiors of the vesicle and cell. Assume that
the solute X dissolves 100 times less readily in the membrane (i.e., the partitioning coefcient is
0.01). Assume the diffusivity of X in the membranes is 107 cm2 /s.
Initially, the concentration of X is zero inside the cell and inside the vesicle. At time t = 0, the
cell is plunged into a bath that contains X with concentration 1 mmol/L.
a) Estimate the time that is required for the concentration of X in the cell to reach 0.5 mmol/L.
Find a numerical value or explain why it is not possible to obtain a numerical value with the
information that is given.
b) Estimate the time that is required for the concentration of X in the vesicle to reach
0.5 mmol/L. Find a numerical value or explain why it is not possible to obtain a numeri
cal value with the information that is given.
Problem 5. As your rst assignment at Tinyuidics Inc., you are asked to design a microuidic
device that will remove small molecules from a sample of uid that contains both large molecules
and small molecules. After some thinking, you design the laminar ow device shown below.
buffer in
waste out
W
sample in
filtrate out
L
buffer in
waste out
The sample is injected in a port with width . The sample ow is surrounded by buffers injected
on both sides of the sample. The combined ow then passes through a channel that has width W
and length L after which the uids are separated into a desired ltrate output (in a channel of width
d) and two waste outputs. Assume that the uid moves with the same speed v in all parts of the
microuidic device (although this is not generally true, it is a convenient starting point). Assume
that << d, and that W is sufciently large that it can be taken to be innity.
To test the device, you mix a solution that contains equal concentrations of 2 proteins, A and B.
The diffusivity of solute B is four times that of solute A.
Part a. Briey explain how this device takes advantage of differences in diffusivities to achieve
separation.
Part b. Let fA represent the ratio of the amount of solute A found in the ltrate divided by the
amount of solute A in the sample. Determine an expression for f A . Determine an expression for
the analogous ratio fB for solute B.
The following gure shows a plot of the dependence of fA and fB on L, when = 1m, d = 20m,
v = 1 mm/s, and DA = 107 cm2 /s.
fA and fB
0.5
0
0
10
L (mm)
Part c. Which curve (dashed or solid) represents fA ? Explain.
Part d. Determine L0 , the value of L that maximizes the difference between fA and fB . Briey
explain why this difference is smaller when L << L0 and when L >> L0 .
2.791J/2.794J/6.021J/6.521J/BE.370J/BE.470J/HST.541J

Reading
Lecture 8 Volume 1: 6.1-6.2.1.4
Lecture 10 Volume 1: 6.4.2-6.4.3 6.6-6.7.4
Lecture 11 Volume 1: 7.2.1 7.2.3 7.2.4.1 7.4
Announcements
Exam 1 will be held on Thursday, October 7, 2004 from 7:30 PM to 9:30 PM
The exam is closed-book: notes on both sides of one 8 12 11 sheet of paper
may be used for reference. Calculators may be used, but computers and wireless
devices may not be used.
There will be no recitations on the day of the exam.
Exercise 1. It is known that the membrane of a certain type of cell is highly permeable to water,
but relatively impermeable to L-glucose, sodium ions, and chloride ions. When the cell is removed
from interstitial uids and placed in a 150 mmol/L NaCl solution, the cell neither shrinks nor
swells.
a) Would the cell shrink, swell, or remain at constant volume if placed in 150 mmol/L solution
of L-glucose? Explain.
b) Would the cell shrink, swell, or remain at constant volume if placed in a 300 mmol/L solution
of L-glucose? Explain.
Exercise 2. If Equation 4.68 in volume 1 of the text is multiplied by A(t), the result can be written
as
dV i (t)
= A(t)LV RT Co (t) Ci (t) .

dt
Using no mathematical formulas or equations, describe the meaning of of this equation in a few
well chosen English sentences.
1
Exercise 3. The following gure shows schematic diagrams of two cells that have the same volume
but quite different shapes.
One cell (left panel) is spherical, the other is approximately cylindrical but contains a large number
of microvilli. The cell membranes have the same hydraulic conductivity to water. If the two cells
are subjected to the same decrease in extracellular osmolarity, which cell swells more rapidly?
Explain.
Exercise 4. Consider the simple, symmetric, four-state carrier model. For each of the following
conditions, nd NiE , NoE , NiES , NoES , and S . Explain the physical signicance of each of your
answers.
a) = 0.
b) = 0.
c) K = 0.
Exercise 5. Consider the simple, symmetric, four-state carrier model when c iS = coS = 0. Sketch
the carrier density in each of its four states as a function of /. Give a physical interpretation of
your results.
Problem 1. A volume element with constant cross-sectional area A has rigid walls and is divided
into two parts by a rigid, semipermeable membrane that is mounted on frictionless bearings so that
the membrane is free to move in the x-direction as shown in the following gure.
c1
c2
10 (cm)
The semipermeable membrane is permeable to water but not to the solutes (glucose or NaCl or
CaCl2 ). At t = 0, solute 1 is added to side 1 to give an initial concentration of c 1 (0) and solute
2 is added to side 2 to give an initial concentration of c2 (0). Concentrations are specied as the
number of millimoles of glucose or NaCl or CaCl2 per liter of solution. The initial position of
the membrane is x(0). For each of the following parts, nd the nal (equilibrium) values of the
membrane position x(), and the concentrations, c1 () and c2 ().
2
(a.) c1glucose (0) = 0; cglucose
(0) = 10; x(0) = 5.
2
(b.) c1
glucose (0) = 30; cglucose (0) = 70; x(0) = 7.
2
(c.) c1
glucose (0) = 20; cglucose (0) = 10; x(0) = 3.
2
(d.) c1
glucose (0) = 30; cN aCl (0) = 20; x(0) = 4.
(e.) c1CaCl2 (0) = 20; c2N aCl (0) = 30; x(0) = 3.
Problem 2. A spherical cell has a freely distensible membrane that is permeable to solute A, im
permeant to solute B, and permeable to water. The cell contains N I moles of impermeant solutes,
and is allowed to equilibrate in a bath in which the concentration of A is zero and the concentration
of B is c1 . The bath is large compared to the cell. The cell volume in this bath is V 0 . At t = 0, the
cell is moved to a bath that contains equal concentrations of A and B, c A = cB = 12 c1 .
a. Is the new bath hyper-, hypo-, or iso-osmotic with the cell at t = 0?
b. If the hydraulic conductivity of the cell is LV , what is the rate of increase of the volume,
dV(t)/dt just after the cell is moved (i.e., at t = 0+ )?
c. What is the equilibrium volume of the cell in terms of V0 ? Explain briey.
Problem 3. The following gure shows the design of a miniature pump that can be implanted in
the body to deliver a drug. No batteries are required to run this pump!
Rigid,
semipermeable
membrane
0.7 cm
Frictionless,
impermeable
piston
Chamber 1
(solute)
Drug
orifice
Chamber 2
(drug)
3 cm
The pump contains two cylindrical chambers lled with incompressible uids: the two chambers
together have a length of 3 cm and a diameter of 0.7 cm. Chamber 1 is lled with a solution whose
concentration is 10 mol/L; the osmolarity of this solution greatly exceeds that of body uids.
Chamber 2 is lled with the drug solution. The two chambers are separated by a frictionless, mass
less, and impermeable piston. The piston moves freely and supports no difference in hydraulic
pressure between the chambers; the piston allows no transport of water, solute or drug between
chambers. The pump walls are rigid, impermeable and cylindrical with an orice at one end for
delivering the drug and a rigid, semipermeable membrane at the other end. The orice diameter is
sufciently large that the hydraulic pressure drop across this orice is negligible and sufciently
small so that the diffusion of drug through the orice is also negligible. The semipermeable mem
brane is permeable to water only, and not permeable to the solute. Assume that T = 300 K.
a) Provide a discussion of 50 words or fewer for each of the following:
i) What is the physical mechanism of drug delivery implied by the pump design?
ii) What is(are) the source(s) of energy for pumping the drug?
iii) Assume there is an adequate supply of drug in the pump for the lifetime of the im
planted subject and that it is necessary to provide a constant rate of drug delivery.
Which fundamental factors limit the useful lifetime of this pump in the body?
b) When implanted in the body, the pump delivers the drug at a rate of 1 L/h. Find the value
of the hydraulic conductivity, LV , of the semipermeable membrane.
Problem 4. A large fraction of the molecules in a cell membrane are phospholipids, which have a
hydrophilic head and hydrophobic tails. When purified phospholipids are added to a saline solution, the phospholipids self assemble into a variety of stable structures, one of which is spherical
and is called a liposome.
Liposomes have saline interiors and exteriors that are separated
by a phospholipid bilayer, much like a biological cell. Liposomes
Bath
can be used as artificial cells to test theories about membrane transport.
Assume that a liposome is created in a solution that contains
200 mmol/L of a solute I that cannot permeate the phospholipid biLiposome
layer. Assume that the inner solution initially contains 200 mmol/L
of solute I and the initial radius is 30m. Assume that the thickness
of the bilayer is much smaller than the diameter of the liposome.
Assume that water can permeate the phospholipid bilayer, and that hydraulic pressure gradients
across the bilayer can be ignored. Assume that the temperature is 300 K.
Assume that the liposome is transfered at time t = 0 to a bath that contains 200 mmol/L of
solute A and 100 mmol/L of solute B. The liposome initially shrinks but then swells and reaches
an ultimate radius of approximately 38m as shown in the following plots. The left plot shows the
time course for the first 1000 seconds. The right plot shows just the first 100 seconds of the same
data.
30
Radius (m)
Radius (m)
40
35
30
25
29
28
0
500
1000
Time (seconds)
50
100
Time (seconds)
Part a. Determine the asymptotic value of concentration cI (t) of solute I in the liposome as time
increases, i.e., determine
lim cI (t).
t
Provide a numerical value (or numerical expression) with units. If it is not possible to determine
the concentration from the information provided, explain why.
Part b. Indicate which, if either, of the solutes A and B can permeate through the artificial membrane? If it is not possible to determine this information, explain why.
Part c. Determine the hydraulic conductivity LV of the artificial membrane. Provide a numerical value (or numerical expression) with units. If it is not possible to determine the hydraulic
conductivity from the information provided, explain why.
Problem 5. A large fraction of the molecules in a cell membrane are phospholipids, which have
a hydrophobic head and hydrophilic tails. When puried phospholipids are added to a saline
solution, the phospholipids self assemble into a variety of stable structures, one of which is called
a liposome.
Bath
Liposome
Liposomes have saline interiors and exteriors that are separated by a phospholipid bilayer, much
like a biological cell, as illustrated above. Liposomes can be used as articial cells to test the
ories about membrane transport. Assume that a liposome is created in a solution that contains
100 mmol/L of a solute A that cannot permeate the phospholipid bilayer. Assume that water can
permeate the phospholipid bilayer, and that the liposome comes to equilibrium with a volume of
1 pL (1012 L) of internal solution containing A with concentration 100 mmol/L.
The liposome is then transferred to one of the following solutions
solution 1: 100 mmol/L of A plus 10 mmol/L of B
solution 2: 90 mmol/L of A plus 10 mmol/L of B
solution 3: 100 mmol/L of B
where B is a solute that can permeate the phospholipid bilayer. Both A and B are nonelectrolytes,
and the baths are large compared to the volume of the liposome. Assume that transport of water
and transport of the permeant solute B are independent of each other, i.e., water transport does not
effect transport of B and vice versa.
(a.) Calculate the equilibrium volume of the liposome in solution 1. Discuss your result briey.
(b.) Calculate the equilibrium volume of the liposome in solution 2. Discuss your result briey.
(c.) Calculate the equilibrium volume of the liposome in solution 3. Discuss your result briey.
Problem 6. A monosaccharide, M , is known to be transported through a cell membrane by a
carrier so that
ci (t)
co
= max
K + ci (t) K + co
where ci (t) is the intracellular concentration of M, co is the external concentration of M, is the
outward ux of M (mol/cm2 s) and max is the maximum ux with which the carrier system
is capable of transporting M . The area of the cell, A, is 106 cm2 , and K is 100 mmol/L. The
following experiment is performed: the cell initially contains zero moles of M , and at t = 0 the
cell is placed in an isotonic solution containing a concentration of M equal to c o (constant), where
co K. The internal concentration of M is found to be
ci (t) = co (1 et/ ), t 0
where = 100 s. The volume of the cell remained roughly constant at 10 10 mL throughout the
experiment. Determine max .
6
2.791J/2.794J/6.021J/6.521J/BE.370J/BE.470J/HST.541J
Issued: October 8, 2004

Due: Thursday October 14, 2004
Reading
Lecture 15 Volume 1: 7.5
Announcements
This homework assignment is smaller than average to give you time to work on your lab reports.
First drafts of your lab reports are due Friday, October 15, 2004 at 10:00 AM. Bring 3 copies.
One will be reviewed by the technical staff. One will be reviewed by the writing staff. One will
be reviewed by a peer student group. You and your partner will be assigned to review the report of
another student group. All reviews are due Tuesday October 19, 2004 when they will be discussed
at the Writing Clinic, to be held at 7:30 PM.
Exercise 1. Dene electroneutrality and briey explain its physical basis.
Exercise 2. Dene the Nernst equilibrium potential and briey explain its physical basis.
Problem 1. Two compartments of a uid-lled chamber are separated by a membrane as shown in
the following gure.

Compartment 1
Membrane
Compartment 2
1 mmol/L NaCl
0.1 mmol/L KCl
0.1 mmol/L NaCl
1 mmol/L KCl
+
V
The area of the membrane is 100 cm2 and the volume of each compartment is 1000 cm3 . The
solution in compartment #1 contains 1 mmol/L NaCl and 0.1 mmol/L KCL. The solution in com
partment #2 contains 0.1 mmol/L NaCl and 1 mmol/L KCL. The temperatures of the solutions are
24 C. The membrane is known to be permeable to a single ion, but it is not known if that ion is
sodium, potassium, or chloride. Electrodes connect the solutions in the compartments to a battery.
The current I was measured with the battery voltage V = 0 and was found to be I = 1 mA.
a) Identify the permeant ion species. Explain your reasoning.
b) Draw an equivalent circuit for the entire system, including the battery. Indicate values for
those components whose values can be determined.
1
c) Determine the current I that would result if the battery voltage were set to 1 volt. Explain
your reasoning.
Problem 2. Three compartments are separated from each other by semi-permeable membranes, as
illustrated in the following gure.
Im
Vm
cNa = 100
cK = 0
cCl = 100
cNa = 20
cK = 80
cCl = 100
cNa = 10
cK = 0
cCl = 10
compartment 1
compartment 2
compartment 3
permeant to
Na+ only
permeant to
Cl only
Each compartment contains well-stirred solutions of sodium, potassium, and chloride ions, with
concentrations indicated in the gure (in mmol/L). The membrane between compartment 1 and 2
is permeant to sodium ions only, and its specic electrical conductivity G N a is 5 mS/cm2 . The
membrane between compartment 2 and 3 is permeant to chloride ions only, and its specic electri
cal conductivity GCl is 2 mS/cm2 . Both membranes have areas A = 10 cm2 . The temperature T is
such that RT /(F log e) = 60 mV.
a) Sketch an electrical circuit that represents the steady-state relation between current and volt
age for the three compartments. Label the nodes that correspond to compartments 1, 2, and
3. Include the switch in your sketch. Label Im , Vm , and the conductances.
b) Let V1 and V2 represent the steady-state potentials in compartments 1 and 2 with reference
to compartment 3 when the switch is open. Calculate numerical values for V 1 and V2 .
c) Compute the steady-state value of the current Im when the switch is closed.
2.791J/2.794J/6.021J/6.521J/BE.370J/BE.470J/HST.541J

Due: October 21, 2004
Reading
Lecture 17 Volume 2: Chapter 1
Lecture 18 Volume 2: 2.1-2.4.2
Lecture 19 Volume 2: 2.4.3-2.5
Announcements
The recitation on October 19 is cancelled so that we can meet that evening for a Writing Clinic. The
Writing Clinic will be held from 7:30 to 9:30 PM. Please return your written critiques of your
peers laboratory report at that time. You will also receive critiques from the technical and
writing staffs.
Exercise 1. Active ion transport is said to have a direct and an indirect effect on the resting
potential of a cell. Dene both effects and discuss the distinction between the two effects.
Exercise 2. Describe the distinctions between the following terms that refer to ion transport across
a cellular membrane: electrodiffusive equilibrium, steady-state, resting conditions, and cellular
quasi-equilibrium.
Exercise 3. Figure 1 shows measurements of the resting potential of a glial cell for different values
of extracellular potassium concentration (left panel). These measurements are to be interpreted in
terms of the network model shown in the right panel of the same gure. Assume that c oN a = 150
0
Im
Resting potential (mV)
20
Mud puppy
glial cell
40
60
p
IN
a
p
IK
GN a
GK
Vmo
80
VN a
100
VK
a
IN
a
a
IK
120
0.1
Slope:
59 mV/decade
1
10
coK (mmol/L)
100
Figure 1: Measurements and model of electrical responses of a glial cell.

mmol/L, ciN a = 15 mmol/L and that the external solution is maintained isotonic with the cytoplasm by controlling impermeant solutes. Assume that sodium and potassium concentrations are
a
constant, except for coK , and that the pump system, which consists of INa a and IK
, is nonelectrogenic.
a) Consider only the region for which the data are well t by the straight line of slope 59
mV/decade. Indicate whether the following statements are true or false and give a brief
reason for each answer.
i
ii)
iii)
iv)
v)
vi)
vii)
viii)
Im = 0.
o
Vm
VK .
GN a GK .
VN a > VK .
ci
K = 100 mmol/L.
a
IK
= INa
a .
p
IK
= INp
a .
INa
a = GN a (Vmo VN a ).
b) It is proposed that deviation of the data from the straight line for the lowest c oK is a result of
a change in GK that occurs when Vmo < 110 mV. For the data shown, is this a reasonable
hypothesis? Does it require that GK for Vmo = 125 mV is larger or smaller than GK for
Vmo > 100 mV? Explain.
Exercise 4. The ionic concentrations of a uniform isolated cell are given in the following table.
Potassium
Sodium
Concentration (mmol/L)
Inside
Outside
150
15
15
150
An electrode is inserted into the cell and connected to a current source so that the current through
the cell membrane is Im . The steady-state voltage across the cell membrane Vm is determined as a
function of the current as shown in the following gure.
+
Vm
Im
Vm
(mV)
0
IN a
IK
GN a
GK
Vm
Im
VN a
0.4
VK
Im (nA)
40
Assume that: (1) the cell membrane is permeable to only K+ and Na+ ions; (2) the Nernst equi
librium potentials are Vn = (60/zn ) log10 (con /cin ) (mV); (3) ion concentrations are constant; (4)
active transport processes make no contribution to these measurements.
a) Determine the equilibrium potentials for sodium and potassium ions, V N a and VK .
b) What is the resting potential of the cell with these ionic concentrations?
c) With the current Im adjusted so that Vm = VK , what is the ratio of the sodium current to the
total membrane current, IN a /Im ?
d) What is the total conductance of the cell membrane Gm = GN a + GK ?
e) Determine GN a and GK .
Problem 1. The resting membrane potential, Vmo , of two uniform, isolated cells is measured as a
function of the external concentration of potassium, coK , with the sodium concentration held xed
o
at its normal value, con
N a , and then as a function of the external sodium concentration, c N a , with
the potassium concentration held xed at its normal value, con
K . The results for these two cells are
shown in the following gure.
Cell 1
Cell 2
50
50
50
50
100
100
Slope: 60 mV/decade
150
150
Slope: 48 mV/decade
10
100
coK (mmol/L)
1000
50
50
50
50
100
100
Slope: 0 mV/decade
10
100
coK (mmol/L)
1000
Slope: 12 mV/decade
150
150
10
100
co
N a (mmol/L)
1000
10
100
o
cN
a (mmol/L)
1000
You may assume that for each cell: (1) external solutions are isotonic; (2) the membranes are
impermeable to ions other than potassium and sodium; (3) the internal concentrations of potassium
and sodium are maintained constant by a non-electrogenic active transport mechanism; (4) the
total membrane conductance is 10 nS; (5) the normal resting potential is 60 mV; (6) the internal
concentration of sodium is 20 mmol/L.
a) For each cell, determine the total conductance of the membrane to potassium and to sodium,
GK and GN a , respectively. If either value is indeterminate from the information given, de
scribe what additional information would be needed.
b) For each cell, determine the internal and external concentrations of potassium and the ex
ternal concentration of sodium at the normal resting potential (60 mV). If the value is
indeterminate from the information given, describe what additional information would be
needed.
4
c) For each cell, determine the simplest equivalent electric network model that relates the de
pendence of the resting potential of the cell on the ion concentrations. Indicate the values of
all elements in the network.
Problem 2. The membrane of a cell is known to be permeable to Na+ and K+ only, with
passive ionic conductances of GN a = 106 S/cm2 and GK = 103 S/cm2 , and contains a
(Na+ K+ )ATPase active transport mechanism that transports 3 molecules of Na + outward and
2 molecules of K+ inward through the membrane for each molecule of ATP split into ADP and
phosphate. In the experiment shown in Figure 2, the cell is kept at a temperature of 24 C. For
Vmo
t1
t2
Injectionof
sodiumions
Perfusion
withouabain
60
60
80
Figure 2: Effect of sodium injection and ouabain on resting potential.
t < t1 , the cell is in its normal resting state with resting potential Vmo 60 mV, and resting ion
concentrations shown in the following table.

Ion
Sodium
Potassium
Concentration (mmol/L)
Internal
External
15
135
156
15
At t = t1 , Na+ is injected rapidly into the cell interior, without the passage of any current through
the membrane, to double the intracellular sodium concentration. When the injection is completed,
the membrane potential hyperpolarizes to approximately 80 mV. At t = t 2 ouabain, a blocker
of the active transport mechanism, is applied to the cell and the membrane potential returns to
approximately its normal resting value.
a) Is the active transport mechanism electrogenic or nonelectrogenic? Explain!
b) Does the active transport mechanism contribute appreciably to the resting potential for t <
t1 ? Explain!
c) How many moles of ATP are split per second by a cm2 of membrane during the interval
(t1 , t2 )?
5
Problem 3. The membrane of a cell contains an active transport mechanism that pumps three
sodium ions out of the cell for every two potassium ions that it pumps into the cell. The membrane
also supports the passive transport of sodium and potassium ions, but is impermeant to all other ions
and is impermeant to water. The sodium conductivity is 105 S/cm2 and the potassium conductivity
is 104 S/cm2 . The cell is allowed to come to steady state and its membrane potential is 52.5 mV.
The Nernst equilibrium potential for sodium is 60 mV and the Nernst equilibrium potential for
potassium is 60 mV. The net outward current density due to active transport is 38 A/cm2 .
a) Draw an electrical circuit to represent ionic transport across the membrane of this cell. In
clude labels for each of the 6 numbered parameters provided in the problem statement.
b) Is the cell at rest? If yes, prove that it is at rest. If no, explain why not.
c) Is the cell in quasi-equilibrium? If yes, prove that it is at quasi-equilibrium. If no, explain
why not.
d) Is the active transport mechanism electrogenic? Explain.
Problem 4. Consider the model of a cell shown in the following gure.
Im
p
IN
a
p
IK
p
ICl
GN a
GK
GCl
VN a
VK
Vmo
a
IN
a
VCl
a
IK
The cell has channels for the passive transport of sodium, potassium, and chloride as well as a
pump that actively transports sodium out of the cell and potassium into the cell. The pump ratio
a
= 1.5. The following table shows the intracellular and extracellular concentrations,
is INa a /IK
Nernst equilibrium potentials, and conductance ratios for sodium and potassium. Some informa
tion is also given for chloride; blank entries represent unknown quantities.
Na+
K+
Cl
Vn
con
cin
(mmol/L) (mV)
10 140 +68
140 10 68
150
Gn /GK
0.1
1
1
The cell also contains impermeant intracellular ions. Assume that the cell is in equilibrium at t = 0,
i.e., assume that at t = 0 the cell has reached a condition for which all solute concentrations, the
cell volume, and the membrane potential are constant.
a) Choose one of the following statements and explain why it is true.
6
i)
ii)
iii)
iv)
v)
vi)
The cell resting potential depends on GCl .

The cell resting potential depends on VCl .
The cell resting potential depends on both GCl and VCl .
The cell resting potential does not depend on GCl .
The cell resting potential does not depend on VCl .

The cell resting potential does not depend on either GCl or VCl .
b) Determine Vmo .
c) At t = 0, the external concentration of chloride is reduced from 150 mmol/L to 50 mmol/L
by substituting an isosmotic quantity of an impermeant anion for chloride. Assume that the
concentrations of sodium and potassium both inside and outside the cell remain the same
and that the volume of the cell does not change.
i) Determine Vmo (0+ ), the value of the membrane potential immediately after the change
in solution. You may ignore the effect of the membrane capacitance.
ii) Determine Vmo (), the value of the membrane potential after the cell has equilibrated.
iii) Determine ciCl (), the intracellular chloride concentration after the cell has equili
brated.
iv) Give a physical interpretation of your results in i), ii), and iii).
v) Discuss the validity of the assumptions that the sodium and potassium concentrations
in the cell are constant and that the volume does not change.
2.791J/2.794J/6.021J/6.521J/BE.370J/BE.470J/HST.541J

Due: October 28, 2004
Reading
Lecture 20 Volume 2: 4.1-4.1.2.3 4.2-4.2.2.2
Lecture 21 Volume 2: 4.2.3-4.2.3.1
Lecture 22 Volume 2: 4.2.3-4.2.3.2
Announcements
Laboratory reports are DUE Monday October 25 at noon. You should submit one copy of the
nal draft of the report. You should include the following items in an appendix: nal proposal,
copy of your critique of a peers rst draft, peer critique of your rst draft, critique of your rst
draft by writing program, critique of your rst draft by technical staff, photocopies of notes taken
during original lab session. Note that there is a SEVERE LATENESS PENALTY. The grade for
a late report will be multiplied by a lateness factor
L = 0.3et/4 + 0.7et/72
where t is the number of hours late. The lateness factor is plotted below. Notice that the maximum
grade for a report that is more than ONE DAY LATE is less than 50%.
Lateness factor L
1.0
0.5
one day
0.0
10
100
Time t past deadline (hours)
This lateness factor is applied regardless of the reason for the lateness, except for health related
problems or personal problems certied by the Deans ofce. Specically, lateness due to computer
and/or printer problems is not exempt.
Exam 2 will be held on Thursday, November 4 from 7:30 PM to 9:30 PM
The exam is closed-book: notes on both sides of two 8 12 11 sheets of paper may be
used for reference. Calculators may be used, but computers and wireless devices may not be used.
There will be no recitations on the day of the exam.
1
Exercise 1. Give a physical explanation for why the conduction velocity is larger in larger diameter
bers, if all other factors are the same.
Exercise 2. Give a physical explanation of the meaning of Equation 2.18 (in volume 2 of the text)
without the use of equations.
Exercise 3. Let the function f (z, t) represent a solution to the wave equation. This solution is
shown in the following gure as a function of time t at the position z = 0.
f (0, t)
0
0
1
t (ms)
Notice that f (0, t) is non-zero for 0 < t < 2 ms and zero elsewhere.
a) Suppose that the wave is propagating in the +z-direction with a propagation velocity of 100
mm/ms. Plot f (z, t) versus z at time t = 2 ms.
b) Suppose that the wave is propagating in the z-direction at a propagation velocity of 100
mm/ms. Plot f (z, t) versus z at time t = 2 ms.
Problem 1. The following two experiments are performed on a squid giant axon:
Experiment #1: The axon is placed in a large volume of sea water, and the size of the
transmembrane action potential is measured by means of an intracellular micropipet and is
found to have a peak-to-peak value of 100 mV. The conduction velocity is 36 m/s.
Experiment #2: The axon is placed in oil and the trans-membrane potential is still found to
be 100 mV peak-to-peak. The peak-to-peak size of the extracellular action potential is 75
mV.
Estimate the expected conduction velocity in Experiment #2. State your assumptions.
2
Problem 2. A ne platinum wire with a resistance per unit length of 130 /cm is inserted inside a
portion of a squid axon as illustrated below.
V1 (t)
action
potential
V2 (t)
Wire
Axon
z (cm)
z1
z2
Intracellular potential
(mV)
The wire is so thin that its volume can be ignored. The axon (500 m diameter) is electrically stim
ulated to produce a propagated action potential traveling in the +z direction. The action potential
is recorded at two intracellular sites: V1 (t) is recorded at z = z1 and V2 (t) is recorded at z = z2 .
The distance between the stimulus electrode (not shown) and z1 is 2 cm. Results are shown in the
following gure.
+50
V1 (t)
V2 (t)
0
50
100
10 15 20
Time (ms)
25
The resistivity of the axoplasm of this axon is 23 -cm. The resistance per unit length of the
external solution is 1.2 /cm. The wire begins at some location between z 1 and z2 , but the exact
position of the beginning is not known and should not be used in any of your calculations.
a) Determine the instantaneous speed of the action potential as its peak passes the point z = z 1 .
b) Determine the instantaneous speed of the action potential as its peak passes the point z = z 2 .
c) Sketch the extracellular potential as a function of space (z) that results at the time that the
peak of the action potential passes the point z = z1 . Include distances z1 4 < z < z1 +4 cm.
Indicate the scale for the y axis. Describe the important features of this plot.
d) Sketch the extracellular potential as a function of space (z) that results at the time that the
peak of the action potential passes the point z = z2 . Include distances z2 4 < z < z2 +4 cm.
Indicate the scale for the y axis. Describe the important features of this plot.
Problem 3. In measurement 1, a cylindrical unmyelinated axon of radius a is placed in a large

volume of isotonic sea water and the conduction velocity of the action potential is measured to
be 1 . The osmotic pressure of the sea water is then doubled by increasing the salt concentration,
and the axon is allowed to come to osmotic equilibrium. Then, in measurement 2, the conduction
velocity is measured to be 2 . Assume that during these experiments
the number of ions transported through the axon membrane is negligible compared to the
number of ions inside the axon,
the volume of the axon is negligible compared to the volume of the bath,
the specic electric properties of the membrane (the capacitance per unit area and the con
ductance per unit area) are the same in both measurements,
the length of the axon remains unchanged, and
the external resistance per unit length of the axon, ro , is negligible compared to the internal
resistance per unit length of the axon.
Part a. Let ri1 and ri2 represent the internal resistance per unit length of the axon in measurements
1 and 2, respectively. Determine the numerical value (or a numerical expression) for the ratio of
these resistances: ri2 /ri1 . Briey explain your reasoning.
Part b. Determine the numerical value (or a numerical expression) for the ratio of speeds: 2 /1 .
Briey explain your reasoning.
2.791J/2.794J/6.021J/6.521J/BE.370J/BE.470J/HST.541J
Issued: November 8, 2004

Due: November 18, 2004
Reading
Lecture 24 Volume 2: 4.4.8
Lecture 25 Volume 2: 4.4.1
Lecture 26 Volume 2: 3.1-3.2.1 3.3-3.4.2.1
Lecture 27 Preparing an oral presentation
Lecture 28 Volume 2: 3.4.2.4-3.4.3.1 3.4.3.3-3.5
Lecture 30 Volume 2: 5.3-5.7
Lecture 31 Volume 2: 6.1-6.1.1 6.4-6.4.1.5 6.2-6.2.2 6.5-p407
Announcements
There is no homework assignment due this week, because of Veterans day. This assignment is due
on the Thursday after Veterans day (November 18).
First Drafts of your HH project is due on November 19 (one day after this homework is due!).
The rst draft should consist of hardcopies of 3-5 technical slides of the type you plan to show
during your nal oral presentation. Each slide should be accompanied by a separate sheet of paper
that lists approximately three bullet points that you will discuss in your presentation of this slide.
The rst draft should also contain a 1 page extended abstract for your HH project. The abstract
should summarize your ndings and explain why they are interesting.
Please take advantage of THIS week to work on your project plus the HH portion of this
homework assignment!
Exercise 1. The following assertions apply to responses calculated according to the HodgkinHuxley model in response to a step of membrane potential applied at t = 0. For each assertion,
state if it is true or false and explain your answer.
a) The leakage conductance is constant.
b) The sodium conductance is discontinuous at t = 0.
c) The potassium conductance is discontinuous at t = 0.
d) The leakage current is constant.
e) The sodium current is discontinuous at t = 0.
f) The potassium current is discontinuous at t = 0.
g) The factors n(t), m(t), and h(t) are discontinuous at t = 0.
h) The time constants n , m , and h are discontinuous at t = 0.
i) The steady-state values n , m , and h are discontinuous at t = 0.
Exercise 2. Figure 1 shows the relation between the membrane potential and the membrane current
density during a propagated action potential as computed from the Hodgkin-Huxley model. The
0.4
Vm
40
0
80
Jm
Jm (mA/cm )
Vm (mV)
0.4
1
Time (ms)
Figure 1: Relation of membrane potential and membrane current density during a propagated
action potential. The dotted vertical line marks the time of occurrence of the peak of the action
potential.
membrane current density consists of an initial outward current followed by an early inward current
whose peak occurs before the peak in the action potential.
a) The initial outward current is due primarily to which of the following:
i)
ii)
iii)
iv)
v)
an ionic current carried by sodium ions.

an ionic current carried by potassium ions.
an ionic current carried by chloride ions.
an ionic current carried by calcium ions.
a capacitance current.
b) The early inward current is due primarily to which of the following:

i)
ii)
iii)
iv)
v)
an ionic current carried by sodium ions.

an ionic current carried by potassium ions.
an ionic current carried by chloride ions.
an ionic current carried by calcium ions.
a capacitance current.
c) Before the peak of the action potential, the membrane potential increases from its resting
value whereas the membrane current density is rst outward (increasing and then decreasing)
and then reverses polarity to become inward (decreasing and then increasing again). Discuss
this complex relation between membrane potential and current. In particular, explain how
the Hodgkin-Huxley model accounts for the fact that the current can be both inward and
outward during an interval of time when the membrane potential is depolarizing.
2
Exercise 3. Does the time constant of a cylindrical cell depend on its dimensions? Does the space
constant of a cylindrical cell depend on its dimensions?
Exercise 4. For each of the following statements, assume that the electrical properties of a patch
of the membrane of the cell can be represented as a parallel resistance and capacitance. Assume
that the cell has a cylindrical shape with a radius that is small compared to the length of the cell.
Determine if each assertion is true or false and give a reason for your choice.
a) For an electrically small cell, the membrane potential in response to a step of current through
the membrane is an exponential function of time.
b) If a step of current is applied through one part of the membrane of an electrically small cell,
the resulting changes in membrane potential will be constant along the length of the cell for
all times after the step.
c) For an electrically large cell, the steady-state value of the membrane potential in response to a
step of current applied through the membrane at one position along the cell is an exponential
function of longitudinal position along the cell.
d) For an electrically large cell, the steady-state value of the membrane potential in response to
a step of current applied through the membrane at one position along the cell is a Gaussian
function of position along the cell.
60
Membrane potential
(mV)
Membrane potential
(mV)
Problem 1. The Hodgkin-Huxley model was used to compute propagated action potentials for
default values of the parameters and for 4 test cases. The following plots show the spatial depen
dence of membrane potential that results 1 ms after the stimulus current was applied at z = 0.
40
20
20
40
60
40
20
20
40
60
80
80
60
1
2
Distance (cm)
Membrane potential
(mV)
Membrane potential
(mV)
60
40
20
20
40
60
60
1
2
Distance (cm)
1
2
Distance (cm)
40
20
20
40
60
80
80
1
2
Distance (cm)
Each of AD shows a plot with two curves: the thin gray curve was obtained for default parameters
and the thick black curve was obtained for one of the tests cases. In each test case, a single
parameter was changed from its default value. Default values of the axon characteristics are as
follows length: 3 cm, radius: 0.0238 cm, cytoplasm resistivity: 35.4 cm, extracellular specic
resistance: 0 /cm.
a. Which of AD shows results when intracellular sodium concentration was reduced from
ciN a = 50 to 25 mmol/L. Explain.
b. Which of AD shows results when the maximum potassium conductance G K was increased
from 36 to 72 mS/cm2 ? Explain.
c. Which of AD shows results when cytoplasmic resistivity was decreased from 35.4 to
30 cm? Explain.
Ionic Current Density

(mA/cm2)
Problem 2. Ionic currents are calculated for a space-clamped squid giant axon using the HodgkinHuxley model, with all parameters set to their default values (as listed on page 191 of volume 2
of the text) except for one parameter. For times t < 0, the membrane potential is held at 75 mV
and the model is at steady state. At t = 0, the membrane potential is stepped to +5 mV and the
resulting ionic current density is computed. Results for six calculations are shown in the following
figure.
J1 J2
1
0
J4
J3
J5
J6
1
2
0
1000
2000
Time (ms)
Part a. Which curve represents the ionic

values except coN a = 50 mmol/L? Explain.
Part b. Which curve represents the ionic
values except coK = 400 mmol/L? Explain.
Part c. Which curve represents the ionic
values except GN a = 0? Explain.
Part d. Which curve represents the ionic
values except GK = 0? Explain.
current that results when all parameters have default

Problem 3. Space-clamped responses of the Hodgkin-Huxley model were calculated with the
leakage conductance set to zero, GL = 0, and with all other parameters set to their default values. The model was stimulated with a pulse of membrane current density of duration 0.5 ms; the
amplitude was varied. The following figure shows the response for an amplitude of 40 A/cm 2 .
100
Jm
mV and A/cm
0
Vm
100
Jion
200
300
400
500
0.5
1
1.5
2
Time (ms)
2.5
Jion (t = 0.7 ms) (A/cm )
For each amplitude of the pulse of membrane current density, the ionic current density J ion and
the membrane potential Vm were determined at t = 0.7 ms, where t = 0 marks the onset of the
current pulse. The relation between Jion at t = 0.7 ms and Vm at t = 0.7 ms that results when
the pulse amplitude is varied is shown in the following gures. The left panel shows results for a
broad range of membrane potential, from 80 to +60 mV. The right panel shows results for the
narrower range from 76 to 62 mV.
0
100
200
0.1
300
400
80 60 40 20 0
20
0.2
40 60
76 74 72 70 68 66 64 62
Vm (t = 0.7 ms) (mV)
Part a. Determine the value of the resting potential to within 1 mV. Explain your choice.
Part b. If the current stimulus is such that Vm (t) = 66 mV at t = 0.7 ms, does the membrane
potential increase with time or decrease with time? Explain.
Part c. Determine the value of the threshold potential to within 1 mV. Explain your choice.
Part d. Between the resting potential and this threshold potential, determine whether |J N a | > |JK |,
|JN a | = |JK |, or |JN a | < |JK |. Explain.
Part e. Just above the threshold potential, determine whether |J N a | > |JK |, |JN a | = |JK |, or
|JN a | < |JK |. Explain.
Problem 4. The Hodgkin-Huxley model of a space-clamped squid giant axon stimulated by a
pulse of membrane current of amplitude 20 A/cm2 and of duration 0.5 ms produces a membrane
action potential. You can demonstrate this to yourself by running the space-clamped version of
the Hodgkin-Huxley simulation software provided with this subject. Start by using the default
parameters. If you change the membrane capacitance from 1 F/cm2 to 20 F/cm2 , no action
potential occurs.
Part a. Explain why no action potential occurs for the larger value of membrane capacitance. You
may base your explanation on comparison of the membrane currents, conductances, and activation
variables for the default parameters and for the increased capacitance condition. Alternatively, you
may wish to perform additional computations with other values of membrane capacitance.
Part b. With membrane capacitance xed at 20 F/cm2 , determine a set of parameters that produce
an action potential with a waveform that is identical to the action potential obtained with the default
parameters. To determine whether or not the action potential is identical to that obtained with the
default parameters, you can superimpose plots and/or look at the parameters computed from the
responses. You should use the computer as a tool to check your ideas and not as a substitute
for thinking. You should avoid a strictly trial-and-error approach. There are simply too many
parameters in the Hodgkin-Huxley model for you to explore them all randomly. When you have
arrived at a satisfactory solution, explain why your parameter change produces the desired result.
Problem 5. Constant currents I1 and I2 are applied to the exteriors of Axons 1 and 2, respec
tively, and the resulting time-independent changes in membrane potential are v m1 (z) and vm2 (z),
respectively. I1 and I2 are adjusted so that vm1 (0) = vm2 (0) = 10 mV. This change in potential is
sufciently small so that the membrane voltage-current characteristic may be assumed to be linear.
You may also assume that ro ri for both axons and that ro is the same for both axons. The
geometries and parameters for Axons 1 and 2 are given below, where a is the axon radius, i is the
cytoplasmic resistivity, and Gm is the specic membrane conductance.
I1
Axon 1
Axon
a
i
#
(m) (cm)
1
100
100
2
10
100
I2
Gm
(S/cm2 )
5103
(1/8)103
Axon 2
0.1
z (cm)
a) Let vm1 (0.1) and vm2 (0.1) be the membrane potential changes at z = 0.1 cm for the
two axons. Determine the value of the ratio A = vm1 (0.1)/vm2 (0.1).
b) Determine the value of the ratio B = I1 /I2 .
Problem 6. A large unmyelinated axon is immersed in oil, and ve different arrangements of

electrodes for delivering current stimuli and for measuring potential responses are attached to the
axon as shown below.
7
ie (t)
v(t)
a
5C
5C
ie (t)
v(t)
b
5C
5C
C
ie (t)
v(t)
c
5C
C
ie (t)
v(t)
+
e
+
v(t)
ie (t)
The stimulus current, a brief positive pulse at t = 0, is the same for each arrangement of electrodes.
The pulse has a duration that is much shorter than the membrane time constant of the cell, and a
strength that is low enough that the cells voltage response remains in its linear range of operation.
The space constant of the cell is C . In arrangement d, the potential is recorded and the current is
delivered at the same longitudinal position. In part e, the electrodes are much longer than C .
For each of the different arrangements (parts a-e in the figure) determine which of the following
waveforms for v(t) represents the deviation of the measured potential from its resting value. For
each waveform, the horizontal axis corresponds to v(t) = 0, and the vertical axis to t = 0. If no
waveform applies, answer None. Explain the basis of your choice in each case.
v1 (t)
v2 (t)
v3 (t)
v4 (t)
v5 (t)
v9 (t)
v12 (t)
v10 (t)
v13 (t)
v11 (t)
v14 (t)
v6 (t)
v7 (t)
v8 (t)
2.791J/2.794J/6.021J/6.521J/BE.370J/BE.470J/HST.541J
Reading
Lecture 32 Volume 2:
Issued: November 18, 2004

Due: December 2, 2004
6.5-p407
p407-416
6.3.2-6.3.6
6.6 6.7
Announcements
This homework assignment is due in 2 weeks, on December 2. Please note, however, that the nal
HH oral presentations take place on December 1 and 3. Therefore, you might want to get started
early on this assignment.
HH Dry Runs are scheduled for November 23 (see schedule in the calendar section). Recitations on
that day are cancelled.
Exercise 1. Estimate the conduction velocity of the action potential from the measurements on a
single myelinated nerve ber shown in Figures 5.19-5.21 in volume 2 of the text..
Exercise 2. Dene the safety factor.
Exercise 3. The following gure shows two putative records of membrane currents recorded from
two membrane patches, each of which contains a single channel, in response to a step of depolar
izing membrane potential.
t
Vm (t)
(1)
(2)
Each of these channels has a linear voltage-current characteristic when the channel is open.
a) Which, if any, of these records could be from a single, voltage-gated channel? Explain.
b) Which, if any, of these records could be from a single channel that is not voltage-gated?
Explain.
+50
+25
0
25
50
Km
16
12
8
4
0
Vm
0.5
Time (ms)
Km (nA/cm)
Vm (mV)
Problem 1. A myelinated axon, shown schematically in Figure 5.8 of volume 2 of the text, has
the dimensions L = 2 mm, D = 14 m, d = 10 m, l = 0.7 m. The resistivity of the cytoplasm
i = 110 cm, and the resistance of the extracellularly space can be assumed to be negligible.
The membrane potential, Vm , and current per unit length, Km , are shown in Figure 1 for a location
at an internode as an action potential propagates down the ber. Assume that the internode can be
1.0
Figure 1: Membrane potential and current at an internode.

represented by a linear cable with the equivalent membrane model shown in Figure 2.
Km
Intracellular
+
gmi
cmi
Vm
Vmo
Membrane
Extracellular
Figure 2: Model for voltage-current relation at an internode.

a) Estimate the conductance, gmi , and capacitance, cmi , per unit length of internode from the
data given. [Hint - the capacitance current is zero when dVm /dt = 0 and largest when
dVm /dt is large.]
b) Find the values of the membrane time constant, M i , and the axon space constant, Ci , of the
internode.
c) Find the specic conductance, Gmi , and capacitance, Cmi , per unit area of internodal myelin.
d) Given that the myelin is composed of 150 lamellae, nd the specic conductance G m , and
capacitance, Cm , per unit area for a single layer of myelin membrane. How do these values
compare to those of unmyelinated bers?
e) Now consider an unmyelinated ber whose diameter is 10 m and whose membrane has a
specic capacitance, Cm , and conductance, Gm , per unit area equal to that found in part d).
What is the time constant, M , and space constant, C , of this ber? Compare these results
to those found in part b). What is the physiological signicance of the difference?
0.8
JK
Squid giant
axon
JN a
J (mA/cm )
0
0.8
5.0
JK
Toad node
of Ranvier
0
JN a
5.0
1
Time (ms)
Figure 3: Comparison of ionic currents during an action potential for an unmyelinated squid giant
axon and a myelinated toad node of Ranvier. These ionic currents are based on calculations of
models of the squid giant axon (adapted from Cooley and Dodge, 1965, Figure 2.4) and toad node
of Ranvier (adapted from Frankenhaeuser and Huxley, 1964, Figure 6).
Problem 2. A squid giant axon (which is an unmyelinated axon) has a diameter of 500 m. The
ionic currents during the passage of one action potential are shown in Figure 3. The normal internal
concentration of sodium is 40 mmol/L. In contrast, consider a frog myelinated ber for which the
axon diameter (not including the myelin) is 10 m, the ber diameter (including the myelin) is
14 m, the internodal length is 2 mm, the nodal length is 0.7 m, and the nodal area is 22 m 2 .
We shall assume that action potentials occur only at the nodes. The ionic currents at the node of
Ranvier during the passage of an action potential are also shown in Figure 3. You may assume that
the sodium current is negligible in the internodes. The normal internal concentration of sodium is
10 mmol/L in the frog ber.
Both the squid unmyelinated ber and the frog myelinated ber conduct action potentials with
about the same conduction velocity. This problem concerns the energetic efciency of these two
bers.
a) Compute the number of moles of sodium entering each ber per action potential per unit
length of ber.
b) Assume that the energy expended to pump the accumulated sodium out of the cell can be
measured in terms of the number of ATP molecules hydrolyzed to ADP and assume that 3
moles of Na+ are transported out of the axon for every mole of ATP hydrolyzed to ADP
inside the axon by the (Na+ -K+ )ATPase pump. Find the ratio of energy expended per unit
length per action potential in order to pump out the accumulated sodium for the squid un
myelinated ber to that for the frog myelinated ber.
c) Describe the advantages of the frog myelinated ber over the squid unmyelinated ber.
Problem 3. Figure 4 shows a detail of a propagating action potential calculated using a model of
a myelinated nerve ber (Figure 5.31 in volume 2 of the text).
a) Describe a method by which the data in Figure 4 could be analyzed to estimate the current
3
Vm (z, to ) Vmo (mV)
110
to = 0.75
100
90
5
6
7
Node Number
Figure 4: Membrane potential along a myelinated ber computed from a model of electrical char
acteristics of the node and internode (Figure 5.31 in volume 2 of the text). The membrane potential
is plotted as a function of distance along the ber (expressed in units of internodal length where
L = 1.38 mm).
Im owing out of a node. Apply your method to calculate the current owing out of node 6
at t0 = 0.75 ms. Assume that ri = 140 M/cm>> ro .
b) Describe a method by which the data in Figure 4 could be analyzed to estimate the current
density Km owing out of an internode. Apply your method to determine whether current is
owing into or out of the internode between nodes 5 and 6 at t0 = 0.75 ms.
Problem 4. Although there is considerable scatter, the ratio of the inner diameter d to outer diam
eter D of the layer of myelin that encircles a myelinated ber tends to be about 0.74, as shown in
the following gure, where every symbol represents measurements of d/D and d for a different
ber.
0.9
0.85
d/D
0.7
0.65

0.8
0.75

0.6
0.55

vagus nerve
sciatic nerve
0.5
0.5 1 1.5 2 2.5 3 3.5 4 4.5 5
d (m)
The point of this problem is to investigate the hypothesis that this relation between d and D results
from an evolutionary optimization of the cable model.
Part a. Assume that the myelinated part (the internode) of a myelinated ber can be represented by
the cable model. Assume the myelin can be represented by a homogeneous electrical material with
resistivity m and permittivity m . Assume the intracellular conductor is a homogeneous conductor
with resistivity w . Assume that the extracellular conductor has negligible resistance. Determine
an expression for the space constant C of this model in terms of the inner diameter d and the outer
diameter D of the layer of myelin. Hint: The radial resistance of a cylindrical shell is given below.
L
d
+
V
R=
V
D
ln
=
I 2L d
Part b. The expression derived in part a is plotted below

0.6
0.4
C/o
0.2
0.5
d/D
where o = D m /8w . Thus, if D is xed (i.e., if the axon is constrained to t into a constant
volume), then o is a constant, and C is maximum when d 0.6D.
b1) Explain in physical terms why the space constant gets smaller as the value of d decreases
below 0.6D.
b2) Explain in physical terms why the space constant gets smaller as the value of d increases
above 0.6D.
Part c. The value of d/D that maximizes the space constant of the cable model is remarkably close
to the ratio of 0.74 seen experimentally. Nevertheless, it is smaller. One possible reason why it is
smaller is that we ignored the resistance of the outer conductor ro . How would the space constants
dependence on d/D change if the resistance of a thin layer of saline (thickness = 0.1D) were
included in the calculation. Make a plot that contains both the old relation (shown in the previous
plot) and the new relation. Briey describe how the addition of the outer resistance changes the
predicted space constant.
2.791J/2.794J/6.021J/6.521J/BE.370J/BE.470J/HST.541J
Issued: December 2, 2004

This homework assignment will not be collected.
Exercise 1. Explain the origin of gating current.

Exercise 2. State whether each of the following are true or false and give a reason for your answer.
a) Tetrodotoxin blocks the ow of potassium through the sodium channel.
b) The macroscopic sodium current recorded by an electrode in a cell is a sum of the singlechannel sodium currents that ow through single sodium channels.
c) The macroscopic sodium current recorded by an electrode in a cell is the average of the
single-channel sodium currents that ow through single sodium channels.
d) Ionic and gating currents give identical information about channel kinetic properties.
Exercise 3. Explain why the gating current is outward in response to a depolarization independent
of the sign of the charge on the gate.
Exercise 4. List 4 distinct properties shown by ionic currents measured from single voltage-gated
ion channels.
Problem 1. The voltage across a membrane patch is stepped from V mo to Vmf at t = 0 and singlechannel ionic currents are recorded as a function of time. Typical records at 6 different values of
Vmf are shown in the following gure.
f
Vm
(mV)
0
0
1
20
1.4
0
40
Current (pA)
1.8
0
60
2.2
0
80
2.6
100
3
0
Time (ms)
a) Is the open-channel voltage-current characteristic of this channel linear or nonlinear?
b) What is the conductance of the open channel?
c) What is the equilibrium (reversal) potential for this channel?
d) It is proposed that this channel is the voltage-gated sodium channel responsible for sodium-
activated action potentials. Discuss this suggestion.
Problem 2. Transport of an ion through a cell membrane can be represented by a population of

voltage-gated channels where each channel contains one two-state gate. The two states are state S 0
and state S1 and transitions between these states obey rst-order kinetics with voltage dependent
rate constants.
(Vm )
S0
S1 .
(Vm )
Single-channel
State
current (pA) occupancy
In response to a step of voltage across the channel, the state occupancy of the channel, the singlechannel current, and the probability that the channel occupies state S 1 are shown in the following
gure.
S1
S0
Membrane
potential
(mV)
Probability of
occupancy
of state 1
0.5
+20
60
4 5 6
Time (ms)
10
a) For which state is the channel non-conducting?

b) Determine both the equilibrium (reversal) potential for conduction through this channel and
the conductance of the channel when the channel is conducting.
c) For Vm = 20 mV determine the rate constant (20) and (20) where the voltage is expressed
in mV.
d) Sketch the probability that the channel occupies state S0 as a function of time.
e) Briey describe one experimental method that can provide an estimate of channel density.
Be specic about which data you propose to use and how you propose to estimate the density
from these data.
f) Measurements indicate that there are 1000 channels per m2 in the membrane of this cell.
Sketch the ionic current density Jm (t) that would be expected with the voltage step shown
in the gure. Indicate relevant dimensions on the sketch.
Problem 3. This problem deals with the relation of current to voltage for single ion channels.
Assume that conduction through an open ion channel is governed by the equation
I = (Vm Ve ),
where I is current through a single open channel, is the conductance of a single open channel,
Vm is the membrane potential across the channel, and Ve is the equilibrium (reversal) potential for
the channel. For each of the channels in this problem, assume that = 25 pS and V e = 20 mV.
a) The membrane potential Vm and the average single-channel current i obtained from three
different single channels (A, B, and C) are shown in Figure 1. Both the membrane potential
Channel A
Vm (t) (mV)
Channel B
Vm (t) (mV)
20
Vm (t) (mV)
20
60
+80
+10
60
i(t) (pA)
i(t) (pA)
0.5
i(t) (pA)
Channel C
0.5
0.75
+0.3
-0.2
Figure 1: Average single-channel currents.

and current are plotted on a time scale such that the changes appear instantaneous and only
the nal values of these variables can be discerned in the plots; i.e., the kinetics are not
shown. For each of these channels, answer the following questions and explain your answers:
i) Is this channel voltage-gated for the illustrated depolarization?
ii) Is the channel activated (opened) or inactivated (closed) by the illustrated depolariza
tion?
b) Assume that each voltage-gated channel contains one two-state gate where is the time
constant of transition between states. For each of the channels, sketch the time course of i(t)
on a normalized time scale t/ . Clearly show the current near t = 0.
Problem 4. Three three-state voltage-gated channels (channels a, b, and c) have the kinetic dia
gram and state occupancy probabilities shown in Figure 2. These channels have the same voltage
dependent rate constants and the same equilibrium potential which is +40 mV. For the membrane
potential shown, the channels are in state 1 with probability 1 for t < 0 and have the indicated rate
constants for t > 0. The channels differ only in their state conductances and state gating charges as
shown in Figure 3. Denote the expected values of the single-channel random variables as follows:
the conductance as ga (t), gb (t), and gc (t); the ionic currents as ia (t), ib (t), and ic (t); the gating
charges as qa (t), qb (t), and qc (t); the gating currents as iga (t), igb (t), and igc (t).
a) Which of the waveforms shown in Figure 4 best represents gb (t)? Explain.
b) Which of the waveforms shown in Figure 4 best represents gc (t)? Explain.
S1
5
1
S2 10
S3
Vm (t)
State occupancy probability
1
x1 (t)
x3 (t)
0.5
x2 (t)
0
0
0.5
1
Time (ms)
1.5
Figure 2: State diagram and occupancy probabilities for a three-state channel. The state occupancy
probabilities for states S1 , S2 , and S3 are x1 (t), x2 (t), and x3 (t), respectively.
Channel a
S1
1 = 10
Q1 = 1
S2
2 = 0
Q2 = 0
10
S2
2 = 10
Q2 = 0
10
S2
2 = 0
Q2 = 0
10
S3
3 = 0
Q3 = 0
Channel b
S1
1 = 0
Q1 = 0
S3
3 = 0
Q3 = 1
Channel c
S1
1 = 0
Q1 = 1
S3
3 = 10
Q3 = 0
Figure 3: State diagrams of three three-state channel models. The models differ in state conduc
tances and state gating charge but not in rate constants.
c) Which of the waveforms shown in Figure 4 best represents iga (t)? Explain.
d) Which of the waveforms shown in Figure 4 best represents igc (t)? Explain.
e) Which of these channel models exhibits activation followed by inactivation of the ionic cur
rent? Explain.
f) Which of these channel models exhibits an ionic current that does not inactivate? Explain.
g) Which of these channel models represents a channel that closes on depolarization? Explain.
5
Vm (t)
Vm (t)
w1 (t)
w5 (t)
w2 (t)
w6 (t)
w3 (t)
w7 (t)
w4 (t)
w8 (t)
Figure 4: Waveforms of responses. The horizontal axis corresponds to w(t) = 0, and the vertical
axis to t = 0.
Problem 5. Figure 5 shows a model of a voltage-gated ion channel with one three-state gate plus
representative single-channel ionic and gating current records.
a) Assume that the voltage-current characteristic of the channel is the same for states 1 and 3
and is linear. Determine the open channel conductance and equilibrium (reversal) potential
for this channel.
b) The ionic current trace shown in Figure 5 has three non-zero segments. Determine which
state the gate is in during each non-zero segment. Explain your reasoning.
c) Figure 6 illustrates the dependence of the steady-state probability that the channel will be
in each of its three states on the membrane potential. Let iss represent the average value
of the ionic current that results after steady-state conditions are reached in a voltage clamp
experiment in which Vm is held constant. Assume that the experiment is repeated for a
number of different values of membrane potential Vm . Plot the relation between iss and Vm .
Describe the important features of your plot.
state 1
+50
50
outside
state 2
t (ms)
outside
state 3
ig (pA)
inside
t (ms)
i (pA)
3
2
1
inside
Vm (mV)
inside
t (ms)
outside
Figure 5: Channel with one three-state gate. The left panels illustrate the three states: states 1 and
3 are open states, state 2 is a closed state. The right panels illustrate the responses of the channel
to a step in membrane potential Vm (t) at time t = 0 (top right) which gives rise to the ionic current
i(t) and gating current ig (t) illustrated in the middle right and lower right panels, respectively.
1
x1
x2
x3
0.5
0
100
100
Membrane potential (mV)
Figure 6: Steady-state probabilities for a channel with one three-state gate. x 1 , x2 , and x3
represent the steady-state probabilities of being in state 1, state 2, and state 3, respectively, as a
function of membrane potential.
2.791J/2.794J/6.021J/6.521J/BE.370J/BE.470J/HST.541J
Hodgkin-Huxley Project
This theoretical project is intended to provide an opportunity to learn about the complex behav
iors that can be exhibited by the Hodgkin-Huxley model and to compare behaviors of the model
with behaviors of electrically excitable cells. We have two simulations. The rst models a spaceclamped axon. That model generates membrane action potentials. The second models an axon
without space-clamp (although the second model can simulate a space clamp since the longitudi
nal resistances can be set to zero). The second model can produce propagated action potentials.
The second model can be used to explore a wider range of phenomena than the rst. The rst
model is faster and simpler than the second. Thus both models are useful, and your project can use
either or both of the models.
Students are STRONGLY encouraged to work in pairs, however, individual projects will be
approved if there are extenuating circumstances. If a pair of students collaborate on a project they
should submit a single proposal and a single report which identies both members of the team and
gives both email addresses. Proposals should be submitted via the form available on the MIT
server. Proposals will be returned as soon as possible so that students can revise them. Only the
nal, accepted proposal will be given a grade.
The demonstration project performed in lecture on the effect of temperature cannot be the basis
of a student project.
Practical considerations in the choice of a topic
Projects can involve almost any of the properties of the Hodgkin-Huxley model. However, to avoid
projects whose aims are vague (e.g., I would like to understand how the Hodgkin-Huxley model
works) the proposed project should be in the form of a specic and testable hypothesis. Projects
that involve months of computation should obviously be avoided. The amount of computation time
should be explicitly taken into account in planning a project. For example, any project that involves
measuring the threshold of occurrence of an action potential for many different parameter values is
bound to be very time consuming, because determining the threshold for a single set of parameters
itself involves many computations. The task is to choose a physiological property of the excitation
of the action potential that is of interest, and then to dene a specic, feasible project.
Choice of topics
Topics can involve comparing predictions of the Hodgkin-Huxley model with measurements on
cells. For example, the text contains data on the effects of many external parameters (e.g., ionic
concentrations, cell type) on action potentials. A project might involve reading the original pa
pers that describe such measurements (some were made before the Hodgkin-Huxley model was
formulated), and testing the hypothesis that these measurements are (or are not) consistent with
1
the Hodgkin-Huxley model. Similarly, a project might involve examining the effect of some phar
macological substance on measurements of the action potential and testing the hypothesis that the
substance produces its effect by changing one or another parameter of the model. These projects
will require some reading of original literature which is often difcult and usually time consuming.
However, such a project can lead to a very rewarding educational experience. Alternatively, the
project might involve a purely theoretical topic in which some property of the model is explained
in terms of its underlying structure. This type of project does not necessarily involve reading the
original literature.
Examples of hypotheses
1. Hypothesis The effect of temperature on the conduction velocity of the squid giant axon
can be t by the Hodgkin-Huxley model. Articles in the literature should be consulted for
this project:
Chapman, R. A. (1967). Dependence on temperature of the conduction velocity of the
action potential of the squid giant axon. J. Physiol. 213:1143-1144.
Easton, D. M. and Swenberg, C. E. (1975). Temperature and impulse velocity in giant
axon of squid loligo pealei. Am. J. Physiol. 229:1249-1253.
2. Hypothesis When two action potentials are elicited, one just after another, the velocity
of the second is slower than the velocity of the rst action potential. This phenomenon is
predicted by the Hodgkin-Huxley model. Articles in the literature should be consulted for
this project:
George, S. A., Mastronarde, D. N., and Dubin, M. W. (1984). Prior activity inuences
the velocity of impulses in frog and cat optic nerve bers. Brain Res. 304:121-126.
3. Hypothesis The threshold current for eliciting an action potential with an intracellular
electrode is higher for a space-clamped than for an unclamped model of an axon.
4. Hypothesis Increasing the membrane capacitance will decrease the conduction velocity.
5. Hypothesis Increasing the membrane conductance (by scaling all the ionic conductances)
will increase the conduction velocity.
6. Hypothesis Increasing the external concentration of sodium will increase the conduction
velocity.
7. Hypothesis Increasing the external concentration of potassium will increase the conduc
tion velocity.
8. Hypothesis Increasing the external concentration of calcium will increase the conduction
velocity.
9. Hypothesis Increasing the temperature will increase the conduction velocity.
10. Hypothesis The difference in waveform of the action potential of a frog node of Ranvier
and of a squid giant axon (Figure 1.9 in volume 2 of the text) can be reproduced by the
Hodgkin-Huxley model of a squid giant axon by a change in temperature.
2
11. Hypothesis The membrane capacitance determines the time course of the rising phase of
the action potential. Increasing the membrane capacitance decreases the rate of increase of
the rising phase of the action potential.
12. Hypothesis The falling phase of the action potential (repolarization) can occur in the
absence of a change in potassium conductance.
13. Hypothesis Increasing the temperature sufciently blocks the occurrence of the action
potential because the membrane time constant limits the rate at which the membrane vari
ables can change and prevents the difference in time course of the sodium and potassium
activation which is responsible for initiation of the action potential.
14. Hypothesis The initiation of the action potential is independent of the potassium conduc
tance.
15. Hypothesis The prolonged plateau of the cardiac muscle action potential can be accounted
for by the Hodgkin-Huxley model with a potassium conductance that has a slow activation.
16. Hypothesis The effect of tetraethylammonium chloride (TEA) on the action potential of
the squid giant axon can be modelled with the Hodgkin Huxley model by decreasing K n and
increasing Kh . Articles in the literature should be consulted for this project:
Armstrong, C. M. (1966). Time course of TEA+ -induced anamalous rectication in
squid giant axons. J. Gen. Physiol. 50:491-503.
Armstrong, C. M. and Binstock, L. (1965). Anomalous rectication in the squid giant
axon injected with tetraethylammonium chloride. J. Gen. Physiol. 48:859-872.
Tasaki, I. and Hagiwara, S. (1957). Demonstration of two stable potential states in the
squid giant axon under tetraethylammonium chloride. J. Gen. Physiol. 40:859-885.
17. Hypothesis The shape of the action potential in the presence of tetraethylammonium chlo
ride (TEA) can be accounted for by the Hodgkin-Huxley model with a reduced maximum
value of the potassium conductance. Articles in the literature should be consulted for this
project:
Armstrong, C. M. (1966). Time course of TEA+ -induced anamalous rectication in
Armstrong, C. M. and Binstock, L. (1965). Anomalous rectication in the squid giant
18. Hypothesis Increasing the external calcium concentration will block the occurrence of the
action potential because this will reduce the difference in the time constant of sodium and
potassium activation which is responsible for the initiation of the action potential.
19. Hypothesis Increasing the external concentration of potassium will decrease the refractory
period; decreasing this concentration will lengthen the refractory period.
20. Hypothesis Increasing the external concentration of sodium will decrease the refractory
3
21. Hypothesis Absolute and relative refractory periods are decreased by increasing the rate
constants for sodium inactivation and for potassium activation.
22. Hypothesis Repolarization cannot occur if the potassium activation rate constant is zero.
23. Hypothesis The threshold of the action potential to a brief pulse of current decreases as
the external potassium current is increased.
24. The Hodgkin-Huxley model with default parameters does not exhibit accommodation. Hy
pothesis Accommodation occurs if the leakage conductance is increased.
25. The Hodgkin-Huxley model with default parameters does not exhibit accommodation. Hy
pothesis Accommodation occurs if the potassium conductance is increased.
26. Hypothesis Increasing the leakage equilibrium potential will block the action potential.
27. Hypothesis The effect of the changes in concentration of sodium ions on the action po
tential of the giant axon of the squid can be accounted for by the Hodgkin-Huxley model.
Articles in the literature should be consulted for this project:
Hodgkin A. L. and Katz, B. (1949). The effect of sodium ions on the electrical activity
of the giant axon of the squid. J. Physiol. 108:37-77.
Baker, P. F., Hodgkin, A. L., and Shaw, T. I. (1961). Replacement of the protoplasm of
a giant nerve bre with articial solutions. Nature 190:885-887.
28. Hypothesis In response to rectangular pulses of current, the rheobase of the strengthduration relation increases as temperature increases.
29. Hypothesis An increase in temperature results in a decrease in the duration of the refrac
tory period.
30. Hypothesis The threshold membrane potential at which the Hodgkin-Huxley model pro
duces an action potential in response to a brief pulse of current is equal to the membrane
potential for which the linearized Hodgkin-Huxley equations have unstable eigenvalues.
31. Application of a long-duration constant current to the Hodgkin-Huxley model produces a
train of action potentials. Hypothesis The frequency of the action potentials increases
with increasing current amplitude.
train of action potentials. Hypothesis The frequency of action potential increases as the
parameter Kn is increased.
train of action potentials. Hypothesis The frequency of action potential increases as the
temperature is increased.
34. Hypothesis An increase in the external concentration of potassium increases the threshold
potential at which an action potential is elicited.
35. Hypothesis Increasing Kh will result in an increase in the steepness of the repolarization
phase of the action potential.
4
Any of these (or other) hypotheses can be the starting point for a project. Most of the hy
potheses given above are simplistic, and a careful investigation will reveal their shortcomings. The
Hodgkin-Huxley model is sufciently complex that investigation of any of the hypotheses will
most likely lead to unexpected results. You should pursue these unexpected results and try to un
derstand their bases. For example, you may nd that in pursuing some hypothesis you choose to
change some parameter of the model that you expect to result in some change in action potential
waveform. The resulting computation might reveal, much to your surprise and chagrin, that no
action potential has occurred. Determine why no action potential occurred. The explanation will
usually be instructive. Your aim should be not simply to reject or accept the hypothesis but to delve
into the topic in sufcient depth so as to a deepen your understanding of the model. One outcome
of the project might be to restate your original hypothesis in a new and more sophisticated form.
Beginning with the proposal and extending through the project, you should keep clearly in
mind that you are not investigating nerve membrane in these exercises. You are investigating
the Hodgkin-Huxley model for nerve membrane. Your explanations of all phenomena must be
in terms of the primitive concepts of this model the ionic conductances, ionic concentrations,
ionic currents, the capacitance, and the variables m, n, and h. Explanations in terms of molecular
channel mechanisms or electrodiffusion of ions in the membrane are irrelevant in so far as they are
not contained in the Hodgkin-Huxley model!

Department of Electrical Engineering and Computer Science
Department of Mechanical Engineering
Division of Bioengineering and Environmental Health
2.791J/2.794J/6.021J/6.521J/BE370J/BE470J/HST541J
Fall, 2003
MicroFluidics Project Laboratory
Introduction
This page contains helpful information about the proposal, experimentation, analysis, and
report-writing stages of this laboratory. You should read through it at each stage to make
sure you understand what is required.
Overview
This laboratory project is intended to provide an opportunity to learn about
1. designing an experiment,
2. acquiring, processing, and interpreting experimental data, and
3. communicating the results to others.
This laboratory project is also intended to introduce the emerging field of microfluidics.
Microfluidics refers to the use of devices in which fluid flows are restricted to channels
with micrometer dimensions. Such devices are interesting for at least 3 reasons:
1. Microfluidic devices can be manufactured using photolithographic techniques that
allow many devices to be constructed simultaneously (just as modern electronic
devices are manufactured). Bulk manufacturing reduces the cost per device.
2. Since they are small, many devices can be fit into a small volume, leading to the
idea of total "labs-on-a-chip" replacing labs that occupy benches or even whole
rooms today.
3. Flows in microscopic chambers can exhibit behaviors that are difficult or
impossible to produce in macroscopic chambers. These flow regimes can be used
to simplify measurements that are difficult or impossible to make
macroscopically.
This laboratory project is intended to take advantage of microfluidics to measure the
properties of molecular transport by diffusion.
Microfluidics
More than any other single factor, bulk fabrication has made possible today's vast array
of powerful and inexpensive electronic devices. The millions of components in a modern
computer are fabricated in parallel, making the manufacture of such integrated circuits
little more costly than the manufacture of circuits that contain only tens of components.
Similar bulk fabrication techniques are currently being developed for fluidic devices, and
the resulting microfluidic devices hold promise to similarly revolutionize chemical and
biochemical analysis systems. For example, the integration of all of the components
needed for the sequencing of DNA (i.e., valves to control flows, incubation chambers,
mixing chambers, heating/cooling chambers) may soon allow "labs-on-a-chip" to replace
whole biochemistry labs.
Microfluidic devices are smaller than conventional macrofluidic components, and their
smaller size facilitates many kinds of analysis. For example, when two fluids come into
contact, they mix by a variety of mechanisms. The most familiar mechanism from our
macroscopic experiences is convection: i.e., the mixing of fluids caused by motions of
fluid, as in stirring. When fluids are constrained to small volumes, convection is
constrained and mixing results almost entirely by diffusion (i.e., by random collisions
between molecules). As a result, it is possible to design microfluidic systems in which
dissimilar fluids flow along side each other over long distances without significant
mixing. Such "laminar-flow" profiles are difficult or impossible to produce
macroscopically and provide unique opportunities to study molecular transport by
diffusion.
Methods
This section describes basic experimental methods used in microfluidic systems. The
descriptions are not complete: you are encouraged to devise more detailed procedures
where appropriate. You may also substitute your own novel methods. However, if your
novel methods require the use of additional equipment, you are responsible for obtaining
that equipment. The staff is only responsible for supplying the equipment described in
this section.
In this experiment, you will use dyes and other chemicals that could stain or irritate your
skin. Wash your hands thoroughly immediately after exposure to any chemicals. Clean up
minor chemical spills immediately. Report major spills to the staff. Rubber gloves will be
available.
No foods or beverages will be allowed in the laboratory.
Chambers
Our experiment chambers are 2-dimensional microscopic channels formed on the surface
of a transparent silicone rubber. The silicone rubber is then bonded to glass slide.
Fabrication methods can be found in the literature (Whitesides-1998).
The following figure shows the topology. The channels are 500 &mum wide and
approximately 100 &mum deep. The inlet channels are approximately 25 mm long. The
outlet channel is approximately 35 mm long.
Establishing Fluid Flow

A variety of methods have been used to pump fluids through microchambers. Some
investigators use macroscopic pumps (e.g., syringe pumps, peristaltic pumps, etc.).
Others use electrically driven flows (e.g., electro-osmosis or electrophoresis). In this lab,
we recommend that you use gravity flow. With our channel designs, a few millimeter
difference in fluid level is sufficient to drive flow rates on the order of micrometers per
second, which are satisfactory for most experiment designs.
Input and output ports connect the microfluidic channels to macroscopic fluid reservoirs,
as shown in the following photograph.
While gravity feed is simple to implement, it is also very sensitive to external

disturbances, such as table vibrations. Be aware that even atmospheric disturbances
(caused by breathing) can affect your results.
Gravity feed can also be difficult to start. We recommend the following procedure for
filling your chamber with fluid.
Fill the input reservoir(s) approximately 2/3's full with the desired liquids, taking
care not to introduce any foreign matter, and not to break the reservoirs off of the
slide.
Carefully attach the provided syringe to the output reservoir, and use the syringe
to gently pull liquid through the channel. Watch the channel carefully to see if
liquid has been pulled through. Because of the small width of the channel, you
may not build up a noticeable amount of liquid in the output reservoir, but if the
channel is full, the experiment will work fine.
Now fill the output chamber with liquid until the liquid reaches approximately the
same height as the input chambers. You are now ready to begin observation of
your channel.
Please take care when using these chambers. They are easily broken. Always flush your
chamber with deionized water after use. If saline solutions are allowed to evaporate, the
salts will clog the channels and solids are not easily removed.
Microscope
Our microscopes have been customized for this microfluidics laboratory, as shown
below.
The microfluidics chambers can be clamped to the stage of the microscope using a slide
holder that has two position control knobs. The microscope has 3 objectives: 4X, 10X,
and 20X. These objectives focus an image of the chamber onto a video camera.
Illumination is provided by LEDs and can come from the top (epi-illumination) or bottom
(trans-illumination). Epi-illumination works best for fluorescent imaging and transillumination works best for brightfield illumination. The microscope has a focus control
knob that allows focusing with &mum resolution.
Please avoid touching the optical components. They are sensitive, and easily scratched.
Even fingerprints can badly degrade the images you will get.
Measuring Flow Rates

Quantitative interpretation of data from microfluidic systems often requires knowledge of
the flow rates. Although flow rates can in principle be determined by measuring the time
it takes for some known volume of fluid to flow through system, it is often more
convenient to measure flow rates by tracking microscopic particles that are suspended in
the fluid. Microscopic polystyrene beads with diameters on the order of 1 &mum are
available for this purpose. Bead solutions can be used in separate experiments to calibrate
flow rates. Alternatively, beads can be added to test solutions to directly measure the flow
rates of test solutions. If the concentration of beads is dilute and if the flow rates are slow,
then individual beads can be tracked across frames that are recorded at a 10-30
frame/second rate (depending on the speed of the computer). If the concentration of beads
is dense or if the flow rates are high, then the LED can be pulsed to produce a
stroboscopic illumination with multiple strobes per frame. Then multiple images of each
bead on a single frame can be analyzed to determine the flow rate.
Computer
A computer running Linux is attached to the video camera via FireWire. A program
called camscope can be used to view and record images and brightness profiles.
Activating the Software

The main program for acquiring and processing data is called camscope. Source code for
camscope is available at http://www.sourceforge.net/projects/camscope.. This program
stores results and temporary files in the current working directory. At the login prompt,
log in with the username knoppix and the password knoppix. To avoid confusing your
data with that of another group, each laboratory group should store results in a separate
directory. Please use the following naming convention. If you are in laboratory group B2,
then type the Linux commands
> cd
> mkdir B2
> cd B2
to make a new directory named B2 and to make that directory the current working
directory. Then type
> camscope
to activate the main program. The camscope program provides facilities to view and
record images and to view and record simple brightness profiles. All of these facilities are
directly accessible from a single main control screen illustrated in the following figure.
Buttons on the right provide the following functions (top to bottom, with keyboard
shortcuts in parentheses):
EXIT (ctrl-q): terminate camscope and return to Linux prompt.
PLAY (ctrl-p): display live images from video camera, or loop through previously
recorded images if the program is in Analyze mode.
PAUSE (ctrl-z): stop displaying new images and hold last one displayed.
RECORD (ctrl-r): start recording images and brightness traces. Records ten images
and then stops (your TA can change this behavior if needed, but it is your responsibility
to make sure your measurements fit on a CD). Note: pressing the record button takes you
out of Analyze mode.
SNAPSHOT (ctrl-s): record a singe image and associated brightness traces.
STOP (ctrl-b): stop recording.
Analyze (ctrl-a): toggles Analyze mode, which displays previously recorded images.
BACK (ctrl-left_arrow): display previous recorded image (only works in Analyze
mode).
NEXT (ctrl-right_arrow): display next recorded image (only works in Analyze mode).
Screen Capture (ctrl-d): save image of screen (screendump).
Using Multiple Data Sets to Organize Your Measurements
In addition to these buttons, the upper left corner of the screen has + and - buttons (with
keyboard shortcuts ctrl-. (period) and ctrl-, (comma) respectively). These buttons control
which data set is currently being recorded or analyzed. All of camscope's other features
(record, analyze, playback, etc) operate on only the current data set (which can be
changed on the fly). Although you can do the entire lab without using multiple data sets,
they are extremely useful for organizing your data. You should use a separate data set for
each type of measurement, and for each measurement location. Be sure to make a note in
your protocol book about which data set corresponds to which measurement!
Manual Gain Control
By default, the camera uses automatic gain control to set the brightness and exposure
time to levels that give a good image. However, in some cases you may wish to manually
set these values in order to quantitatively compare brightnesses under different lighting
conditions (for example, comparing brightnesses with two different dye concentrations in
the chamber). Although there are no buttons to adjust these values, you can use the
following keyboard shortcuts:
Ctrl-1: turn down the brightness by 3 points (brightness varies from 0 to 511).
Ctrl-2: turn up the brightness by 3 points.
Ctrl-3: turn on auto-brightness (Ctrl-1 and Ctrl-2 both turn it off).
Ctrl-5: turn down the exposure by 3 points (exposure varies from 0 to 511).
Ctrl-6: turn up the exposure by 3 points.
Ctrl-7: turn on auto-exposure (Ctrl-1 and Ctrl-2 both turn it off).
Ctrl-9: turn down the color saturation by 3 points (saturation varies from 0 to 255, and
has no auto mode).
Ctrl-0: turn up the saturation by 3 points. When any of these keys is pressed, the
current values of these parameters are printed to the console.
Taking Measurements
Camscope allows you to make quantitative measurements both in real-time and from
previously recorded images, by switching to/from Analyze mode. Several types of
measurements can be made:
1. Pixel Values: When the cursor is moved into the image, the position of the cursor
and the RGB values of the pixel at that position are displayed in the lower right.
2. Line Plots: When the cursor is moved into the image, its vertical (and horizontal)
position selects a line (and column) whose brightness is displayed below (and to
the side of) the image. When images are being recorded, the red, green, and blue
intensities in these brightness contours are also saved as text files (the Ctrl-r and
Ctrl-s keyboard shortcuts are handy for saving files while the cursor is in the
image).
3. Average Brightness: When a box is drawn with the right mouse button, the
average RGB values within the box are displayed in the lower right corner of the
screen.
4. Distance/Velocity: When a line is drawn by holding the left mouse button and
dragging the mouse, the x, y, and total distance of the line is displayed in pixels at
the bottom of the screen. In addition, the velocity is computed automatically by
subtracting the time at which the line was started from the current time (in
Analyze mode, the times at which the images were acquired are used instead). To
measure the velocity of a bead in Analyze mode, for example, you would click
and hold the mouse button over a bead, press Ctrl-right_arrow to switch to the
next image (or to skip through several images), and move the pointer to the new
bead position. The velocity of the bead will be reported at the bottom of the
screen, next to the distance.
File Formats
Images are recorded sequentially as .BMP files. The first image recorded into an empty
directory is named image.000.000000.bmp, the second is named
image.000.000001.bmp, and so on. Changing the data set changes the three-digit
number near the beginning of the file, and resets the six-digit counter to zero. If the
cursor is in the image at the time of recording, a text file is also created that contains the
red, green, and blue intensities that were displayed below and to the right of the image.
The text file associated with image.000.000000.bmp is named info.000.000000.txt.
Screen dumps are saved in a similar sequential fashion, with the first one named
print.000.000000.bmp.
Saving Your Results

When you are ready to leave the lab, you should save your data. We cannot guarantee
that your data will be preserved on the lab computer, so copy everything before you
leave. The easiest way to save your data is to record it on a CD. Put a blank CD into the
CD burner and type
cdcp .
at the linux prompt. This command will record a CD that contains all of the files the
working directory (i.e., ".") and its subdirectories. If your directory is larger than the size
of one CD (about 700 MB), you will need to split your data into multiple subdirectories
and copy each onto a separate CD. Your TA can help you do this.
Analyzing Results
The camscope program is intended to provide sufficient information for you to monitor
how your experiment is proceeding while you are in the lab. This is important so that you
can discover problems and fix the problems before taking your final data. It is also
important so that you have a good idea that your experiment was successful or not before
you leave the lab. If you discover problems with your data, it is generally easier to take
new data now than it is to come back at a later time and start again.
Results from camscope can also be directly incorporated into your final report. However,
quantitative statistics to test specific hypotheses generally require additional analyses,
based on images and brightness profiles saved by the camscope program. Every time
camscope takes a picture, it saves the image as a .BMP file. When the cursor marks a
"line-of-interest" and a "column-of-interest" at the time that an image is recorded, the red,
green, and blue intensitives of those lines and columns of interest are also recorded as
"info" files (see "File Formats" above). The following figure shows a graphical
representation of these two files.
Intensity Profiles
The numbers in the info files can also be read by text processing / spreadsheet / plotting
programs and used to generate plots. The following figure shows the red, green, and blue
traces obtained from the center lines of two images saved at different times by camscope.
Some trends are easy to see just from the traces. However, the traces are noisy, and
averaging can give more reliable statistics. Brightnesses can be averaged in the horizontal
or vertical direction from the line-of-interest and column-of-interest numbers contained in
a single info file. Brightnesses can be averaged across time by combining information
contained in many info files. Arbitrary analyses are possible by calculating directly from
the images. Many software packages, including Matlab, provides functions that access
brightness values in .bmp image files.
More meaningful statistics can be generated from analytic theories and/or simulations.
The course software (available on the MIT server) can be used to calculate solutions to the
diffusion equation. The following plots show calculated concentration profiles for solute
confined in a 1D box for 3 successive times starting from an initial step concentration.
These plots illustrate that as time proceeds, the concentration profile flattens. Based on
this observation, one might measure the slope of the brightness contour measured in the
center of the laminar flow chamber and compare that slope the one measured in the
simulation. Alternatively, one might measure the minimum and maximum brightnesses
and compare those statistics to the simulation. The following figure illustrate some
potentially meaningful statistics to extract from brightness contours. You may be able to
suggest better statistics for your particular study.
You could also analyze your data by comparing it to an analytic theory. Such a theory is
developed in the course text (volume 1, Figure 3.16). Based on that theory, we expect the
concentration profiles to be integrals of the gauss function (i.e., the error function, erf).
One could find the erf function that best fits the measured brightness contours as a way to
estimate how much diffusion has occured.
Each of these analysis methods has advantages and disadvantages. Fitting the data with a
known function takes advantage of ALL the brightness data, and may therefore be good
for reducing the effects of measurement noise. However, the erf analysis does not take
the walls of the laminar flow chamber into account. Numerical analysis, using the course
software or some user written code, can take the walls into account, and thereby be more
accurate. However, numerical analysis may be more difficult to implement.
There is not single best way to analyse your data. Simple methods are fine so long as
their limitations are taken into account. Part of your project should be developing an
analysis method that makes sense for the question that you are addressing.
Experiments
Basic Observations: Laminar Flow and Diffusion
Before beginning your project, you should perform a vew basic observations to
familiarize yourself with the equipment.
Draw about 1 mL of deionized water into an empty syringe. Add 100 &muL of
microspheres to the syringe. Draw a few mL of air into the syringe and shake to disperse
the microspheres. Fill one input reservoir of a laminar flow chamber with this fluid.
Repeat the procedure, substituting food coloring for deionized water, and fill the second
input reservoir.
Filling the input reservoirs will not necessarily start the flow. To start the flow, carefully
attach the provided syringe to the output reservoir, and use the syringe to gently pull
liquid through the channel. Watch the channel carefully to see if liquid has been pulled
through. Because of the small cross-sectional area of the channel, you may not be able to
see fluid in the output reservoir even after the flow has started.
Move the chamber to the video microscope. Start the camscope program. Position the
stage so that you see the microchannel. Positioning can be tricky: you must get the
microchannel centered under the objective AND in focus in order to see any image at all!
When properly focused, you should see microspheres streaking across the image. Add or
remove liquid to the input and output reservoirs to adjust the flow rate. Measure the flow
rate by recording a sequence of images and measuring the distance traved by one
microsphere per frame. Are all of the beads moving at the same velocity? Should they
move at the same velocity?
You should see laminar flow. Estimate the maximum spatial gradient of brightness. is the
maximum centered in the microchannel? Should it be centered? Can you make it more
off center?
Projects
Your project is the main educational experience of this laboratory. You and your partner
should plan your project well in advance of going to the laboratory. This section lists
several topics that you could explore as your project. You may choose one of these or
you can construct an entirely new one. The descriptions given here are incomplete. Your
plan should be well-defined. Keep it simple so that you can complete the work, including
some preliminary plotting of results and thinking about interpretation within a severalhour lab session. You may also want time to check your interpretation by taking
additional measurements.
Linearity of Fick's Law

Motivation: Fick's law states that the diffusive flux of a solute should be proportional to
the gradient of concentration of that solute. Design an experiment to test if this is true.
Hypothesis: The flux of a solute is proportional to the gradient of the concentration of
that solute and is independent of the absolute concentration of solute.
Method: Perform laminar flow experiments with pairs of solutions with concentrations X
and X+Y of dye. Vary X keeping Y constant and test whether the diffusive flux depends
on X.
Diffusion of one Species in the Presence of Others

Motivation: Fick's law states that the diffusive flux of a solute should be proportional to
the gradient of concentration of that solute and independent of the presense of other
solutes. Design an experiment to test if this is true.
Hypothesis: The flux of a solute is proportional to the gradient of the concentration of
that solute and is independent of the presence of other solutes.
Method: Perform laminar flow experiments with pairs of solutions with fixed differences
in the concentration of dye but variable amounts of added glucose.
Effect of Solvent on Diffusivity

Motivation: According to the random walk model, solutes diffuse because they collide
with water molecules. Replacing water by a different solvent might change the number or
magnitude of these collisions.
Hypothesis: The diffusivity of a dye in water is greater than that of the same dye in oil.
Method: Perform laminar flow experiments with food coloring in one input reservoir and
either water or oil in the other.
Analysis of Microfluidic Data

Motivation: A typical laminar flow experiment can generate many megabytes of data.
How should one analyze this data to get the most information about diffusivity?
Hypothesis: Tracking the slope of concentration near the center of a laminar flow
provides more information about diffusivity that does tracking the width of the mixed
region.
Method: Determine transverse concentration profiles across a laminar flow at multiple
locations along the channel. Determine the spatial derivative of these concentrations
across that channel. According to the simple theory developed in lecture, these derivative
curves should have gaussian shapes. Compare estimates of diffusivity based on the
heights and widths of these gaussian shapes.
Microfluidic Mixing
Motivation: Microscale flows are dominated by viscosity. Therefore, mixing is primarily
by diffusion. But can we actually ignore other mechanisms?
Hypothesis: Diffusion is not the only important mixing mechanism in laminar flow.
Method: Measure mixing of two fluids that contain particles that are so large that they
should not diffuse during the experiment (e.g., microspheres). Any mixing that occurs
could not be due to diffusion.
Practical Considerations in Choosing a Topic

Projects can involve any of the topics discussed above or a topic of your own creation. A
well thought-out project, whether based on one of the ones above or not, will usually
promote better data collection, better report writing, and ultimately a better grade. If you
create a novel project, you must obtain any supplies or equipment that is not part of the
standard laboratory setup described in Methods. For example, studying the diffusivity of
some large biological molecule like a drug molecule might be an interesting project.
However, you are responsible for obtaining the biological molecule and determining a
method to measure its concentration.
When you choose your topic, remember that your experiment should take only a few
hours to complete. Think through how many measurements you will need to make and
how long it will take to make each measurement.
Formulate a specific and testable hypothesis, and center your project on that hypothesis.
Avoid vague hypotheses, such as: "I would like to understand how concentration affects
the diffusivity of dyes." Instead choose a more narrrowly focused hypothesis, such as:
"Increasing the concentration of dye to near saturation values will decrease the diffusivity
of the dye." This more-focused hypothesis is testable: it can be true or false. If you form a
clear hypothesis, you will be able to plan a logical set of measurements to test the
hypothesis, and you will be able to come to a clear conclusion when you write your
report.
When you do your experiment, you may get unexpected results. For example, you may
have planned to measure effects of glucose on the diffusivity of a dye. However, you may
find that the added glucose affects the velocity of flow in the chambers. You should
explore unexpected results and try to understand their bases. Your aim should be not
simply to reject or accept your hypothesis, but to develop insight into the phenomena. For
example, perhaps changes in velocity result from changes in viscosity and changes in
viscosity of the medium affect your estimate of diffusivity. If so, the unanticipated
changes in velocity could be key to understanding the measured changes in diffusivity.
Keep in mind that this is an experimental project. Your goal is to characterize what
happens, not why it is happening. Theoretical analyses may support your experimental
findings. However, your grade will be primarily based on the reliability of your data.
Control Observations
Control observations are important parts of the design of any experiment. The purpose of
a control observation is to determine whether the variable that is directly manipulated by
the experimenter is the one that controls the change in response. Two common kinds of
control experiments test repeatability (i.e., if you make the same measurement several
times, do you get the same answer) and reversibility (i.e., if you make a change and then
undo it, does the response go back to what it was before the change), although other
control observations are often used. Suppose, for example, that you wish to determine the
effect of adding glucose to the diffusion of a dye. You could measure the time-space
evolution of dye concentration with no glucose, repeat the measurement with glucose,
and compare. If the results are different, can you conclude that the reason is the glucose?
What if you inadvertently filled the supply reservoirs differently in the two experiments?
Perhaps the difference is because the flow rates were different, not because glucose was
added. Control observations are intended to assess the extent to which factors that are not
part of the experimental design are contributing to response patterns. Simply repeating
the experiment with no glucose is a good way to assess many sources of error. Repeated
sequences of measurements can be even better.
Proposals, Reports, and Logistics

Scheduling a Laboratory Session
Students should schedule a time slot for their laboratory session by submitting an
electronic schedule form. At that time, you may also request a partner. The laboratory
accomodates 10 students in each session. We will work out the laboratory schedule in
lecture 6. You have the best chance to get your most desired time slot by submitting your
schedule form by lecture 5. After initial laboratory assignments have been made, you will
be permitted to change your laboratory session only if you request the change more than
24 hours before your assigned slot and only if there is an open slot in the schedule at your
desired time.
Proposal
You and your partner should meet to plan your project and to write a proposal. The
proposal should contain a brief statement of the hypothesis you propose to test and the
method that you will use to test it. Include a list of the experiments you will perform and
the measurements you plan to make in each experiment. Indicate how the measurements
will be used to help you test your hypothesis. The proposal should fit on a single sheet of
paper. A sample proposal is shown in following figure. The proposal should be submitted
by lecture 5. You can submit your proposal electronically. The staff will review the
proposals and make suggestions. Acceptable proposals will be APPROVED; flawed
proposals will be REJECTED. Proposals that are not approved may be revised and
resubmitted.
Proposal: Linearity of Mixing in Microchambers
Partner Names (E-mail):} Partner One (pone@email) and Partner Two

(ptwo@email)
Hypothesis: The process by which fluids mix as they flow through microchambers is
linear.
Background: The primary mechanism by which fluids mix when they flow through
microchambers is diffusion. Since diffusion is a linear process (i.e., the relation between
flux and concentration gradient is linear), we expect that the fluid mixing in
microchambers will be linear.
Procedure: A laminar flow chamber with two inputs will be used to assess fluid mixing
in microchambers. The concentration of dye in the two chambers will be investigated in 3
conditions:
input 1 input 2
condition 1 0%
50%
condition 2 50% 50%
condition 3 50% 100%
Mixing will be assessed by analyzing video images of the flow at a point 3 mm
downstream from the point where the laminar flow begins. Under the assumption that
mixing is linear, the results for condition 3 should be the sum of the results for conditions
1 and 2.
To increase the confidence in these results, images will also be obtained at 2 additional
locations. The entire experiment will then be repeated to assess effects of uncontrolled
variables, such as flow rate.
Laboratory Notebook
The written record of your experiment is the original record of your work and the basis
for everything that you conclude. Such records should be kept in a laboratory notebook,
which is typically a special notebook with sewn binding (not a loose-leaf notebook),
whose pages were numbered when the notebook was printed. Records should be written
in ink. The laboratory notebook is the permanent record of your experiment.
Laboratory notes should be sufficiently detailed so that (1) the experiment could be
repeated at some later time, (2) results from different experiments can be compared, and
(3) so that your procedures can be reconstructed at a later time without relying on your
memory. The first page for each experiment should give the date and time, as well as a
brief description of the purpose of the experiment. All relevant procedures and
observations should be entered in the protocol book and the time should be indicated
regularly.
Nothing should ever be erased. If an error is detected in some procedure or some reading,
that should be noted in the book. The original observation should under no circumstances
be obliterated so that it cannot be read. Perhaps you will subsequently find that the
original observation was correct and that the correction was in error. The general rule is
to write down everything that is done that may later become relevant. Scientists are rarely
sorry that they wrote too much in the protocol book -- only that they wrote too little.
You do not have to purchase a special laboratory notebook for this project. However, we
do ask that you take laboratory notes during your experiment, as a step toward learning
about effective practices in experimental work. You will be asked to attach your notes to
your laboratory report, and we will assess these notes as part of the grading procedure.
Project Report
The project report should be concise. Do not repeat material that is easily referenced. For
example, there is no need to reproduce any figure from this laboratory manual or from the
course text: simply refer to it. Technical writing is necessarily directed at some particular
intended audience. Write the project report as though it were to be published in a journal
that is read primarily by students who have taken this subject. Thus, you can assume
some working knowledge about the subject. The project report should contain the
following sections.
Cover Page. On the cover page include the title of the laboratory session, the
authors' names, your laboratory subsection, the dates of the laboratory session(s),
and the name of your partner (if not a co-author).
Abstract. The abstract is a one paragraph (<100 words) summary of the report
including the question investigated, the methods used, and the principal results
and conclusions. Your intended audience should be able to understand the abstract
without having to read any of the report. This section should be written last.
Introduction. The introduction is a brief section (about 1 page) designed to
motivate the reader. Include background information on the problem, hypotheses
to be tested, significance of the work, etc. You may give citations to material in
this laboratory manual or elsewhere. The introduction should be directly relevant
to your report; broad discussions of microfabrication or biology are not necessary
or desireable.
Methods. Briefly describe any special methods that you used that are not in this
laboratory description. Give details of calculations used to obtain the results. Do
not repeat material that is in this description; just refer to it.
Results. Describe the measurements (whether or not they fit with expectations) in
the results section. Generally, results can be communicated more efficiently and
accurately with pictures and graphs than with words alone. Describe those aspects
that are important to your interpretation, but omit interpretations from this section.
A collection of printed graphs without a written description of their relevance is
unacceptable as a results section. Students frequently err on the side of including a
large number of graphs and little description of their relevance. You need only
include results that are relevant to your conclusions. Most of us have trouble
leaving things out. Ask yourself why a particular result is a necessary part of your
story; omit those that aren't necessary.
Discussion. In the discussion section, assess the results for dependability and
accuracy, and interpret results in the light of other knowledge. The discussion
section can include relevant speculations and ideas for improving the experiment
to test the hypotheses more rigorously.
Appendix. The appendix should include a copy of the notes taken in your lab
notebook during the laboratory session.
Reports that are written haphazardly and without planning are usually unintelligible and
receive poor grades. We strongly recommend that you start by writing an outline to
structure the logic of the report. Revise your outline until the flow of your argument
makes sense (ask yourself, "If this were someone else's report, would I believe the
conclusion?"). At that point, you can usually write the report by fleshing out the outline.
Grade
The grade for the experimental project will be based on the proposal and on the project
report using the following considerations:
First draft & Critique (15%). Your first draft and your critique of a colleague's
first draft will be graded primarily for completeness.
Report structure (15%). The sections of the report should be coherent.
Clarity/Conciseness (20%). A good report is easy to read. The content of each
paragraph and each graph should be clear. Everything included in the report
should be there for a reason. Points will be deducted for extraneous material.
Reports should be less than 10 pages long, unless there are good reasons for
additional pages.
Conceptual correctness (20%). Is the report free of obvious errors,
exaggerations, and omissions? Are the prominent features of the data described
accurately? Are the results (which follow directly from the measurements) clearly
separated from the interpretations (which rely on information other than what was
observed)? Can the conclusions be derived from the results?
Insightfulness (30%). Insightfulness can be demonstrated by (1) proposing an
experimental method that can resolve some scientific issue, (2) carrying out
experiments and/or analyses that lead to clear conclusions, (3) preparing a report
that demonstrates a clear understanding of the strengths and weaknesses of your
results and analyses. Simply performing one of the standard experiments and
showing unmotivated measurements will receive 0 points. Clever design of an
experiment or imaginative analysis of the results will receive 30 points.
Demonstrating a clear understanding of your experiment, your analyses, and what
can be concluded is sufficient for 15 points.
DUE DATES ARE FIRM, AND THERE IS A SEVERE LATENESS PENALTY.

The grade for a late report will be multiplied by a lateness factor
L = 0.3 exp(-t/4) + 0.7 exp(-t/72)

where t is the number of hours late. The lateness factor is plotted below. Notice that the
maximum grade for a report that is more than ONE DAY LATE is less than 50%.
6.021J AUTHOR GUIDELINES
CONTENT: A lab report in 6.021J Quantitative Physiology is a description and analysis of your
research. The primary audience of your report is other 6.021J students. It is expected that your research
was jointly conducted and authored. We do not expect you to reach grand theories or expect all your
research to be successful. We do expect you to offer a rationale that explains why this research is
relevant, provide a detailed and accurate methodology description, disclose your results, and discuss
reasons why your experiment succeeded or failed by linking that discussion to your results and methods.
STYLE: We prefer an informal but not colloquial style of writing to a textbook style or jargon-laden
prose. You may use occasional instances of personal pronouns in your report. Your readers, the students
and faculty of this course, all have some background in this subject, but only a very small percentage are
experts. A clear conceptual discussion is far better than a plethora of technical details that have no overarching meaning or organization.
MANUSCRIPT FORMATTING: All pages should be numbered, beginning with the first page of the
report body. Please include a Cover Page that includes authors names as well as title of your report and
submission date. Please include your Abstract on this Cover Page. Do not number the Cover Page. Every
report needs to include in the body the following major section headings: Introduction, Methods, Results,
Discussion. Within each of these sections, you may use more descriptive subheadings. A Table of
Contents is optional.
LENGTH: Please limit your reports to 3,500 words. We prefer single-spaced texts with clear page
breaks. Appendices are not included in the word count limit. Avoid lengthy Appendices as most readers
will not read them carefully.
FIGURES: We recognize that sometimes a picture is worth a thousand words, but avoid the gratuitous
use of figures in your results. Five to 10 figures should be sufficient for your report. Use figures to
synthesize results and show trends or comparisons across findings. Integrate your figures with your text
to create a story between text and figure. Large figures should not run across pages. Each figure needs
to be numbered and include a caption and label. Please clean up your figures from MatLab by
removing unnecessary grid lines and shading. In addition, please make figures legible by using a 10 or
12-point font size for captions and axis labels.
REFERENCES: You need at least one reference for your report. Most 6.021J students reference the
Weiss text. Many reports also include references to research in the Introduction.
FURTHER RESOURCES: 6.021J has its own Report and Proposal Guide which is available in the
study materials section. This guide is a supplement to the MIT style guide, The Mayfield
Handbook of Technical and Scientific Writing.
SUBMISSION OF MANUSCRIPTS: Please see the calendar section for report due dates.
First Drafts: Include three copies of your report. Copies will be distributed to peer reviewers as
specified in lecture. All reviews are returned during the writing clinic. Please make sure that your review
of your peers report is complete and ready to be returned at the writing clinic.
Final Reports: (7 items) Include one clean copy of your report, the three reviewed copies of your report,
a copy of the report you critiqued, a copy of your lab protocol, and proposal. Clip or bind all materials
together.
Changes and Errata to

Cellular Biophysics, Volume 1: Transport
by Thomas F. Weiss
May 3, 1999
Page xxix, Seventh line, replace 133.3 105 N m2 with 133.3 N m2
Page xxix, Insert as rst entry in table [Name]Acceleration of gravity[Symbol]
g [Value] 9.807 m s2
Page xxx, Second entry in table (for Dielectric constant), third column, remove
cm2 s1
Page 8, Sixth line from bottom of the page, change and disassembled to (and
disassembled)
Page 84, Line 1, change To study diusion to For example, to study diu
sion
Page 88, replace Figure 3.2 with
Surface
area A
(x, t)
(x + x, t)
x + x

Surface
area A
xl
x+l
2
Page 158, Exercise 3.10, Sentence 33, replace The volume of bath 2 is V2 .
with Bath 2 has volume V2 and a concentration of solute n that is zero.
Membrane
C1
C2
D1
D2
d2
d1
Page 167, Line 3, replace equilibration time of X in the with time for X to
reach steady state in the
Page 171, Item c., line 2, replace membrane, i.e., does with membrane at
Page 171, In the equation of Item c., replace n = Ps (c1n c2n )? with
n (t) = Ps (c1n (t) cn2 (t))?
Page 171, Item d., line 2, replace membrane, i.e., does with membrane at
Page 171, In the equation in Item d., replace n = Pl (c1n cn2 )? with
n (t) = Pl (c1n (t) c2n (t))?
Surface
areaA
F(x)
p(x)
x + x
p(x + x)
3
Surface
areaA
V (x, t)
V (x + x, t)
x + x
Page 204, In the rst line of the section Water Diusion, remove by means
of and replace with with water that contains
Page 204, In the second line of the section Water Diusion, replace water
(e.g., deuterium, tritium, etc.) with hydrogen (tritium)
Page 235, Line 6 of Figure 4.28 caption, replace (pm s1 Pa) with (pm
s1 Pa1 )
Page 255, Fifth line from bottom of page, replace Vc . with Vc , and Vc Vc .
Page 255, Last line on page, replace Are with Determine if and change
volume, d(t)/dt at to volume (d(t)/dt at
Page 256, Line 1, replace t = 0+, and () with t = 0+) and the nal value
(()) of the normalized volume are
Page 263, Line 1, replace a. with 1. and replace was with is
Page 263, Line 2, replace stood with stands
Page 263, Line 3, replace had with has, replace 30.7 with 36.5, and
replace could with can
Page 263, Line 4, replace had with has and was with is
Page 263, Line 6, replace b. with 2.
4
Glasstube
AreaA
Sucrose
solution
h(t)
Water
Membrane
Page 268, In rst line of item a., replace less with fewer
Page 270, Line 5, replace C

o (t) < Co
(t) with C
o (t) < Ci (t)
Page 283, Line 9 in Figure 5.2 caption, change test to tests
-1
(t)
Impermeantsolute
0 1 2 3 4 5
-1
0.9
0.9
0.8
0.8
(t)
0.7
0.7
0.6
0.6
0.5
0.5
1.0
1.8
Permeantsolute
0 1 2 3 4 5
=10
=1.0
=0.1
=10
1.6
n(t) 1.4
n
(t) 0.5
=1.0
1.2
=0.1
1.5
1.5
c(t) 1
c(t) 1
0.5
1 0 1 2 3 4 5
Normalizedtime, t
0.5
6
1 0 1 2 3 4 5
Normalizedtime, t
5
Page 293, Line 8 of Figure 5.6 caption, replace (pm s1 Pa) with (pm
s1 Pa1 )
Page 297, Line 5 of rst paragraph, replace water molecules, e.g., tritium.
with water molecules, e.g. with tritium replacing hydrogen. and replace
solvent and tritium with solvent and tritiated water
-1
1 0 1 2 3 4 5
Normalizedtime, t
0.9
(t)
0.8
0.7
0.6
0.5
2.0
n(t)
1.0
2.0
ci (t) 1.0
2
1.5
co (t) 1
0.5
6
-1
1 0 1 2 3 4 5
Normalizedtime, t
0.9
(t)
0.8
0.7
0.6
0.5
1.8
1.6
n(t) 1.4
1.2
2
1.5
cA (t)
cB (t) 1
0.5
Page 323, Line 7, replace are with is

Page 323, Line 8, replace largest? with larger?
Page 324, Line 18, replace by radioactive with with heavy
Page 347, Lines 9 and 10. Remove Since we assume the enzyme is conserved,
Page 347, Line 20 replace Michaelis-Menton with Michaelis-Menten
Page 348 Line 1 in Figure 6.8 caption, replace Michaelis-Menton with MichaelisMenten
7
2.5
)
r 2 (A
1.5
0.5
0.5
1.5
r 1 (
A)
2.5
Page 388, Line 16, replace the the with the

Page 422, Second Line from bottom of page, replace e with eq
Page 423, Line 1, replace e with eq
Page 423, Line 3, replace d , with ss ,
Page 423, Line 5, replace d with ss
Page 424, In the equation in Problem 6.4, replace ci with ci (t) in both
instances
Page 424, In the fourth line of Problem 6.4, replace ci with ci (t)
Page 426, Line 7, replace concentration with densities
Page 429, Problem 6.9, Add after initial concentration is C. the sentence
Assume that the change in intracellular osmolarity is negligible.
Page 456, Line 6, replace Using with With
8
Surface area A
J(x, t)
J(x + x, t)
x + x
Page 463, Last line, replace sinh (x) with sinh (X)
Page 464, Equation 7.27, replace with
=
RT /(zF )
Page 473, Line 7 of Figure 7.11 caption, add The electric field was 0.548 V/cm.
Page 491, Line 12, replace 68 with 60
Page 501, Fourth line from bottom of page, change flux ion to flux of ion
Page 510, Third line from bottom of page, replace low-sodium with sodium
Page 511, Line 7 of Figure 7.42 caption, replace low-sodium with sodium
Page 512, Line 9, replace effect with dependence
Page 514, Second paragraph, third line, replace First, addition with Addition
Page 517, Line 10 of Figure 7.46 caption, remove , obviating and replace with
which interferred with
Page 530, third line from bottom of page, the two coefficients of Vm should be
(zn2 F Pn cin ) and (zn2 F Pn con ), respectively.
9
20
Jn
2
zn F Pn con
10
15
10
5
0.1
4
2
zn Vm
Page 531, add to the end of the caption of gure 7.52 The parameter is con /cin .
Page 546, Third line from bottom of page, replace 0.2mol/L with 0.2 mol/L
0
20
40
0
LingandGerard
(1950)
JJ
Slope:
44mV/decade
60
80
Slope:
58mV/decade
0 1
10
100
co
K (mmol/L)
Restingpotential(mV)
Restingpotential(mV)
20
20
Adrian
(1956)
40
60
J
J
80
100
120
140
1000
0.1
J
Slope:
58mV/decade
10
100
1
coK (mmol/L)
1000
Page 584, Line 14, replace cip with cii

Page 584, Line 15, replace cip (t) = nip (t)/V (t) with cii (t) = nii (t)/V(t)
Page 584, Line 16, replace cip (t) = (nip (t) with cii (t) = (nii (t)
Page 628, Line 11, remove for a z+ -z electrolyte
Page 628, Line 14, remove equilibrium
Page 630, Part a, Line 1, replace Vm with Vmo and replace the potential
with the resting potential
Page 630, Part a, Line 2, replace Vm with Vmo
Page 630, Part a, Part v, Line 1, replace Equilibrium with Quasi-equilibrium
Page 630, Part c, Line 1, replace equilibrium with quasi-equilibrium
10
Page 630, Part c, Line 2, replace equilibrium with quasi-equilibrium
Page 631, in the last line, the denominator of the righthand side of the equation
should read x(t)(L x(t))
Page 632, Line 12, the denominator of the righthand side of the equation should
read x(t)(L x(t))
co
Page 633, Third line from bottom of page, replace oK with K
Page 634, every instance of equilibrium should be preceded by electrodiu

sive
Page 635, every instance of equilibrium should be replaced with quasi
equilibrium
Page 683, Column 3, Line 8, replace Michaelis-Menton with MichaelisMenten
Changes and Errata to

Cellular Biophysics, Volume 2: Electrical Properties
by Thomas F. Weiss
December 29, 1998
Page xxv, Seventh line, replace 133.3 105 N m2 with 133.3 N m2
Page xxv, Insert as rst entry in Physical Contents table [Name]Acceleration
of gravity[Symbol] g [Value] 9.807 m s2
Page xxvi, Second entry in table (for Dielectric constant), third column, remove
cm2 s1
Page 56, Line 12 from bottom of page, replace if there is an with an
Page 56, Line 10 from bottom of page, replace cell, that must with cell,
must
Page 60, Equation 2.31, in the third numerator replace 2 Vm with 2 Vm (z, t)
Page 83, Replace Figure 2.33 with
Trough
Seawater
Axon
600m
600m
Page 117, Line 3, replace the the with the

Page 140, replace item b. of Problem 3.10 with Explain why the internal
potential, vi () approaches zero as ri /ro goes to zero.
2
3
J
J
tp
M
+2
tp
M
JJ J
5
2
z 2 (mm )
10
o (z)
o (z)
Page 156, In the equation in Problem 3.19, replace vz
with dvdz

Jm
JC
JK
GK (Vm , t)
JN a
GN a (Vm , t)
+
VN a
Intracellular
Vm
Membrane
JL
GL
Cm
+
VK
+
VL
Extracellular
Page 171, In the unnumbered equations after Eq. 4.3, replace both instances of
log with ln
Page 214, In equation 4.28, in the second numerator replace (Vm) with (Vm )
Page 224, Last paragraph, line 7, replace We also with We have also
Page 229, First paragraph, fth line from bottom, replace parameters the
system of with parameters, the
Page 229, First paragraph, fourth line from bottom, replace is unstable with
are unstable
3
Page 233, Line 6, replace all with each of and replace in Taylors with
in a Taylors
Page 239, Line 7, replace their with there
Page 271, Last line on page, replace of membrane current with of current
Page 272, Lines 3 and 4, delete The vertical scales for waveforms b through f
are identical, but the scale for waveform a is dierent.
Vm (mV)

20
0
60
(a)
0
(b)
0
0
(c)
(d)
(e)
0
(f)
0
1
2
Time(ms)
Page 276, Second line from bottom of page, change that indicates to to
indicate
4
dIm /dt (mA/s)
Im (t)
+
V (t)
6 4 2
0.4
4 6 8
Im (mA)
10
V (t) (mV)
0.8
+50
1.2
t
1.6
2.0
50
Page 283, Line 1, replace the the membrane with the membrane
Page 295, Lines 8 and 9, replace cells, either one unmyelinated fiber in one
supporting cell with cell. A supporting cell may ensheath one
Page 295, Lines 9 and 10, remove in a single supporting cell, as seen in cross
section
Nucleus
Schwann cell
Cytoplasm
Compacted
membrane
Cytoplasmic
ridge
Axon
5
L
Node1
100m
Internode
Node2
l
d
D
500
Page 301, Figure 5.8 caption, Line 3, add after and l = 1m. the following
sentence The inset shows the region around a node scale by 500.
Page 302, Figure 5.9 caption, line 6, add after for these bers. the sentence
The average SD was: 0.731 0.056 for the vagus nerve; 0.742 0.065 for
the sciatic nerve.
Page 302, Figure 5.10 caption, line 8, add after in m. the sentence The
correlation coecient is 0.80.
Page 303, Figure 5.11 caption, line 4, add after of lamellae. the sentence The
correlation coecient is 0.89.
Page 305, Second paragraph, sixth line, replace suggests with suggest
Page 310, Last line on page, replace (as with as and replace potential)
with potential (Figure 4.32) [NB Use symbolic reference to Figure 4.32]
Page 311, Last line of Figure 5.19 caption, add after each record was obtained.
the sentence The external longitudinal current is plotted in a direction opposite
to the direction of propagation.
Page 315, Line 3, replace reject with rule out
Page 315, Line 7 from bottom of page, replace The pattern of maxima and
minima occurred with The maxima and minima occur
Page 319, Figure 5.28 caption, line 3, replace potential with potentials
Page 319, Last line on page, replace values are with values of electrical and
geometric properties of frog myelinated bers are
Page 322, Line 6, replace the reference (Figures 5.21) with (Figure 5.21)
6
120
0.245 0.450
1.00
1.25
100
60
0.225
5
0 .20
0.185
80
1.50
1.75
Vm (z, t)Vmo (mV)
40
20
0
4
120
0 2
8
12
16
NodeNumber
4 6
8 10 12
100
20
14
80
60
40
20
0
0
0.4
0.8
1.2
Time(ms)
1.6
2.0
Page 325, Line 7 of Figure 5.33 caption, replace v = 2.0D (left panel) with
v = 2.0D with a correlation coecient of 0.67 (left panel)
Page 325, Line 8 of Figure 5.33 caption, replace v = 2.6D (right panel) with
v = 2.6D with a correlation coecient of 0.88 (right panel)
Page 325, Figure 5.34 caption, third line from bottom, replace v = 5.7D with
v = 5.7D with a correlation coecient of 0.97

Page 326, Equation 5.11, replace

Ld with
d
L
Page 327, Equation 5.14, in the third numerator replace V (z, t) with Vm (z, t)
7
Time(ms)
0.5
4
6
8
10
Distance(mm)
12
Internodaldelay(s)
300
100V
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
200
100
0
1
200s
2 3 4 5 6 7 8
NodeNumber
Page 331, Line 9 of Figure 5.37 caption, replace those in Figure 5.25. The
with those in Figure 5.25. The arrows in the upper right panel delineate the
rst and last record shown on the left. The
Page 331, Line 11 of Figure 5.37 caption, replace time in with time
Page 331, Line 12 of Figure 5.37 caption, replace successive internodes. with
versus distance (same scale as above); successive nodes are indicated.
Page 331, Line 13 of Figure 5.37 caption, replace The dotted line with The
dashed line
Page 332, Line 4, replace capacitance with membrane capacitance and re
sistance with membrane resistance
Page 338, In Problem 5.3, Item b., replace Vm (z, t) = Vm (t z/) with
Vm (z, t) = f (t z/)
8
Active
node
Internode
Stimulated
node
va (t)
Va
Rn
t
+
va (t)
Internode
Cn
Vm (z, to )Vmo (mV)
110
to = 0.45
100
90
4
5
6
7
NodeNumber
Page 344, Problem 5.10, Item a., Line 3, add after 0.45 ms. the sentence
Assume that ri = 140 M/cm ro .
Page 344, Problem 5.10, last line of item b., replacet with to
Page 351, First paragraph, third line from the bottom, replace singe-channel
with single-channel
Page 352, In the eighth and ninth lines of the rst paragraph, remove However,
as with all important work, this and replace with This
Page 353, Second line from bottom of page, replace voltage clamps with
changes in membrane potential
Page 354, Line 5, replace for very large cells only. with only for very large
cells.
Page 354, Line 13, replace wide with wider
Page 354, Line 17, replace the entire line with in the cytoplasm, the antibiotic
Nyastatin can be placed
Page 354, Line 18, replace the pipette, with the patch pipette,
Page 354, Last line on page, replace We call these currents with We call
currents measured this way
9
Page 358, Line 2, replace and one that normally with and normally
Page 362, Paragraph 3, replace lines 3 and 4 with to cell membranes and to
membrane fractions that contain the appropriate channels. These blockers
Page 362, Paragraph 3, Line 6, replace that result with which result
Page 363, Third line of rst paragraph, replace interpreted with explained
Page 363, Line 5, replace which are permeable with which is permeable and
replace If one channel predominates with If one channel is most prevalent
Page 367, Line 5, replace variety of cells than with variety of cell parts than
Page 375, Paragraph 3, Line 2, replace and are inward with and have inward
Page 375, Paragraph 3, Line 3, replace of calcium with of free (unbound)
calcium
Page 380, Third line from bottom of page, replace Gausss law with Gausss
integral theorem
2000
t
Vm (t)
Ig (t)
Qon (pC)
1500
Qon
Qof f
1000
500
0
0
E
EE EE
E
t
EE
E EEEE
EE
EEE EEEE
EE
E
E EEE E E
EE E E
500
1000
1500
Qof f (pC)
2000
Page 390, Figure 6.24 caption, last line, add after current through the mem
brane. the sentence The dashed regression line has the equation Qon =
1.07Qof f 47 with a correlation coecient of 0.95.
Page 393, Last paragraph on page, line 3, replace voltage-gated sodium with
voltage-gated
Page 393, Last paragraph on page, line 4, replace opening immediately after
a depolarization with opening
10
Page 393, Last paragraph on page, line 5, replace open immediately after a
depolarization with open for V = 190 mV than for V = 110 mV
Ligand-gatedchannel
Voltage-gatedchannel
19mV
+21mV
+61mV
4pA
+
V
1pA
110mV
100ms
130mV
150mV
170mV
50ms
+101mV
190mV
Page 395, Lines 1 and 2, replace magnitude of the membrane potential is

increased. with potential V is made more negative.
Page 396, Last line on page, replace channel open with channel-open
Page 399, fth line from bottom of page, replace gate that opens with gate
that tends to open
Page 404, In the second equation, replace both instances of
g(t) with
gk (t)
Page 409, Line 10, replace EC EO kT , with |EC EO | kT ,
Page 412, Second line following Equation 6.31, remove Note that x is inde
pendant of
Page 412, Tenth line from bottom of page, replace Thus, with That is,
Page 414, In the rst equation, replace Vm with (Vm VO )
Page 414, In the second equation, replace Vm with (Vm VC )
Page 415, in the sixth line of the last paragraph, remove i(Vm , t),
Page 423, Second part of Equation 6.48, replace C pO (C ) with C pC (C )
Page 427, in the last line of the rst paragraph, replace the the with the
Page 441, Seventh line from bottom of page, replace decided with decidedly
Page 453, (FIGURE 6.71 GRAY SCALES ARE NOT DISTINCT)
11
Page 468, Example 6.10, replace water channels with water channels (Weiss,
1996) [NB use symbolic citation]
Page 472, Problem 6.6, Line 1, replace through the a cell with through a
cell
Page 487, Line 4, replace Figure 6.89 with Figure 6.89 (Weiss, 1996) [NB
use symbolic citation]
Page 495, Line 6, replace Is so, with If so,
6.021J Guide to Report and
Proposal Writing
Quantitative Physiology
Fall 2002
Table of Contents
PREFACE ......................................................................................................................................................4
WRITING RESOURCES AT MIT .....................................................................................................................4
1.0 EFFECTIVE TECHNICAL COMMUNICATION..............................................................................5
1.1 ACCURACY, CLARITY, CONCISENESS, AND COHERENCE .......................................................................5
1.2 AUDIENCE .............................................................................................................................................6
1.3 POINT OF VIEW ......................................................................................................................................6
1.3.1 Active voice versus passive voice..................................................................................................6
1.3.2 Verb Tense ....................................................................................................................................7
1.4 ORGANIZING INFORMATION ...................................................................................................................7
1.5 AVOIDING COMMON STYLE PROBLEMS IN 6.021J .................................................................................7
2.0 PROPOSALS ...........................................................................................................................................9
2.1 GENERAL INFORMATION ABOUT PROPOSAL WRITING ...........................................................................9
2.1.1 Purpose. The Proposal: ................................................................................................................9
2.1.2 Quick Tips.....................................................................................................................................9
2.1.3 Format ..........................................................................................................................................9
2.1.4 Organization .................................................................................................................................9
2.2 FROG PROPOSALS ..................................................................................................................................9
2.3 HODGKIN-HUXLEY PROPOSALS ...........................................................................................................10
2.3.1 Proposal Submission ..................................................................................................................10
2.3.2 Practical considerations in the choice of a topic........................................................................10
2.3.3 Choice of topics ..........................................................................................................................10
2.3.4 Examples of hypotheses ..............................................................................................................11
3.0 REPORTS ..............................................................................................................................................14
3.1 ELEMENTS OF A TECHNICAL REPORT ...................................................................................................14
3.1.1 Title.............................................................................................................................................14
3.1.2 Abstract.......................................................................................................................................14
3.1.3 Table of Contents ........................................................................................................................14
3.1.4 Introduction ................................................................................................................................15
3.1.5 Methods ......................................................................................................................................15
3.1.6 Results.........................................................................................................................................15
3.1.7 Discussion...................................................................................................................................16
3.1.8 Conclusion (Optional) ................................................................................................................16
3.1.9 References - IEEE style...............................................................................................................16
3.1.10 Appendices................................................................................................................................16
3.2 GRAPHICS: PRESENTING INFORMATION IN TABLES, FIGURES, AND EQUATIONS ..................................17
3.2.1 Tables..........................................................................................................................................17
3.2.2 Figures........................................................................................................................................17
3.2.3 Equations ....................................................................................................................................17
3.3 IEEE STYLE ........................................................................................................................................18
3.3.1 Two parts to IEEE style: (1) in-text citation and (2) references page ........................................18
3.3.2 Examples of IEEE References for Reference page of report ......................................................18
3.4 FROG REPORT SPECIFICS .....................................................................................................................20
3.4.1 Commonly Misunderstood Concepts ..........................................................................................20
3.4.2 The Report: Common Issues .......................................................................................................20
3.5 HODGIN-HUXLEY REPORT SPECIFICS ..................................................................................................20
3.5.1 Commonly Misunderstood Concepts ..........................................................................................20
3
3.5.2 The Report: Common Issues .......................................................................................................21
4.0 TIPS ON COLLABORATING ............................................................................................................22
4.1 WAYS TO MAKE COLLABORATING EASIER............................................................................................22
4.2 TIPS FOR COLLABORATIVE EDITING......................................................................................................22
4.3 EDIT FOR CONTENT .............................................................................................................................22
4.4 EDIT FOR STYLE ..................................................................................................................................23
5.0 TIPS ON EDITOR'S COMMENTS ....................................................................................................24
5.1 WRITING MEANINGFUL COMMENTS ON OTHER REPORTS .....................................................................24
5.2 MAKING SENSE OF EDITOR'S COMMENTS .............................................................................................24
Preface
This guide is meant to provide 6.021J students a comprehensive tool for writing proposals and
reports in this course. This guide includes information developed by 6.021J technical and writing
staff as well as information from The Mayfield Handbook of Technical Style.
Writing Resources at MIT

Your 6.021J staff is the best resource you have about writing in 6.021J. If you want help outside of
6.021J, visit the Writing and Communication Center <http://web.mit.edu/writing>.
The Mayfield Handbook of Technical and Scientific Writing and other on-line resources are
available at the Writing Program homepage. Note that the Mayfield Handbook is a GENERAL
GUIDE and not tailored to the expectations of 6.021J.
1.0 Effective Technical Communication

"The fundamental purpose of scientific discourse is not the mere presentation of information and
thought but rather its actual communication. It does not matter how pleased an author might be to
have converted all the right data into sentences and paragraphs; it matters only whether a large
majority of the reading audience accurately perceives what the author had in mind"
- George Gopen and Judith Swan, "The Science of Scientific Writing"
1.1 Accuracy, Clarity, Conciseness, and Coherence

Good technical communication is accurate, clear, concise, coherent, and appropriate.
Accuracy, which is the careful conforming to truth or fact, has three main aspects:
1. Document accuracy refers to the proper coverage of your topics in appropriate detail.
Document accuracy is generally cultivated by a clear problem statement and by a preliminary
outline.
2. Stylistic accuracy concerns the careful use of language to express meaning. Accurate
language requires the careful use of paragraph and sentence structure and word choice to
describe and analyze your topics effectively. Stylistic accuracy is also a matter of using words
precisely.
3. Technical accuracy depends on the writer's conceptual mastery of the subject and its
vocabulary, as well as on his or her ability to analyze and shape data with a minimum of
distortion.
Clarity, which refers to ease of understanding, is a special problem in science and technology
writing. Increase the clarity of your material in several ways:
1. Structural clarity makes it easy for the reader to get the large picture. Tables of contents,
problem statements, and even strategic repetition also promote structural clarity. Graphs and
tables, effectively worded headings guide readers and help keep the large picture in focus.
2. Stylistic clarity is promoted by simple, direct language. Word choice is a factor in stylistic
clarity: use simple language wherever possible to counteract the abstract, highly specialized
terms of science and technology.
3. Contextual clarity, in which the importance, authorization, and implications of your work are
made available, also contributes to ease of understanding. All work has a context, and your
readers want to understand what the context of your document is. What prompts you to write?
What is your purpose? Whose work precedes or has influenced yours? What is the
organizational and intellectual context of your problem? Answer those questions in
introductions and problem statements and in your citations and other references.
Conciseness, which refers to the expressing a great deal in few words has a special value in
technical fields. Writers are often tempted to include everything that could be relevant to their
subject, rather than merely what is focused, relevant material for their report. The concise
document is a piece of writing that conveys only the needed material. Increase conciseness by:
1. Narrow the document scope to a manageable problem and response.
2. Prepare a clear introduction and develop a detailed outline. These are two strategies that give
you control over document length and scope.
3. Identify and eliminate material that is not necessary to support your claims. Look for sections,
including appendixes, that are not essential to your work.
Graphics are powerful aids to conciseness because they cut down on the amount of prose
necessary to describe objects and processes, summarize data, and demonstrate relationships.
6
Coherence is the quality of hanging together, of providing the reader an easily followed path.
Writers promote coherence by making their material logically and stylistically consistent, and by
organizing and expressing their ideas in specific patterns. Coherence can dramatically improve
the reader's ability to understand your material by promoting its flow or readability. Coherence is
especially valued in science and technology because of the inherent complexity of the subjects.
1. Give readers a road map to help them anticipate the content of your work.
2. Use expected organization. Divide your report into standard sections and place information in
the appropriate section.
3. Develop paragraphs logically. By organizing material into a topic sentence and supporting
sentences, paragraphs pull together material and emphasize various forms of conceptual
development.
4. Transitional devices also operate at the paragraph level to provide links between sentences
and between paragraphs.
1.2 Audience
Determine your audience's needs by assessing their expertise and their purpose in reading the
document. Effective technical writing recognizes several types of readers, reflecting different
levels of expertise:
experts
technicians
managers
laypersons
In 6.021J, you can assume that your primary readers are general experts as each report is written
for a "peer audience" (not your professor). General experts possess extensive knowledge about a
field in general, but they might be unfamiliar with particular technical terms, specific equipment, or
recent advances in your document's subject matter. Specific experts, on the other hand, share or
surpass your knowledge about a document's subject matter.
1.3 Point of View

Point of View refers to how you tell the story of your experiment. There are certain conventions in
report and proposal writing that readers expect and that lend your writing more credibility.
1.3.1 Active voice versus passive voice
Most of your 6.021J work should be written in passive voice. Passive voice in technical writing
keeps the emphasis on the experiment, not the researcher. Passive voice also lends a
professional tone to your writing as overuse of active voice seems childlike. For example,
Simplistic sounding - Over-use of Active Voice
I dissected the frog according to the guidelines in the lab manual. Then, I placed the
sciatic nerve in the nerve chamber. I placed the recording electrodes at R7 and R8.
More professional-sounding - Passive Voice
The frog was dissected according to the guidelines in the lab manual. The sciatic nerve
was then placed in the nerve chamber.
Careful use of active voice is quite effective, however, in a report to add resonance to the writing.
Active voice is usually most effective in the Discussion section of a report. Why? In the Discussion
you can foreground your own ideas about why you achieved the results of your experiment
Second person is not acceptable in 6.021J report writing (Second person = "you")
1.3.2 Verb Tense

In proposals and reports you will find it necessary to alternate verb tenses, depending on which
section of the document you are writing.
Proposals: Present and future tense
What you know is written in present tense
What you will do is written in future tense.
Reports: Combination of present, past, and future tense
Abstract - Past tense (although an introductory sentence may be written in present tense)
Introduction - Present tense for rationale. Purpose statement may be written in past tense.
Methods - Past Tense
Results - Past Tense, although in certain instances present tense is appropriate
Discussion - Your choice of tense
Conclusion (optional) - Your choice of tense
1.4 Organizing Information

Organization is the arrangement of elements into a structure, a whole. Organization is essential in
making your document coherent to your audience. A predictable and logical structure helps
readers understand the information presented in your document.
Organization is a specific approach to document planning. The key instrument of document
organization is the outline. Outlines help you work out both the general structure of your document
and specific sections and topics. An outline will force you to partition material,
develop a point
of view, establish the scope of your document, sequence your topics, and develop a writing
strategy.
1.5 Avoiding Common Style Problems in 6.021J

1. Keep it together. Don't separate the noun and verb of a sentence with lengthy phrases.
Readers look for syntactic resolution --i.e. what is the subject of the sentence doing?
2. Logic: Follow reader expectations that the topic comes first in a sentence and the resolution
comes at the end of the sentence.
For example these two sentences have different meanings because of the reversed topicresolution order: "Bees disperse pollen" versus "Pollen is dispersed by bees"
3. Link old ideas to new ones Use transitions or common vocabulary to create cognitive
coherency and fill logical gaps.
4. Avoid jargon. Jargon is convoluted prose. Technical terms are concise and aid reader
comprehension.
5. Avoid vague pronoun references:
"This." The antecedent "this" needs a noun. This what?
"It." The pronoun "it" is not descriptive. Use specific nouns.
6. You do not need to use phrases like "as stated above." In written communication, readers
generally don't need such pointers as they remember what they've read previously in short
reports. However, do reference figures and graphs: "As shown in Figure 3 . . ." or (Figure 3)
7. Don't be the teacher. Avoid writing as though you were instructing someone. For example, "As
you can see, the response changed after 10 ms."
8. Do not write Methods like a cookbook series. For example, "Wash the nerve with Ringer's
solution."
9. Do not overuse personal pronouns.
10. Know the correct technical terminology for what you are doing.
8
11. The word "data" is plural (datum is the singular form). For example, "The data were defined
such that . . "
12. Do not use bullets to list Methods or Results. Write your report in paragraph form.
13. Do not begin sentence with numbers.
14. In IEEE style you do not use footnotes.
2.0 Proposals
2.1 General Information about Proposal Writing
Proposals develop a plan of action in response to a specific need or problem. In content,
successful proposals demonstrate that you understand the scope of the problem and that you
have developed a valid and well-focused approach for reaching proposed objectives. The goal in
writing proposals is to effectively communicate a plan of action in concise, specific language.
2.1.1 Purpose. The Proposal:

Defines the problem or question that the experiment is trying to answer

Develops an appropriate experimental approach with variables and controls to test the
hypothesis
Specifies the methods that will be used to carry out the experiment
Outlines the expected results
2.1.2 Quick Tips

Think through your research project before writing. Exactly what are you testing? Why? How?
Avoid universal words like "all" and "every" as well as vague words like "some" and "a few."
Also, understand the technical meaning of words like "control" before suggesting that an initial
measurement will be your "control." (If you are unsure about usage of the term "control" see
the frog lab handout provided in class for a technical definition.)
A good rule of thumb when writing a proposal is the "peer test" -- i.e. based on your written
proposal, can your colleague, friend, or roommate understand exactly what you are doing?
Can they restate your research project in one sentence?
2.1.3 Format

Single-spaced
One page
2.1.4 Organization
For your 6.021J proposal, you do not need to submit a proposal with all the elements of a
professional proposal. However, your proposal does need to include certain basic elements:
Title: Specific and meaningful
Authors: Include the names and e-mail addresses of all group members
Hypothesis: The hypothesis states -- in one sentence -- exactly what you are testing. That
statement should be answerable with "yes" or "no"
Background: The background statement explains the motivating problem or rationale for
pursuing a research project. The background statement should clearly articulate the
reasoning behind your hypothesis.
Procedure: The procedure presents your method for reaching your stated hypothesis. What
kind of data will you collect? How will that data be analyzed? Even the most promising
research will fall flat if you cannot design a scientifically valid way to investigate it.
2.2 Frog Proposals
10
2.3 Hodgkin-Huxley Proposals

This theoretical project is intended to provide an opportunity to learn about the complex behaviors
that can be exhibited by the Hodgkin-Huxley model and to compare behaviors of the model with
behaviors of electrically excitable cells. We have two simulations. The first models a spaceclamped axon. That model generates MEMBRANE action potentials. The second models an
axon without space-clamp (although the second model can simulate a space clamp since the
longitudinal resistances can be set to zero). The second model can produce PROPAGATED
action potentials. The second model can be used to explore a wider range of phenomena than the
first. The first model is faster and simpler than the second. Thus both models are useful, and
your project can use either or both of the models.
Beginning with the proposal and extending through the project, you should keep clearly in mind
that you ARE NOT investigating nerve membrane in these exercises. You ARE investigating the
Hodgkin-Huxley model for nerve membrane. Your explanations of all phenomena must be in
terms of the primitive concepts of this model --- the ionic conductances, ionic concentrations, ionic
currents, the capacitance, and the variables m, n, and h. Explanations in terms of molecular
channel mechanisms or electrodiffusion of ions in the membrane are irrelevant in so far as they
are not contained in the Hodgkin-Huxley model!
2.3.1 Proposal Submission
Partners should submit a single proposal and a single report which identifies both members of the
team and gives both email addresses. Proposals should be submitted using the proposal
submission form on our home page.
2.3.2 Practical considerations in the choice of a topic
Projects can involve almost any of the properties of the Hodgkin-Huxley model. However, to
avoid projects whose aims are vague (e.g., ``I would like to understand how the Hodgkin-Huxley
model works'') the proposed project should be in the form of a specific and testable hypothesis.
Projects that involve months of computation should obviously be avoided. The amount of
computation time should be explicitly taken into account in planning a project. For example, any
project that involves measuring the threshold of occurrence of an action potential for many
different parameter values is bound to be very time consuming because determining the threshold
for a single set of parameters itself involves many computations. The task is to choose a
physiological property of the excitation of the action potential that is of interest, and then to define
a specific, feasible project.
2.3.3 Choice of topics
Note: The demonstration project performed in lecture on the effect of temperature cannot be the
basis of a student project.
Topics can involve comparing predictions of the Hodgkin-Huxley model with measurements on
cells. For example, the text contains data on the effects of many external parameters (e.g., ionic
concentrations, cell type) on action potentials. A project might involve reading the original papers
that describe such measurements (some were made before the Hodgkin-Huxley model was
formulated), and testing the hypothesis that these measurements are (or are not) consistent with
the Hodgkin-Huxley model. Similarly, a project might involve examining the effect of some
pharmacological substance on measurements of the action potential and testing the hypothesis
that the substance produces its effect by changing one or another parameter of the model. These
projects will require some reading of original literature which is often difficult and usually time
10
11
consuming. However, such a project can lead to a very rewarding educational experience.
Alternatively, the project might involve a purely theoretical topic in which some property of the
model is explained in terms of its underlying structure. This type of project does not necessarily
involve reading the original literature.
2.3.4 Examples of hypotheses
Any of these (or other) hypotheses can be the starting point for a project. Most of the hypotheses
given above are simplistic, and a careful investigation will reveal their shortcomings. The
Hodgkin-Huxley model is sufficiently complex that investigation of any of the hypotheses will most
likely lead to unexpected results. You should pursue these unexpected results and try to
understand their bases. For example, you may find that in pursuing some hypothesis you choose
to change some parameter of the model that you expect to result in some change in action
potential waveform. The resulting computation might reveal, much to your surprise and chagrin,
that no action potential has occurred. Determine why no action potential occurred. The
explanation will usually be instructive. Your aim should be not simply to reject or accept the
hypothesis but to delve into the topic in sufficient depth so as to a deepen your understanding of
the model. One outcome of the project might be to restate your original hypothesis in a new and
more sophisticated form.
Hypothesis --- The effect of temperature on the conduction velocity of the squid giant
axon can be fit by the Hodgkin-Huxley model.

Chapman, R. A. (1967). Dependence on temperature of the conduction velocity of the
action potential of the squid giant axon. J. Physiol. 213:1143-1144.

Easton, D. M. and Swenberg, C. E. (1975). Temperature and impulse velocity in giant
axon of squid loligo pealei. Am. J. Physiol. 229:1249-1253.
Hypothesis --- When two action potentials are elicited, one just after another, the velocity
of the second is slower than the velocity of the first action potential. This phenomenon is
predicted by the Hodgkin-Huxley model.

George, S. A., Mastronarde, D. N., and Dubin, M. W. (1984). Prior activity influences
the velocity of impulses in frog and cat optic nerve fibers. Brain Res. 304:121-126.
Hypothesis --- The threshold current for eliciting an action potential with an intracellular
electrode is higher for a space-clamped than for an unclamped model of an axon.
Hypothesis --- Increasing the membrane capacitance will decrease the conduction
velocity.
Hypothesis --- Increasing the membrane conductance (by scaling all the ionic
conductances) will increase the conduction velocity.
Hypothesis --- Increasing the external concentration of sodium will increase the
conduction velocity.
Hypothesis --- Increasing the external concentration of potassium will increase the
Hypothesis --- Increasing the external concentration of calcium will increase the
Hypothesis --- Increasing the temperature will increase the conduction velocity.
11
12
Hypothesis --- The difference in waveform of the action potential of a frog node of Ranvier
and of a squid giant axon (Figure 1.9 in volume 2 of the text) can be reproduced by the
Hodgkin-Huxley model of a squid giant axon by a change in temperature.
Hypothesis --- The membrane capacitance determines the time course of the rising phase
of the action potential. Increasing the membrane capacitance decreases the rate of
increase of the rising phase of the action potential.
Hypothesis --- The falling phase of the action potential (repolarization) can occur in the
absence of a change in potassium conductance.
Hypothesis --- Increasing the temperature sufficiently blocks the occurrence of the action
potential because the membrane time constant limits the rate at which the membrane
variables can change and prevents the difference in time course of the sodium and
potassium activation which is responsible for initiation of the action potential.
Hypothesis --- The initiation of the action potential is independent of the potassium
conductance.
Hypothesis --- The prolonged plateau of the cardiac muscle action potential can be
accounted for by the Hodgkin-Huxley model with a potassium conductance that has a
slow activation.
Hypothesis --- The effect of tetraethylammonium chloride (TEA) on the action potential of
the squid giant axon can be modelled with the Hodgkin Huxley model by decreasing K_n
and increasing K_h.

Armstrong, C. M. (1966). Time course of TEA-induced anamalous rectification in

Armstrong, C. M. and Binstock, L. (1965). Anomalous rectification in the squid giant

Hypothesis --- The shape of the action potential in the presence of tetraethylammonium
chloride (TEA) can be accounted for by the Hodgkin-Huxley model with a reduced
maximum value of the potassium conductance.

Armstrong, C. M. (1966). Time course of TEA-induced anamalous rectification in

Armstrong, C. M. and Binstock, L. (1965). Anomalous rectification in the squid giant

Hypothesis --- Increasing the external calcium concentration will block the occurrence of
the action potential because this will reduce the difference in the time constant of sodium
and potassium activation which is responsible for the initiation of the action potential.
Hypothesis --- Increasing the external concentration of potassium will decrease the
refractory period; decreasing this concentration will lengthen the refractory period.
Hypothesis --- Increasing the external concentration of sodium will decrease the refractory
12
13
Hypothesis --- Absolute and relative refractory periods are decreased by increasing the
rate constants for sodium inactivation and for potassium activation.
Hypothesis --- Repolarization cannot occur if the potassium activation rate constant is
zero.
Hypothesis --- The threshold of the action potential to a brief pulse of current decreases
as the external potassium current is increased.
The Hodgkin-Huxley model with default parameters does not exhibit accommodation.
Hypothesis --- Accommodation occurs if the leakage conductance is increased.
The Hodgkin-Huxley model with default parameters does not exhibit accommodation.
Hypothesis --- Accommodation occurs if the potassium conductance is increased.
Hypothesis --- Increasing the eakage equilibrium potential will block the
action potential.
Hypothesis --- The effect of the changes in concentration of sodium ions on the action
potential of the giant axon of the squid can be accounted for by the Hodgkin-Huxley
model.

Hodgkin A. L. and Katz, B. (1949). The effect of sodium ions on the electrical activity
of the giant axon of the squid. J. Physiol. 108:37-77.

Baker, P. F., Hodgkin, A. L., and Shaw, T. I. (1961). Replacement of the protoplasm
of a giant nerve fibre with artificial solutions. Nature 190:885-887.
Hypothesis --- In response to rectangular pulses of current, the rheobase of the strengthduration relation increases as temperature increases.
Hypothesis --- An increase in temperature results in a decrease in the duration of the
refractory period.
Hypothesis --- The threshold membrane potential at which the Hodgkin-Huxley model
produces an action potential in response to a brief pulse of current is equal to the
membrane potential for which the linearized Hodgkin-Huxley equations have unstable
eigenvalues.
Application of a long-duration constant current to the Hodgkin-Huxley model produces a
train of action potentials. Hypothesis --- The frequency of the action potentials increases
with increasing current amplitude.
train of action potentials. Hypothesis --- The frequency of action potential increases as the
parameter K_n is increased.
train of action potentials. Hypothesis --- The frequency of action potential increases as the
temperature is increased.
Hypothesis --- An increase in the external concentration of potassium increases the
threshold potential at which an action potential is elicited.
Hypothesis --- Increasing K_h will result in an increase in the steepness of the
repolarization phase of the action potential.
13
14
3.0 Reports
In 6.021J you will write two reports--frog lab report and Hodgin-Huxley report. Both reports follow a
standard format for a technical report.
3.1 Elements of a technical report

A report should tell a story. The story is your lab project and its implications. Scientific reports
follow a general organization that includes the following sections:
Table 1: Elements of a 6.021J Report
Front Matter
Body
End Matter
Cover Page (Title +
Introduction
References
Abstract)
Methods
Appendix
Table of Contents
Results
Discussion
Conclusion (optional)
6.021J reports also usually follow the following conventions:

Use standard font; 10 or 12 point

Double space drafts (for comments). Single-space final reports.

Number pages, beginning with Introduction.

Each section of the body of the report and report end matter is numbered
3.1.1 Title
The purpose of the report title is to be informative, specific, understandable at a glance.
Avoid "cute" titles
The title is on a Cover Page
All nouns are capitalized in the title
The title is centered on the page
Your names and date appear below the title
Do not use abbreviations in the Title
3.1.2 Abstract
The abstract is a one paragraph summary of the report. The abstract of a scientific paper is the
most important section, because it usually determines whether someone will read your paper or
not. You should write the abstract last. The abstract should include a rationale for the study, your
experimental approach, results, and conclusion. Generally, each of these topics should be
handled in a sentence or two.
The abstract is the shortest (150-200 words) and generally most challenging part of your
report to write.
Do not include figures, figure references, or extraneous information--i.e., information not
found in the report--in your abstract.
3.1.3 Table of Contents
The Table of Contents helps readers quickly find the information they need from your report and
provides a guide to the report content.

List the headings and subheadings exactly as they appear in your report
Through formatting show the hierarchy of heading and subheadings.
For example:
14
15
2.0 Methods
.
.
2.1 Dissection Procedure
2.2 Tests Conducted
.
.
.
.
3
3
4
3.1.4 Introduction
The introduction provides the motivation for conducting the study. You should briefly summarize
what is known (appropriate literature citations are encouraged) and indicate what new knowledge
you hope to discover. Include only relevant background, including key terms, then state the
problem that is being addressed. In your Introduction, you do not need to state everything that you
have ever learned which is in any way relevant to the topic. Just summarize the relevant facts.
While the implications of what you may discover are relevant, you need not state that your findings
will be of cosmological importance.

DO NOT include findings or methods in your Introduction

Introductions usually follow a funnel style, starting broadly with general ideas and then
narrowing to your hypothesis.
You should specifically state the hypothesis you tested
When you first use a term that you abbreviate later, use the full name at first usage. After it,
put the abbreviation in parenthesis. For example, "The compound action potential (CAP) . . ."
In following instances, you may use "CAP" in place of compound action potential.
3.1.5 Methods
The Methods section describes the process you undertook to complete the research. Methods
describes the FINAL APPROACH that you took to your experiment, which may not be the
approach that you initially intended. Describe the experimental methods as well as any
mathematical or statistical methods you used to analyze the data. Include Methods for all results
presented in your report. By definition any experimental measurements or experimental data you
collected are not reported here. They are reported under the Results section. Provide sufficient
detail to enable another investigator to exactly reproduce your experiments and, hopefully, obtain
the same results. The essence of scientific research is the ability to reproduce results.

Only include methods for data and results presented in your report.
Methods are not written like a cookbook (a series of orders) or a numbered series of steps.
Write Methods in paragraph form, divided into subsections by topic.
Distinguish between preliminary measurements/studies and your main experiment.
Describe your Methods in past tense since you have already completed the experiment.
Data processing (e.g. statistics, using ANOVA) is a Method and needs to be described.
3.1.6 Results
The Results section DESCRIBES but DOES NOT INTERPRET the major findings of your
experiment. Organize Results logically with subsections to emphasize order. Results should
correlate organizationally to the Methods. Collaborative Writer's Tip: If you write the Methods of
the report, also write the Results so you know that the two sections are organized respectively.
Present the data using graphs and tables to reveal any trends that you found. Do not
tabulate/graph raw data. Each table or graph should document one of your findings. This will most
likely involve synthesizing your raw data into an appropriate format before graphing them.
Simply presenting tables and figures is not acceptable. Coherent prose is necessary to introduce
and explain tabular and graphical material. Often each grouping of information in Results is
organized as follows:
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16
1. Paragraph explaining a figure following the paragraph. The paragraph description
describes in words what is shown in the figure.
2. Figure showing visual representation of data.

3. Figure caption (below the figure) that explains what is shown in the figure.
A key issue in Results is to determine whether the effects you measured are a result of the
intervention you studied or rather just reflect random variations in the data or a drift of
experimental parameters over time. Well-designed control experiments and statistical analysis of
your data should be used to resolve this question.

Avoid presenting raw data (e.g. showing ten superimposed waveforms to demonstrate a trend
of decreasing amplitude) and instead use synthesis graphs (e.g. a plot of amplitude vs.
concentration) which explicitly show the trends you are trying to prove
Figures should appear in the order which they are referenced in the text of the paper.
Each figure should be a standalone entity, and the caption should be clear, specific and
detailed enough to describe what is shown without reading the whole text.
Avoid captions that begin with A graph of Just state what is shown.
Make sure the legend is specified and easy to read
3.1.7 Discussion
The Discussion offers your interpretations and conclusions about your findings. At the beginning
of the Discussion, return to the main point of your study -- Did you answer your hypothesis? How
do your Results relate to the goals of the study, as stated in your introduction? How do they relate
to the results that might have been expected from background information obtained in lectures,
textbooks, or outside reading? How do you explain deviations in your findings? Were there
limitations to your study? What might be useful for future investigations?
The Discussion is your chance to demonstrate your ability to synthesize, analyze, evaluate,
interpret, and reason effectively. Draw generalizations from your results or conclusions about
theoretical/practical implications. Use evidence to support these claims. Do not include new
findings in your Discussion. You do NOT need to bring in theories to explain your ideas beyond
what you have learned in class. Your readers are looking for well-supported explanations, not for
leaps of fancy or mere repetitions of your findings.

Do not repeat the visuals shown in the Results section (although some authors choose to add
additional visuals to clarify their discussion). Include textual references to figures if you need
for readers to reference a figure (For example, "As shown in Figure 3: title . . .").
3.1.8 Conclusion (Optional)

Some writers like to end their reports with a short conclusion that summarizes the main "jist" of
their research and includes recommendations for future study.
3.1.9 References - IEEE style

If you reference an outside source in your report, you should cite where you found that source.
You should also cite sources that your reader, a fellow student, may be unfamiliar with. The
appropriate style for citing sources in this report is IEEE style. Cite only material that you have
actually read. See Section 4.3 for guidelines on citing sources in IEEE style.
3.1.10 Appendices
Appendices include the original data taken during the laboratory session. Appendices should be
numbered A, B, C, etc. Appendices are useful for additional data and mathematical analyses that
16
17
are important reference material for the study but which would interrupt the flow of the
presentation in the main body of the report.
3.2 Graphics: Presenting Information in Tables, Figures, and Equations

Graphics in reports are invaluable aids to your audience because they condense text, clarify
relationships, and highlight patterns. Good graphics display the significance of your data and allow
the reader to follow your discussion.

Use graphics to condense complicated textual content for your audience.

The nerve was placed on the nerve chamber with the proximal end on the stimulating
electrode, as shown in Figure 1.
Use graphics to clarify relationships between results.
Although conduction velocity increased with temperature, this relationship is not linear, as
can be seen in Figure 2.
Use graphics to highlight patterns in your data that are not immediately evident in your text.
Figure 3 displays the effects of exercise on heartbeat in an experiment to study energy
expenditure in a partial gravity environment, such as an orbiting space station.
3.2.1 Tables
Each table must contain a title and a caption.

Tables are numbered, and they appear in the order they are referenced in the text.
3.2.2 Figures

Each figure must have a title and a caption beneath the figure
Figures are numbered, and they appear in the order they are referenced in the text
Axes are labeled at bottom and side of graph
For graphs with multiple plots, provide a legend
Units of measure are visible. Each visual does not extend across more than one page.
C o n tr o l
Electrode Voltage (mV)
2 m in
4 m in
400
6 m in
200
0
-2 0 0
M a x V a lu e R e a c h e d
M in V a lu e R e a c h e d
-4 0 0
-6 0 0
1
51
101
151
T im e ( m s e c )
Figure 3: The stimulus response from an addition of 0.06% alcohol. The

maximum value reached is a decrease in the absolute magnitude of the peak and
occurs after the alcohol is allowed to settle for 6 minutes. The offset was added
in order to center the resting potential at 0.
3.2.3 Equations

Equations are numbered.

Use mathematical symbols.
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Decimal quantities include a zero before the decimal point.

Add a space before the equation and after the equation to separate from the text
G Na = G Na m 3 (V m , t )h(V m , t )
(Eq. 1)
3.3 IEEE Style

The Institute of Electrical and Electronics Engineers (IEEE), one of the largest professional
organizations in the world, oversees numerous journals and regularly publishes its own Letters,
Transactions, and Proceedings of the technical conferences it sponsors.
IEEE style uses a single sequentially ordered note number to cite all references to each source
mentioned in the text. The IEEE reference listis arranged by the order of citation in the text, not in
alphabetical order. IEEE style also prohibits the use of content notes, preferring instead that
supplementary explanations and examples be included in the text (often in parentheses).
3.3.1 Two parts to IEEE style: (1) in-text citation and (2) references page
Example of IEEE citation in the body of a report:
The oncogene jun has presently become one of the best-known oncogenes because of
its ability to act as a transcription factor [1]. One study [2] examined the mRNA levels of
jun C, jun B and jun D in various mouse tissues and concluded that each of these genes
is expressed independently in different tissues and that they may play a role in growth,
development and cellular differentiation.
Example of the above report's References page
[1] F. Cavalieri, T. Ruscio, R. Tinoco, S. Benedict, C. Davis, and P. K. Vogt, "Isolation of
three new avian sarcoma viruses: ASV9, ASV17, and ASV 25," Virology, vol. 143, pp.
680-683, 1985.
[2] S. I. Hirai, R. P. Ryseck, F. Mechta, R. Bravo, M. Yaniv, "Characterization of jun D: a
new member of the jun protooncogene family," Embo Journ., vol. 8, pp. 1433-1438, 1989.
--Taniya Sarkar, Wei Zhao, and Nurul H. Sarkar, "Expression of Jun Oncogene in Rodent and
Human Breast Tumors," World Wide Web Journal of Biology
3.3.2 Examples of IEEE References for Reference page of report

Books
Book by One Author
[1] A. Lightman, Ancient Light: Our Changing View of the Universe. Cambridge, MA:
Harvard University Press, 1991.
Edited Book or Anthology
[1] J. L. Spudich and B. H. Satir, Eds.,Sensory Receptors and Signal Transduction.
New York: Wiley-Liss, 1991.
Selection in an Edited Book
[1] E. D. Lipson and B. D. Horwitz, "Photosensory Reception and Transduction,"
in Sensory Receptors and Signal Transduction, J. L. Spudich and B. H.
Satir, Eds. New York: Wiley-Liss, 1991, pp. 1-64.
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19
Book by an Institutional or Organizational Author
[1] Council of Biology Editors, Scientific Style and Format: The CBE Manual for
Authors, Editors, and Publishers, 6th ed., Chicago: Cambridge University Press, 1994.
Technical Report
[1] C. F. Heohan, M. C. Liepins, C. A. Meuse, M. M. Wolfson, "Summary of triple Doppler
data, Orlando, 1991," MIT Lincoln Laboratory, Lexington, MA. Tech. Rep.
ATC-186 (DOT/FAA/NR-92-2), 7 Apr. 1992.
Government Publication
[1] National Aeronautics and Space Administration, NASA Pocket Statistics.
Washington, DC: Office of Headquarters Operations, 1991.
Journal Articles
Article in a Journal Paginated by Annual Volume
[1] K. A. Nelson, R. J. Dwayne Miller, D. R. Lutz, and M. D. Fayer, "Optical
generation of tunable ultrasonic waves," Journal of Applied Physics, vol. 53, no. 2,
Feb., pp. 1144-1149, 1982.
Article in a Professional Journal Paginated by Issue
[1] J. Allemang, "Social studies in gibberish," Quarterly Review of Doublespeak, vol. 20,
no. 1, pp. 9-10, 1993.
Article in a Popular Monthly or Bimonthly Periodical
If the journal is a monthly or bimonthly periodical, use the month and year of publication
instead of the volume number.
[1] J. Fallows, "Networking technology," Atlantic Monthly, Jul., p. 34-36, 1994.
Article in a Daily, Weekly, or Biweekly Magazine or Newspaper
Include the year, month, and day.
[1] B. Metcalfe, "The numbers show how slowly the Internet runs today," Infoworld, 30
Sep., p. 34, 1996.
Websites
[1] T. Land, "Web extension to American Psychological Association
style (WEAPAS)," [Online document], 1996
Mar 31 (Rev. 1.2.4), [cited 1996 Sep 14], Available HTTP:
http://www.nyu.edu/pages/psychology/WEAPAS/
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3.4 Frog Report Specifics

3.4.1 Commonly Misunderstood Concepts

Differences between Compound Action Potential (which is being measured in this lab) and an
Action Potential.
Why a diphasic response is seen.
What is a control.
3.4.2 The Report: Common Issues

Introduction
Since you do not have much background knowledge at this point, your background
research may be sparse. However, make sure you explain to readers why you chose to
study you did.
Do not spend a lot of time and space defining CAP and terms that peer readers
understand.
Methods
Do not repeat the frog dissection process described in the lab manual. You only need to
describe your specific experimental method.
Cite the lab manual
Methods are not just procedures, but also your method(s) for taking measurements.
Explain exactly how amplitude was defined and measured.
Explain the controls you took.
Detail how many trials and at what levels.
Results
Results are more than just graphs. Explain in words what is shown in each figure.
Separate your Basic Observations from your Experimental Results using subheadings
Do not spend too much time explaining basic observations.
Organize results to show trends or comparisons in the data.
3.5 Hodgin-Huxley Report Specifics

The Hodgin-Huxley report comes late in the semester when students are tired. Leave yourself
enough time to write your report and run your simulations.
3.5.1 Commonly Misunderstood Concepts

The Frog Lab is an experimentally-based project. The HH lab is based on simulation.

Time controls are not necessary for simulations. There can be controls performed for other
variables, such as the numerical method used by the software.
The HH software models the responses of the giant squid axon, a single, very specific cell
Well-defined procedures for measuring various properties are necessary. (e.g., In determining
threshold current amplitude, how will you determine whether a given response is an action
potential or not?)
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21
3.5.2 The Report: Common Issues

Methods
This lab does not have procedural methods.
The methods will mainly be explanations of how and why data was gathered
The notion of control is different than the frog experiment. In the HH experiment there is
no need to control for time.
Results
Explain results in terms of the model. What did the model predict? Compare those
predictions with experimental findings.
Explain results in terms of the variables of the model
Discussion
Be careful about drawing conclusions. If you use a definition and then change a definition
and get a different result, how robust is your finding really?
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4.0 Tips on Collaborating

One of the most useful education experiences in this course is learning to work with others. Most
scientific writers collaborate on projects and through the experience of working collaboratively
researchers develop techniques for working with others so that the work is evenly distributed.
4.1 Ways to make collaborating easier

1. Work together to select your project. Decide which specific issue to study, and outline your
proposal report.
2. Create a work plan that clearly defines which partner is responsible for each of the duties to
be performed.
3. Divide the work load fairly, using each person's strengths. For example, if you are good at
MATLAB, take responsibility for producing the graphs for your report.
4. Get contact information so you can find your partner out of the lab.
5. Set due dates. Stick to those dates.
6. Agree on word processing program so it is easier to merge your work.
7. Each write different sections of the report. If you write the Methods, you should also write the
Results since Methods and Results should correlate.
8. Synthesize your efforts in advance. Do not wait until the day your report is due (or the night
before!!) to combine your work.
9. Always keep only one master draft.
10. Work in parallel on different sections, then in series (one person at a time) on the whole draft.
11. Edit. Edit. Edit.
12. Proofread. Proofread. Proofread.
4.2 Tips for collaborative editing

When writing collaboratively, stay professional and focused on your task. Try using a two-part
editing process for editing your work. First, edit for content. Second, edit for style.
4.3 Edit for Content

Read through your draft, stopping at the end of each section, and ask yourself the following
questions:
Is the information accurate? Are there any incorrect data entries? Are all outside sources
documented? Is all information from outside sources either paraphrased or quoted exactly
and enclosed in quotation marks? Are any graphics misleading?
Is the information complete? Have you omitted any facts, concepts, equations or processes
necessary for the document's aim and for the audience type and the audience's purpose? Are
there any steps missing from instructions, procedures, or descriptions of processes?
Is the information comprehensible to your audience? Are all technical terms that need to be
defined for your audience clearly defined? Are all acronyms explained when first used?
Does the report tell a story? Does it bring up the important points you are trying to make? Are
the methods and results clearly and precisely described? Are the discussion points relevant to
your results? Is each result discussed and properly documented?
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4.4 Edit for Style
If you have not already done so, divide your document into sections and subsections by
inserting headings and subheadings into your document.
Does each section and subsection follow logically from the preceding one?
Early in the text, is there a clear road map of the entire document? Does the document follow
that road map?
Review the graphics in the order presented in your document. Do they present the key
information to the reader in a logical order?
Read a printed copy of the report aloud to find typographical errors and page break errors.
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5.0 Tips on Editor's Comments

5.1 Writing Meaningful comments on other reports
By far some of the most helpful comments on 6.021J reports come from other students! Yes, it is
true. Often tech readers and the writing instructor do not offer "the complete picture." Only another
student can tell you if your report is really clear and wll organized because peer-readers are the
primary audience for your reports.
Observe the following general strategies in reviewing a colleague's document.
1. Take the time to review it right. Spend an hour on your review out of courtesy to the other
writers.
2. Read the report at least twice -- first time for surface coherence and obvious errors;
second time for deep editing issues (logic, coherence between sections). You will
probably need to skip back and forth in the report to do a thorough editing job.
3. Start by praising what the document does well.
4. Spend much of your time responding to the author's specific requests. (That assumes
that the writer left you questions.)
5. Avoid performing an editorial review, unless asked to by the author. You do not need to
mark every comma error in the report. Mark a few and the author should understand the
problem from a few examples.
6. Do not just criticize harshly (i.e. "This sucks.") no matter how poor the draft. Make
suggestions on how to solve the problems you notice in the document.
7. Ask questions if you do not understand a part of the report.

8. If something is "vague" or "unclear" explain why.
9. If a sentence is difficult to read or unclear, underline it and write in the margin your note.
10. Write an end note in which you summarize the main problems with the report in order of
importance.
11. Sign your review with your name and email address.
5.2 Making sense of editor's comments

For both the frog report and the Hodgin-Huxley report, you will receive comments on your first
draft from three readers -- peer readers, a technical reader, and a writing reader. All professional
writers must manage multiple edits from multiple editors, so 6.021J is good practice. As the writer
you get the final word on whether you change your report or not. Editor's comments are only
SUGGESTIONS. Use your own judgment in choosing how to revise your report. Feel free to add a
cover letter on your final report if you feel strongly about rejecting a comment. In the end, editor's
comments are meant to HELP YOU. Take their advice as help, not as personal criticism.
Tips for making sense of edits:
If editor's suggest similar edits. It's probably a good hint that something really is wrong with a
part of your report if multiple editor's comment on it.
If editor's comments are contradictory. Try to understand why the editor's were commenting
contradictorily on a point. Did one misread? Are they saying the same thing in different ways?
Was there another problem elsewhere in the report that led to this disagreement?
If editor's simply make poor comments -- maybe they were confused about a point, maybe
they missed a point. Do not think your editor does not know what he or she is doing. Editor's
are human. Sometimes they make mistakes.
If you do not understand a comment or cannot decipher your editor's handwriting, ask your
editor to explain. All 6.021J readers are willing to answer questions in person and via email.
24
Tips to Writing a Successful Proposal for 6.021J

Adapted from the Mayfield Handbook of Technical & Scientific Writing and the 6.021J proposal handout
Goals:
Proposals develop a plan of action in response to a specific need or problem. In content, successful
proposals demonstrate that you understand the scope of the problem and that you have developed a valid
and well-focused approach for reaching proposed objectives.
The goal in writing proposals is to effectively communicate a plan of action in concise, specific language.

Think through your research project before writing. Exactly what are you testing? Why? How?
Avoid universal words like "all" and "every" as well as vague words like "some" and "a few."
Also, make sure you understand the technical meaning of words like "control" before suggesting that
an initial measurement will be your "control." (If you are unsure about usage of the term "control" see
the frog lab handout provided in class for a technical definition.)
A good rule of thumb when writing a proposal is the "peer test" -- i.e. based on your written proposal,
can your colleague, friend, or roommate understand exactly what you are doing? Can they restate your
research project in one sentence?
Format:
Single-spaced
One page
Organization:
Most proposals share a general structure, including title, objective, background, and proposed research
plan. See the Mayfield Handbook of Scientific and Technical Writing (Section 2.6) for a description of
elements found in professional proposals.
For your 6.021J proposal, you do not need to submit a proposal with all the elements of a professional
proposal. However, your proposal does need to include certain basic elements:
Title
Often the title is the only basis on which readers decide if your work will be useful to them. Make
your title descriptive enough to give a specific idea of what is covered in the proposal.
WEAK: Effects of Alcohol on a Frog Sciatic Nerve
What kind of effects? What exactly is this proposal suggesting to research?
BETTER: The Relationship Between Amplitude of the Compound Action Potential and Diameter of
the Frog Sciatic Nerve

Name
Your name and the name of your partner (with your email addresses)
Hypothesis
The hypothesis should state -- in one sentence -- exactly what you are testing. That statement should
be answerable with "yes" or "no"
WEAK: We predict that the speed and amplitude of the compound action potential of the frog sciatic
nerve will both change with temperature
This hypothesis cannot be answered "yes" or "no." In addition, it is not clear what kind of response
the researchers are studying, as the wording "change with temperature" is too vague.
BETTER: Decreasing temperature will decrease the velocity of the compound action potential of the
Poe
09/13/01
frog sciatic nerve
Background
The background statement should explain the motivating problem or rationale for pursuing a research
project. The background statement should clearly articulate the reasoning behind your hypothesis.
WEAK: The speed of a chemical reaction depends on temperature. Therefore, we expect the speed of
the compound action potential to depend on temperature. Also, the duration will depend on
temperature. Finally, the amplitude of the compound action potential should depend on temperature.
This statement is too general. What do the researchers mean when they write "depend on"? How do
these three expectations lead the researchers to the hypothesis?
BETTER: Decreasing temperature decreases the rates at which many chemical reactions proceed.
Therefore, it seems plausible that the speed of neural conduction would decrease as temperature
decreases.
Procedure
The procedure should present your method for reaching your stated hypothesis. What kind of data
will you collect? How will that data be analyzed? Even the most promising research will fall flat if
you cannot design a scientifically valid way to investigate it.
WEAK: We will measure the compound action potential as described in the Laboratory Manual but
at a variety of temperatures. We will record action potentials for all conditions and compare them.
This procedure does not clearly outline the research method. The researchers are unclear about how
they will conduct their study and what they will do with their data. Where will action potentials be
recorded? What will be compared and how? How will these measurements help test the hypothesis?
BETTER: After dissecting the sciatic nerve from a frog, we will stimulate the nerve and measure the
responses as outlined in the lab manual. The velocity of the compound action potential will be
determined by dividing the distance between the stimulating and recording electrodes by the time to
the first negative peak of the response potential. The distance between the stimulus and the response
electrodes will be made as large as possible (using R11 and R12 if the nerve is long enough) to
improve the accuracy of the velocity measures (by minimizing the effects of small errors in measuring
times and distances). After determining the velocity at room temperature, we will chill the nerve by
applying chilled Ringer's solution. We will then measure and record the compound action potential.
We will then apply room-temperature Ringer's solution to see if the effects of chilling are reversible.
We will then repeat this procedure at least 3 times to make sure that the effects are, in fact, due to the
chilling.
Poe
09/13/01
CELLULAR BIOPHYSICS
SOFTWARE BASED ON MATLAB
Thomas Fischer Weiss

and
Tanmaya Shubham Bhatnagar
Massachusetts Institute of Technology
Fall 1997
Date of last modication: October 25, 1997
ii
iii
Preface
Historical perspective
During the 1980s the use of computers and information technologies began to
have an impact on higher education (Kulik and Kulik, 1986; Balestri, 1988; Wil
son and Redish, 1989; Athena, 1990a; Athena, 1990b). As an integral part of this
trend, in 1983 MIT in partnership with the Digital Equipment Corporation and the
IBM Corporation launched Project Athena which was designed to make computa
tion available to undergraduate students through a network of computers located
in public clusters on the MIT campus (Athena, 1990a; Athena, 1990b). A major
objective of Project Athena was to improve undergraduate education through
the use of computation and information technologies. Faculty were encouraged
to participate, and support for faculty software developers was provided on a
competitive basis.
One of us (TFW) has been involved in teaching cellular biophysics at MIT since
the 1960s. The possibility of using software as a pedagogical aid was intriguing.
With support from Project Athena, a software package on the Hodgkin-Huxley
model for nerve excitation was developed as part of an undergraduate thesis (by
David Huang), and was rst used to teach cellular biophysics in the Fall 1984
semester. The software was designed to be easy to use so that a students atten
tion would be focussed on the Hodgkin-Huxley model and not on the computer.
Informal discussions with students and a survey of student views showed that the
software was an enormous success. During the rst semester, the software was
used primarily in lecture demonstrations and as the basis for student projects.
Both pedagogic methods were found to be effective. The use of the software
in lecture was very effective in motivating and engaging students. The student
projects were effective in allowing students to pursue a research project of their
choice with staff assistance. For many students this was their rst experience
with a research project. The use of these projects, developed in the rst year,
was so successful that it has been used ever since.
The initial results with the Hodgkin-Huxley software were so successful ed
ucationally, that several other software development projects involving student
programmers were launched. In all, 5 software packages were developed and
have been used every year to teach the subject. All of these packages were re
vised extensively in response to suggestions from students and staff. The original
software runs on UNIX workstations under MITs Project Athena and is available
to the MIT community on a network of about 1000 UNIX workstations located in
public clusters on the MIT campus as well as in some living groups. All this soft
ware was written in C and XWindows and was based on a library of graphic user
interface subroutines written by one of the students (Giancarlo Trevisan). The
software has been used in lectures, in recitations held in an electronic classroom
in which each student uses a workstation, in homework assignments, and in stu
iv
dent projects. Various modes of use of the software in teaching were developed
and are described briey elsewhere (Weiss et al., 1992) and more extensively in
the last chapter of this manual. The software has become an integral part of the
subject, and it is difcult to imagine teaching the subject without the software.
Several problems became apparent in the development and utilization of the
software. First, it was very expensive, in time and in money, to develop the soft
ware with the software tools available in the late 1980s. Much of the time was
expended in the development of graphic user interfaces that make the software
easy for the user but which are tedious for the programmers to specify. These
graphic user interfaces had to be written in a low-level language (XWindows).
When Project Athena ended in 1991 and the funds from corporate sponsors were
no longer available to support the development of new software, this develop
ment slowed considerably. Second, maintenance of the software became a major
headache. It became difcult for a single faculty member with research, teaching,
and other academic commitments to maintain a library of software in the face
of changes in the operating systems. Third, as word spread about the existence
of the software, educators and students outside of MIT requested the software.
These requests accelerated dramatically after one of the software packages en
titled Hodgkin-Huxley Model won the 1990 EDUCOM/NCRIPTAL Higher Educa
tion Software award for Best Engineering Software. However, almost all of the
requests came from students and faculty with access to Macintosh or PC com
puters and not to UNIX workstations. Thus, when these people were informed
that the software ran only on UNIX workstations, they invariably lost interest.
At the time the software was written, the computational power of workstations
so exceeded that of personal computers (PCs) that it was simply not possible
to provide the type of performance on PCs that was achieved on the worksta
tions. Furthermore, MITs Project Athena was committed to a network of UNIX
workstations. Thus, for both software and hardware considerations, it did not
make sense to port the existing software to PCs. Furthermore, the high cost of
software development and maintenance did not justify further development of
educational software on UNIX workstations alone. Thus, the development of new
software was terminated in 1991.
By 1995, a number of developments made it feasible to address the problems
described above and to develop software for teaching cellular biophysics in a
manner that would make it easier to maintain, easier to modify, and widely avail
able. Thus, all the software was rewritten to operate under MATLAB, which is a
software package produced by The MathWorks, Inc., for the following reasons:
MATLAB is a powerful interpretive computational and visualization soft
ware package with a large number of higher-level built-in functions. Thus,
it is suitable for the development of educational software packages.
MATLAB is available for Macintosh computers running on MacOS, PCs run
ning Microsoft Windows, and UNIX workstations running XWindows. Thus,
v
MATLAB runs on all the platforms commonly found in academic settings.
The vendor supports changes in MATLAB that are required as changes in
computer platforms occur. With the use of software built on MATLAB, this
major maintenance job is transferred from individual faculty members to
the vendor who has both the nancial incentive and expertise to maintain
the vendor software.
Large improvements in performance of PCs have made the development of
computationally intensive educational software feasible on these platforms.
MATLAB has provided increasingly sophisticated tools for building graphic
user interfaces (GUIs). These GUIs are essential for building user-friendly
educational software packages.
MATLAB has rapidly become the de facto leader in supporting educational
computational subjects at MIT and elsewhere. Thus, students are exposed
to MATLAB in other subjects and the different exposures are mutually re
inforcing.
The effort to port the software to MATLAB was supported for 3 years by the Na
tional Science Foundation. The present software manual describes this software.
Although the software is not linked directly to any textbook, it was developed in
parallel with textbooks in cellular biophysics (Weiss, 1996a; Weiss, 1996b).
Acknowledgement
A number of people contributed to the success of the development of this soft
ware. We thank Project Athena, especially its two directors Steven Lerman and
Earll Murman, for their support. In addition Gerald Wilson, Joel Moses, Richard
Adler, Paul Peneld, and Jeffrey Shapiro were unfailingly supportive of this effort.
A number of students were involved in this effort. David Huang wrote the rst
version of the Hodgkin-Huxley model package. David Koehler also contributed to
this package. Devang M. Shah wrote the rst version of the random-walk model
package which was also revised by Elana B. Doering. Chapter 2 is based heav
ily on Devangs thesis (Shah, 1990). Scott I. Berkenblit wrote the rst version of
the macroscopic diffusion package. Chapter 3 is based heavily on Scotts thesis
(Berkenblit, 1990). Stephanie Peek and Leela Obilichetti helped to develop the
carrier-mediated transport package. Giancarlo Trevisan was a major contributor
to all the packages. He wrote the rst version of the voltage-gated ion channel
package. He later rewrote the Hodgkin-Huxley package and the carrier-mediated
transport package. He wrote all the graphic user interface routines that were
ultimately used by all the packages. Generations of students beneted from his
efforts. The recipients of the 1990 EDUCOM/NCRIPTAL Higher Education Soft
ware Award for Best Engineering Software for the Hodgkin-Huxley package were
vi
Thomas Weiss, Giancarlo Trevisan, and David Huang. More than a dozen gener
ations of the students who took the subject helped to nd aws in the software
and made valuable suggestions for its improvements.
Besides the support from Project Athena, the development of the software
was supported by the Howard Hughes Medical Institute for which we are grate
ful. TFW was supported in part by the Thomas and Gerd Perkins professorship.
The porting of the software to MATLAB was supported by the National Science
Foundation (NSF), Division of Undergraduate Education. We would particularly
like to thank Dr. Herbert Levitan, Section Head of Course and Curriculum De
velopment of NSF. Dr. Karen C. Cohen has been helpful in the evaluation of the
software.
The division of labor on the present MATLAB-based software is as follows:
The software was designed by both TSB and TFW but is based heavily on the
previous software. The MATLAB code was written by TSB. Both TSB and TFW
tested the software extensively. The manual was written primarily by TFW.
Contents
1 INTRODUCTION
1.1 Overview Of Software Packages . . . . . .
1.2 Brief Introduction To MATLAB . . . . . .
1.2.1 Jargon . . . . . . . . . . . . . . . . .
1.2.2 Help . . . . . . . . . . . . . . . . . .
1.3 Starting And Quitting The Software . . .
1.3.1 Directory structure . . . . . . . . .
1.3.2 Starting the software . . . . . . . .
1.3.3 Quitting the software . . . . . . . .
1.4 Common Features Of Software Packages
1.4.1 Controls . . . . . . . . . . . . . . . .
1.4.2 Quitting a package . . . . . . . . .
1.4.3 Printing/saving a gure . . . . . .
1.4.4 Reading from and saving to a le
1.4.5 Flexible graphic resource . . . . .
1.4.6 Scripts . . . . . . . . . . . . . . . . .
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12
2 RANDOM WALK MODEL OF DIFFUSION

2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.1.1 Historical background . . . . . . . . . . . . . . . . . . . . . . .
2.1.2 Macroscopic and microscopic models . . . . . . . . . . . . . .
2.1.3 Overview of software . . . . . . . . . . . . . . . . . . . . . . . .
2.2 Description Of The Random-Walk Model . . . . . . . . . . . . . . . .
2.2.1 Particle parameters within a region . . . . . . . . . . . . . . .
2.2.2 Boundary conditions . . . . . . . . . . . . . . . . . . . . . . . .
2.2.3 Parameters that change the number of particles in the eld
2.2.4 Statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.3 Users Guide To The Software . . . . . . . . . . . . . . . . . . . . . . .
2.3.1 RW controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.3.2 Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.3.3 Particles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.3.4 Histogram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.3.5 Graph . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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viii
CONTENTS
2.3.6 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.3.7 Miscellaneous issues . . . . . . . . . . . . . . . . . . . . . . . . .
2.4 Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3 MACROSCOPIC DIFFUSION PROCESSES

3.1 Introduction . . . . . . . . . . . . . . . . .
3.1.1 Background . . . . . . . . . . . . .
3.1.2 Macroscopic model of diffusion
3.1.3 Overview of software . . . . . . .
3.2 Methods of Solution . . . . . . . . . . . .
3.2.1 Exact solutions . . . . . . . . . . .
3.2.2 Numerical Solutions . . . . . . . .
3.2.3 Summary . . . . . . . . . . . . . .
3.3 Users Guide To The Software . . . . . .
3.3.1 MD controls . . . . . . . . . . . . .
3.3.2 Initial concentration prole . . .
3.3.3 Numerics . . . . . . . . . . . . . .
3.3.4 Analysis gures . . . . . . . . . .
3.3.5 Arbitrary concentration proles
3.4 Problems . . . . . . . . . . . . . . . . . . .
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56
4 CARRIER-MEDIATED TRANSPORT
4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.2 Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.2.1 Steady-state behavior of a simple, four-state carrier that binds
one solute . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.2.2 Steady-state behavior of a simple, six-state carrier that binds
two solutes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.2.3 Transient and steady-state behavior of a general, four-state
carrier that binds one solute . . . . . . . . . . . . . . . . . . . .

4.3 Numerical Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.3.1 Numerical methods . . . . . . . . . . . . . . . . . . . . . . . . . .
4.3.2 Choice of numerical parameters . . . . . . . . . . . . . . . . . .
4.4 Users Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.4.1 CMT controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.4.2 Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.4.3 Steady-state interactive analysis . . . . . . . . . . . . . . . . . .
4.4.4 Steady-state graphic analysis . . . . . . . . . . . . . . . . . . . .
4.4.5 Transient analysis . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.5 Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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5 HODGKIN-HUXLEY MODEL
5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.1.1 Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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CONTENTS
5.2
5.3
5.4
5.5
5.6
ix
5.1.2 Overview of the software . . . . . . . . . . . . . . . . . . . . . .

Description Of The Model . . . . . . . . . . . . . . . . . . . . . . . . . .
5.2.1 Voltage-clamp and current-clamp congurations . . . . . . . .
5.2.2 The membrane current density components . . . . . . . . . .
5.2.3 The membrane conductances . . . . . . . . . . . . . . . . . . . .
5.2.4 The activation and inactivation factors . . . . . . . . . . . . . .
5.2.5 The rate constants . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.2.6 Time constants and equilibrium values of activation and in
activation factors . . . . . . . . . . . . . . . . . . . . . . . . . . .
Numerical Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.3.1 Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.3.2 Choice of integration step t . . . . . . . . . . . . . . . . . . . .
5.3.3 Method for computing solutions . . . . . . . . . . . . . . . . . .
Users Guide To The Software . . . . . . . . . . . . . . . . . . . . . . . .
5.4.1 Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.4.2 Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.4.3 Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.4.4 Scripting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
PROJECTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.6.1 Practical considerations in the choice of a topic . . . . . . . .
5.6.2 Choice of topics . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.6.3 The proposal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.6.4 The computations . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.6.5 The report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6 VOLTAGE-GATED ION CHANNELS

6.1 Introduction . . . . . . . . . . . .
6.1.1 Historical background .
6.1.2 Overview of software . .
6.2 Description Of The Model . . .
6.3 Numerical Methods . . . . . . .
6.3.1 Integration step . . . . .
6.3.2 Initial conditions . . . . .
6.4 Users Guide . . . . . . . . . . . .
6.4.1 Controls . . . . . . . . . .
6.4.2 Channel parameters . . .
6.4.3 Membrane potential . . .
6.4.4 Numerics . . . . . . . . .
6.4.5 Analysis . . . . . . . . . .
6.5 Problems . . . . . . . . . . . . . .
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CONTENTS
List of Figures
1.1
1.2
1.3
1.4
1.5
Softcell gure showing the available software packages .

The print gure . . . . . . . . . . . . . . . . . . . . . . . . .
Example of the use of the exible graphic resource . . .
The select x,y gure . . . . . . . . . . . . . . . . . . . . . . .
The axis scale gure . . . . . . . . . . . . . . . . . . . . . . .
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2.1 Denition of grid of particle locations . . . . . . . . . . . . . . .

2.2 Denition of simulation eld, regions, and boundaries . . . . .
2.3 Motion of a particle in a homogeneous region . . . . . . . . . . .
2.4 Motion of a particle at a vertical perimeter boundary . . . . . .
2.5 Motion of a particle at an internal vertical boundary . . . . . . .
2.6 The rw controls gure . . . . . . . . . . . . . . . . . . . . . . . . .
2.7 Parameters gure . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.8 Initial locations of particles . . . . . . . . . . . . . . . . . . . . . .
2.9 Locations of particles after a 100 step random walk . . . . . . .
2.10 Histogram of particle locations after a 100 step random walk .
2.11 Standard deviation of particle location versus step number . .
2.12 Numerical summary of statistics after a 100 step random walk
2.13 Parameters for a random walk in 3 regions . . . . . . . . . . . .
2.14 Initial locations of particles for a random walk in 3 regions . .
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3.1 Classes of initial concentration proles simulated by the software

3.2 The MD controls gure . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.3 Initial concentration gure for impulses . . . . . . . . . . . . . . . .
3.4 Initial concentration gure for sinusoids . . . . . . . . . . . . . . . .
3.5 Initial concentration gure for discontinuities . . . . . . . . . . . .
3.6 Initial concentration gure using the arbitrary option . . . . . . . .
3.7 Initial concentration gure for the two compartments option . . .
3.8 The diffusion parameters gure . . . . . . . . . . . . . . . . . . . . .
3.9 The numerics gure . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.10 Plots versus position gure . . . . . . . . . . . . . . . . . . . . . . . .
3.11 Plots versus time gure . . . . . . . . . . . . . . . . . . . . . . . . . . .
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4.1 Kinetic diagram of the simple, four-state carrier . . . . . . . . . . . .

4.2 Kinetic diagram of a simple, six-state carrier that binds two solutes
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xii
LIST OF FIGURES
4.3
4.4
4.5
4.6
Kinetic diagram of a general, four-state carrier model . . . . . . . . .

Controls gure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Units of all variables in the carrier models . . . . . . . . . . . . . . . .
Parameters and state gures for the simple, four-state carrier model
that binds one solute . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

4.7 Parameters and state gures for the simple, six-state carrier that
binds two solutes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

4.8 Parameters and state gures for the general, four-state carrier that
binds one solute . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

4.9 The steady-state graphic analysis gure . . . . . . . . . . . . . . . . .
4.10 The transient analysis gure . . . . . . . . . . . . . . . . . . . . . . . .
4.11 The set up transients gure . . . . . . . . . . . . . . . . . . . . . . . . .
4.12 The transient numerics gure . . . . . . . . . . . . . . . . . . . . . . . .
68
72
72
5.1 Voltage-clamp conguration . . . . . . . . . . . . . . . . . . . . . . . . .

5.2 Current-clamp conguration . . . . . . . . . . . . . . . . . . . . . . . .
5.3 The controls gure after the software is initiated . . . . . . . . . . . .
5.4 The controls gure after the software is initiated . . . . . . . . . . . .
5.5 The parameters versus membrane potential gure . . . . . . . . . . .
5.6 The select y gure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.7 Stimulus gure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.8 Example of a stimulus waveform . . . . . . . . . . . . . . . . . . . . . .
5.9 The numerics gure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.10 The block diagram gure . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.11 Expansion of the current clamped block . . . . . . . . . . . . . . . . .
5.12 The simulink gure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.13 The sink gure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.14 Block diagram with oscilloscope attached . . . . . . . . . . . . . . . .
5.15 The oscilloscope screen . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.16 The plot versus time gure . . . . . . . . . . . . . . . . . . . . . . . . .
5.17 The variable summary gure. . . . . . . . . . . . . . . . . . . . . . . . .
5.18 Comparison gure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.19 Phase-plane plot of membrane conductance versus membrane po
tential . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.20 Membrane potential obtained at different temperatures . . . . . . .
5.21 Simulation results for different parameters that block the action
potential . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.22 Examples of action potentials . . . . . . . . . . . . . . . . . . . . . . . .
5.23 Dependence of the action potential on temperature . . . . . . . . . .
5.24 Effect of extracellular sodium concentration on the action potential
5.25 Sample project proposal . . . . . . . . . . . . . . . . . . . . . . . . . . .
87
87
92
93
95
95
96
98
98
100
100
101
101
102
103
103
104
105
73
74
75
78
79
80
81
106
107
114
117
118
118
123
6.1 Kinetic diagram of a channel that has 5 states . . . . . . . . . . . . . 127
6.2 The probability of occurrence of more than 1 event in an interval t 131
LIST OF FIGURES
6.3
6.4
6.5
6.6
The controls gure after the software is initiated . . . . . . . . . . . .

The channel parameters gure . . . . . . . . . . . . . . . . . . . . . . .
Rate constant window . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
View rate constant gure after both the forward and reverse rate
constants have been dened . . . . . . . . . . . . . . . . . . . . . . . .

6.7 Membrane potential gure . . . . . . . . . . . . . . . . . . . . . . . . . .
6.8 Numerics gure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6.9 State occupancy gure . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6.10 Single channel ionic current . . . . . . . . . . . . . . . . . . . . . . . . .
6.11 Summary gure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6.12 Comparison gure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
xiii
132
133
134
135
136
136
138
139
140
141
xiv
LIST OF FIGURES
List of Tables
2.1 The macroscopic laws of diffusion . . . . . . . . . . . . . . . . . . . . .
16
3.1 Summary of computational methods.
. . . . . . . . . . . . . . . . . .
45
4.1 Modiable parameters of the carrier models . . . . . . . . . . . . . . .
76
xv
xvi
LIST OF TABLES
Chapter 1
INTRODUCTION
1.1
Overview Of Software Packages
The software for cellular biophysics consists of 5 software packages. The titles
of the software packages, with acronyms in parentheses and brief descriptions,
are:
Random Walk Model of Diffusion (RW) allows users to select parameters of the
random walks of particles in a eld and to observe the resulting spacetime evolution of particle location. This package is intended to link the
macroscopic laws of diffusion to its probabilistic, microscopic basis.
Macroscopic Diffusion Processes (MD) allows users to select the initial spatial
distribution of solute concentration, the diffusion parameters, and to ob
serve the resulting space-time evolution of solute concentration and ux.
This package is intended to give users intuition about macroscopic diffu
sion processes.
Carrier-Mediated Transport (CMT) allows users to examine simple models of
carrier-mediated transport through cellular membranes. For each of three
models, the user can change any parameter and can instantly see the effect
on the state of the carrier-model. This interactive mode is intended to build
intuition about these models. In addition, there is a graphic mode that
allows display of steady-state and transient responses to changes in any
parameter.
Hodgkin-Huxley Model (HH) allows users to change parameters of the HodgkinHuxley model of a space-clamped giant axon of a squid, and to perform
simulation experiments in either the voltage-clamp or the current-clamp
conguration. This package is built on a block-diagram language providing
users a graphic access to the model.
Voltage-Gated Ion Channels (IC) allows users to design a voltage-gated ion chan
nel. The user selects the number of states, the conductance and gating
1
CHAPTER 1. INTRODUCTION
charge associated with each state, and the voltage-dependence of state tran
sition rates. The user can then perform simulation experiments on the
channel.
These packages are all designed to enhance comprehension of topics in cellular

biophysics by providing pedagogic tools that can be used as a basis for lecture
demonstration, open-ended problems that lend themselves to classes held in an
electronic classroom in which students have access to computers, homework
problems, and research projects. Although independent of any textbook, this
suite of software packages was developed in parallel with textbooks in cellular
biophysics (Weiss, 1996a; Weiss, 1996b).
1.2
Brief Introduction To MATLAB
All the software packages are written in MATLAB/SIMULINK which is an interac

tive programming environment for numerical and symbolic computations and for
visualization of computational results. MATLAB is especially effective in systems
analysis and signal processing. Because MATLAB runs on all the major computer
platforms, the cellular biophysics software operates on all the major platforms:
PCs using Windows, Macintosh computers using MacOS, and Unix workstations.
Both MATLAB (version 4.2c) and SIMULINK (version 1.3) are required to operate
this software.1
The MATLAB environment is interpretive. That is, commands can be entered
at a prompt and interpreted within the scope of a MATLAB session. Thus, com
putational results generated by a simulation are available to the user for further
analysis. The software is designed to perform all the simulations with mini
mal typed commands. The graphical user interface allows navigation through
the software using a sequence of mouse events (e.g., clicking the mouse, pulling
down a menu, dragging the mouse).
Users of the software do not need to learn MATLAB to use the software. How
ever, knowledge of MATLAB can enhance users usage of the software. A number
of texts on MATLAB are available (Hanselman and Littleeld, 1996). In addition,
MATLAB manuals can be ordered directly from MathWorks. Section 1.2.1 is a
glossary of some useful terms in the MATLAB vocabulary. Section 1.2.2 men
tions resources that can provide on-line help with MATLAB.
1.2.1 Jargon
The following terms are useful in navigating in the MATLAB environment.
1
Although not tested extensively, RW, MD, CMT, and IC run on the Student Version of MAT
LAB. However, it may be that parameters can be chosen for these packages which will not satisfy
the limitations of the Student Version. HH requires SIMULINK in addition to MATLAB. However,
currently HH does not run on the Student Versions of MATLAB plus SIMULINK.
1.2. BRIEF INTRODUCTION TO MATLAB
workspace A collection of variables in the current session of MATLAB. When

MATLAB is started, the workspace is empty. Each software package denes
its own variables and parameters which it adds to the workspace.
command window The window that appears when MATLAB is started. Com
mands entered at the MATLAB prompt (>>) in this window are evaluated in
the workspace.
gure A rectangular window containing graphical objects, such as axes, buttons,
and menu items. See the MATLAB command figure.
axes The area in a gure containing plots and annotation. See the MATLAB com
mand axes.
buttons Rectangular regions allowing a sequence of commands to be executed
when they are clicked, selected, or edited. See the MATLAB command
uicontrol.
popup-menu A rectangular region showing the current popup-menu selection.
When clicked, the menu is expanded to show all the options. See the MAT
LAB command uicontrol.
menubar A bar at the top of a gure (Windows and UNIX implementations) or at
the top of the monitor screen (MacOS implementation) associated with the
currently selected gure. When selected, the menu item expands to show
its related submenu items. Submenu items marked with a check-mark are
currently active selections.
M-le A text le containing a sequence of commands to be evaluated in the MAT
LAB workspace. The software contains a collection of m-les which can be
recognized by the extension .m.
MAT-le A binary data le containing MATLAB variables. Each software package
uses and stores a different set of variables.
parameters Numeric values that dene each model.
variables Numeric values of independent variables set by the user or of depen
dent variables calculated from the model.
SIMULINK A block-diagram language that extends MATLABs capabilities to sim
ulate dynamic systems.
1.2.2 Help
Help on MATLAB and SIMULINK is available through the command window using
the following commands at the MATLAB prompt (>>)
who lists the variables in the current workspace.
help function provides some help on the command function.
help help provides help on getting started using help.
lookfor word nds functions that involve word.
Additional help is available in the descriptions of individual software packages.
1.3
Starting And Quitting The Software
1.3.1 Directory structure

The software is designed to be run from a directory that includes the following
les/directories:
cmt is a directory that contains the carrier-mediated transport software.
hh is a directory that contains the Hodgkin-Huxley model software.
ic is a directory that contains the voltage-gated ion channel software.
md is a directory that contains the macroscopic diffusion processes software.
rw is a directory that contains the random walk model software.
softcell.m is a MATLAB m-le that initializes the software and allows the user to
choose software packages from a menu.
tlib is a directory that contains a library of software routines used by all the
packages.
1.3.2 Starting the software

The software is accessible through MATLAB/SIMULINK via a menu that allows
selection of the software packages and initializes all packages. The startup pro
cedure is given for the different platforms.
1.3. STARTING AND QUITTING THE SOFTWARE
Figure 1.1: Softcell gure showing the

available software packages.
UNIX workstation on Project Athena. From the dashboard at the top of the mon
itor select
Courseware
Electrical Engineering and Computer Science
6.021J/6.521J Quantitative Physiology

New MATLAB Software
This procedure displays the softcell gure shown in Figure 1.1. Clicking on
any package, initializes that package and hides the softcell gure.
Windows, MacOS, UNIX, and other operating systems. Initialize MATLAB, and
type the following instruction (in the MATLAB window) at the MATLAB
prompt (>>)
>> cd directory
where directory is the name of the directory (folder) that houses the cel
lular biophysics software.2 Then type
>> softcell
This command displays the softcell gure shown in Figure 1.1. Clicking on
any package, initializes that package and hides the softcell gure.
In addition, there are two m-les used by the software that may not be part
of the standard distribution of MATLAB 4.2c.
ODE Suite. One feature of the packages (transient response for CMT) makes
use of MATLABs ODE Suite (specically, the ode solver ode15s), a col
lection of algorithms optimized for solving ordinary differential equa
tions. To use transient response with CMT, it is imperative that the
ODE Suite be on MATLABs search path. Use the following checklist
to insure that the ODE Suite is accessible to the cellular biophysics
software:
2
To verify that the directory is the right one, either type pwd to indicate the name of the
present directory or type ls to list the contents of the directory. It should contain the le
softcell.m. If it does not contain this le then either the selected directory is wrong or the
cellular biophysics software is not installed on your computer.
1. At the MATLAB prompt, type
which ode15s.
If MATLAB returns the name of a le, the ODE Suite is already

installed; skip the rest of the checklist.
2. Check if the ODE Suite is resident in your computer. If the suite
came with MATLAB, it is most likely in the directory (folder) hier
archy
matlab/toolbox/contrib.
If you can nd the le ode15s.m, skip to step 4.
3. Install a copy of the ODE Suite on your computer. You can down
load it from the MathWorks website at the URL
http://www.mathworks.com/
Place the new directory (folder) into contrib.
4. Append the folder which contains the ODE Suite to MATLABs search
path. If the ODE Suite resides in
matlab/toolbox/contrib/ode,
type the command
>> path(path,matlab/toolbox/contrib/ode);
[For a Windows/PC system the directory (folder) is specied by an
address that looks like c:\matlab\toolbox\contrib\ode, whereas
on MacOs, the directory (folder) is specied by an address that
looks like MacHD:matlab:toolbox:contrib:ode.]
For the remainder of the session, MATLAB will look through the
folder matlab/toolbox/contrib/ode when searching for les from
the ODE Suite. To make this change permanent, see MATLAB doc
umentation on setting the default MATLAB search path.
Printing. All the packages make use of an m-le (printdlg.m) for printing.
Use the following check list to insure that printdlg.m is accessible to
the software.
1. At the MATLAB prompt, type
which printdlg.
If MATLAB returns the name of a le, printdlg.m is already in

stalled; skip the rest of the checklist.
2. The m-le printdlg.m is distributed in a folder called uitools. Check
if uitools is resident in your computer. If the uitools came with
MATLAB, it is most likely in the directory (folder) hierarchy
matlab/toolbox/uitools.
If you can nd the le printdlg.m, skip to step 4.
3. Install a copy of the uitools folder on your computer. You can
download it from the MathWorks website or their ftp site which
can be reached through their web site:
1.4. COMMON FEATURES OF SOFTWARE PACKAGES
ftp://ftp.mathworks.com/pub/mathworks/toolbox/uitools
.
Place the new directory (folder) into toolbox.
4. Append the folder which contains the uitools folder to MATLABs
search path, i.e., type the command
>> path(path,matlab/toolbox/uitools);
1.3.3 Quitting the software

Quitting any package displays the softcell gure again. To quit MATLAB, click
on QUIT in the menubar and select Exit MATLAB. The menubar is located at the
top of the gure in UNIX and Windows implementations and at the top of the
monitor screen in the MacOS implementation.
1.4
Common Features Of Software Packages
Certain features are common to all the software packages and these are described
here. When any of the software packages is selected in the softcell gure, one or
more windows is displayed on the screen. MATLAB refers to these as gures.
1.4.1 Controls
Each package has a controls gure that allows the user to control the package.
Although individual packages have different controls gures, all controls gures
contain a log panel and a message panel. The log panel contains options for
recording log entries of the session. Log entries are records of actions of the
user during the simulation session. Clicking on Select le displays a window
that allows choosing the name of the log le into which the log entries will be
saved. The log entries can also be displayed in the message panel. In general,
the message panel is used to send messages to the user.
1.4.2 Quitting a package

Each gure associated with each package contains a menubar. The menubar
occurs at the top of the gure in UNIX and Windows implementations and at the
top of the screen in Macintosh versions of the software. This menubar enables
the user to quit the software package by clicking on XX and then selecting quit
XX, where XX is the acronym for the package (e.g., CMT for carrier-mediated
transport).
Figure 1.2: The print gure after Print

was selected in the RW package (Parti
cles #1 gure).
1.4.3 Printing/saving a gure

The menubar for each gure associated with each package also contains Print
which if selected brings up the print gure (Figure 1.2). The user can either print
the gure to the default printer, print to any printer by editing Device Option (to
see how to do it type help print at the MATLAB prompt), or store a postscript
le of the gure.
1.4.4 Reading from and saving to a le

A variety of information about the software can be saved in MAT-les using the
standard MATLAB binary le format (see MATLABs save and load commands).
For example, all the packages allow storage of simulation parameters to allow a
simulation to be repeated at a later time. In addition, results of simulations can
also be saved in les for later retrieval. However, the information stored varies
for different software packages, and the individual descriptions of the packages
should be consulted for more detailed information.
To restore state variables from a prior simulation, use Read parameters pushbuttons which are found on some of the gures of all of the packages. Although
data can be restored using load from the command-line, this method will not, in
general, restore all relevant state variables necessary to run the software.
1.4.5 Flexible graphic resource

A exible graphics resource is used by all the software packages to compare
results of simulations. This resource is customized for each software package
but contains features that are common to all the software packages and these are
described in detail here. We illustrate the usage of this resource with examples
from the carrier-mediated transport package. Selection of graphic analysis in the
controls gure of the carrier-mediated transport package results in the display
of the steady-state graphic analysis gure (Figure 1.3). This is a typical usage of
the graphic resource. This gure contains a number of panels.
Plot control. The panel in the upper left corner controls plotting in the manner
described below.
Figure 1.3: An example of the use of the exible graphic resource in the CMT package.
The steady-state graphic analysis gure shows a plot of uxes and carrier densities
versus the inside concentration of solute S, cSi , in linear ordinate and abscissa scales.
10
Figure 1.4: The select x,y gure that produced the

plot shown in Figure 1.3. Note that cSi (which is
highlighted in blue) was selected as the indepen
dent variable that denes the abscissa (horizontal
axis) in the plot. The variables E , ES , niE , noE ,
niES , and noES were selected as the dependent vari
ables and plotted as the ordinates (vertical axis).
Select x,y. Clicking on this entry results in the display of the Select x,y g
ure (Figure 1.4) which allows selection of one independent variable
which determines the abscissa of the plot and multiple dependent vari
ables which determine the ordinates. Clicking on an independent vari
able selects it for the abscissa variable and deselects a previously se
lected variable. Clicking on an unselected dependent variable adds it to
the collection of selected variables. Clicking on a selected dependent
variable deselects it. A maximum of four types of dependent variables
can be selected for plotting. In some packages (CMT), the range of the
independent variable is selected in this gure.
Select data les. Clicking on this entry displays a gure that allows selec
tion of a le from which previously stored parameters can be read. The
types of data that are read varies with each package.
Graph x,y. Clicking on this entry results in a plot of the selected data.
Overlay. When this button is activated, the next set of plots are overlayed
over the current set. When this option is not checked, the following
plots replace the current ones.
Use data les. When this button is activated, the next set of plots are de
rived from the selected data les.
Save results. Clicking this button displays a gure that allows selection of
a le into which the current data can be stored. The types of data that
are stored varies with each package.
Clear. Clicking this button clears the plot area as well as the legend and
cross-hair information.
11
Figure 1.5: The axis scale gure after the

abscissa was selected in Figure 1.3.
Axes control. The lowest panel in the gure shows the selected plots. The axes
can be changed by clicking on either the ordinate or the abscissa variable
which results in the display of the axis scale gure (Figure 1.5). The axis
scale can be chosen to be linear, logarithmic, and/or reciprocal. If none of
the options is chosen, the scale is linear. If log scale is chosen, the scale is
logarithmic. If invert is chosen (available only in CMT) then the reciprocal of
the abscissa variable is plotted either on a linear or on a logarithmic scale.
In logarithmic coordinates, negative values of a variable (i.e., the uxes) are
truncated. Clicking on done hides the gure.
Legend. The legend panel records a list of all data plotted. The following are
recorded.
Time stamp. The time and date when the curves were generated are indi
cated. Clicking on the time stamp alternately displays and hides all
the curves associated with this legend item.
Line and symbol type. The color, line style, and symbol type are used to
encode a particular variable; this marker is shown in the legend.
Variable name. The name of the variable that was plotted is shown. Click
ing on the variable name alternately displays and hides the curve as
sociated with this entry. When variables are added or deleted, the axis
is auto-scaled if that option is selected it is selected by default in
the axis gure.
Cross-line value. When the cross line is used, the value of all variables at a
particular value of the independent variable is displayed. These values
are accurate only when cross line is selected in the mouse-event controls
panel (see below).
Message window. Messages to the user are displayed in the message window.
12
Mouse-event controls. The plot can be modied or queried in several ways.

Annotate. Click on annotate and then click on a desired location in the plot
area. A text edit box appears at that location. Type the annotation in
the text edit box and type <RETURN> when the annotation is completed.
Clicking on the annotation and dragging the mouse moves the annota
tion to a desired location in the plot eld. Clicking on clear removes
the annotation.
Cross hair. Clicking on cross hair places a mouse-controlled cross hair in
the plot eld. Clicking the mouse at some location in the plot eld
places (in the cross-hair panel) the values of all variables at the location
of the cursor. Clicking on hide removes the cross-hair values.
Cross line. Clicking on cross line displays a vertical line, the cross line, in
the plot eld at the location of the pointer cursor. The line follows
the cursor as it moves across the plot eld. The values of all plotted
variables at the intersection with the cross line are displayed in the
legend. The value of the independent variable is displayed above the
legend. Clicking on reset removes the cross-line values from the legend
and clicking off cross line removes the cross line from the plotting eld.
Zoom. Clicking on zoom allows the user to magnify a region of the plot
ting eld. Clicking and dragging the mouse produces a rectangle in a
portion of the plot eld; the rectangle denes the region to be mag
nied. Additional magnication can be achieved by zooming again.
Click unzoom to undo the effects of all prior zooms.
1.4.6 Scripts
Scripting commands alleviate the burden of being present while repetitive, time
consuming simulations are computed.3 The set of commands available to the
software user can be found by issuing the command help XXscr, where XX is
the acronym for the package.
Scripting can also be used to create customized plots of variables. For exam
ple, in the Hodgkin-Huxley package, after running a simulation, the time depen
dance of the sodium conductance can be plotted on a separate gure using the
following commands:
u_gna = hhscr(get,G_Na); %get the sodium conductance vector
u_time = hhscr(get,t); %get the vector of sampled time values
figure; %create a new figure
plot(u_time,u_gna); %plot sodium conductance vs. time
3
A sample script is given in the chapter on the Hodgkin-Huxley model.
13
Once the values of these variables are so obtained, they can be manipulated,
modied, and saved to les. It is important to practice safe-workspace-integrity
techniques by creating names of variables that are similar to but different from
those dened in the workspace. To see a list of variables in the workspace, type
who. In general, prex the names of your own variables with a set of characters
such as u_. In this way, variables can be manipulated or plotted without danger
of creating inconsistencies in the workspace.
Although the set of scripting commands in the various XXscr les is not ex
haustive enough to allow operating all aspects of the software from the commandline, it is sufcient to carry out some of the time-consuming elements of the sim
ulation. Furthermore, by issuing only sanctioned scripting commands from the
MATLAB >> prompt, the user is assured that variables in the workspace will not
be corrupted with inconsistencies.
14
Chapter 2
RANDOM WALK MODEL OF

DIFFUSION
15
16
2.1
CHAPTER 2. RANDOM WALK MODEL OF DIFFUSION
Introduction
2.1.1 Historical background

A bolus of soluble material will gradually spread out in its solvent until a uniform
solution results. This diffusion process must have been familiar to humans in
antiquity. However, a mathematical description of these macroscopic changes in
concentration was not available until the 1850s (Fick, 1855), and a microscopic
or particle-level model, not until the turn of this century (Einstein, 1906).
Diffusion plays an important role in such a wide range of disciplines, that it is
important for students of science and engineering to develop an understanding
of the macroscopic laws of diffusion and their microscopic basis. We will review
some important characteristics of the macroscopic laws of diffusion and their
relation to random-walk models. A fuller treatment is available elsewhere (Weiss,
1996a).
2.1.2 Macroscopic and microscopic models

Macroscopic laws of diffusion
The macroscopic laws of diffusion for the simple case when the particles are not
subject to a body force, the medium does not convect the particles, the diffusion
coefcient is a constant, and the particles are conserved are summarized in one
and three dimensions in Table 2.1. These equations relate the ux of particles
Equation
Ficks rst law
Continuity equation
Diffusion equation
One Dimension Three Dimensions

c
= Dc
= D
x
c
= c
=
t
x
t
c
c
2 c
=D 2
= D2 c
t
x
t
Table 2.1: The macroscopic laws of diffusion for a concentration of particles diffusing
in a homogeneous region with a constant diffusion coefcient D, in the absence of a
body force on the particles or convection of the medium, and where the particles are
conserved.
(), which is the number of moles of particles transported through a unit area in
a unit time, to the concentration of particles (c), which is the number of moles
of particles per unit volume. Ficks rst law relates ux to particle concentra
tion; it is analogous to other laws that relate a ow to a force such as Ohms
law of electric conduction, Darcys law of convection, and Fouriers law of heat
2.1. INTRODUCTION
17
ow. Ficks rst law implies that a solute concentration gradient causes a solute
ux in a direction to reduce the concentration gradient. The continuity equation
follows from conservation of particles, and the diffusion equation is obtained by
combining Ficks rst law with the continuity equation.
Microscopic basis of diffusion
An important notion in understanding diffusion processes is to relate the macro
scopic laws of diffusion to microscopic models of diffusing particles. The sim
plest microscopic model that captures the essence of diffusion is the discretetime, discrete-space random walk. In a one-dimensional random walk in a ho
mogeneous region of space, we assume a particle moves along the x-axis in a
series of statistically independent steps of length +l or l, where the time be
tween steps is . In an unbiased walk, positive and negative steps are equally
likely, i.e., each has probability 1/2. It can be shown that statistical averages of
properties of a population of particles obey the macroscopic laws of diffusion.
In particular, this simple model can be shown (Weiss, 1996a) to yield Ficks rst
law with a diffusion coefcient,
l2
D=
.
2
Therefore, the connection between the random walk of a particle and the laws of
macroscopic diffusion can be made clear if the motion of a number of particles
(on the order of 50) can be visualized for a number of steps.
2.1.3 Overview of software

The software described here is intended to allow users to investigate the prop
erties of the simplest microscopic model that captures the essence of diffusion:
the discrete-time, discrete-space random-walk model.
In the discrete-time, discrete space random walk model described here, there
is a population of particles which execute statistically-independent, but otherwise
identical two-dimensional random walks in a rectangular eld. The eld can be
divided into one, two, or three homogeneous regions whose widths are speci
able, and whose properties may differ. Each particle undergoes a random walk
with parameters that include: the probability that the particle takes a step to the
left or right, and the step size. These parameters can be set independently in the
three regions. The particles can be set to have a speciable lifetime. One source
and one sink of particles can be placed in the eld and the initial concentration
of particles can be specied in each of the three regions. Characteristics of the
boundary conditions between regions can also be specied. With this software
package it is possible: to visualize the spatial evolution of particle concentra
tion from a variety of initial distributions selectable by the user; to examine the
evolution of particle concentration from a source and in the presence of a sink;
18
1 unit
j +2
j +1
Figure 2.1: Denition of grid of particle locations. A particle

is shown at the grid location (i, j). The distance between
adjacent grid locations, in both the horizontal and vertical
directions, is the unit distance.
j
j 1
j 2
i 2 i 1 i
i +1 i +2
to examine diffusion in regions of differing diffusion coefcients; to simulate

diffusion of particles subjected to a body force; to simulate diffusion between
two compartments separated by a membrane; to investigate the effects of chem
ical reactions or recombination which consume particles at a xed rate; and to
investigate the effects of different boundary conditions between regions. Two
diffusion regimes can be run and displayed simultaneously to allow direct com
parison between the space-time evolution of two different diffusion processes.
In addition, a variety of statistics of the spatial distribution of particles can also
be displayed.
By watching the particles move and by comparing simulation results to ex
pectations, the user can develop an intuition for the way in which the random
motions of particles lead to their diffusive spread.
2.2
Description Of The Random-Walk Model
In this simulation, the discrete-time, discrete-space random walk takes place on

a nite two-dimensional grid of locations accessible to the particles and called
the eld. The location of each particle is specied by giving its coordinates on
this grid (i, j) where i is the horizontal coordinate and ranges from 0 to 399 and
j is the vertical coordinate and ranges from 0 to 99 (Figure 2.1). The horizontal
distance between adjacent grid locations is 1 unit of distance and all spatial di
mensions of the random walk are expressed as multiples of this unit distance.
The location of the particle in the grid can change probabilistically at each step
of the random walk. Thus, successive steps represent successive times that are
separated by a unit time interval. All times are expressed in terms of the number
of steps of the random walk.
The eld can be divided into one, two or three homogeneous regions (Fig
ure 2.2). Certain parameters of the simulation are dened for the entire eld,
others at boundaries between regions, and still others are dened independently
for each region. The latter parameters will be described rst and include: region
size, particle step size, directional probabilities, and initial particle distribution.
2.2. DESCRIPTION OF THE RANDOM-WALK MODEL
Region 1
Region 2
Region 1 size
vertical internal
boundaries
19
Region 2
perimeter boundary:
vertical
horizontal
Figure 2.2: Denition of simulation eld, regions, and boundaries. Solid lines delimit the
perimeter boundaries of the eld; dashed lines indicate the internal vertical boundaries
that separate the regions.
2.2.1 Particle parameters within a region

The parameters that dene the random walk are identical at each location within
a region each region is homogeneous. These parameters are described below.
Region size
The width of each region can be specied, but the sum of the widths cannot
exceed 400. This allows a variety of diffusion regimes to be dened. For exam
ple, if Region 1 has width of 400 then the other two regions must have width 0
and the random walk is dened for one homogeneous region. By specifying two
regions with non-zero widths, it is possible to dene a diffusion process with
different initial conditions in the two regions. This allows a rich variety of initial
distributions to be dened. Three non-zero width regions allows simulation of
diffusion between two regions separated by a third region with different prop
erties. This might be used to investigate diffusion between two baths separated
by a membrane.
Step size
The step size denes the distance, in multiples of unit distances, that particles
may move in each step of time. Varying the step size simulates varying the
diffusion coefcient. The size of a region is always set to a multiple of the step
size in that region; all particles in a region are located at integer multiples of
the step size starting from the left boundary of the region. This ensures that
particles at a boundary fall on the boundary and simplies the specication of
particle motion at a boundary.
20
upper left
upper right
step size
expired
lower left
lower right
step size
Figure 2.3: Schematic diagram of motion of a particle in a homogeneous region. The grid
of possible particle locations, separated by unit distances, are indicated by + symbols.
A particle is shown in the center of the gure at one instant in time. One time step later
the particle either stays in the same location or moves to one of 4 possible locations
(indicated by the shaded particle) or it expires (is removed from the eld). If the particle
moves, it translates one step size (here shown as 2 units of distance) in both the vertical
and the horizontal direction.
Particle motion directional probabilities

At each instant in time, a particle is at some location in the region. The dis
position of the particle at the next instant in time is determined by one of six
mutually exclusive and collectively exhaustive possibilities as illustrated in Fig
ure 2.3. The particle can move one step size to the upper left, upper right, lower
left, or lower right; stay in the same location (center); or be eliminated (expire).
The probabilities for each of the six outcomes is as follows:
P[expired] = 1/L ,
P[center] = (1 1/L) (1 p q) ,
P[upper left] = 0.5 (1 1/L) q ,
P[upper right] = 0.5 (1 1/L) p ,
(2.1)
P[lower left] = 0.5 (1 1/L) q ,

P[lower right] = 0.5 (1 1/L) p ,
where L is the average lifetime of the particle, i.e. the average number of time
steps to expiration; p is the conditional probability that the particle moves to the
right given that it has not expired; q is the conditional probability that the particle
moves to the left given that it has not expired. Note that while the probability
of moving to the left and to the right can differ, the probability of moving up
or down is always the same. Because the six probabilities dene all the possible
outcomes at each instant in time, they sum to unity.
Different types of random walks are described by changing the directional
probabilities. The random walk dened by assuming p = q = 1/2 is the simple,
21
unbiased random walk described in Section 2.1. In general, if p = q the random

walk is unbiased; there is no statistical tendency for particles to move preferen
tially in either horizontal direction. However, if p q, the random walk is biased
so that there is a tendency for particles to move in one horizontal direction. For
a step size of S, the mean distance E[m] that the particle moves to the right in
n units of time is
E[m] = Sn(1 1/L)(p q) .
Initial distribution of particles
The initial distribution of particles can be specied in each of the three regions.
Particles start at locations that are integral multiples of the step size in each
region. Particles are distributed randomly (with a uniform distribution) in the
vertical direction and have the selected distribution in the horizontal direction.
The initial distribution of particles can be selected to be one of the following.
Empty implies that initially there are no particles in the region.
Pulsatile implies that a specied number of particles are placed at a spec
ied horizontal location in the region and spaced randomly in the vertical
direction.
Linear implies that a linear concentration prole is generated whose slope
and number of particles are specied. A uniform distribution of particles is
obtained if the slope is set to zero. Negative concentrations are not allowed:
if the parameters are chosen such that the concentration would become
negative at some point in the region, these putative negative concentrations
are set to zero.
Sinusoidal implies that the spatial distribution is sinusoidal with a specied
period and number of particles.
2.2.2 Boundary conditions

The eld contains three different types of boundaries (Figure 2.2) which are, in
order of increasing complexity, horizontal perimeter boundaries at the top and
bottom of the eld, vertical perimeter boundaries at the left and right ends of
the eld, and vertical internal boundaries that separate regions.
Horizontal perimeter boundaries
Horizontal perimeter boundaries act as perfectly reecting walls. If a particle
is located within one step size of such a boundary and takes a step toward the
boundary then the new vertical location of the particle is determined in the fol
lowing manner: the vertical distance the particle travels to reach the wall plus
22
upper right
step size
left vertical
perimeter
boundary
expired
lower right
Figure 2.4: Schematic diagram of motion

of a particle at a vertical perimeter boundary. For purposes of illustration the parti
cle motion at the left boundary is shown.
Conditions at the right boundary are the
mirror-image of those shown here.
step size
the vertical distance the particle travels after reecting from the wall must sum
to the step size. This relation determines the new location given the old location
and the value of the step size.
Vertical perimeter boundaries
The vertical perimeter boundaries are also reecting walls. Because the prob
abilities of stepping to the left and right need not be the same, we found that
purely reecting wall of the type described for the horizontal perimeter bound
aries created undesirable artefacts especially when the conditional probabilities
of moving to the left and right were not equal (p q). Therefore, we modied the
boundary condition so that a particle that would have crossed a vertical perime
ter boundary at a given step was placed on the boundary and then subject to
the following boundary condition which is illustrated for the left boundary in
Figure 2.4 and whose directional probabilities are:
P[expired] = 1/L ,
P[center] = (1 1/L) (1 p) ,
(2.2)

i.e. the particle cannot move to the left.
Vertical internal boundaries
The motion of particles at a vertical internal boundary is similar to that within a
homogenous region. The differences are that: the step sizes in the two adjacent
regions may differ; and special directional probabilities, specied by the user,
apply at the boundary. These have been provided to allow users to explore the
consequences of a rich variety of boundary conditions. To simplify boundary
conditions, the software ensures that particles do not cross this boundary in one
time step but rather they land on the boundary. This is guaranteed by forcing the
width of boundaries, initial particle locations, locations of sources and sinks to be
left region
23
right region
upper right
upper left
step size in
right region
expired
lower left
lower right
Figure 2.5: Schematic diagram of mo

tion of a particle at an internal vertical
boundary between two regions. The
step size is 1 to the left of the bound
ary and 2 to the right of the boundary.
step size in step size in

left region right region
internal vertical
boundary
commensurate with the step size. Given this restriction, the possible outcomes
for a particle on a boundary are shown schematically in Figure 2.5. The directional
probabilities are identical to those in a homogeneous (region given above) except
that the conditional probability of moving to the left and to the right given that
the particle did not expire (p and q in the homogeneous region) are independently
specied at each internal boundary. The step size to the left is equal to the step
size in the region to the left of the boundary; the step size to the right is equal
to the step size in the region to the right of the boundary.
2.2.3 Parameters that change the number of particles in the eld

After the initial distribution of particles is chosen, there are three ways in which
the total number of particles in the eld can change.
Particle lifetime
The average lifetime L of particles at any location in the eld is speciable. The
effect of particle lifetime on the directional probabilities was described earlier.
Source
One source can be placed at a horizontal location in the eld and covers the entire
vertical height of the eld. The source must be located at an integer multiple of
the step size from the left boundary of each region in which it is located. The rate
of generation of particles is specied by giving the number of particles (specied
as a two-digit number) produced in some number of time steps (specied as a
two-digit number). Thus the rate of generation of particles can be a rational num
ber. The particles are generated at the horizontal location of the source and are
distributed randomly along the vertical direction using a uniform distribution.
24
Sink
A sink can be placed at a horizontal location in the eld and covers the entire
vertical height of the eld. The sink is located at an integer multiple of the step
size from the left boundary of each region in which it is located. Particles that
land on the sink are absorbed; hence the number of particles at the sink is always
zero.
2.2.4 Statistics
Two sets of computations are performed simultaneously during a simulation:
statistics based on the actual locations of particle and statistics based on the
expected locations of particles. Given a particle location at one step and a set
of directional probabilities, a random number generator is used to determine
which of the possible new locations occurs at the next step. These sequence
of locations determines the locations of the particles on the screen and all the
statistics labelled actual. However, given a particle location at one time and the
same directional probabilities, an expected location of the particle in the next step
is also computed. Thus, during a simulation both the set of actual and expected
locations for the particles are computed and can be displayed.
Histogram of horizontal particle locations
Histograms summarize the spatial distribution of particle locations. Each his
togram consists of a set of bins that spans the eld in the horizontal direction;
the number of bins depends upon the specication of the bin size. With a bin size
of 16, there are 25 bins that span the entire eld of 400 locations. The histogram
shows the number of particles in each bin as a function of bin location. Choice of
bin size is important. A small bin size depicts the particle distribution with high
spatial distribution. However, a small bin size implies that each bin will contain
relatively few particles and the number of particles will uctuate randomly from
bin to bin. Conversely, a large bin size gives a histogram with poor spatial res
olution but a larger amount of statistical averaging of the spatial distribution of
particles.
The shape of the histogram is sensitive to the choice of bin size and can lead to
confusing patterns. For example, suppose the bin size is ve and the step size is
two. Suppose further that particles are located uniformly in the eld; one particle
per accessible location. However, the step size constrains the possible locations
that a particle may occupy to be separated by 2. Therefore, with a bin size of
ve, successive bins in the histogram alternate between 2 and 3 particles. Thus
the histogram will not appear uniform, but oscillatory. This problem is cured if
the bin size is an integral multiple of the step size. If the step sizes differ in the
three regions, then the bin size should be set equal to the least common multiple
of the three step sizes.
2.3. USERS GUIDE TO THE SOFTWARE
25
Statistics as a function of step number

A number of statistics (both actual and expected) can be plotted versus step num
ber. These are:
Mean is the mean location of the particles in the entire eld.
Standard Deviation is the standard deviation of particle location in the
entire eld.
#Generated is the cumulative number of particles generated by the source
since the beginning of the simulation.
#Absorbed is the cumulative number of particles absorbed by the sink since
the beginning of the simulation.
#Expired is the cumulative number of particles lost (due to their nite life
times) since the beginning of the simulation.
Total #Particles is the total number of particles in the entire eld at each
step number.
Region 1 #Particles is the total number of particles in Region 1 at each step
number.
number. For this total only, the particles located at the boundary between
Region 1 and Region 2 are counted as belonging to Region 2.
These statistics allow a quantitative evaluation of simulation results. We give
a number of examples of the use of these statistics. A systematic change in
the mean location of the particles as a function of step number demonstrates a
drift or migration of the particles as can be achieved by a bias in the directional
probabilities. A difference in the standard deviation of two distributions can
be achieved by changing the step size. The dependence on step number of the
number of particles in the eld, in a region, generated, absorbed, or expired can
be used to assess whether a particle distribution has reached steady state. The
change in the total number of particles in each region can be used to estimate
the rate of transport of particles between regions.
2.3
Users Guide To The Software
When this software package is selected, 3 gures are displayed (in addition to
MATLABs command window) RW Controls, Parameters #1, and Particles #1.
26
Figure 2.6: The controls gure.
2.3.1 RW controls
The controls gure controls the random walk software and is shown in Figure 2.6.
The part of the controls gure below the menubar is divided into four horizontal
panels. The top panel indicates which aspects of the simulation(s) are to be
displayed. Two independent simulations can be run simultaneously. The lefthand side contains the controls for Simulation #1 and the right-hand side for
Simulation #2. Clicking on Histogram #1, for example, displays a histogram of
particle locations for Simulation #1. Clicking on it again hides this histogram.
These displays are described in detail below. The next panel down allows the
simulation to be started, paused, continued, or stopped. The number of steps in
the random walk before the simulation pauses can be entered in the text edit box.
The end step indicates the current maximum value of the number of steps. This
value is incremented if the simulation pauses and is continued. Clicking 1-step
executes one step of the random walk. The third horizontal panel from the top is
a message window that displays information to the user. The log panel contains
options for recording log entries of the session and is described in Chapter 1. The
bottom right panel allows reading parameters from a le and saving parameters
to a le.
2.3.2 Parameters
The parameters gure is shown in Figure 2.7. The parameters gure allows se
lection of the parameters of the simulation(s). The parameters are given below.
Region Size. The user may dene up to three regions, whose combined
width may not exceed 400. To eliminate a region, enter 0 for the region
size. Regions can also be of size k(step size) where k = 3, 4, 5, .... That
is, regions of size stepsize and 2(stepsize) are not allowed.
27
Figure 2.7: Parameters gure.
Step Size. The step size can be specied independently in each region.
Initial Distribution Of Particles. The initial distribution of particles can be
specied independently in the three regions. Each initial distribution has
parameters that are specic for that distribution.
Right Step Prob. The conditional probability of a step to the right given that
the particle has not expired can be specied independently in each region.
Left Step Prob. The conditional probability of a step to the left given that
the particle has not expired cannot be specied. It is set automatically so
that in each region, the sum of the probabilities of all possible outcomes is
one.
Stay Prob. The conditional probability that the particle stays in the same lo
cation given that the particle has not expired can be specied independently
in each region.
Probabilities at Boundaries. The perimeter boundaries of the eld act as
reecting boundaries; the boundaries between regions are characterized
by user-dened boundary conditions. Boundary conditions are dened as
shown in Figure 2.7: left-step-probability L, stay probability S , and rightstep-probability R at the boundary between regions. For example, if the
Region #1-#2 has the set of probabilities (L, S, R) = (0, 0, 1) then particles
28
Figure 2.8: Initial locations of particles for the parameters shown in Figure 2.7. Initially
there are 50 particles located at position 200 and spread randomly with a uniform
distribution in the vertical direction.
at the boundary may only step to the right. Therefore, to a particle from Re
gion #2, this looks like a reecting boundary, whereas all particles reaching
the boundary from Region #1 will cross into Region #2. As with the direc
tional probabilities within a region, the user selects the conditional (on not
expiring) probability of a step to the right and the conditional probability
of no step; the conditional probability of a step to the left is then computed
so that probabilities of all possible outcomes sum to one.
Source. The location of the source can be specied as well as the number
of particles generated in a specied number of steps. When the source is
turned on, a small + is placed at the horizontal location of the source just
above the eld.
Sink. The particle sink may be turned ON and its location specied. When
the sink is turned on, a small is placed at the horizontal location of the
sink just above the eld.
Average Lifetime. The user may dene the average particle lifetime dened
as the number of steps it takes, on average, for the particle to expire.
2.3.3 Particles
The particles gure shows the locations of particles in the eld as shown for an
initial distribution of particles in Figure 2.8. When the simulation is started by
clicking the Start button in the controls gure, the random walks of the particles
are exhibited in the particles gure. A step counter indicates the number of steps
taken in the random walks. After 100 steps of the random walks of particles, the
particles gure is as shown in Figure 2.9.
29
Figure 2.9: Locations of particles after a 100 step random walk for the same parameters
as shown in Figure 2.7 and for the initial locations of particles shown in Figure 2.8.
2.3.4 Histogram
Selecting Histogram in the controls gure displays the histogram gure (Fig
ure 2.10). The binwidth of the histogram can be selected in the upper righthand corner. The binwidth determines the resolution of the histogram. Small
bin widths produce histograms of particle locations with high spatial resolution
but a great deal of statistical variation. Large bin widths result in histograms
with poorer spatial resolution but less statistical variation in the histogram. The
binwidth should be a multiple of the particle step size to avoid artefacts that
result from incommensurate values. Clicking on the ordinate axis label displays
an axis gure that allows the user to change the ordinate scale.
2.3.5 Graph
Selecting Graphs in the control gure displays the graphs gure. The temporal
evolution of any of the statistics described in Section 2.2 can be plotted versus
the step number. Figure 2.11 shows an example of the standard deviation of
particle locations plotted versus step number. Clicking on the ordinate axis label
displays an axis gure that allows the user to change the ordinate scale.
2.3.6 Summary
Numerical values of statistics can be displayed in the summary gure as shown
in Figure 2.12
30
Figure 2.10: Histogram of particle locations after a 100 step random walk for the same
parameters as shown in Figure 2.7 and for the initial locations of particles shown in
Figure 2.8. The histogram is for the particle locations shown in Figure 2.9.
Figure 2.11: Standard deviation of particle location versus step number for the same
parameters as shown in Figure 2.7 and for the initial locations of particles shown in
Figure 2.8.
Figure 2.12: Numerical summary of statistics

after a 100 step random walk for the same
parameters as shown in Figure 2.7 and for
the initial locations of particles shown in Fig
ure 2.8.
2.4. PROBLEMS
31
2.3.7 Miscellaneous issues

Time taken for random walks
All of the gures can be displayed simultaneously as the random walks are exe
cuted for two independent simulations. However, the display of each additional
gure slows down the simulation. Increasing the number of particles also slows
down the simulation.
Color coding of regions
Region #1 is indicated in blue in both the parameters gure and the particles
gure; magenta is used for region #2 and green for region #3.
2.4
Problems
Problem 2.1 This problem deals with random walks of particles that begin from
the same horizontal location.
a. Use the default simulation parameters with a pulsatile initial distribution
of particles but set the step size to 2 and 4 for Simulations #1 and #2, re
spectively. Run the simulation for 100 steps. Note that the parameters of
Simulation #1 and #2 differ only in step size. Examine graphs of the aver
age and the standard deviation of the horizontal locations of the particles
versus step number.
i. Explain quantitatively the differences in the graphs in terms of the
difference in step size of the two simulations.
ii. Why does the slope of the standard deviation decrease with step num
ber? What type of dependence on step number do you expect? Explain.
b. Now set the step size to 2 for both simulations and decrease the number
of particles in the pulsatile initial distribution for one of the simulations
to 25. Rerun the simulation. How does the number of particles affect the
dependence of average location and standard deviation on step number?
c. Set all the parameters at their default values and then set the step size
for both Simulation #1 and #2 to 2. For simulation #1 set the right step
probability to 0.75, the left step probability to 0.25, place an impulse of 50
particles at location 100. For simulation #2 set the right step probability
to 0.25, the left step probability to 0.75, place an impulse of 50 particles at
location 300. Run the simulation for at least 100 steps. Examine graphs of
the average and the standard deviation of the horizontal locations of the
particles versus step number. Explain these results quantitatively.
32
Problem 2.2 This problem deals with the steady-state distribution of particles in
the presence of a source and sink for both unbiased and biased random walks.
For all parts of this problem set the parameters for both Simulation #1 and #2
as follows: make the size of Region #1 400; the step size 20; and make the initial
distribution of particles empty. Also place a source at location 0 and a sink at
location 400 and make the histogram bin size 20.
a. Make the random walks for both Simulation #1 and #2 unbiased with a right
step probability of 0.5. For simulation #1 make a source that generates 1
particle every 2 steps and for Simulation #2 make a source that generates
1 particle every 1 step. Make the particle lifetime innite for both simula
tions. Now run the simulation. In the steady-state, by denition the particle
distribution will not depend upon step number.
i. Before you run the simulation, estimate the form of the steady-state
particle distribution. Is it uniform, exponential, pulsatile, linear, Gaus
sian, or none of these?
ii. Using the statistics available, determine a criterion for estimating when
the particle distribution is in steady state.
iii. Now run the simulation until your criterion for steady state is met.
What is the steady-state particle distribution? Does it t with your
initial expectation?
iv. How can you explain the difference in steady-state distribution for the
two simulations?
v. Show that the steady-state particle distribution you have found for the
random walks is consistent with Ficks laws.
b. Use the same parameters for Simulation #2 as in part a, but change those
of Simulation #1 so that the source rate is also 1 particle every 1 step; and
so that the probability of a right step is 0.55. Run the simulation until it
has reached a steady state.
i. Compare the steady-state distributions for the biased and unbiased
random walks. How do they differ?
ii. What is the shape of the steady-state distribution for the biased walk?
iii. How would you modify Ficks rst law to account for not only diffusion
of particles but a steady drift of particles of velocity v ? What steadystate distribution of particles is predicted from Ficks laws and the
continuity equation in the presence of this steady drift of particles? Is
this consistent with the simulation results you obtained?
c. Keep the parameters of Simulation #1 and #2 the same as in part b, but
change the right step probability of Simulation #2 to 0.48. Explain the dif
ferences in the shapes of the steady-state distributions for the two simula
tions.
2.4. PROBLEMS
33
Problem 2.3 This problem deals with the effect of a nite particle lifetime on the
statistics of random walks.
a. Dene a simulation with an initial particle distribution that is a uniform
distribution of particles in space, but with a nite average particle lifetime.
Run the simulation until all the particles have expired. Examine a graph of
# particles versus step number. Explain the shape of this function.
b. Dene another simulation that is identical with the one in part a, but this
time with a source of particles. Do you expect a steady state to be reached
between the the source and expirations? Determine a criterion for steady
state and check out your intuition.
c. Design a combination of source rate and lifetime such that the distribu
tion reaches a steady state. This might correspond, for example, to a drug
concentration reaching steady state in the body, as it is both infused and
eliminated.
d. Design a combination of source rate and lifetime such that most particles
in the region have expired by the time the source injects the next batch.
This might correspond to the drug concentration when the dosing interval
is longer than the elimination half-life of the drug.
Problem 2.4 This problem deals with a random walk in three regions. Set up
the parameters as shown in Figure 2.13. For both simulations, the two end re
gions contain uniform concentrations of particles; but the number of particles
differs. There is a concentration difference between the end regions as shown
in Figure 2.14 for one of the simulations; the other is similar. The center region
can be regarded as a membrane that separates the two end regions and contains
no particles initially. The random walk in the membrane region is unbiased in
one simulation and biased in the other. Run the simulation for several hundred
steps.
a. Explain the differences between the distributions of particles for the two
simulations.
b. Quantitatively describe the ux of particles between the two end compart
ments both the magnitude and sign of the ux.
c. What physical process might be represented in Simulation #2?
Problem 2.5 Design a three region diffusion regime where the center region is
considered to be a membrane. Design membrane characteristics such that the
membrane is transparent for particles moving from left to right but purely re
ecting for particles moving from right to left. Test your design by running the
simulation.
34
Figure 2.13: Parameters for a random walk in 3 regions (Problem 2.4).
2.4. PROBLEMS
35
Figure 2.14: Initial locations of particles for a random walk in 3 regions (Problem 2.4).
Problem 2.6 Start with two identical simulations with Regions #1 and #2 that
have: a region size of 400; a step size of 2; unbiased random walks; no sources
or sinks; innite particle lifetimes; and sinusoidal initial particle distributions.
Choose one simulation with a period of 200 and the other with a period of 50.
Choose an appropriate bin size for the histograms. Run the simulation.
a. What is the shape of the equilibrium distribution of particles?
b. Which particle distribution approaches this equilibrium faster?
c. Experiment with different frequencies and generalize your conclusion from
part b.
36
Chapter 3
MACROSCOPIC DIFFUSION PROCESSES
37
38
3.1
CHAPTER 3. MACROSCOPIC DIFFUSION PROCESSES
Introduction
3.1.1 Background
Diffusion is an important transport process in physical, chemical, and biological
systems. Two theoretical models of diffusion capture complementary aspects of
the phenomenon. The microscopic model describes the probabilistic behavior
of a population of individual solute particles which execute statistically indepen
dent, but otherwise identical, random walks. Software dealing with such a mi
croscopic model of diffusion is described in Chapter 2. The software described
in this chapter involves macroscopic diffusion which describes the aggregate be
havior of large populations of solute particles.
3.1.2 Macroscopic model of diffusion

In 1855, Adolph Fick proposed a macroscopic model for passive diffusion (Fick,
1855). By analogy to Fouriers law of heat conduction and Ohms law for electrical
conduction, Fick proposed that the ux of solute at a point in space is propor
tional to the concentration gradient at that point. Mathematically, this relation
is expressed by Ficks rst law, which, in its one-dimensional form, is as follows:
= D
c
,
x
(3.1)
where c(x, t) is the solute concentration and (x, t) is the solute ux. The con
stant of proportionality, D, is known as the diffusion coefcient. Conservation of
solute (in the absence of sources or sinks or of chemical reactions that create or
destroy solute) results in a second relation between concentration and ux, the
continuity equation:
c
= .
(3.2)
x
t
Differentiating both sides of Equation 3.1 with respect to x and using the continu
ity equation yields Ficks second law, or the one-dimensional diffusion equation:
2c
c
=D 2
t
x
(3.3)
In principle, any one-dimensional diffusion process can be modelled by solving

this equation subject to the appropriate initial conditions and boundary condi
tions.
We next consider the same problem but with two changes: (1) a body force
acts uniformly on the solute so that it drifts (migrates) and (2) a chemical reac
tion occurs that removes solute. The solute ux, (x, t), is now the sum of the
diffusive ux, given by Ficks law, and the ux due to drift. Thus, in this case,
= D
c
+ vc,
x
(3.4)
3.1. INTRODUCTION
39
where v is the drift velocity of the solute; i.e., the velocity of the solute in response
to the body force in the absence of diffusion. If r is the reaction rate at which
solute is removed, then the continuity equation becomes
c
=
r c.
x
t
Combining these expressions yields a modied diffusion equation:
(3.5)
c
2c
c
=D 2 v
r c.
(3.6)
t
x
x
Thus, solute drift and a chemical reaction that removes solute contribute addi
tional terms to the diffusion equation.
If the initial concentration, c(x, 0) is known in some region of space and if the
relation between the concentration and ux is known at each boundary of this
region, then a unique solution exists for t > 0. This agrees with intuition. Given
an initial concentration prole, c(x, 0), Ficks laws govern the unique evolution
of the concentration prole for all later times.

While macroscopic diffusion has been successfully modelled by Ficks equations,
studying the equations alone provides only limited insight into the behavior of
diffusion processes. The goal of this software is to help users gain intuition about
diffusion in one dimension. The solutions to the diffusion equation are functions
of two variables: one spatial variable, x, and time, t. These solutions can be
plotted either as a function of time at a particular point in space or as a function
of the spatial variable at a particular instant in time. Such isolated snapshots,
however, do not fully convey the dynamic behavior of diffusion processes. With
this software, the user can view a movie of the solute concentration or ux prole,
as a function of position, as it evolves in time. Thus, the software enables the user
to gain intuition about the dynamic behavior of macroscopic diffusion processes.
Furthermore, the software provides an opportunity for users to experiment
with the macroscopic diffusion processes. For example, the user can explore
how changing the diffusion coefcient affects the time-course of the simulation.
The user can also specify transparent or reecting boundaries and can explore
how a body force acting on the solute or a chemical reaction that removes solute
inuence the diffusion process. Thus, the software can be used as a tool for in
vestigating how various parameters and boundary conditions inuence diffusion
processes.
Five options for initial concentration proles, corresponding to ve charac
teristic diffusion problems, are implemented in the software (Figure 3.1). Four
of these problems involve diffusion from a specied initial concentration prole
in a one-dimensional region of space (which may be innite in extent), while the
fth involves diffusion between two nite, well-mixed compartments separated
by a membrane.
40
Impulse
Initial concentration
Sinusoid
Discontinuity
Arbitrary
Bath 1 M
Bath 2
Two compartment
Position
Figure 3.1: Schematic representation of the ve

classes of initial concentration proles simulated
by the software. M designates the membrane.
3.2. METHODS OF SOLUTION
41
One-dimensional diffusion
In one-dimensional diffusion, the initial concentration can be chosen to be one
of four options: impulses, sinusoids, discontinuities, and an arbitrary spatial
distributions. An impulse of solute concentration is a mathematical idealization
corresponding to a nite amount of solute initially concentrated at a single point
in space. In the impulses option, the user can specify the magnitude and posi
tion of up to four impulses. This option illustrates diffusion from point sources.
The sinusoids option illustrate the spatial frequency response of a system gov
erned by the diffusion equation, specically, the low-pass spatial ltering effect
of diffusion. By superimposing up to four sinusoids, the user can observe the de
pendence of the space-time evolution of concentration on its spatial frequency
content. In the discontinuities option, the initial concentration prole may be
piecewise-constant but contain discontinuities. The user can specify the magni
tude and location of up to four such discontinuities. For example, this allows
simulation of the diffusion that results from an initial rectangular pulse of so
lute concentration. The user can also explore the response for more complicated
initial conditions which can be specied by drawing an arbitrary initial concen
tration on the monitor screen with a mouse.
For these different initial distributions, the user can specify the boundary
type (transparent or reecting), the value of the drift velocity, and the chemical
reaction rate at which solute is removed.
Two-compartment diffusion through a membrane

In the two compartment option, the user can also investigate diffusion between
two well-stirred compartments, or baths, through a membrane which is perme
able to the solute. Two-compartment diffusion through a membrane is an impor
tant transport process in biological systems. It can model, for example, diffusion
between the cytoplasm of a cell and the extracellular uid, across the plasma
membrane. The baths are assumed to be well-stirred, so that the concentration
within each bath varies with time but not with position in the bath. The total
amount of solute in the system is assumed to be nite. The user can specify the
width of each bath and of the membrane, the initial concentration of each bath,
and an arbitrary initial concentration prole in the membrane.
3.2
Methods of Solution
For several of the diffusion problems implemented in the software, exact solu
tions of the modied diffusion equation (Equation 3.6) are available in a form
that makes computation efcient. Such solutions have been used wherever pos
sible. The remainder of the solutions were obtained by numerical methods. The
42
methods are described in some detail elsewhere (Berkenblit, 1990); only a brief
summary of the methods is given here.
The method used to obtain solutions depends upon the type of boundary con
dition. Two types of boundary conditions for the diffusion problems can be se
lected by the user: transparent or reecting boundary conditions. If transparent
boundaries are specied, then the region over which diffusion occurs is innite;
the spatial limits of the region over which diffusion is displayed are set by the
user. At a reecting boundary, on the other hand, the solute ux is constrained
to be zero, since no solute particles can cross such a boundary.
3.2.1 Exact solutions

Exact solutions were used to compute the response for all one-dimensional diffu
sion problems with transparent boundaries. These are described in this section.
Impulse response Greens function
No drift, no chemical reaction. First, we consider the case when the drift ve
locity is zero and the chemical reaction rate is zero. Let the initial concentration
be a unit impulse located at position x = and delivered at time t = 0,
c(x, 0) = (x ).
(3.7)
The solution of the diffusion equation (Equation 3.3), called the Greens function
G(x, t; , 0), is
1
2
c(x, t) = G(x, t; , 0) =
e(x) /4Dt .
4 Dt
(3.8)
Thus, the concentration prole is a Gaussian

function of the spatial variable.
The standard deviation of the concentration, 2Dt, increases with increasing
time, but the total area of the concentration remains constant because solute is
conserved.
Drift but no chemical reaction. We next consider the same problem but with
a non-zero drift velocity. In this case, the concentration satises the modied
diffusion equation, Equation 3.6, with r = 0:
c
2c
c
=D 2 v
,
t
x
x
(3.9)
c(x, 0) = (x ).
(3.10)
with the initial condition

The solution can be shown to be
c(x, t) =
1
2
e(xvt) /4Dt = G(x vt, t; , 0).
4 Dt
(3.11)
43
Thus, the response in this case is a Gaussian function, as before, but the entire
prole drifts in the positive x-direction with drift velocity v.
Drift and chemical reaction. With a non-zero chemical rate, r , and drift velocity,
v, we need to solve Equation 3.6 which has a solution
c(x, t) = er t G(x vt, t; , 0).
(3.12)
In general, if c (x, t) is the solution to Equation 3.3, with a specied initial concentration prole and transparent boundaries, then the solution to the modied
equation, 3.6, satisfying the same initial conditions, is given by
c(x, t) = er t c (x vt, t).
(3.13)
Sinusoid
First we consider the solution to Equation 3.3 with the initial condition
c(x, 0) = A (1 + sin(x + ))
(3.14)
for some arbitrary constant amplitude, A, spatial radian frequency, , and phase,
. The solution for t > 0 is given by
2
c(x, t) = A 1 + eD t sin(x + ) ,
(3.15)
which can be veried by substituting this expression into Equation 3.3. Thus,
an initially sinusoidal concentration prole remains sinusoidal for all later time,
but the amplitude decreases exponentially with time. The rate of attenuation is
proportional to the square of the spatial frequency.
With drift and a chemical reaction between solute and solvent, the solution is
2
c(x, t) = Aer t 1 + eD t sin (x vt) + ,
(3.16)
where v is the drift velocity and r is the reaction rate.
Discontinuous initial prole
We next consider the case of an initial prole that is piecewise-constant but con
tains a jump discontinuity at x = . The initial condition is that
cL , x <
c(x, 0) =
,
(3.17)
cR , x >
which can also be written as
c(x, 0) = cL + (cR cL )
(x x ) dx .
(3.18)
44
For t > 0, we can integrate the Greens function dened by Equation 3.8 to obtain
the solution:
c(x, t) = cL + (cR cL )
G(x, t; x , 0) dx
1
2
e(xx ) /4Dt dx
= cL + (cR cL )
4 Dt
1
x
= cL + (cR cL ) 1 erfc
,
(3.19)
2
2 Dt
where the complementary error function, erfc(x), is dened by the integral
2
2
et dt.
(3.20)
erfc(x) =
x
With a drift velocity, v, and reaction rate, r , the solution is
1
x vt
r t
r t
c(x, t) = cL e
1 erfc
+ (cR cL )e
.
2
2 Dt
(3.21)
3.2.2 Numerical Solutions

One-dimensional problems with reecting boundaries and the two-compartment
problem are solved using numerical methods. To solve a diffusion problem nu
merically over some specied spatial region and some specied time interval, the
position and time variables are discretized. Denoting the time increment by t
and the position increment by x, we dene
j
ui = c(xi , tj ),
(3.22)
where
xi = x0 + ix, i = 1, . . . , N
tj = t0 + jt,
j = 1, . . . , M.
(3.23)
A general approach to solving partial differential equations numerically is to

replace the partial derivatives by nite-difference approximations. The nitej
difference expressions involve the ui terms dened above and result in sets of
algebraic equations that can be solved by numerical methods for solving ma
trix equations. In the software, the equation with no drift term is solved by
the implicit Crank-Nicolson algorithm, while for problems with a non-zero drift
term, this algorithm is combined with the explicit Two-Step Lax-Wendroff method
(Press et al., 1988; Gerald and Wheatley, 1989). When a non-zero chemical reac
tion rate, r , is specied, the computed concentration is multiplied by the atten
uation factor, er t . The Crank-Nicolson and Lax-Wendroff formulas involve the
parameters = Dt/(x)2 and = vt/x. The numerical methods give sta
ble solutions provided < 0.5 and || 1. For the two compartments option,
the boundary conditions at the membrane solution interface is that the concen
tration in the membrane at the interface is equal to the bath concentration.
45
Option
Boundary Type
Computational Method
Impulse
Transparent
Exact solution
Reecting
Crank-Nicolson
Sinusoid
Transparent
Exact solution
Discontinuity
Transparent
Exact solution
Reecting
Crank-Nicolson
Reecting
Crank-Nicolson
Arbitrary
Two-Compartment
Crank-Nicolson
Table 3.1: Summary of computational methods.
3.2.3 Summary
A variety of techniques are used to nd exact solutions to one-dimensional dif
fusion problems with transparent boundaries. The specic methods used in the
software to solve one-dimensional problems depend on the initial conditions and
are summarized in Table 3.1. With two reecting boundaries and in the absence
of drift, the exact solutions consist of innite series. Thus it is cumbersome to
compute these exact solutions. With two reecting boundaries and with drift,
exact solutions are in general not available. Therefore, we have chosen to solve
these problems numerically using the Crank-Nicolson and Lax-Wendroff meth
ods. The latter methods are also used to compute the solutions to the twocompartment problem.
3.3
MATLABs command window) MD Controls, Initial concentration prole, Plots
versus position, and Plots versus time. A typical session with the software consists
of selecting one of ve initial concentration prole options, selecting the values
of parameters, executing a simulation, and analyzing the results.
3.3.1 MD controls
The controls gure controls the macroscopic diffusion software and is shown in
Figure 3.2. The part of the controls gure below the menubar is divided into six
panels. The upper left panel controls the display of the initial concentration and
the numerics. The upper middle panel controls timing of the simulation. The
upper right panel (the analysis panel) controls the display of simulation results.
46
Figure 3.2: The MD controls gure.
Clicking on a selection box display the appropriate gure; clicking again hides
it. The next horizontal panel down allows the simulation to be started, paused,
continued, or reset. The log panel contains options for recording log entries
of the session and is described in Chapter 1. The bottom horizontal panel is a
message window that displays information to the user.
Timing
The user can select the number of steps in time for computing the simulation
results and the interpoint integration time. The product gives the duration of
the simulation time interval. The end time indicates the projected end of the
simulation at any time. This number is updated if the simulation is continued.
The time is the present value of the simulation time, it is the elapsed simulation
time since the simulation was started. Clicking on 1 Time step results in the
computation of one step of the simulation.
3.3.2 Initial concentration prole

The initial concentration prole gure (Figure 3.3) allows control of the initial
concentration and all the parameters of the diffusion process. The four onedimensional diffusion problems and the two-compartment problem are imple
mented in the software as ve options called: Impulses (Figure 3.3), Sinusoids
(Figure 3.4), Discontinuities (Figure 3.5), Arbitrary (Figure 3.6), and Two Com
partments (Figure 3.7). For each option, the user can modify the values of the
option-specic parameters (described in the captions), change the graph param
eters, and run a simulation. To modify the value of a parameter, the user clicks
on the parameter and then types in the new value, followed either by a carriage
return or by selection of another parameter. A change in most parameter values
requires that gures be updated to reect the new value of the initial concentra
tion prole. Since this update takes some time, it may be helpful to deselect Plots
47
Figure 3.3: Initial concentration gure for impulses. When the software is initiated,
Impulses is the default initial concentration prole. In general, the magnitudes and po
sitions of four impulses can be specied. The positions of each impulse can be set only
if its magnitude is non-zero. The boundary type (transparent or reecting) is selectable,
and, if the boundaries are reecting, the positions of the two reecting boundaries can
be set.
48
Figure 3.4: Initial concentration gure for sinusoids. The frequencies and amplitudes
of the four sinusoids were chosen to correspond to the rst four terms in the Fourier
series of a square wave. In general, the amplitudes, frequencies, and phases of four
sinusoids can be specied. The frequency and phase of a sinusoid can be set only if
its amplitude is non-zero. Only transparent boundaries are available for the sinusoids
option.
49
Figure 3.5: Initial concentration gure for discontinuities. Two discontinuities were
used to generate an initial concentration prole that is a rectangular pulse. In general,
the magnitude and position of four discontinuities can be specied. The position of a
discontinuity can be set only if its magnitude is non-zero. The boundary type (trans
parent or reecting) is selectable, and, if the boundaries are reecting, the positions of
the two boundaries can be set.
50
Figure 3.6: Initial concentration gure drawn using the arbitrary option. Only the re
ecting boundary condition is available for this option, and the positions of the two
boundaries is speciable. The initial prole is drawn on the monitor screen by moving
the mouse cursor. The details are described in Section 3.3.5.
51
Figure 3.7: Initial concentration gure for the two compartments option. In general,
specication can be made for the width and the initial concentration in each bath, the
membrane width, and the initial membrane concentration prole, drawn with a mouse
cursor (as described in Section 3.3.5). The user can also chose how the two baths and
the membrane are to be displayed. Selecting the View membrane option displays the
membrane and a bit of each bath on each side. Selecting the View baths option displays
the membrane and both baths to scale.
52
Figure 3.8: The diffusion parameters gure.
vs. position and Plots vs. time from the MD controls gure. All the parameters
for each option can be saved in a le and read from a le.
Diffusion parameters
Clicking on Diffusion parameters in the Initial concentration prole gure displays
the Diffusion parameters gure (Figure 3.8). This gure allows the user to spec
ify the diffusion parameters (diffusion coefcient, drift velocity, and chemical
reaction rate) for each option independently. For the two compartments option
these diffusion parameters apply to the membrane and not to the baths.
Graph of initial concentration
The initial concentration is plotted in the Initial concentration prole gure (Fig
ures 3.3-3.7). A check box in the upper right-hand corner allows display of the
initial ux. An axis scale can be changed by clicking on its label to display the
axis-scale gure which is described in Chapter 1. The new axis limits can be typed
into the edit boxes to change the axis. In addition, there are two markers that are
indicated by two triangles on the abscissa. These markers indicated positions
at which the concentration and ux can be displayed as a function of time. The
positions of these markers can be controlled numerically or graphically. Numer
ical control is achieved by typing into the appropriate text edit box. Graphical
control is achieved by clicking on the abscissa axis. The left marker is controlled
by clicking the left button on a two-button mouse or by clicking the button on
a single-button mouse. The right marker is controlled by clicking the right but
ton on a two-button (or three-button) mouse or by shift-clicking the button on a
single-button mouse.
3.3.3 Numerics
Clicking on Numerics in the MD Controls gure displays the Numerics gure (Fig
ure 3.9). The numerics gure controls the spatial resolution of the simulation.
The upper portion of this gure deals with those computations that make use
of exact solutions of the diffusion equation (i.e., all one-dimensional diffusion
problems with transparent boundaries). For this case, the user can select the
53
Figure 3.9: The numerics gure.
number of spatial points at which the solution is computed. The larger the num
ber of points, the higher the spatial resolution of the computation and the longer
it will take to complete the computation. The lower portion of this gure deals
with those computations that use numerical integration of the diffusion equation
(i.e., all one-dimensional diffusion problems with reecting boundaries and the
two-component diffusion problem). The user can choose to select the number
of points in space at which the solution is computed. The user has a choice in
how the interpoint integration time is to be determined. The numerical method
is stable provided an inequality that relates the temporal and spatial resolution
is satised. If Auto-link with DELTA_T is selected, the simulation determines
the integration time to satisfy the inequality and to guarantee a stable integration
method which results in an accurate solution. If this choice is not selected, the
user can choose the temporal resolution (integration time) and spatial resolution
independently. However, with this choice there is no guarantee that the solution
will be accurate.
3.3.4 Analysis gures

There are two gures that display the solute concentration and ux during a
simulation. The Plots versus position gure displays the concentration and/or
the ux as a function of position at each instant in time during the simulation
(Figure 3.10). The current simulation time is displayed near the top of the gure.
Axes limits can be changed by clicking on the axes labels to display the axis-scale
gure. The two green triangular markers mirror the markers shown in the Initial
concentration prole gure. With the Two compartments option, the user can
also chose how the two baths and the membrane are to be displayed. Selecting
the View membrane option displays the membrane and a bit of each bath on each
side. Selecting the View baths option displays the membrane and both baths to
scale.
The Plots versus time gure (Figure 3.11) displays the concentration and/or
the ux as a function of time during the simulation for two positions selected
by the markers found in both the Initial concentration prole gure and the Plots
versus position gure (Figure 3.10). The locations of the markers are indicated at
54
Figure 3.10: Plots versus position gure.
Figure 3.11: Plots versus time gure.
55
the top of the gure. Axes limits can be changed by clicking on the axes labels
to display the axis-scale gure.

For the Arbitrary and Two compartments options, the user can draw an arbitrary
initial concentration prole by clicking on the Draw initial prole button and can
erase an existing prole by selecting the Erase initial prole button. Clicking on
the Draw initial prole button will erase the existing prole.
Drawing a prole consists of generating a list of concentration values at a
corresponding array of positions. The user selects these points by moving the
mouse and clicking any mouse button. As the pointer moves within the plotting
eld in the Initial concentration prole gure, a line joins the last point which
was selected to the current pointer position. There are two modes of action that
the user can use to draw the prole:
Clicking a mouse button within the axes of the graph adds a position and
concentration value to the coordinate lists and draws a line segment from
the previous point to the current point. In this manner, the user can con
struct a prole made up of line segments.
Moving the mouse while a mouse button is held down causes a series of
points to be added to the coordinate lists. In this manner, the user can
construct more complicated curves.
The two methods can be combined in drawing a single prole. As soon as a
complete prole has been drawn, the drawing routine terminates and stores the
prole data.
There are some additional rules of operation for drawing initial proles. When
a button is pressed, the position and concentration that are added to the coordi
nate arrays depend on the pointer location:
A button press at a position that does not lie to the right of the previous
point is ignored, in order to ensure that the user-drawn concentration pro
le is a single-valued function of position.
If a button is pressed within the graph axes, then the coordinates of the
pointer location are added to the list.
If a button is pressed outside the boundaries of the graph (but still within
the graph window), then the point that is added to the list is the point of
intersection between the graph boundary and a line from the previous point
to the current position. Thus, while a prole is being drawn, it is constrained
to lie entirely within the boundaries of the graph.
56

By default in the arbitrary option, the concentration at the left-hand point of
the prole is zero. The user can change the rst value, however, by making
the rst button press at the desired vertical location but to the left of the
concentration axis. In the two components option, the concentration at the
left-hand point of the prole is set equal to the concentration in the left
bath (bath #1), and the concentration at the right-hand point of the prole
is set equal to the concentration in the right bath (bath #2).
Clicking outside the Initial concentration prole gure at any time aborts the
drawing procedure.
3.4
Problems
Problem 3.1 In this problem you will investigate the space-time evolution of so
lute diffusion from a point source. For all parts of this problem use a single im
pulse and transparent boundaries. Set the impulse strength to 100 moles/cm2 ,
place the impulse at position 0.5 cm, and set the drift velocity and the reaction
rate to zero. Set the marker positions to 0.55 and 0.6 cm unless indicated other
wise. Set the diffusion coefcient to 105 cm2 /s and run the simulation for 1000
seconds. Obtain a plot of the concentration and ux on appropriate ordinate
scales. You should obtain the spatial distribution of the concentration and the
ux at 1000 seconds and both variables as a function of time at the two marker
positions. Repeat these two steps for a diffusion coefcient of 4 105 cm2 /s.
a. Describe qualitatively the effect of the change in diffusion coefcient on
the spatial distribution of concentration. Be brief.
b. For both values of the diffusion coefcient, determine the maximum am
plitude of the concentration versus position and the width of the spatial
distribution of concentration at an amplitude that is e1 of its peak value.
Explain the numerical values of all four measurements. Be brief and precise;
state your assumptions explicitly.
c. For the diffusion coefcient at 105 cm2 /s, examine the concentration ver
sus time at the two positions 0.55 and 0.6 cm. Describe qualitatively the
differences in concentration versus time at the two positions. Be brief.
d. For the diffusion coefcient at 105 cm2 /s, measure the maximum concen
tration as a function of time at the two positions and the time of occurrence
of this maximum. Explain the values of all four measurements. Be brief and
precise; state your assumptions explicitly.
e. Explain the shape of the spatial distribution of ux for a diffusion coef
cient of 105 cm2 /s.
3.4. PROBLEMS
57
f. Explain the relation between the ux and concentration versus time at lo

cation 0.55 cm for a diffusion coefcient of 105 cm2 /s.
g. Rerun the simulation for a diffusion coefcient of 105 cm2 /s at positions
0.45 and 0.55 cm. Explain the differences in the ux as a function of time
for these two locations.
Problem 3.2 This problem deals with the solution from a point source in the
presence of drift. Set the impulse strength to 100 moles/cm2 ; place the impulse
at position 0.5 cm; set the diffusion coefcient to 105 cm2 /s, and the reaction
rate to zero. Set the marker positions to 0.75 and 0.9 cm unless indicated other
wise. The parts of this problem that deal with reecting boundaries are solved
numerically. To decrease the time taken for these computations, consider de
creasing the spatial resolution of the computation to 10 points.
a. Set the boundary conditions to transparent and the drift velocity to zero
and run the simulation for 1000 s. Now set the drift velocity to 104 cm/s
and run the simulation again for 1000 s. Describe the effect of the drift
on the spatial distribution of concentration. Account quantitatively for the
position of the peak of the spatial distribution at 1000 s.
b. Set the boundary conditions to reecting and the drift velocity to zero. Run
the simulation until the spatial distribution is no longer a function of time.
This is the equilibrium distribution. What is the spatial distribution at equi
librium? Explain your answer.
c. Set the boundary conditions to reecting, the drift velocity to 104 cm/s,
and run the simulation. Describe the effect of drift on the spatial distribu
tion of concentration. Illustrate your description with printed copies of the
distribution at characteristic times.
d. With the boundary conditions still set to reecting and the drift velocity
104 cm/s, determine the equilibrium spatial distribution of concentration.
Account quantitatively for this distribution.
e. It is known that the density of air decreases exponentially with distance
above the earths surface. Explain this phenomenon.
Problem 3.3 As shown elsewhere (Weiss, 1996a, Chapter 3), two-compartment
diffusion is based on 4 assumptions:
1. The two compartments are well-mixed so that the concentrations of solute
n are uniform and have values at time t of cn1 (t) and cn2 (t).
2. Solute particles are conserved, e.g., there is no chemical reaction present
that either creates or destroys particles.
58

3. The membrane is sufciently thin and the number of solute particles con
tained in the membrane at any time is negligibly small.
4. The membrane is sufciently thin that at each instant in time the concen
tration prole in the membrane is in steady state.
This problem concerns the conditions for the validity of assumptions 3 and 4.
Specically, you will explore the effect of bath dimensions on two-compartment
diffusion without making these two assumptions.
In all parts of the problem, use the Two compartments option of the software.
Set the membrane width to 0.01 cm, and the concentration of bath #1 to 70 and
bath #2 to 10 mol/cm3 . Leave the drift velocity and reaction rate at 0 and the dif
fusion coefcient at 105 cm2 /s. Set the parameters of the plot of concentration
versus position so that the membrane and a little of each bath are visible on the
screen select membrane view. Note that the left edge of the membrane is at a
position of 0 cm. Draw some initial concentration in the membrane. Make sure
all ordinate scales on all plots are 0 to 100 mol/cm3 . Keep these parameters xed
throughout this problem. To reduce the time taken for the computation reduce
the spatial resolution in the membrane to 10 points in space. The software will
determine the time increment (DELTA_T). Initially set the number of steps so that
the end time is 5 s.
For each of the pairs of bath widths Bath #1 = 1 cm, Bath #2 = 1 cm; Bath #1
= 0.1 cm, Bath #2 = 0.1 cm; Bath #1 = 0.01 cm, Bath #2 = 0.01 cm; Bath #1 = 0.01
cm, Bath #2 = 0.05 cm; Bath #1 = 0.001 cm, Bath #2 = 0.001 cm; answer the
following questions.
a. Assess the validity of assumption 4.
i. Make rough estimates of both the steady-state (ss ) and equilibrium
(eq ) time constants from the computations.
ii. Estimate the same two time constants based on theoretical considera
tions (Weiss, 1996a, Chapter 3).
iii. What is your conclusion based on your computations and your esti
mates of time constants?
b. Assess the validity of assumption 3.
i. Before you do the computation, make an estimate of the nal concen
tration in each bath. Then do the computation, and check your initial
estimates against the computed values
ii. If they differ, explain the basis of the difference.
iii. How good is the assumption that the quantity of solute in the mem
brane is negligible? If you decide that the quantity of solute in the
membrane is not negligible, design a simulation experiment to test
your conclusion.
3.4. PROBLEMS
59
e. Are the bath concentrations exponential functions of time? Explain.

Problem 3.4 Some problems in diffusion with a reecting boundary can be solved
by using the solution for a transparent boundary and the method of images to
match the reecting boundary condition. This problem explores the successes
and pitfalls of this method. In all parts of this problem, set the drift velocity to
zero, the reaction rate to zero, and the diffusion coefcient to 105 cm2 /s unless
state otherwise. The parts of this problem that deal with reecting boundaries
are solved numerically. To decrease the time taken for these computations, con
sider decreasing the spatial resolution of the computation to 10 points.
a. Use reecting boundaries, and an initial impulse of concentration of strength
100 moles/cm2 located at 0.2 cm. Run the simulation for 1000 s and obtain
a print of the spatial distribution of concentration at time 1000 s and the
concentration versus time at locations 0 and 0.3 cm.
b. At a reecting boundary, the ux must be zero. Change the boundary con
dition to transparent and determine the parameters of two impulses: one
to match the left boundary condition and another to independently match
the right boundary condition. Run the simulation again and compare with
the results in part a. Does this method of images work exactly? Explain.
Problem 3.5 Diffusion from an initial sinusoidal concentration distribution gives
important insights into the space-time evolution of diffusion processes. In all
parts of this problem, use a drift velocity of zero, a reaction rate of zero, and a
diffusion coefcient of 105 cm2 /s unless state otherwise.
a. Use an initial concentration that is sinusoidal with amplitude 50 moles/cm2
and a spatial frequency of 1 cycle/cm. Run the simulation for 1000 s and
print the spatial distribution of concentration at 1000 s and the concentra
tion versus time at 0.25 and 0.75 cm. Repeat this procedure for sinusoids
with the same amplitudes but the following spatial frequencies: 3, 5, and 7
cycles/cm. Summarize your results both qualitatively (in words) and then
quantitatively (with suitable calculations).
b. Construct a periodic waveform from four sinusoids with the following am
plitudes (moles/cm2 ) and spatial frequencies (cycles/cm): 105, 1; 35, 3; 21,
5; 15, 7. Run the simulation and observe the spatial distribution of concen
tration. Summarize your results and relate them to results of part a.
c. Switch to the arbitrary initial distribution option and set the boundary con
ditions to reecting. Using the mouse draw an arbitrary, preferably jagged,
initial prole. This part of this problem uses a numerical solution method
that is time consuming. To decrease the time taken for these computa
tions, consider decreasing the spatial resolution of the computation to 10
60

points. Run the simulation and watch the spatial distribution of concentra
tion change. Summarize your results. What is the effect of diffusion on the
spatial distribution?
Chapter 4
CARRIER-MEDIATED TRANSPORT
61
62
4.1
CHAPTER 4. CARRIER-MEDIATED TRANSPORT
Introduction
Transport of many solutes including important metabolites (e.g. monosaccha

rides, amino acids, mononucleotides, phosphates, uric acid, etc.) through cel
lular membranes is accomplished by membrane-bound carrier molecules that
combine with the solute molecule on one face of the membrane, then translo
cate in the membrane and uncombine at the other face. Thus, transport involves
chemical reactions in which the solute binds and unbinds with a carrier. This
type of transport is called carrier-mediated transport. Carrier-mediated trans
port has distinctive properties. For example, the relation of ux to concentration
saturates, i.e., it does not obey Ficks law for membranes. In addition, differ
ent molecules compete for the carrier. For example, glucose and sorbose (two
monosaccharides) compete for the sugar carrier. Hence, transport of one sugar
can inhibit transport of another simply by occupying a site to which both can
bind.
There are canonical models of carrier-mediated transport that capture impor
tant properties of the transport of metabolites through cellular membranes. It
is important to understand these canonical models in order to understand how
metabolites are transported across these membranes. Derivations of predictions
of these models are not particularly difcult to follow; the individual steps are
simple. However, the models typically result in messy algebraic expressions that
relate ux to concentration and transport parameters. Thus, it is easy to get lost
in algebraic manipulation as well as in a sea of parameters so that an intuitive
grasp of the models becomes illusive. The intent of this software is to allow the
user to develop intuition for these models.
4.2
Description Of The Models
Descriptions of carrier-mediated transport as well as models of such transport

processes can be found elsewhere (Stein, 1986; Weiss, 1996a). Here we consider
three models and list both the assumptions and the important results. First, we
consider the steady-state behavior of a simple, four-state carrier that binds one
solute Then, we consider the steady-state behavior of a simple, six-state carrier
that binds two solutes with different afnities. Finally, we consider both the
transient and the steady-state behavior of a general, four-state carrier model that
binds one solute.
4.2. MODELS
63
Membrane
S +
Intracellular
cSi
noE
ES
Eo
ES
KSi
ES i
niES
KSo
E
E
S = ES
+ So
cSo
Extracellular
niE
Figure 4.1: Kinetic diagram of
the simple, four-state carrier

that binds one solute.
ES o
no
ES
4.2.1 Steady-state behavior of a simple, four-state carrier that

binds one solute
Assume that the membrane contains NET moles of carrier per unit area of membrane.1 Each of these carriers exist in one of four states labeled ES i , ES o , E i , and
E o (Figure 4.1). In the ES states, the solute S is bound to the carrier E; in the
E state the carrier is unbound. In the ES i and E i states, the carrier, bound and
unbound, communicates with the solution on the inner side of the membrane.
In the ES o and E o states, the carrier, bound and unbound, communicates with
the solution on the outer side of the membrane. The densities of carrier in the
four states are niES , noES , niE , and noE moles per unit area of membrane. The uxes
of bound and unbound carrier are ES and E and the ux of solute is S . The
ux is dened as positive when the ux is in the outward direction; the units
are in moles per unit area per second. The model is dened by the following
assumptions:
The total amount of carrier, bound and unbound, is constant, i.e. the sum
of the carrier density over all of its states equals the total density of carrier
in the membrane
o
NET = niES + nES
+ nEi + nEo .
(4.1)
Since the carrier resides permanently in the membrane, the total ux of
carrier must be zero, i.e.
ES + E = 0.
(4.2)
The only time the solute crosses the membrane is when it is bound to the
carrier; ES o is assumed to undergo a reversible change in conformation to
the form ES i . The unbound carrier is assumed to undergo a similar reaction
1
Because the kinetic equations for binding of the carrier to the solute are analogous to those
of the binding of an enzyme to its substrate, the carrier is denote by E which stands for enzyme.
64

between the two conformations E i and E o . These two reactions are assumed
to be rst-order reactions with forward and reverse rate constants, E , ES ,
E , and ES , so that the uxes are dened as follows:
ES = S = ES niES ES noES ,
E =
E niE
E noE .
(4.3)
(4.4)
In the simple model, the binding reactions at the membrane interfaces are
assumed to be so rapid, compared to the rate of transport of solute across
the membrane, that the membrane interface reactions are assumed to be at
equilibrium, i.e.,
cSo noE
cSi niE
o
=
K
and
= KSi ,
(4.5)
S
noES
niES
where KSo and KSi are the dissociation constants on the two membrane in
terfaces.
These equations can be solved to determine the ns in terms of the concentra
tions and transport parameters. Equations 4.3 and 4.4 can be used to determine
the s. Combining Equations 4.2, 4.3, and 4.4 yields
(ES niES ES noES ) + (E niE E noE ) = 0.
(4.6)
Equations 4.1, 4.5, and 4.6 can be expressed as a matrix equation as follows:
i
0 cSi 0
0
nES
KS

o
0 cSo noES 0
0 KS
.
i =
(4.7)
ES ES E E
n
E

0
NET
1
1
1
1
noE
The rst two rows correspond to the two relations in Equation 4.5. The third row
results from Equation 4.6, and the fourth row corresponds to Equation 4.1. This
set of simultaneous equations has the following solutions (Weiss, 1996a):
cSi (E KSo + ES cSo )
,
D1
(4.8)
cSo (E KSi + ES cSi )

= NET
,
D1
(4.9)
niE = NET
KSi (E KSo + ES cSo )

,
D1
(4.10)
noE = NET
KSo (E KSi + ES cSi )

,
D1
(4.11)
niES = NET
noES
where
D1 = (E KSo + ES cSo )(KSi + cSi ) + (E KSi + ES cSi )(KSo + cSo ).
(4.12)
4.2. MODELS
ES i
Intracellular
cSi
Ri
cRi
Ei
ES o
ES
KSo
E
E
E
KRi
ER i
niER
noES
ES
KSi
niE
Si
Membrane
S = ES
noE
Eo
KRo
ER
ER
R = ER
cSo
So
Ro
Extracellular
niES
65
Figure 4.2: Kinetic diagram of a simple,
six-state carrier that binds two solutes (S
and R).
cRo
ER o
o
nER
S and E can be obtained from Equations 4.3 and 4.4.

The ux of solute can also be expressed in terms of the uni-directional uxes
as
S = S S ,
where
S = ES niES and S = ES noES .

two solutes
The simple, four-state carrier shown in Figure 4.1 can be extended to account for
the binding of two solutes that compete competitively for binding sites on the
carrier (Figure 4.2). In this scheme, solutes S and R combine with carrier E but
with different afnities. The binding to solute S has dissociation constants KSi
and KSo and the binding to R has dissociation constants KRi and KRo .
The kinetic equations are analogous to those derived for the simple, four-state
carrier except that the carrier now has 6 states:
of the carrier density over all of its six states equals the total density of
carrier in the membrane
i
NET = niES + noES + nER
+ noER + niE + noE ,
(4.13)
66

where NET is the total density of carrier in the membrane.
Since the carrier remains in the membrane, the net ux of carrier must be
zero
ES + ER + E = 0.
(4.14)
The uxes are related to the carrier densities so that

ES = S = (ES niES ES no
ES ).
(4.15)
ER noER ).
E noE ).
(4.16)
ER = R =
E =
(ER niER
(E niE
(4.17)
In the simple model, the reactions at the membrane interfaces are assumed
to take place so rapidly, compared to the rate of transport of solute across
the membrane, that the membrane interface reactions are assumed to be at
equilibrium, i.e.,
i i
i i
cSo noE
cRo noE
o c S nE
i
o cR nE
=
K
,
=
K
and
=
K
,
= KRi ,
R
S
S
noES
noER
niES
niER
(4.18)
where KSo , KSi , KRo and KRi

are the dissociation constants for solutes S and R,
respectively at the two membrane interfaces.
Combining Equations 4.14 and 4.15, 4.16, and 4.17 yields

(ES niES ES noES ) + (ER niER ER noER ) + (E niE E noE ) = 0.
(4.19)
It is of interest to obtain the ux of solutes S and R as a function of both con

centrations and the transport parameters KSi , KSo , KRi , KRo , ES , ER , E , ES , ER ,
E , and NET . Therefore, it is useful to regard the system of algebraic equations
given by Equations 4.14 through 4.19 as a set of 6 equations in the 6 unknowns
i
niES , noES , nER
, noER , nEi , and noE . These can be written in matrix form as follows:
i
KSi
0
0
0 cSi 0
nES
o
o
0 Ko
0
n
0
0
c
S
S
ES
0
KRi
0 cRi 0 niER
0
o
0
0
KRo
0
0 cRo
nER
ES ES ER ER E E
niE
1
1
1
1
1
1
noE
0
0

0
=

0
NET
(4.20)
The rst four rows correspond to the four relations in Equation 4.18. The fth
row results from Equation 4.19, and the sixth row corresponds to Equation 4.13.
This set of simultaneous equations has solutions (Weiss, 1996a):
niES
cSi KRi (E KSo KRo + ES cSo KRo + ER KSo cRo )

= NET
,
D2
(4.21)
4.2. MODELS
67
cSo KRo (E KSi KRi + ES cSi KRi + ER KSi cRi )
= NET
,
D2
(4.22)
niER = NET
KSi cRi (E KSo KRo + ES cSo KRo + ER KSo cRo )

,
D2
(4.23)
noER = NET
cRo KSo (E KSi KRi + ES cSi KRi + ER KSi cRi )

,
D2
(4.24)
niE = NET
KSi KRi (E KSo KRo + ES cSo KRo + ER KSo cRo )

,
D2
(4.25)
noE = NET
KSo KRo (E KSi KRi + ES cSi KRi + ER KSi cRi )

,
D2
(4.26)
noES
where
D2 = KSi (cRi ER + KRi E )(KSo KRo + cSo KRo + KSo cRo ) +
KSo (cRo ER + KRo E )(KSi KRi + cSi KRi + KSi cRi ) +
cSi KRi ES (KSo KRo + cSo KRo + KSo cRo ) +
cSo KRo ES (KSi KRi + cSi KRi + KSi cRi ).
(4.27)
The uxes can be computed using Equations 4.15-4.17.

The solute uxes can also be expressed in terms of the uni-directional uxes
as
S = S S ,
R = R R ,
where
S = ES niES and S = ES noES ,

R = ER niER and R = ER noER .

carrier that binds one solute
Transient solution
Suppose that in the simple, four-state carrier model shown in Figure 4.1, the as
sumption that the interfacial binding reactions are fast is dropped. The model
which results is called the general, four-state carrier model and the kinetic dia
gram for this model is shown in Figure 4.3.
This model is dened by the following assumptions:
68

Membrane
S + E
Intracellular
cSi
nEo
ai
ao
Eo + S o
ho go cSo
g i hi
bi
ES i
niES
Extracellular
niE
Figure 4.3: Kinetic diagram of a general,
four-state carrier model that binds one so

lute.
ES o
bo
no
ES
S = ES
The total amount of carrier, bound and unbound, is constant, i.e. at each
instant in time the sum of the densities of carrier over all of its states equals
the total density of carrier
NET = niES (t) + noES (t) + niE (t) + noE (t).
(4.28)
Since both transient and steady-state values will be considered, the notation
will be to specify a variable that changes in time as, for example, niES (t) and
its steady-state value as niES ().
ES (t) + E (t) = 0.
(4.29)
the form ES i . The unbound carrier is assumed to undergo a similar reaction
between the two conformations E i and E o . The kinetic equations for the
general, four-state carrier model can be written for the rate of change of
carrier in each of the four states by a matrix differential equation which is
n
iE (t)
o
nE (t)
i
.
nES (t)
noES (t)
(4.30)
The binding reactions are not assumed to be arbitrarily fast. Since the bind
ing reactions are assumed to be second-order kinetic equations, the solute
concentrations enter the binding reactions.
niE (t)
o
d

nE (t)
i
dt

nES (t)
noES (t)
gi
0
ao
ai hi cSi

go
ai
ao ho cSo
0

=
bi gi
hi cSi
0
bo
ho cSo
0
bi
bo go
4.2. MODELS
69
The four kinetic equations are not independent; e.g., the fourth can be derived
from the rst three equations. Thus, the fourth equation can be eliminated and
noES (t) can be eliminated using the conservation of carrier relation,
i
noES (t) = NET niE (t) no
E (t) nES (t),
(4.31)
to yield the matrix equation

ao
gi
nE (t)
nE (t)
ai hi cSi
0
d o
o

go
nE (t)
+
go
NET .
nE (t)
=
ai go ao go ho cSo
dt
niES (t)
niES (t)
hi cSi bo
bo
bi gi bo
bo
(4.32)
This matrix equation can be solved for the three carrier densities and Equa
tion 4.31 can be used to solve for the fourth density. The solution for each
of the carrier densities has the form
nj (t) = Aj1 e1 t + Aj2 e2 t + Aj3 e3 t ,
(4.33)
where the nj s are the four carrier densities, the s are the three non-zero eigen
values of the system, and the As are the residues. This solution is valid when
the eigenvalues are distinct. All 4 carrier densities have the same 3 eigenvalues,
but in general, the residues differ. Since the rate constants and concentrations
are all positive quantities, it can be shown that all the eigenvalues have negative
real parts. Both the eigenvalues and residues are functions of the rate constants
and the solute concentrations. Hence, the solutions yield the carrier densities
(niES (t), noES (t), niE (t), and noE (t)) as functions of time for any values of the con
centrations of solute S and of the transport parameters ai , ao , bi , bo , gi , go , hi ,
ho , and NET .
Steady-state solution
In the steady state, the density of carrier in each of its four states is constant and
the derivative terms on the left-hand side of Equation 4.30 are zero. As noted
previously, the four equations are not independent. Thus, one of the equations
can be eliminated. However, conservation of carrier leads to an independent
constraint which can be added to the three independent steady-state equations
to yield the following four steady-state equations
i

(ai + hi cSi )
gi
0
ao
n
E ()
0
go noE () 0
ai
(ao + ho cSo )
0
. (4.34)
=
0
(bi + gi ) bo
niES ()

0

hi cSi
NET
1
1
noES ()
1
1
The solutions (Weiss, 1996a) are ratios of sums of products of rate constants
i
o
o
MES
MES
nES
()
MEi noE ()
MEo niES ()
niE ()
=
=
=
=
,
,
,
,
NET
D
NET
D
NET
D
NET
D
(4.35)
70
where
MEi = ao bi go + ao gi go + ao bo gi + bo gi ho cSo ,
MEo = ai bi go + ai gi go + ai bo gi + bi go hi cSi ,
i
MES
= ai bo ho cSo + ao go hi cSi + ao bo hi cSi + bo hi ho cSi cSo ,
o
MES
D =
ai bi ho cSo + ai gi ho cSo +
i
o
MEi + MEo + MES
+ MES
.
ao bi hi cSi
(4.36)
bi hi ho cSi cSo ,
The steady-state ux is found elsewhere and equals (Weiss, 1996a)

E () = S () = ES () =
bi go hi cSi niE () bo gi ho cSo noE ()

.
bi go + bo gi + gi go
(4.37)
These equations yield the values of the n()s and the ()s in steady state as
a function of the concentrations of solute S and of the transport parameters ai ,
ao , bi , bo , gi , go , hi , ho , and NET .
as
S () =S () S (),
where
S () =
S () =
4.3
bi go hi cSi niE ()
,
bo gi ho cSo noE ()
.
Numerical Methods And Parameters
4.3.1 Numerical methods

The steady-state values of the carrier densities and the carrier uxes are alge
braic functions of the solute concentrations and of the parameters. They could
have been computed directly from the steady-state matrix equations for each
carrier model. However, it proved to be faster to compute these quantities di
rectly from the solutions of these matrix equations which are: Equations 4.3-4.4
and Equations 4.8-4.11 for the simple, four-state carrier, Equations 4.15-4.17 and
Equations 4.21-4.26 for the simple, six-state carrier, and Equations 4.35-4.37 for
the general, four-state carrier.
The transient solution for the general, four-state carrier was obtained by solv
ing Equation 4.32 numerically using MATLABs ode15s routine for solving sets of
ordinary differential equations. The solution for 3 of the 4 carrier densities were
computed; the fourth was computed from Equation 4.31. Eigenvalues of the ma
trix of rate constants (Equation 4.32) were computed to aid the user in choosing a
time scale for displaying transient responses. Eigenvalues were computed using
MATLABs eig function.
4.4. USERS GUIDE
71
4.3.2 Choice of numerical parameters

Simple models
The software enables the user to compute the ns and s for any values of the
parameters, the s, s, Ks, NET , and the concentrations of solute, the cs. The
software is initiated with default parameters chosen to approximate hexose trans
port in human erythrocytes (Carruthers, 1984; Stein, 1986) assuming a symmet
ric transport scheme. The density of carriers was set to NET = 10 pmoles/cm2 .
The dissociation constant of solute S was set to approximate that of D-glucose,
KSi = KSo = 2 moles/cm2 , and that of R was set to that of a solute to which
the carrier binds with lower afnity, approximating that of D-xylose, so that
KRi = KRo = 200 moles/cm2 . All the rate constants were set equal with a value
that made the maximum ux 100 pmoles/cm2 -s so that ES = ES = ER =
ER = E = E = 20 s1 . The concentrations of solute were chosen arbitrarily as
0
follows: cSi = 2, cS
= 1, cRi = 2, cRo =
1 moles/cm3 .
General model
[To be written]
4.4
Users Guide
When the program is selected, 3 gures are displayed (in addition to MATLABs
command window): Controls, Parameters, and State. The controls gure controls
the software. The remaining gures are for steady-state interactive analysis of the
simple, four-state carrier. In the interactive mode, any parameter of the carrier
model can be changed and the resulting steady-state values of carrier densities
and uxes are displayed immediately. The same steady-state interactive analysis
is available in all three models: the simple symmetric, four-state carrier; the sim
ple symmetric, six-state carrier; and the general, four-state carrier. Additional
modes of analysis allow plotting the steady-state values of carrier densities and
uxes as continuous functions of a user-specied model parameter. In addi
tion, for the general, four-state carrier, the user can observe transient changes
in carrier densities in response to a change in parameters. All of these modes of
analysis are selected using the controls gure.
4.4.1 CMT controls

The part of the controls gure (Figure 4.4) below the menubar is divided into
ve panels. The model panel allows the user to choose a particular model for
analysis. The analysis panel allows the user to choose among the various modes
of analysis available in the software by clicking on the appropriate button. The
72
Figure 4.4: Controls gure.
Figure 4.5: Units of all variables

in the carrier models.
miscellaneous panel allows the user to display the units for all variables used by
the software (Figure 4.5). The log panel contains options for recording log entries
of the session and is described in Chapter 1. The message panel at the bottom
of the controls gure is used to send messages to the user.
4.4.2 Model
Clicking on model in the controls gure allows selection of three models of
carrier-mediated transport. Selecting a different model will initiate the steadystate, interactive analysis for that model. The models are listed below.
Simple, four-state: refers to the simple, four-state carrier that binds one solute.
This is the default model that is displayed when the software is initialized.
The parameters and state gures associated with this model are shown in
Figure 4.6.
Simple, six state: refers to the simple, six-state carrier that binds two solutes
shown in Figure 4.7.
General, four-state: refers to the general, four-state carrier that binds one solute
4.4. USERS GUIDE
73
Figure 4.6: Parameters and state

gures for the simple, four-state
carrier model that binds one so
lute.
74

gures for the simple, six-state
carrier that binds two solutes.
4.4. USERS GUIDE
75

gures for the general, four-state
carrier that binds one solute.
76
Simple
Simple
General
four state
six state
four state
Total carrier density
NET
NET
NET
Rate constants
E , E ,
E , E , ES , ES ,
ai , ao , bi , bo
ES , ES
ER , ER
gi , go , hi , ho
Solute concentrations
cSi , cSo
cSi , cSo , cRi , cRo
cSi , cSo
Dissociation constants
KSi , KSo
KSi , KSo , KRi , KRo
Table 4.1: Modiable parameters of the carrier models the independent variables.
4.4.3 Steady-state interactive analysis

Interactive, steady-state analysis involves two gures the parameters and the
state gures. Any parameter (independent variable) can be changed in the pa
rameters gure and the resulting changes in the steady-state values of the car
rier state densities and carrier uxes (dependent variables) are displayed in the
state gure. The parameters for all three carrier models are listed in Table 4.1.
In both the parameters and state gures, clicking on any variable (parameter,
carrier density, or carrier ux) displays information about that variable in the
message window of the gure.
Parameters
The numerical value of each parameter is displayed in the button located either
above or below each parameter. Parameter values can be changed en masse by
clicking the appropriate buttons in the lower right part of the parameters gure.
Parameters can be restored to their default values or read from a le. Parameters
may also be saved to a le.
Parameters may be changed individually in three ways.
A value may be changed arbitrarily by clicking on the button for each pa
rameter. The button is changed to a text-edit box which allows editing the
parameter value. After typing RETURN, the new values of carrier densities
and carrier uxes are computed and displayed in the state gure. A non
numeric entry or a negative entry is not accepted and the prior value is
restored.
A parameter, selected by clicking on its button, may be incremented or
decremented by clicking on + or in the lower left of the parameters g
ure. The magnitude of the increment can be selected by typing in the text
4.4. USERS GUIDE
77
edit box in the lower left part of the parameters gure. The state gure is
updated with each incremental change in the parameter.
decremented repeatedly by clicking on the repeat button to the right of the
+ or to the left of the , respectively. The state gure is updated with each
incremental change in the parameter. Clicking on the repeat button again
stops the repetitive process.
In the general, four-state carrier, passive transport of solute (also called the
principle of detailed balance) requires that (Weiss, 1996a)
ai ho bo gi = ao hi bi go .
When this condition is violated, a warning messages is displayed in the message
window of the parameters gure, and the ratio
r =
ao hi bi go
ai ho bo gi
is displayed.
State
The steady-state values of carrier densities and carrier uxes are displayed below
each quantity for the particular set of parameters shown in the parameters gure.
These quantities are also displayed graphically. Carrier densities are displayed
with bar graphs that represent the relative densities of carrier in each states. Both
four-state carriers display niE , noE , niES , and noES . The six-state carrier displays niE ,
noE , niES , noES , niER , and noER . The carrier uxes are displayed with thick arrows
in the center of the gure. No arrow is displayed when the ux is zero . The
direction of the arrow indicates the direction of the ux. The color of the arrow
indicates the relative magnitude of the carrier ux; a small magnitude ux has a
black arrow, a large magnitude ux has a bright red arrow.
4.4.4 Steady-state graphic analysis

Selection of graphic analysis in the controls gure, displays the steady-state
graphic analysis gure (Figure 4.9). This gure allows the user to plot any vari
able versus any of the parameters of the carrier-mediated transport model. Use
of this gure is described in detail in Chapter 1. The variables are listed as: ux E
for E , ux ES for ES , n E i for niE , . . . , efux S for S .
78
Figure 4.9: The steady-state graphic analysis gure showing a plot of uxes and carrier
densities versus cSi on linear ordinate and abscissa scales.
4.4. USERS GUIDE
79
Figure 4.10: The transient analysis gure showing the transient response to the change
in parameters shown in Figure 4.11 and using the numerical data shown in Figure 4.12.
4.4.5 Transient analysis

Transient analysis is available only for the generalized, four-state carrier by click
ing on transient in the controls gure. This action displays the transient analysis
gure (Figure 4.10). Use of the transient analysis gure is described in detail in
Chapter 1. Differences occur only in the control of transient analysis panel shown
in the upper left panel of the gure. We describe this panel only.
Set up transients. Clicking on this item displays the set up transients gure shown
in Figure 4.11. The rst column of this gure shows all the 11 independent
variables for the general, four-state carrier. The initial values are shown in
the second column and the nal values are shown in the fourth column.
The initial values can be changed individually by typing in the new value
in the appropriate text edit box. The third column gives several options
for changing any particular variable. Several independent variables can be
changed. Clicking on Done terminates selection of variables to be changed.
80
Figure 4.11: The set up transients gure.
4.5. PROBLEMS
81
Figure 4.12: The transient nu

merics gure.
The bottom of the gure gives several additional options for changing vari
ables that are explained by positioning the mouse cursor over the option.
Graph ns. Clicking on this item displays the carrier densities as a function of
time.
Numerics. Clicking on this item displays the transient numerics gure which
gives information to the user and allows for control of the time scale of
the transient response (Figure 4.12). The transient numerics gure displays
the eigenvalues of the transient response at the top. These eigenvalues can
be computed for the initial or the nal values of all parameters by clicking
on the appropriate button in this gure. The nal value of the time in the
plot is determined by the information in the maximum time for transient
response panel.
Absolute scale. Selecting this item displays plots of all carrier densities on the
same absolute scale.
Relative scale. Selecting this item displays plots of all carrier densities on indi
vidual scales so that all the carrier densities are discernible.
Clear plotting axes. Selecting this item clears the plot eld.
4.5
Problems
Problem 4.1 This problem is intended to develop your intuition for the steadystate behavior of the simple, four-state carrier model for a single solute. You will
observe the effects of changes in parameters on both the ux and the carrier den
sities. Use the simple, four-state carrier model and start with all the parameters
at their default values.
a. What is the relation of S and E ? Explain.
82

b. What is the relation of the direction of S to the sign of cSi cSo ? Explain.
c. How does the state of the carrier depend on solute concentration?
i. Do changes in cSi change niES and niE ? If so, how? If not, why not?
ii. Do changes in cSi change noES and noE ? If so, how? If not, why not?
iii. Do changes in cSo change niES and niE ? If so, how? If not, why not?
iv. Do changes in cSo change noES and noE ? If so, how? If not, why not?
Reset all the parameters to their default values, except set ES = 100 s1 .
d. What is the relation of the direction of S to the sign of cSi cSo ? Explain.
Reset all the parameters to their default values, except set E = E = 0 s1 .
e. What is the relation of S to cSi cSo ? Explain.
Problem 4.2 This problem is designed to explore the functional relation between
ux and solute concentration when expressed in different coordinates. Use the
simple, four-state carrier model and start with all the parameters at their default
values, except set cSo = 0. In parts a through c your job is to estimate the values
of (S )max and KSi from the graphs specied, where (S )max is the maximum
ux of S with cSo = 0.
a. Obtain a graph of S versus cSi in linear coordinates.
b. Obtain a graph of S versus cSi in double logarithmic coordinates.
c. Obtain a graph of 1/S versus 1/cSi .
d. Determine the values of (S )max and KSi from the model parameters.
e. Compare the 4 sets of values you have obtained for (S )max and KSi .
Problem 4.3 Use the simple, four-state carrier model and start with all the pa
rameters at their default values, except set cSo = 0. Obtain a graph of all four
carrier states as a function of cSi . Some of the these ns increase, others de
crease, while others remain constant. Summarize and explain the results you
found.
Problem 4.4 Use the simple, six-state carrier model and start with all the param
eters at their default values. Set the solute concentrations of S and R to zero on
both sides of the membrane.
a. Explain the initial carrier states and ux values.
4.5. PROBLEMS
83
b. Increase cSi and observe both the carrier states and the ux. What is the
relation of the ux of S to cSi ?
c. Now set cSi = 10 and increase cRi . How do the uxes of S and R depend
upon cRi ?
o
d. Set cSi = 10 and cS
= 5. Now increase cRi from an initial value of 0. How

do the uxes of S and R depend upon cRi
? Pay particular attention to the
direction of the ux of S.
Problem 4.5 The transient response shown in Figure 4.10 appears to show that
the carrier densities change discontinuously at t = 0 in response to the change
in parameter shown in Figure 4.11. Reproduce this result.
a. On the basis of the theoretical development given in Section 4.2, can the car
rier densities change discontinuously in response to a discontinuous change
in any of the parameters? Explain.
b. By experimenting with the transient response, explain the results shown in
Figure 4.10. Make your explanation as quantitative as possible.
84
Chapter 5
HODGKIN-HUXLEY MODEL
85
86
5.1
CHAPTER 5. HODGKIN-HUXLEY MODEL
Introduction
5.1.1 Background
Electrically excitable cells produce action potentials which are important for
transmission of information in neurons, for contraction of muscle cells, and for
secretion of chemical substances by neurosecretory cells (Aidley, 1989; Hodgkin,
1964; Katz, 1966; Kandel et al., 1991; Keynes and Aidley, 1991; Nicholls et al.,
1992; Weiss, 1996b). The macroscopic mechanisms of production of action po
tentials can be understood in terms of the nonlinear electrical characteristics of
cellular membranes rst described by Hodgkin and Huxley for the membrane
of the giant axon of the squid (Hodgkin and Huxley, 1952). Since the nonlinear
properties of the membranes of electrically excitable cells are controlled by the
membrane potential, it is relatively simple to understand these mechanisms when
the membrane potential is constant, but vastly more difcult when the membrane
potential is not constant such as occurs during an action potential. Of course,
it is the properties of electrically-excitable cells under the latter conditions that
are the most important for the function of these cells.
5.1.2 Overview of the software

The purpose of this software is to allow users to enhance their comprehension
of the Hodgkin-Huxley model by providing a complete simulation of the model
under space clamped conditions. Any of the parameters of the Hodgkin-Huxley
model can be changed by the user and simulation experiments can be done to
examine the consequences of the parameter changes. Extensive graphics utilities
allow the user to plot any variable versus any other variable in the model. Since
the model is built on a block diagram language (SIMULINK), the user can also
make changes in the model structure.
5.2
Description Of The Model
Descriptions of the Hodgkin-Huxley model are available elsewhere (Aidley, 1989;

Hodgkin, 1964; Katz, 1966; Plonsey and Barr, 1988; Johnston and Wu, 1995;
Weiss, 1996b). A summary of this model is given in this section. The model
that is the basis of this software is a one-compartment model that represents a
space-clamped axon stimulated by means of two electrodes so that the membrane
current density and membrane potential are uniform along the length of the axon.
5.2. DESCRIPTION OF THE MODEL
87
Jm (t)
+
V (t)
m
Jm (t)
JC
JK
JN a
GK (Vm , t)
GN a (Vm , t)
+
VK
+
VN a
JL
GL
+
V (t)
m
Cm
+
VL
+
Vm (t)
JC
JK
GK (Vm , t)
JN a
GN a (Vm , t)
JL
Jm (t)
GL
Vm (t)
Cm
+
VK
+
VN a
Figure 5.1: Schematic di

agram and circuit model
of a space-clamped axon
in the voltage-clamp con
guration.
Jm (t)
Figure 5.2: Schematic diagram and circuit model

in the current-clamp conguration.
+
VL

5.2.1 Voltage-clamp and current-clamp congurations

Two simple and mutually exclusive stimulus congurations can be used to in
vestigate the model: the voltage-clamp and current-clamp congurations. In the
voltage-clamp conguration (Figure 5.1), the simulated space-clamped axon is
driven by a voltage source and the membrane current density is computed. In
the current-clamp conguration, the simulated space-clamped axon is driven by
a current source and the membrane potential is computed.
5.2.2 The membrane current density components

The total membrane current density, Jm , is the sum of the capacitance current
density plus the ionic current density
Jm = JC + Jion ,
(5.1)
88
where the capacitance current density is

JC = Cm
dVm (t)
,
dt
(5.2)
and Vm is the membrane potential. The ionic current density can be expressed
in terms of its components
Jion = JNa + JK + JL ,
(5.3)
where the ionic current densities due to sodium, potassium and leakage are
JNa = GNa (Vm , t)(Vm (t) VNa ),
(5.4)
JK = GK (Vm , t)(Vm (t) VK ),
(5.5)
JL = GL (Vm (t) VL ),
(5.6)
and where the Nernst equilibrium potential for the nth ion is dened in terms of
the concentrations as follows
o
c
RT
Vn =
(5.7)
ln ni ,
zn F
cn
where R is the molar gas constant, T is absolute temperature, F is Faradays
constant, and zn , cno and cni are the valence, outside, and inside concentrations
of ion n, respectively. For a univalent ion, the Nernst equilibrium potential is
expressed as
o
c
Vn = 0.08616 (Tc + 273.16) ln ni (mV),
(5.8)
cn
where Tc is the temperature in Centigrade.
5.2.3 The membrane conductances

The sodium and potassium conductances are dened as
Na m3 (Vm , t)h(Vm , t),
GNa (Vm , t) = G
K n4 (Vm , t).
GK (Vm , t) = G
(5.9)
(5.10)
5.2.4 The activation and inactivation factors

The rst-order kinetic equations for the activation and inactivation factors are
written in terms of the rate constants as follows:
dm
dt
dh
dt
dn
dt
= m m(m + m ),
(5.11)
= h h(h + h ),
(5.12)
= n n(n + n ),
(5.13)
where the s and s depend upon Vm .
89
5.2.5 The rate constants

The dependence of the rate constants on membrane potential has been gener
alized from the original Hodgkin-Huxley model to allow control of the potential
dependence of individual rate constants and to represent approximately the ef
fects of changes in calcium concentration and temperature.
The rate constants are
0.1(35 + Vm + VCa + Vm )
K T Km ,
e0.1(35+Vm +VCa +Vm ) 1
= 4e(Vm +VCa +Vm +60)/18 KT Km ,
m =
m
h = 0.07e
h =
n
n
0.05(Vm +VCa +Vh +60)
KT Kh ,
KT Kh ,
1+e
0.01(Vm + VCa + Vn + 50)
K T Kn ,
=
e0.1(Vm +VCa +Vn +50) 1
= 0.125e0.0125(Vm +VCa +Vn +60) KT Kn ,
0.1(Vm +VCa +Vh +30)
(5.14)
(5.15)
(5.16)
(5.17)
(5.18)
(5.19)
where KT is a temperature factor, that is dened as

KT = 3(T c 6.3)/10 .
(5.20)
KT multiplies all the rate constants; this effect approximates the effect of tem
perature on the electrical properties of the membrane of the squid giant axon
(Huxley, 1959). The factors Km , Kh and Kn have been added to the original
Hodgkin-Huxley model to allow changes to be made in the individual rate con
stants of m, h, and n. The factor VCa is used to approximate the dependence
of rate constants on calcium concentration and is
o
cCa
VCa = 0.03335 (Tc + 273.16) ln
12.995 (mV).
(5.21)
i
cCa
At the normal calcium concentration, the potential VCa has the value 0. For cal
cium concentration ratios that differ from the normal value, VCa differs from 0
and the dependence of the rate constants on the membrane potential is shifted
by a term that is proportional to the calcium equilibrium potential. This ap
proximates the effect of a change in calcium concentration on the parameters of
squid giant axon membrane (Frankenhaeuser and Hodgkin, 1957). The potentials
Vm , Vm , Vh , Vh , Vn , and Vn have the value 0 in the original Hodgkin-Huxley
model. These potentials can be used to shift the dependence of individual rate
constants on membrane potential.
5.2.6 Time constants and equilibrium values of activation and

inactivation factors
Equations 5.11-5.13 are expressed in terms of rate factors, but it is also useful
to express these equations in terms of time constants and equilibrium values, as
90
follows
dm
dt
dh
dt
dn
dt
=
=
=
m m
,
m
h h
,
h
n n
.
n
(5.22)
The time constants and equilibrium values can be dened in terms of the rate
constants by comparing Equations 5.11-5.13 to Equation 5.22.
m =
h =
n =
5.3
1
m + m
1
h + h
1
n + n
and
m =
and
h =
and
n =
m
,
m + m
h
,
h + h
n
.
n + n
(5.23)
Numerical Methods
5.3.1 Background
In order to compute the membrane potential for a given set of parameters, the
equations describing the Hodgkin-Huxley model (listed in Section 5.2) must be
approximated in a form that is appropriate for numerical solution on a digital
computer. A variety of methods exist for the numerical integration of a set of
coupled differential equations (Press et al., 1986). The simplest method, called
the Euler method, is to approximate all derivatives by rst differences, and to
solve the resulting collection of algebraic equations at a series of discrete times
separated by a time increment t. Although simple in concept, the Euler method
is not a particularly accurate or efcient method. Because the Hodgkin-Huxley
software is built on MATLAB/SIMULINK which includes a variety of methods of
numerical integration, the user can choose the method of integration from a num
ber of choices. The default method of integration used in the Hodgkin-Huxley
simulation is called the fth-order Runge-Kutta method.
5.3.2 Choice of integration step t

The accuracy of all numerical methods is dependent on the choice of the integra
tion step t. Simulation users will need to concern themselves with the choice of
t. If t is decreased, the accuracy of a single step increases but the time it takes
to compute the solution increases. Furthermore, if computations are continued
for a large number of steps, the accumulation of round-off errors, due to the lim
ited precision for representing numbers in a computer, can become appreciable.
5.3. NUMERICAL METHODS
91
Conversely, if t is increased, the accuracy of the computation decreases and

the solution may even diverge. This divergence can lead to spurious phenomena
that may mistakenly be attributed to the Hodgkin-Huxley model when they are
really artifacts of the numerical methods. A plausible empirical test of whether
or not a solution is sufciently accurate is to test the sensitivity of the solution
to changes in t. If increasing the value of t does not appreciably change the
solution, then the value of t used initially is too small and time was wasted
in performing the computation. If decreasing the value of t does not appre
ciably change the computational result, then the larger value is preferable. The
simulation of the Hodgkin-Huxley model is set initially with default numerical pa
rameters. For changes in parameters of the model that do not appreciably change
the various time constants of the model, the default numerical parameters are
adequate. However, if changing a model parameter (such as the temperature,
membrane capacitance, etc.) appreciably decreases some time constant of the
system, then a smaller value of t should be used. Therefore, it is advisable to
explore briey the effects of varying t on simulation results.
5.3.3 Method for computing solutions

In the voltage clamp simulation, the solution is obtained as follows: Suppose the
solution is known at time tp t and the solution at time tp is desired. The value
of the membrane potential Vm (tp ) at tp is determined from specication of the
stimulus (see Equations 5.24 and 5.25 on Page 97). This value is substituted into
Equations 5.14 and 5.19 to determine the rate constants at tp . Using these rate
constants, and given the values of m, h, and n at time tp t, the values of m,
h, and n are determined at tp by solving Equations 5.11-5.13 by an integration
method; the default method is the fth-order Runge-Kutta method. The values
of these factors are used to compute the values of the conductances and current
densities from Equations 5.1-5.6. The computation is begun with initial values of
m, h, and n that are determined from Equation 5.23 for a membrane potential
equal to the source voltage for t < 0.
In the current clamp simulation, the initial values of m, h, n, and Vm are
computed rst. This is done by using MATLABs trim function to solve the set
of Equations 5.1, 5.3-5.21 and a specication of the source current (Equation 5.24
on Page 97) with the derivatives of all the variables set to zero. Starting with these
initial values, the time-varying equations are solved numerically by an integration
method that can be chosen by the user. The default method is the fth-order
Runge-Kutta method.
92
Figure 5.3: The controls gure af

ter the software is initiated.
5.4
When this software is selected, 3 gures are displayed (in addition to MATLABs
command window): controls, parameters, stimulus. The controls gure controls
the software (Figure 5.3). The parameters gure allows the user to change any
of the parameters of the model. The stimulus gure allows the user to specify
the stimulus. Once the parameters and the stimulus are specied, selecting Start
simulation results in the computation of the response as a function of time. Upon
completion of the computation, the software is in the analysis mode to allow the
user to examine the results graphically and numerically.
5.4.1 Controls
The part of the controls gure (Figure 5.3) below the menubar is divided into six
panels. The left side of the top panel allows the user to choose the model.1 The
right side allows the user to choose between voltage-clamp and current-clamp
congurations. In the next panel down, the simulation is started by clicking
on the button Start simulation. The setup panel allows the user to select the
parameters gure (which is used to specify the parameters), the stimulus gure
(which is used to specify the stimulus as a function of time), the numerics gure
(which control the numerical methods and numerical parameters), and the block
diagram gure (which gives the user access to a block diagram of the system in
the SIMULINK language). The analysis panel becomes active after the simulation
is completed and allows the user to select three options for analysis of the results.
The rst option allows the user to plot any model variable as a function of time.
This gure is displayed automatically at the completion of a simulation. The
second option displays a numerical summary of simulation results. The third
option allows the user to access a quite general plotting facility that not only
plots any of the model variables versus any other model variable, but allows
plotting results stored in les. The message panel is used to send messages to
1
At the present time only the default HH model is available.
93

the user. The log panel contains options for recording log entries of the session
and is described in Chapter 1.
5.4.2 Setup
Parameters
Selecting parameters in the controls gure displays the Parameters gure (Fig
ure 5.4) which is used to view parameters and to change parameters.
Changing parameter values. The Parameters gure contains three columns for
each parameter: the rst column identies the parameter, the second gives its
default value, and the third column shows the value of the parameter if it is
modied from its default value. Clicking on the parameter name displays the
denition as well as the units of the parameter in the message panel. Parameters
are selected for modication by clicking the button in the third column of the
parameter eld. When a parameter is selected, its third column button will be
replaced by an edit box. Clicking any mouse button inside the edit box allows the
parameter to be changed. The new value of the parameter is entered from the
keyboard; < RETURN > terminates the parameter entry. If the new value differs
from the default value, then the new value will appear in the third column. With
this method of display, the parameter list can be scanned quickly to indicate
which parameters differ from their default values.
There are some restrictions on the numerical values of parameters; Gs 0,
94
Cm 0, cs > 0, Ks > 0, and the temperature must be above absolute zero. The
derived parameters cannot be changed but are derived from the other parameters
and are displayed for the convenience of the user. For example, the sodium
equilibrium potential VNa cannot be changed directly by the user, but changes
automatically when the sodium concentrations or temperature are changed.
Reading and saving parameters in les. Near the bottom of the parameters
gure there are options that allow parameters to be read from a le or saved to
a le.
Viewing the voltage dependent parameters. The Hodgkin-Huxley model con
tains several parameters that are instantaneous functions of the membrane po
tential. Plots of parameters are available as a function of Vm for the following:
m (Vm ), m (Vm ), m (Vm ), m (Vm ), h (Vm ), h (Vm ), h (Vm ), h (Vm ), n (Vm ),
n (Vm ), n (Vm ), n (Vm ). These can be accessed by clicking on Plot parame
ters versus voltage which displays a new gure (Figure 5.5). This gure makes
use of the graphics package described in Chapter 1 with a few differences that
are described here. Since the independent variable for these plots is the mem
brane potential, only the dependent variables can be chosen by clicking on select
y which displays the select y gure (Figure 5.6). The select y gure allows selec
tion of multiple dependent variables which determine the ordinates of the plot.
Identication. The lower right-hand corner of the parameters gure contains

room for a text string of the users choice. This is intended to identify the param
eters gure. The user might consider entering the date and time, a run number,
or other identication. Clicking in that area displays a text edit box into which
the user types the identication.
Stimulus
Selecting Stimulus in the controls gure displays the Stimulus gure as shown in
Figure 5.7. The stimulus is the membrane potential in the voltage-clamp cong
uration and the membrane current density in the current-clamp conguration.
Use of stimulus m-les. By default, the stimulus is generated by the MATLAB
m-le hhstim.m which uses the parameters listed in the lower part of the stim
ulus gure. This specication of the stimulus is quite rich, as will become clear
below. However, a user who wishes to dene a stimulus that differs from the one
provided can write a MATLAB m-le to generate that stimulus. That le can then
be selected in the stimulus gure, and the stimulus it generates will be displayed
95
Figure 5.5: The parameters versus membrane potential gure after selection of param
eters as in Figure 5.6.
Figure 5.6: The select y gure that was used

to produce the plot shown in Figure 5.5.
96
Figure 5.7: Stimulus gure with the default stimulus waveform for a current-clamp
conguration.
97
in the stimulus gure. The script for the available m-les can be used to dene
new user-specied m-les.
Use of the m-le hhstim.m The default m-le, hhstim.m, uses the numerical
parameters in the stimulus gure. The stimulus is the sum of a constant plus
two independently speciable pulses. Each pulse can be a rectangular pulse, a
ramp pulse or an exponential pulse or a combination of these. If the slope and
the time constant are set to zero, then the remaining parameters specify the
amplitude, duration and onset time of a rectangular pulse. If the slope has a
non-zero value, a ramp of that slope is added to the rectangular pulse for the
duration of the pulse. Similarly, if the time constant has a non-zero value, then
an exponential pulse with the selected time constant is added to the waveform.
The time constant can be positive or negative.
The stimulus, s(t), is dened as follows
s(t) = s o + s 1 (t) + s 2 (t),
(5.24)
where s o is a constant and s 1 (t) and s 2 (t) are independently speciable pulses.
Each pulse has the form
mi (t toi ) + Ai e(ttoi )/ i if to t to + tdur ,

i
s
(t) =
0
otherwise,
(5.25)
where pulse i (i = 1 or 2) starts at to and has a duration tdur . The amplitude of

the pulse is Ai , the slope is mi , and the time constant is i . With this specication,
a rich variety of stimuli can be produced; an example is shown in Figure 5.8.
The stimulus parameters can be read from or saved to a le by selecting the
appropriate button at the bottom of the stimulus gure.
Identication. The upper right-hand corner of the stimulus gure also contains
room for a text string of the users choice for identifying the stimulus. This works
identically to the identication of the parameters gure.
Numerics
Selecting Numerics in the controls gure displays the numerics gure (Figure 5.9).
This gure allows selection of the numerical method used to solve the ordinary
differential equations (or ode solver) as well as the numerical parameters of the
simulation. The dialog-box that appears at the top allows direct selection of
one of seven ode solvers: Euler, Third Order Runge-Kutta, Fifth Order RungeKutta, Adams, Gear, a hybrid Adams/Gear, Linsim. The MATLAB manuals or
MATLABs help facility should be consulted for further information about these
98
Figure 5.8: Example of a stimulus current waveform consisting of a constant plus two
pulses: the rst pulse is a ramp plus rectangular pulse; the second is an exponential
pulse.
Figure 5.9: The numerics g

ure.
99
methods. More detailed descriptions are available elsewhere (Shampine and Re

ichelt, 1997). By default, the software uses the fth-order Runge-Kutta method of
integration with a variable integration step size (t). The integration methods re
quire that the following parameters be dened: Minimum step-size, Maximum
step-size, Tolerance. The tolerance is an estimate of the accuracy of the so
lution, i.e., a tolerance of 0.001 implies that the error in the solution is less than
0.1% of the correct value. Decreasing the tolerance will increase the accuracy of
the solution, but will increase the computation time.
Block diagram
The Hodgkin-Huxley model is simulated in SIMULINK which is a block diagram
language addition to MATLAB. The model simulation consists of a nested set
of block diagrams.2 Although the software can be run without reference to the
block diagram, convenient access to the block diagram has been provided for
the interested user. Since the block diagrams are easily edited, the user has the
option of modifying many aspects of the model. However, modication of the
block diagrams should be done with some caution.
Selecting Block diagram in the controls gure results in the display of the
block diagram shown in Figure 5.10. Double clicking on the block labelled Cur
rent clamped displays a block diagram of this block as shown in Figure 5.11.
Each of the blocks in Figure 5.11 can be double-clicked and each of the resulting
block diagrams can also be revealed by double clicking. In addition, the controls,
parameters, and stimulus gures can be accessed from this block diagram by
double clicking on the appropriate block.
An example of customization of the software. A simple example of the usage

of SIMULINK to customize the software is described here. Suppose for a par
ticular investigation of the model, it is desirable to plot some variable (e.g., the
sodium conductance) in the Hodgkin-Huxley model as a function of time during
the simulation. This is easily done with SIMULINK. Double clicking on the G(V )
block in Figure 5.11 displays a block diagram of the conductance computation.
To obtain a plot of the sodium conductance during a computation, an oscillo
scope is attached to the sodium conductance. Typing simulink in the MATLAB
command window displays the SIMULINK elements (Figure 5.12). Double clicking
on sinks displays the sinks available in SIMULINK which includes an oscilloscope
or Scope (Figure 5.13). To attach the oscilloscope to the sodium conductance,
click on the oscilloscope and drag the oscilloscope to the appropriate place in
the block diagram and connect it to the sodium conductance by clicking and
2
It is important to keep in mind that the block diagrams in SIMULINK reect not just the ow
of signals in the Hodgkin-Huxley model, but some of the idiosyncratic properties of linking the
block diagram description to MATLAB.
100
Figure 5.10: The block diagram gure after the block diagram option is selected in the
controls gure. This block diagram is for the current-clamp conguration.
Figure 5.11: Expansion of the current clamped block in Figure 5.10.
101
Figure 5.12: The simulink

gure obtained by typing
simulink at the MATLAB
prompt.
Figure 5.13: The sink gure obtained after double clicking

on sinks in the simulink gure (Figure 5.12).
102
Figure 5.14: Block diagram with oscilloscope attached to the sodium conductance signal.
This block diagram is obtained by double clicking on the G(V ) block in Figure 5.11.
dragging between the terminals. This results in a new block diagram with the os
cilloscope attached as shown in Figure 5.14. Double clicking on the oscilloscope
displays the oscilloscope screen (Figure 5.15). The horizontal and vertical gains
must be specied by the user. Starting the simulation now displays the sodium
conductance on the oscilloscope screen as the computation proceeds.
5.4.3 Analysis
The software provides one numeric and two graphic displays of simulation re
sults. These three displays are selected and deselected in the controls gure.
Analysis is available after a simulation has been run if the parameters have not
been changed after the simulation was run.
Plots versus time

Selecting this item in the controls gure displays the plots versus time gure as
shown in Figure 5.16. This gure provides a simple and rapid means of plot
ting any of the simulation variables versus time on xed scales. The variable
is selected by clicking on the dropdown menu at the top of the gure and then
dragging the mouse to the variable of interest.
103
Figure 5.15: The oscilloscope screen showing

a plot of the sodium conductance which is dis
played as the computation proceeds.
Figure 5.16: The plot

versus time gure
with Vm chosen for
plotting.
104
Figure 5.17: The variable summary gure af

ter the simulation has been completed using
the default parameters for a current-clamp
conguration.
Variable summary
Selecting this item in the controls gure displays the variable summary gure
as shown in Figure 5.17. This gure contains four columns of text. The rst
column identies the simulation variable. The second contains the initial value of
the variable. The third and fourth columns contain the minimum and maximum
values of the variables during the course of the simulation.
Comparison
Selecting this item in the controls gure displays the comparison gure as shown
in Figure 5.18. This exible graphic resource is described more fully in Chapter 1.
Briey, this gure allows plotting any result of the simulation against any other
in coordinates chosen by the user. Several dependent variables can be plotted
simultaneously. In addition, results saved in les can be plotted so that results
for different parameters can be compared. In addition, results of consecutive
simulations can be overlayed. We give a few examples of the types of graphics
that are readily available with this resource.
As shown in Figure 5.19, parametric plots of one variable versus another with
time as the parameter are easily obtained. Figure 5.20 shows the membrane
potential obtained at several different temperatures. This gure was obtained by
overlaying successive computations. It could also have been created by saving
the results of simulations performed for different temperatures in les and then
plotting the results from these les.
105
Figure 5.18: Comparison gure showing the membrane potential and ionic conduc
tance obtained from a simulation with model parameters and the stimulus dened in
Figures 5.4 and 5.7.
106
Figure 5.19: Phase-plane plot of membrane conductances versus membrane potential

during an action potential. All the parameters were the default parameters shown in
Figure 5.4 and the stimulus was the same as shown in Figure 5.7 except that the duration
was increased to 20 ms.
107
Figure 5.20: Membrane potential obtained at different temperatures. All the parameters
were the default parameters shown in Figure 5.4 except for the temperature and the
stimulus was the same as shown in Figure 5.7.
108
5.4.4 Scripting
As mentioned in the Introductory chapter, some of the software packages lend
themselves to user written scripts that automate a sequence of computations.
The following is an example of a script used to perform current clamp simulations
at different temperatures.
%A Hodgkin-Huxley script demonstration
%(contents are in HHDEMO1.M)
%This script can be used to generate simulation data using the
%current-clamped configuration. The temperature is varied while
%all other parameters remain unchanged.
%With each setting of the temperature, the simulation is run
%and the resulting data are saved to data files which can then be
%used to display the results in the Comparison figure.
%Before using the script, make sure that the Hodgkin-Huxley
%biophysics software has been started.
%If it hasnt been started, start the software using SOFTCELL.M
%
softcell(hh);
%hhscr(set) will list the parameters that can be changed
%The parameter names are case-sensitive, so make sure that
%you type them exactly as shown.
%Insure that the current clamped configuration is being used.
hhscr(set,Configuration,Current clamped);
%Since a lot of files will be created, it is best to store
%them in a separate folder.
foldername = pwd;
%Examples of foldername are
%foldername = C:\data\temp;
%foldername = /user/tsb/data/temp;
%Make sure that a separator character ends the pathname
pathname = tfname(foldername);
%Set up a loop that samples through a temperature range.
%In this case, we use the range T = [0 10 20 30] Celsius
for temp = 0:10:30
5.5. PROBLEMS
109
%set the models temperature parameter
newtemp = hhscr(set,T_C,temp);
%perform simulation
hhscr(start);
%give yourself a note: indicate in the console what the
%settings are
disp([Temperature is set to num2str(newtemp)]);
%create a unique filename that contains the simulation data
filename = [temp num2str(temp) .mat];
%save the simulation data to the file

hhscr(save,simulation,filename,pathname);
end
%Thats it -- all the data have been saved.
%Now, put up all the data simultaneously by following these steps:
%1. call up the "Comparison plots" figure,
%2. insure that the "Use data files" radiobutton is on,
%3. using "Select x,y", select whichever variable(s) to plot,
%4. use "Graph x,y" in the "Comparison plots" figure to view all
%
the data.
5.5
Problems
Problem 5.1 Use the default parameters of the Hodgkin-Huxley model under
voltage-clamp conditions to complete the following problems. You may change
only the stimulus parameters.
a. The potassium conductance
i. Find the amplitude and duration of a rectangular pulse of membrane
potential such that the potassium conductance reaches its nal of
GK (Vm , ) = 9 0.2 mS/cm2 .
ii. What is the value of the time constant of n, n , during this pulse?
b. The sodium conductance
potential such that the peak sodium conductance is 15 0.2 mS/cm2 .
110

Make sure that the pulse duration is sufcient so that there is a peak
in the sodium conductance before the pulse terminates.
ii. What are the values of m and h at the time of the peak value of the
sodium conductance?
iii. Increase the amplitude of the pulse 20 mV from the value you found
above and determine the peak sodium conductance and the values of
m and h at the time of the peak value of the sodium conductance.
iv. Decrease the amplitude of the pulse 20 mV from the value you found
Problem 5.2 This problem deals with the differences in time dependence of the
[in]activation factors in voltage-clamp and current-clamp experiments.
a. Run the simulation in the voltage-clamp conguration using the default
parameters, except delay the onset of the pulse of voltage by 1 ms to make
the on and off transients more readily visible. Examine the results of the
simulation and answer the following questions.
i. Describe and explain the dependence on time of m , m , and m.
ii. Describe and explain the dependence on time of h , h , and h.
iii. Describe and explain the dependence on time of n , n , and n.
iv. Plot the voltage dependence of m , h , n , m , h , and n . Check the
numerical values of these variables against those obtained in parts i,
ii, and iv.
b. Run the simulation in the current-clamp conguration using the default
parameters. Examine the results of the simulation and answer the following
questions.
c. Succinctly summarize the differences in the time dependence of all these
variables in voltage-clamp and current-clamp congurations.
Problem 5.3 In this problem we illustrate another useful aspect of performing
simulation experiments on the model; the model can be used to test ideas con
cerning proposed measurements on cells.
Assume that the membrane of neuron X has voltage-current characteristics
as described by the Hodgkin-Huxley model except that the voltage dependences
5.5. PROBLEMS
111
of the parameters of the factors n, m, and h are unknown. In this problem you
are asked to develop methods to estimate the voltage dependence of some of
these parameters and to assess the accuracy of your methods. To make the sim
ulations realistic, in all parts of the problem you may only change the following
parameters: the concentrations of sodium, potassium, and calcium either inside
or outside the cell, and the temperature. You may use either voltage-clamp exper
iments or current clamp experiments. You can choose any stimulus waveform
that you can construct with the simulation. However, you must base your estima
tion method on the membrane current in voltage clamp experiments and/or on
the membrane potential in current-clamp experiments. For example, you cannot
base your estimation method on a direct measurement of m(t).
a. Develop a method to estimate the voltage dependence of m . Use the sim
ulation to assess the accuracy of your method by comparing the results of
your estimation of m with a direct computation of m .
b. Develop a method to estimate the voltage dependence of h . Use the sim
ulation to assess the accuracy of your method as in part a.
Problem 5.4 By changing the amplitude of the stimulus pulse, while keeping all
other parameters at their default values, determine the threshold of the action
potential to a precision of 4 signicant digits.
a. Describe the changes in action potential waveform as a function of current
amplitude.
b. Does the change in waveform of the action potential as a function of stim
ulus amplitude violate the all-or-none principal? Explain.
c. Investigate the basis of the change in waveform of the action potential by
examining the behavior of variables in addition to the membrane potential
as the current amplitude is varied.
Problem 5.5 Examine the refractory properties of the model by applying two
current pulses, each of amplitude 30 A/cm2 and duration 0.5 ms and separated
by 12 ms in time. Set the simulation duration to 20 ms. Run the simulation. You
should observe two action potentials. Reduce the inter-pulse interval to 10 ms.
What happens? Now change the amplitude of the second pulse to 50 A/cm2
and observe the response. Change the inter-pulse interval to 5 ms and observe
the outcome.
a. Have you observed properties of the absolute or the relative refractory pe
riod?
112
b. By examining the behavior of the factors m, n, and h during these twopulse simulations, determine which of these factors are most inuential in
refractory properties.
Problem 5.6 Observe the phenomena of repetitive activity and depolarization
block by performing a sequence of simulations with the following parameters.
Use a single current pulse of duration 40 ms, a simulation duration of 50 ms,
and stimulus amplitudes of 10, 25, 50, 100, and 200 A/cm2 .
a. Note that both the number of action potentials and their amplitudes vary
with the current amplitude. Sketch the relation between the number of
action potentials and current amplitude and between action potential am
plitude and current amplitude.
b. By examining the behavior of the factors m, n, and h determine which of
these factors are most inuential in determining repetitive activity. Explain
your reasoning.
Problem 5.7 The phenomenon of anode-break excitation can be demonstrated
by applying a pulse of current of duration 20 ms and amplitude 20 A/cm2 .
Use a simulation duration of 40 ms.
a. Why is this phenomenon called anode-break excitation?
b. By exploring the model variables explain this phenomenon.
Problem 5.8 The phenomenon of accommodation can be illustrated by applying
a ramp of current of slope 0.4 A/(cm2 ms) starting at an amplitude of 0 for a
duration of 6 seconds (also set the simulation duration to 6 seconds). The model
Na = 120 mS/cm2 but
does not show accommodation for the default value of G
2
does for a value of 80 mS/cm . When the simulation is completed, plot the
sodium, potassium and membrane current versus the membrane potential.
a. Perhaps no action potential has occurred in response to the ramp of cur
rent because the reduced value of the sodium conductance prevents action
potential from being generated for any stimulus. Test this hypothesis.
b. Explain the underlying basis of accommodation.
c. What does the phenomenon of accommodation suggest about the notion of
the threshold for eliciting an action potential?
Problem 5.9 Sub-threshold oscillations can be observed by using the default pa
rameters with current pulses of 50 ms duration and simulation durations of 100
ms. Use current amplitudes of .01, .1, 1, 2, and 2.5 A/cm2 .
5.5. PROBLEMS
113
a. Describe your observations.

b. Can the response of the model to a step of current be represented by the
response of a network consisting of a constant resistance in parallel with a
constant capacitance. Explain.
c. If your answer to part b was no, then devise a current stimulus such that
the models response will approximate that of a network consisting of a
constant resistance in parallel with a constant capacitance. Explain your
method.
Problem 5.10 Determine the threshold current amplitudes (to three signicant
gures) for eliciting action potentials for current pulses of duration 0.01, 0.05,
0.1, 0.5, 1, 2, 5, 10, and 20 ms.
a. How does the threshold depend on current duration for low durations?
Explain this behavior.
b. How does the threshold depend on current duration for long durations?
Problem 5.11 The Hodgkin-Huxley model with the default parameters stimu
lated by a pulse of membrane current of amplitude 20 A/cm2 and of duration
0.5 ms produces an action potential as shown in Figure 5.21. In each of the
following computations, one membrane parameter only differs from the default
parameters, and for each of these computations no action potential occurs. The
parameter changes are:
i. A change in the temperature from 6.3 C to 35 C blocks the action potential
as shown in Figure 5.21.
ii. A change in the maximum potassium conductance from 36 to 72 mS/cm2
blocks the action potential. [Results not shown.]
iii. A change in the internal calcium concentration from 0.0001 to 0.0002 mmole/l
iv. A change in the membrane capacitance from 1 F/cm2 to 20 F/cm2 blocks
the action potential as shown in Figure 5.21.
v. A change in the external calcium concentration from 44 mmole/l to 22
mmole/l blocks the action potential. [Results not shown.]
Examination of the results for the above computations (e.g., Figure 5.21) re
veals that there is no large change in membrane potential, i.e., no action potential
has occurred. For each of the computations:
114
Figure 5.21: Results of simulation with all model parameters at their default val
ues except where indicated. The curve labelled default was obtained with the de
fault parameters. The curve labeled temp35 was obtained with the temperature set
to 35 C. The curve labeled cm20 was obtained with the membrane capacitance set to
Cm = 20 F/cm2 .
5.6. PROJECTS
115
a. Explain why no action potential occurred. You may wish to base your ex
planation on the results obtained with each of the above computations. For
example, you may wish to examine the membrane currents, conductances,
and activation variables that occurred for each computation. You may also
wish to perform additional computations using different model parameters.
For example, to see why no action potential occurs for a large temperature
change, it might be instructive to examine the effects produced by smaller
changes in temperature. Since for many of the parts of this problem, there
are large changes in parameters you may wish to explore the role of the
numerical methods in arriving at the solutions.
b. Determine a set of parameters so as to produce an action potential with a
waveform that is identical, except for a change in time scale and a change
in resting potential, to the action potential obtained with the default pa
rameters. However, for each of the above parts, you may not change the
parameter that differs from its default value. For example, for computation
in part i, you may not change the temperature. Your task is to change some
other parameter or group of parameters such that the action potential is
restored. For computation in part ii, you may not change the maximum
potassium conductance. For computations in parts iii and v, you may not
change either the internal or the external calcium concentration, etc. RE
MEMBER the objective is not just to produce an action potential, that
is too easy, but to obtain an action potential whose waveform is identi
cal to that obtained with the default parameters. To determine whether
or not the action potential is identical to that obtained with the default
parameters, you can superimpose plots and/or look at the variables sum
mary gures from the responses. You should use the computer as a tool
to check your ideas and not as a substitute for thinking. You should avoid
a strictly trial-and-error approach. There are simply too many parameters
in the Hodgkin-Huxley model for you to explore them all randomly. When
you have arrived at a satisfactory solution, print a hard copy of the model
parameters gure showing the parameters you used to solve the problem
and include this with your solution. Explain why your parameter change
produces the desired result. [HINT: simulations are not required to solve
these problems, but they are helpful for checking ideas quickly.]
5.6
PROJECTS
The simulation software lends itself to more extensive study than that included
in the Problems. These more extensive studies are called Projects and these are
described here.
116
5.6.1 Practical considerations in the choice of a topic

Projects can involve almost any of the properties of the Hodgkin-Huxley model.
However, to avoid projects whose aims are vague (e.g., I would like to under
stand how the Hodgkin-Huxley model works) the proposed project should be in
the form of a specic and testable hypothesis. Projects that involve months of
computation should obviously be avoided. Experience should indicate the dura
tion required to run simulations of the Hodgkin-Huxley model. These durations
should be taken into account explicitly in planning a project. For example, any
project that involves measuring the threshold of occurrence of an action poten
tial for many different parameter values is bound to be very time consuming,
because determining the threshold for a single set of parameters itself involves
many computations. The task is to choose a physiological property of the ex
citation of the action potential that is of interest, and then to dene a specic,
feasible project.
5.6.2 Choice of topics

Topics can involve comparing predictions of the Hodgkin-Huxley model with
measurements on cells. For example, the effects of changes in sodium ion con
centration on the action potential have been measured (Hodgkin and Katz, 1949a;
Baker et al., 1961). A project might involve reading the original papers that de
scribe such measurements (some were made before the Hodgkin-Huxley model
was formulated), and testing the hypothesis that these measurements are (or
are not) consistent with the Hodgkin-Huxley model. Similarly, a project might in
volve examining the effect of some pharmacological substance on measurements
of the action potential and testing the hypothesis that the substance produces its
effect by changing one or another parameter of the model. These projects will re
quire some reading of original literature which is often difcult and usually time
consuming. However, such a project can lead to a very rewarding educational
experience. Alternatively, the project might involve a purely theoretical topic
in which some property of the model is explained in terms of the underlying
structure of the model. This type of project does not necessarily involve reading
the original literature. To make the process of project denition more tangible,
we shall discuss one property of the Hodgkin-Huxley model of a space-clamped
axon, the shape of the action potential, and suggest some appropriate projects
based on this property.
Background
The waveform of the action potential is different in different types of electricallyexcitable cells. As demonstrated in Figure 5.22, while the action potential wave
form has a peak-to-peak amplitude of about 100 mV, the duration and time course
vary greatly. It is also known that the action potential waveform of a cell can
5.6. PROJECTS
117
+50
+50
Squidgiant
axon
0
50
50
100
Membranepotential(mV)
Electriceel
electroplaque
100
0
+50
4
Time(ms)
+50
Cat
motoneuron
Frogsartorius
musclefiber
50
3
6
Time(ms)
50
100
100
0
Time(ms)
10
20
Time(ms)
30
+50
+50
Catmyelinated
fiber
50
-50
100
100
0
1
Time(ms)
Sheeppurkinje
fiber
0.5
1
Time(s)
1.5
Figure 5.22: Examples of action potentials measured in a variety of cell types (Keynes
and Aidley, 1991, adapted from Figure 2.4).
Vm(t) Vmo(mV)
118
100
20.2
3.6
32.5
50
6.3
9.8
13.3
0
0
1
2
Time(ms)
Membranepotential(mV)
Figure 5.23: Dependence of the action potential on temperature for measurements ob

tained from a giant axon of the squid (Hodgkin and Katz, 1949b).
40
1
3
-40
-80
0
2
Time(ms)
Figure 5.24: Effect of extracellular sodium concentration on the membrane potential of

a giant axon of a squid (Hodgkin and Katz, 1949a, adapted from Figure 4). Traces 1 and
3 are the action potentials obtained in normal sea water before and after trace 2 which
was obtained in sea water with 50% sodium content. Isotonic solutions were obtained
by using mixtures of sea water and a glucose solution.
be changed by changing a number of experimental variables. For example, in

creasing the temperature tends to decrease the duration of the action potential
(Figure 5.23), and reducing the external sodium concentration reduces the am
plitude and increases the duration of the action potential (Figure 5.24). Since
action-potential waveforms vary from cell to cell and vary for one cell if environ
mental variables are changed, this raises a question To what extent are changes
in action-potential waveforms seen in different cells due to inherent differences in
the membrane mechanisms rather than to differences in membrane parameters
with identical membrane mechanisms? For example, the action potentials of the
squid axon and the frog and rat nodes of Ranvier shown in Figure 5.22 were
measured at different temperatures. In fact, the briefest action potentials were
obtained at the highest temperatures. Since Figure 5.23 indicates that the dura
tion of the action potential does become shorter at higher temperatures in squid
axon, it may be that the temperature differences in the measurements could ex
plain the differences in the waveforms of the action potentials of these three
preparations. It is clear that temperature changes alone cannot explain all the
5.6. PROJECTS
119
variations seen in Figure 5.22 since the long-duration action potential of frog car
diac muscle was obtained at a higher temperature than was the action potential
of the squid giant axon. However, perhaps some combination of changes of pa
rameters in addition to temperature (e.g., ion concentrations, ion conductances,
membrane capacitance, etc.) might explain the long-duration action potential of
cardiac muscle.
The list of projects given below includes a number that deal with the waveform
of the action potential generated by the Hodgkin-Huxley model as well as a few
that deal with other topics.
1. Hypothesis The difference in waveform of the action potential of a frog
node of Ranvier and of a squid giant axon (Figure 5.22) can be reproduced by
the Hodgkin-Huxley model of a squid giant axon by a change in temperature.
2. Hypothesis The membrane capacitance determines the time course of the
rising phase of the action potential. Increasing the membrane capacitance
decreases the rate of increase of the rising phase of the action potential.
3. Hypothesis The falling phase of the action potential (repolarization) can
occur in the absence of a change in potassium conductance.
4. Hypothesis Increasing the temperature sufciently blocks the occurrence
of the action potential because the membrane time constant limits the rate
at which the membrane variables can change and prevents the difference in
time course of the sodium and potassium activation which is responsible
for initiation of the action potential.
5. Hypothesis The initiation of the action potential is independent of the
potassium conductance.
6. Hypothesis The prolonged plateau of the cardiac muscle action poten
tial can be accounted for by the Hodgkin-Huxley model with a potassium
conductance that has a slow activation.
7. Hypothesis The effect of tetraethylammonium chloride (TEA) on the ac
tion potential of the squid giant axon can be modelled with the HodgkinHuxley model by decreasing Kn and increasing Kh . Articles in the literature
should be consulted for this project (Armstrong, 1966; Armstrong and Binstock, 1965; Tasaki and Hagiwara, 1957).
8. Hypothesis The shape of the action potential in the presence of tetraethy
lammonium chloride (TEA) can be accounted for by the Hodgkin-Huxley
120

model with a reduced maximum value of the potassium conductance. Arti
cles in the literature should be consulted for this project (Armstrong, 1966;
Armstrong and Binstock, 1965; Tasaki and Hagiwara, 1957).
9. Hypothesis Increasing the external calcium concentration will block the

occurrence of the action potential because this will reduce the difference in
the time constant of sodium and potassium activation which is responsible
for the initiation of the action potential.
10. Hypothesis Increasing the external concentration of potassium will de
crease the refractory period; decreasing this concentration will lengthen the
refractory period.
11. Hypothesis Increasing the external concentration of sodium will decrease
the refractory period; decreasing this concentration will lengthen the refrac
tory period.
12. Hypothesis Absolute and relative refractory periods are decreased by
increasing the rate constants for sodium inactivation and for potassium
activation.
13. Hypothesis Repolarization cannot occur if the potassium activation rate
constant is zero.
14. Hypothesis The threshold of the action potential to a brief pulse of cur
rent decreases as the external potassium current is increased.
15. The Hodgkin-Huxley model with default parameters does not exhibit ac
commodation (Weiss, 1996b). Hypothesis Accommodation occurs if the
leakage conductance is increased.
16. The Hodgkin-Huxley model with default parameters does not exhibit ac
commodation (Weiss, 1996b). Hypothesis Accommodation occurs if the
potassium conductance is increased.
17. Hypothesis Increasing the leakage equilibrium potential will block the
action potential.
18. Hypothesis The effect of the changes in concentration of sodium ions on
the action potential of the giant axon of the squid can be accounted for by
the Hodgkin-Huxley model. Articles in the literature should be consulted
for this project (Hodgkin and Katz, 1949a; Baker et al., 1961).
19. Hypothesis In response to rectangular pulses of current, the rheobase of
the strength-duration relation increases as temperature increases.
20. Hypothesis An increase in temperature results in a decrease in the dura
tion of the refractory period.
5.6. PROJECTS
121
21. Hypothesis The threshold membrane potential at which the HodgkinHuxley model produces an action potential in response to a brief pulse
of current is equal to the membrane potential for which the linearized
Hodgkin-Huxley equations have unstable eigenvalues.
22. Application of a long-duration constant current to the Hodgkin-Huxley model
produces a train of action potentials. Hypothesis The frequency of the
action potentials increases with increasing current amplitude.
produces a train action potentials. Hypothesis The frequency of action
potential increases as the parameter Kn is increased.
produces a train action potentials. Hypothesis The frequency of action
potential increases as the temperature is increased.
25. Hypothesis An increase in the external concentration of potassium in
creases the threshold potential at which an action potential is elicited.
26. Hypothesis Increasing Kh will result in an increase in the steepness of
the repolarization phase of the action potential.
Any of these (or other) hypotheses can be the starting point for a project.
Most of the hypotheses given above are simplistic, and a careful investigation
will reveal their shortcomings. The Hodgkin-Huxley model is sufciently complex
that investigation of any of the hypotheses will most likely lead to unexpected
results. You should pursue these unexpected results and try to understand their
bases. For example, you may nd that in pursuing some hypothesis you choose
to change some parameter of the model that you expect to result in some change
in action potential waveform. The resulting computation might reveal, much to
your surprise and chagrin, that no action potential has occurred. Determine why
no action potential occurred. The explanation will usually be instructive. Your
aim should be not simply to reject or accept the hypothesis but to delve into the
topic in sufcient depth so as to a deepen your understanding of the model. One
outcome of the project might be to restate your original hypothesis in a new and
more sophisticated form.
Beginning with the proposal and extending through the project, you should
keep clearly in mind that you are not investigating nerve membrane. You are
investigating the Hodgkin-Huxley model for the membrane of the squid giant
axon. Your explanations of all phenomena must be in terms of the primitive
concepts of this model the ionic conductances, ionic concentrations, ionic
currents, the capacitance, and the variables m, n, and h. Explanations in terms
of molecular channel mechanisms or electrodiffusion of ions in the membrane or
ion pumps are irrelevant in so far as they are not contained in the Hodgkin-Huxley
model!
122
5.6.3 The proposal

The proposal should contain a brief statement of the hypothesis you propose to
test, as well as your proposed method of procedure. Include a list of the compu
tations you will perform and the measurements you plan to make. Indicate how
the measurements will be used to help you come to a conclusion. The proposal
should be written on one 8 1/2 11 sheet of paper. A sample proposal is shown
in Figure 5.25.
5.6.4 The computations

After carefully dening the computations needed to determine the validity of
your hypothesis, you should perform the necessary computations. You should
keep careful track of the computations you perform by entering relevant informa
tion in a notebook. The notebook should indicate the date of each computational
session as well as the identity of the computer you used (make and model). Keep
an accurate record of each computation so that you can reconstruct what you
did at a later date. Save your results in les. Make composite plots to summa
rize a series of measurements. For example, to show the effect on the action
potential of some parameter, plot the action potentials for selected values of the
parameter on one set of axes. Arrange you work so that you have time for some
nal computations after you begin writing the report. You may nd that new
questions will arise as you write the report. If you leave adequate time, you may
be able to resolve these questions.
5.6.5 The report

The report is an opportunity for you to work on your ability to express yourself
succinctly. Your report should contain text, gures, tables, etc. whatever you
need to make your point most effectively. Assume that the background of your
readers is that of the students and faculty in your class.
Your report should contain several sections.
Hypothesis
Briey restate your original hypothesis.
Rationale
Briey explain your approach to testing your hypothesis. In broad terms, explain
what you did to test your hypothesis and why you did it.
5.6. PROJECTS
123
PROPOSAL: HODGKIN-HUXLEY MODEL PROJECT

Name: Hy I.Q. Student
Email address: hiqstudent
Hypothesis: The difference in observed action potential shape between
the giant axon of the squid and the node of Ranvier of the rat is due to a
difference in temperature.
Background: The rate constants that determine the variables m, n, and
h in the Hodgkin-Huxley model increase as the temperature is increased.
Hence, I would expect that with increased temperature the time course of
the action potential would be briefer. The observed action potential of the
rat node of Ranvier measured at 37 C. is briefer than the action potential of
the squid giant axon measured at 16 C. Hence, I will determine whether this
difference in temperature is adequate to explain the difference in actionpotential waveform. In this study, I will assume that the Hodgkin-Huxley
model accounts for action potentials in both preparations. Since the intra
cellular and extracellular ionic concentrations of sodium, potassium and
calcium also differ in these two preparations, if time permits I will also
investigate the effect of this difference.
Procedure: I will obtain the intracellular and extracellular concentrations of
sodium and potassium ions for the rat node of Ranvier from the literature. I
will perform a series of simulation studies with a single pulse of membrane
current whose amplitude will be set at a constant suprathreshold value. I
propose the following series of simulations
#
Temp.
Ion Concentrations
16
default values for squid giant axon
37
16
values found for rat node
37
The waveforms of the action potentials obtained under the various condi
tions will be compared on the graphics display and the summary statistics
for each condition will be examined. If condition 4 yields an action poten
tial that resembles that which is measured on the rat node of Ranvier, then
the hypothesis will be supported by these calculations. If they differ, then
I will investigate the bases of the differences.
Figure 5.25: Sample proposal for a project.
124
Methods and procedures

In this section you should explain any methodological or procedural issues. For
example, if you measured the time of the peak of the action potential as a function
of some parameter, explain how you measured the time of the peak and how you
dened when an action potential occurred, i.e., how did you separate the action
potential from the local response.
Results
Describe your computational results and provide documentation such as that
shown in Figures 5.18-5.20, as well as summary plots and tables. This section
should be organized to lead the reader through a logical sequence of results that
terminates inexorably in a conclusion. Your objective is to construct an airtight
case for some conclusion whether or not it supports or rejects your original hy
pothesis. This is not the place to interpret or to discuss your results.
Conclusions and Discussion
State your conclusions concisely and point out how your results support your
conclusions. You might also suggest additional computations to further test
your hypothesis. Your conclusions and discussion should be focussed on the
relation between your results and your hypothesis.
Grade
Your grade on this report will be determined largely by the extent to which you
follow the above directions, avoid extraneous and irrelevant discussion, and ex
press your thoughts clearly.
Chapter 6
VOLTAGE-GATED ION CHANNELS
125
126
6.1
CHAPTER 6. VOLTAGE-GATED ION CHANNELS
Introduction
6.1.1 Historical background

Passive transport of ions through cellular membranes is mediated by membranebound channel proteins that form selectively permeable ion channels. Although
their existence was long suspected, the rst direct physiological evidence for
these channels became available in 1976 (Neher and Sakmann, 1976). Subse
quently, many different types of channels have been identied (Hille, 1992).
Channels can be categorized on the basis of the physical/chemical variable that
opens or gates the channel. For example, the channels that underlie the prop
erties of electrically excitable cells are gated by the membrane potential and are
called voltage-gated channels. These channels are opened by a change in mem
brane potential. Other channels are gated by the binding of specic chemical
substances, mechanical deformation of the membrane, etc. In all of these cases,
the channels behave as if they have a discrete number of states, of which a few
(usually only one) are conducting or open states and the others (usually more
than one) are non-conducting or closed states. The channel switches rapidly and
randomly among its allowable states, and the probability that a transition occurs
at a particular time depends on the value of the gating variable.
Models of the gating of single ion channels were developed almost immedi
ately after single-channel data were obtained (Colquhoun and Hawkes, 1977).
Descriptions of these models can be found elsewhere (Colquhoun and Hawkes,
1995a; Weiss, 1996b).

This software package enables users to enhance their understanding of models
of the gating of single voltage-gated ion channels. The software allows the user
to design a channel by choosing the number of states, the voltage dependence
of transitions between states, the conductance and gating charge of each state,
and the equilibrium potential for the channel. After the channel is designed, the
user can analyze the behavior of the channel to a change in membrane potential.
Any of the variables associated with the channel can be displayed including the
state occupancy probability, conductance, ionic current, gating charge, and gating
current. Both random variables and their expected values can be displayed as a
function of time. The software is sufciently powerful and exible to allow users
to synthesize realistic, state-of-the-art models for the gating of voltage-gated ion
channels.
6.2
127
A brief description of the channel model is given here; a more complete descrip
tion is given elsewhere (Weiss, 1996b). We assume that a channel has N states
and that at each instant in time t, the channel is found in one of its states (Fig
ure 6.1). The states are enumerated as {S1 , S2 , S3 , . . . SN }. Each state has state at-
S1
1 , Q1
12
21
15
S2
2 , Q2
23
32
51
S3
3 , Q3
45
34
43
S4
4 , Q4
54
S5
5 , Q5
Figure 6.1: Kinetic diagram of a channel that has 5 states. The states are shown linked
by rate constants for transitions between states, where ij is the rate of transition from
state i to state j. When the channel is in state j the conductance of the channel is j
and the gating charge of the channel is Qj .
tributes: the state conductance and the state gating charge. The state attributes
for these states are denoted as {1 , 2 , 3 , . . . N } for the state conductances and
{Q1 , Q2 , Q3 , . . . QN } for the state gating charges. Given the membrane potential Vm
and the equilibrium potential Veq , the state ionic currents are {I1 , I2 , I3 , . . . IN }.
Thus, when the channel is in state Sj , the state conductance is j , the state ionic
current is Ij = j (Vm Veq ), and the state gating charge is Qj . Gating currents
occur at the transitions of the gating charge.
The temporal evolution of the electrical properties of a channel depend upon
the state occupancy probabilities which we discuss briey. Dene the probability
that the channel is in state j at time t as xj (t), and the transition probability that
the channel is in state j at time t + t given that it was in state i at time t as
yij (t + t). The fundamental assumption of the model for state transitions is
that the transition probabilities depend on the present state of the channel and
not on previous states. Such a probabilistic process is called a Markov process.
Formally, we assume that
yij (t + t) = ij t + o(t) ,
where o(t) has the property that limt0 o(t)/t = 0 and ij is a rate con
stant for transitions from state i to state j. The rst term is the probability of
128
occurrence of a single transition in the interval of duration t when this interval

is short and the rate of transitions is ij . The second term takes into account the
probability of the occurrence of multiple transitions in the interval. For intervals
t that are sufciently small so that no more than one transition is likely to oc
cur in the interval, the o(t) term is negligible; we will ignore this term in the
development that follows. The probability that the channel is in state j at time
t + t and in state i at time t is yij (t + t)xi (t) ij xi t.
The increase in probability that the channel is in state j in the time interval
(t, t + t) is xj (t + t) xj (t). In this time interval, this probability increases
as a result of transitions from states i into state j and decreases as a result of
transitions from state j into state i. By collecting all such terms we obtain,
xj (t + t) xj (t)
ij xi (t)t
i=1,i=j
ji xk (t)t ,
i=1,i=j
where the rst summation is due to transitions into state j and the second summation is due to transitions out of state j . If we rearrange the terms and take
the limit as t 0, we obtain the differential equation
N
N
dxj (t)
ij xi (t)
ji xj (t).
=
dt
i=1,i=j
i=1,i=j
This equation can be written in matrix form by

probabilities to be
11 12
21 22
=
N1 N 2
(6.1)
dening the matrix of transition
1N
2N
.
NN
where ij is the transition rate from state i to state j when i = j, and ii is

N
chosen so that i=1 ij = 0. The state occupancy probability satises the matrix
differential equation
dx(t)
= x(t),
(6.2)
dt
where x(t) is a row matrix of state occupancy probabilities. In addition, since
the channel is in one of its N states at each instant in time,
N
xj (t) = 1 .
j=1
The equilibrium state occupancy probability can be obtained directly from Equa
tion 6.2 by setting dx(t)/dt = 0 to yield
0 = x(),
(6.3)
129
to obtain the equilibrium state occupancy probability x().

If the matrix is constant, then the solution to the matrix equation for the
state occupancy probability is (Colquhoun and Hawkes, 1995a)
x(t) = x(0)et ,
where x(0) is the matrix of the initial value of x(t). Evaluation of the exponential
matrix yields the result
N
x(t) = x(0)
S j ej t ,
(6.4)
j=1
where j is the jth eigenvalue of and S j is the jth spectral matrix of . Therefore,
we see that the state occupancy probabilities are weighted sums of exponentials
whose exponents are the eigenvalues of the transition rate matrix. Because the
matrix is singular, one eigenvalue has value zero. All other eigenvalues have
negative real parts (Cox and Miller, 1965). Thus, the non-zero eigenvalues lead
to solution exponentials that decay with time.
For a voltage-gated channel, the transition rates depend explicitly on the mem
brane potential which in turn may vary with time. If the rate constants are
assumed to satisfy the theory of absolute reaction rates (Weiss, 1996a; Weiss,
1996b), then they depend exponentially on the membrane potential,
Aij eaij Vm if i j,
ij (Vm ) =
0
if i = j,
where Aij is a rate factor and aij is an exponential factor. ij (Vm ) depends on
the membrane potential which in turn depends upon time. Therefore, the rate
constants will in general depend upon time.
During intervals of time when the membrane potential is a constant, Equa
tion 6.2 is a linear, rst-order matrix differential equation with constant coef
cients. The solution determines the state occupancy probabilities, the {xj (t)}s.
The expected values of the channel conductance, channel current, and gating
charge are computed directly from the state occupancy probabilities. If the con
ductance of the channel is j when the channel is in state j, then the expected
value of the conductance of the channel, g(t), is
g(t) =
j xj (t).
(6.5)
j=1
If we assume that the current through the channel when the channel is in state j
is j (Vm Veq ), the expected value of the single-channel current, i(t), is
i(t) =
j=1
j xj (t)(Vm Veq ) = g(t)(Vm Veq ).
(6.6)
130
Similarly, if the gating charge of the channel when the channel is in state j is Qj ,
the expected value of the single-channel gating charge, qg (t), is
qg (t) =
Qj xj (t).
(6.7)
j=1
The expected value of the single-channel gating current, ig (t), is

ig (t) =
6.3
dqg (t)
.
dt
(6.8)
Numerical Methods
6.3.1 Integration step

The differential equation for the state occupancy probability (Equation 6.2) is
solved numerically using methods described elsewhere (Colquhoun and Hawkes,
1995b). The accuracy and efciency of the numerical solution depends upon the
value of the integration step, t. The value of t needs to be chosen small enough
so that the time rate of change in the occupancy probabilities can be resolved ac
curately and so that the random variables are represented accurately. The choice
of an adequate value of t depends upon the eigenvalues of the state transi
tion rate matrix. Typically, t should be chosen so that t 1/|max |, where
max is the eigenvalue with the largest magnitude. The smaller t is chosen
the more accurate the integration in any one step, but the longer the computa
tion will take. In addition, long computations can result in the accumulation of
round-off errors. Thus, the choice of t is a compromise between the speed and
accuracy of the simulation. Solution of the matrix equation (Equation 6.4) deter
mines the occupancy probabilities of each state. From these probabilities, the
expected values of the conductances, currents and gating charge are computed
using Equations 6.5-6.8.
Random variables are computed from state transition probabilities. Transi
tions probabilities from state i to state j are computed from the relation yij (t +
t) ij t at each instant in time. The time interval for computing random
variables is set equal to the integration step t. The occurrence of a transition
is determined by a random number generator. The sequence of state transi
tions determines the sequence of conductance values and gating charges since
each state has a unique conductance and gating charge. The conductance values
determines the current since this current is determined by specifying the con
ductance, the membrane potential, and the channel equilibrium potential. The
gating current random variable is represented by impulses at the times of tran
sition of the gating charge and whose areas equal the discontinuities in gating
charge.
6.4. USERS GUIDE
131
0.2
(t)
0.1
Figure 6.2: The probability of occurrence of

more than 1 event in an interval t where
the rate of events is and the events are dis
tributed according to a Poisson distribution.
0.05
0.02
0.01
0.005
0.1
0.2
0.5
In order to accurately represent the random variables, the time interval must
be chosen sufciently brief that the probability of occurrence of more than 1
change in state in the interval is negligible. The probability of occurrence of k
events in an interval t with an average rate of events of is given by the Poisson
distribution
(t)k t
Pr(k, t) =
.
(6.9)
e
k!
Hence, the probability of occurrence of more than 1 event in an interval is
(t) = 1 Pr(0, t) Pr(1, t) = 1 (1 + t)et .
(6.10)
The probability of more than one event in an interval (t) is shown plotted
versus t in Figure 6.2. Note that for t 0.2, (t) 0.018.
6.3.2 Initial conditions

In order to obtain a solution to Equation 6.2, initial conditions must be specied.
There are several plausible choices for the initial conditions, i.e., the initial states
of the channel. One choice is simply to specify the initial state deterministically.
A second choice is to choose the most probable state as the initial state. The
most probable state can be obtained by solving Equation 6.3 and choosing the
initial state as the one with the highest probability. A third choice is to choose
the initial state probabilistically according to the equilibrium probability for state
occupancy as determined by Equation 6.3. All three choices are implemented in
the software.
6.4
When this package is selected, 2 gures are displayed (in addition to MATLABs
command window): controls and channel parameters. The controls gure con
trols the software (Figure 6.3). The channel parameters gure allows the user to
design a single channel. Once the channel is designed, the membrane potential is
specied as a function of time, and the numerical variables chosen, the software
allows the user to analyze the statistical properties of the channel variables as a
function of time.
132

6.4.1 Controls
The portion of the controls gure (Figure 6.3) below the menubar is divided into
ve panels. The setup panel allows the user to select the channel parameters
gure (which is used to design the channel), the membrane potential gure (which
is used to specify the membrane potential as a function of time), and the numerics
gure (which is used to specify the initial conditions and the integration step
of the solution). A panel just below the setup panel controls the simulation.
The simulation can be started, stopped, paused, or continued. The analysis panel
allows display of a variety of the results of a simulation. The log panel contains
options for recording log entries of the session and is described in Chapter 1.
This message panel is used to send messages to the user.
6.4.2 Channel parameters

After the program is initiated, the channel parameters gure displays the default
channel kinetic diagram as shown in Figure 6.4. In general, the user constructs
a channel model by editing the default channel model. Editing entails adding
new states, adding or modifying rate constants that link the states, assigning
ionic conductances and gating charges to states, and assigning an equilibrium
potential to the channel model.
Each box in the channel parameters gure (Figure 6.4) represents a particular
state of the channel and is given a number from 1 to 8 (a maximum of 8 states
is possible). The arrows connecting these states depict the transition rates be
tween states. Each box also contains the ionic conductance of the channel when
the channel is in that state; the ionic conductance can be changed by clicking on
its value and typing the new value into the edit box. The ionic conductance is
expressed in picosiemens (pS). A value of zero denotes a non-conducting state.
Each box also contains the gating charge valence z of the channel when the chan
nel is in that state; the gating charge valence can be changed by clicking on its
6.4. USERS GUIDE
133
Figure 6.4: The channel parameters gure. The rate constant 12 has already been
dened and is displayed in the message panel at the bottom of the gure.
134
Figure 6.5:
Appearance of
the display after the user has
clicked on the forward rate con
stant in Figure 6.4 and changed
the parameters of the the rate
constant.
value and typing the new value into the edit box. The gating charge valence
can be positive or negative and need not be an integer. The gating charge is ze,
where e = 1.602 1019 C. The value of the channel equilibrium potential can be
changed by clicking in the text edit box at the bottom of the channel parameters
gure and typing the new value.
Add new state
A new state can be added to the diagram by clicking on Add New State. A new
state will be created and positioned in the upper left corner of the eld. A new
state or any existing state can be repositioned in the window by clicking on the
grey region at the top of the state boxes and dragging the state box to a new
position. To delete a state the user clicks on the red delete box in the upper
left-hand portion of the state box.
Add rate constant
Rate constants are dened in the rate constant gure. Two cases arise both of
which result in the display of the rate constant gure: (1) the user wishes to
modify an existing rate constant and (2) the user wishes to dene a new rate
constant linking two states. To modify an existing rate constant the user simply
points to the desired rate constant arrow between two states and clicks the mouse
to obtain the rate constant gure (Figure 6.5). To add a rate constant linking state
6.4. USERS GUIDE
135
Figure 6.6: View rate con

stant gure after both the for
ward (12 ) and reverse (21 )
rate constants have been de
ned.
In this simulation,
12 = 2.5e0.01Vm (1/ms) and
21 = 3e0.04Vm (1/ms), where
Vm is in mV.
i to state j, the user rst clicks on Add Rate Constant, then clicks in the state
box for state i, and then clicks in the state box for state j. During this operation,
the cursor becomes a +. The rate constant gure is displayed either when a
rate constant is added or when an existing rate constant is selected. To modify
the voltage dependence of the rate constant, the user can either type numerical
values into the text edit boxes in the lower left-hand corner of the rate-constant
window or use the mouse to enter the voltage dependence of the rate constant
graphically. Clicking on two locations in the plot of rate constant versus potential
puts an exponential function through those two points. The parameters of this
exponential function of membrane potential are displayed in the text edit boxes.
Clicking on Update Rate Constant sets the voltage dependence of the selected
rate constant which is then displayed in the message window at the bottom of
the channel parameters gure (Figure 6.4). To view the voltage dependence of
several rate constants, choose View Rate Constants. A gure is displayed which
allows rate constants to be plotted (Figure 6.6). Clicking and dragging on any of
the menu items allows the rate constant to be selected.
Miscellaneous features
If Reset Diagram is selected the current channel kinetic diagram is erased and
the default channel kinetic diagram is drawn. A previously stored diagram can
be retrieved by selecting Get an old diagram. The current diagram can be saved
to a le by selecting Save this diagram.
136
Figure 6.7: Membrane potential

gure after selection of a pulse
of potential.
Figure 6.8: Numerics gure appropriate for rate constants shown in Figure 6.6 and
membrane potential shown in Figure 6.7.
6.4.3 Membrane potential

Selection of Membrane Potential in the controls gure displays the membrane
potential gure (Figure 6.7). The membrane potential can be a rectangular pulse
of potential superimposed on a steady holding potential. The user can select the
holding potential, the duration of the stimulus, the onset time of the pulse starts,
the pulse duration, and pulse amplitude.
6.4.4 Numerics
The numerics gure (Figure 6.8) controls the choice of the integration step and
initial conditions for the simulation. The gure consists of four panels. The two
upper panels deal with integration steps for the two allowable membrane poten
6.4. USERS GUIDE
137
tial levels. The next panel down deals with choice of initial conditions (initial
states). The nal panel is a message window that includes an estimate of the
time it will take to complete the simulation for the chosen parameters.
Integration step
For a given choice of membrane potential and voltage-dependent rate constants,
the software computes the eigenvalues of the transition rate matrix and displays
these results to the user. The smallest time constant is computed from the fastest
eigenvalue and the user can choose, by editing the text edit box, to make the
integration step a fraction (or a multiple) of this smallest time constant. Alter
natively, the user can choose a xed integration time. The integration time that
results from the users choice is displayed as is the probability of more than one
transition during an interval of time that equals the integration step.
Initial state
The initial state for a simulation can be chosen deterministically to be any of
the allowable states or the most probable state for the given initial values of the
membrane potential. By default, the initial state is chosen probabilistically by
computing the state occupancy probabilities for the chosen initial value of the
membrane potential and choosing the initial state randomly using these proba
bilities.
6.4.5 Analysis
Clicking on the analysis panel of the controls gure allows access to a variety of
displays of simulation results including such variables as: the state occupancy,
the state occupancy probability, the ionic conductance, the ionic current, the
gating charge, and the gating current. Both the random variables and their ex
pected values can be displayed. Ten channels with similar characteristics can
be examined simultaneously to allow users to relate macroscopic to microscopic
variables. Results of multiple simulations can also be plotted on a single set of
axes for the sake of direct comparison.
Three different types of graphs are available. The rst type allows plotting a
single variable as a function of time in xed coordinates. An example is the state
occupancy gure shown in Figure 6.9. The top panel shows the simulation for 10
independent channels, the middle panel shows the results for channel 1 alone,
and the bottom panel shows the state occupancy probabilities for both states of
the channel. A second example of this type of graph is the ionic current shown in
Figure 6.10. Both the ionic current random variable and its expected value have
been selected for plotting. In addition, the average ionic current of 10 identically
distributed but statistically independent channels can also be displayed. Similar
138
Figure 6.9: State occupancy gure with all variables selected for display.
6.4. USERS GUIDE
139
Figure 6.10: Single channel ionic current showing the relation between the random
variable and its expected value.
plots are available for the ionic conductance, gating charge, and gating current.
These displays are helpful for relating macroscopic to microscopic variables and
random variables to their expected values.
A second type of graph is the summary graph which allows comparison of
the time dependence of channel variables to each other in xed coordinates (Fig
ure 6.11). Most of the variables are self-evident from the display. However, the
representation of the gating current random variable requires some comment.
The gating charge random variable is a random rectangular wave. Hence, the
gating current random variable, which is dened as the derivative of the gating
charge random variable, is a random impulse train (train of Dirac delta functions).
We represent these impulses with lollipops. The time of occurrence of a lollipop
equals the time of occurrence of an impulse and the height of the lollipop equals
the area of the impulse. On the scale of visibility of the gating current random
variable, the expected value is often too small to see. Hence, in the plot of the
gating current, deselecting the random variable will allow its expected value to
be observed. Clicking on the radio button for Cross line displays a vertical line
that tracks the position of the mouse cursor. The values of the intersection of
the line with each variable is displayed.
The third type of graph allows comparison of results obtained in different
simulations in coordinates dened by the user. Clicking on Comparisons in the
control gure displays the comparisons gure (Figure 6.12). This gure makes
140
Figure 6.11: Summary gure with all variables selected for display.
6.4. USERS GUIDE
141
Figure 6.12: Comparison gure showing the expected value of the ionic current and of
the gating charge for the channel dened in Figures 6.4-6.7.
142
use of the graphics package described in detail in Chapter 1.
6.5
Problems
Problem 6.1 This problem deals with a channel that has one two-state gate (which
we refer to as a two-state channel) whose rate constants are not a function of
membrane potential; this channel is not voltage-gated. Dene a two-state chan
nel for which state 1 is closed (nonconducting) and state 2 is open (conducting),
12
1
2 .
21
Use rate constants that are constant (independent of membrane potential). In all
parts of this problem use rate constants such that 12 + 21 = 10 ms1 .
a. Determine opening and closing rate constants such that the channel is
equally likely to be in state 1 or state 2.
b. Determine opening and closing rate constants such that the channel is three
times as likely to be in state 2 than in state 1.
c. Use the same rate constants as in part b. Set the membrane potential so
that it is 50 mV for t < 0.5 ms and +50 mV for t > 0.5 ms. The objective
of this part is to design a channel that has a single-channel current when
the channel is open (I ) of 1.2 pA when the membrane potential is 50 mV
and +0.8 pA when it is +50 mV.
i. Determine the equilibrium potential and single-channel conductance
when the channel is open (). Check your answer by running the simu
lation using the values of the equilibrium potential and single-channel
conductance you determined.
ii. What is the average single-channel current (i) for t < 0.5 ms? What is
the average single-channel current for t > 0.5 ms?
Problem 6.2 This problem deals with a two-state channel whose rate constants
are functions of membrane potential; the channel is voltage-gated. Dene a twostate channel for which state 1 is closed (nonconducting) and state 2 is open
(conducting),
12
1
2 .
21
Set the membrane potential to 60 mV for t < 0.2 ms and to +40 mV for t > 0.2
ms.
a. Determine voltage-dependent rate constants such that: the channel is closed
(with probability > 0.8) for t < 0.2 ms; the channel is open (with probability
> 0.8) for t 0.2 ms; and the channel opens with a time constant of about
0.2 ms.
6.5. PROBLEMS
143
b. Determine parameters of the channel such that when the channel is open,
the single-channel current (I ) is +0.5 pA at a membrane potential of +40
mV and is zero when the membrane potential is 10 mV.
c. Is this an activation gate or an inactivation gate?
d. Change the equilibrium potential to 70 mV. Repeat the simulation. Could
this channel describe the kinetics of the potassium channel in the HodgkinHuxley model? In what ways does it resemble the potassium channel? In
what ways does it differ from the potassium channel?
e. Change the equilibrium potential to +50 mV. Repeat the simulation.
i. Is the average channel conductance a continuous function of time?
Explain!
ii. Is the average channel current a continuous function of time? Explain!
iii. Could this channel describe the kinetics of the sodium channel in the
Hodgkin-Huxley model? In what ways does it resemble the sodium
channel? In what ways does it differ from the sodium channel?
Problem 6.3 In this problem you will investigate two channels that each have
two states with the same kinetic diagram, namely
12
1
2 ,
21
where the rate constants are

12 = 4e0.04Vm and 21 = 2e0.01Vm .
Each channel is subject to a membrane potential prole that is 60 mV from
t = 0 to t = 1 ms after which the membrane potential is +10 mV for 2 ms. The
equilibrium potential for each channel is +40 mV. The channels differ only in
the conductance assigned to each state. Channel 2 has 1 = 0 and 2 = 20 pS;
Channel 2 has 1 = 20 pS and 2 = 0.
a. Which channel opens in response to a depolarization? Explain.
b. Which channel closes in response to a depolarization? Explain.
c. Does the time-dependence of the probability that the channel is in state 1
differ for these two channels? Explain.
Problem 6.4 This problem deals with a three-state channel whose rate constants
are not a function of membrane potential; this channel is not voltage-gated. De
ne a three-state channel with the following kinetic scheme
12
23
21
32
1
2
3 ,
144
where states 1 and 2 are closed and state 3 is open. In all parts of this prob
lem, make the rate constants independent of membrane potential, and use rate
constants in the range 0.1-10 ms1 .
a. Determine a set of rate constants such that the channel is equally likely to
be in any one of its three states.
b. Try a set of rate constants such that ij = ji . What are the probabilities
of occupying each state? Try another such set having this property. What
are the probabilities of occupying each state with this new set? What can
you conclude about this case?
c. Determine a set of rate constants such that the probabilities that the channel
is in states 1:2:3 are approximately 0:0.5:0.5.
d. Determine a set of rate constants such that the probabilities that the channel
is in states 1:2:3 are approximately 0:0.25:0.75.
e. Determine a set of rate constants such that the probabilities that the channel
is in states 1:2:3 are approximately 0.2:0.3:0.5.
Problem 6.5 In this problem you will examine the properties of voltage-gated
channels with two, three, and four states. Assume that the equilibrium potential
of each channel is 40 mV and that the membrane potential starts at 60 mV and
switches to +10 mV at 1 ms and is maintained at this value for 2 ms. The three
channels are dened as follows:
The two-state voltage-gated channel has a kinetic diagram
12
1 2,
21

12 = 4e0.04Vm and 21 = 2e0.01Vm .
The three-state voltage-gated channel has a kinetic diagram
12
23
21
32
1 2
3 ,
12 = 23 = 4e0.04Vm and 21 = 32 = 2e0.01Vm .
The four-state voltage-gated channel has a kinetic diagram
12
23
34
21
32
43
1 2
3
4 ,
12 = 23 = 34 = 4e0.04Vm and 21 = 32 = 43 = 2e0.01Vm .
6.5. PROBLEMS
145
In exploring the following issues, it is instructive to examine graphs that show

the membrane potential as well as both the random variables and mean values or
probabilities associated with the record of state occupancies, the conductance,
and the current through the channel.
a. For each of the channels, make the last state (the state with the highest
state number) the conducting state with a conductance of 20 pS and make
all other states non-conducting. Compare the mean conductance of the twostate, the three-state, and the four-state channels. What can you say about
the effect on channel conductance of increasing the number of closed states
that precede the open state?
b. Now consider the four-state channel. Compute the mean conductance when
state 1 has a conductance of 20 pS and all other states are nonconducting.
Repeat this computation except make state 2 the conducting state with all
others nonconducting. Repeat again with state 3 and then state 4. Com
pare the mean conductance for these four conditions. Which of these con
ductances most closely resembles the sodium conductance of squid axon?
Explain.
Problem 6.6 Design a three-state channel that activates and then inactivates. The
channel activates at about 0 mV at a rate that is three times as fast as it inactivates.
a. Consider a channel that must open before it inactivates, e.g.
12
23
21
32
1 2
3 ,
where both states 1 and 3 are closed and state 2 is open.
b. Consider a channel that need not open before it inactivates.
146
Bibliography
Aidley, D. J. (1989). The Physiology of Excitable Cells. Cambridge University

Press, Cambridge, Great Britain.
Armstrong, C. M. (1966). Time course of tea+ -induced anomalous rectication
in squid giant axons. J. Gen. Physiol., 50:491503.
Armstrong, C. M. and Binstock, L. (1965). Anomalous rectication in the squid
giant axon injected with tetraethylammonium chloride. J. Gen. Physiol., 48:859
872.
Athena (1990a). Computation and Educational Community: A Background Pa
per. Committee on Academic Computation for the 1990s and Beyond, Mas
sachusetts Institute of Technology.
Athena (1990b). Computing for Education at MIT: Final Report. Committee on
Academic Computation for the 1990s and Beyond, Massachusetts Institute of
Technology.
Baker, P. F., Hodgkin, A. L., and Shaw, T. I. (1961). Replacement of the protoplasm
of a giant nerve bre with articial solutions. Nature, 190:885887.
Balestri, D. (1988). Ivory towers, silicon basements. Infor. Tech. Quaterly, 7:517.
Berkenblit, S. I. (1990). Design of a software diffusion simulator and analysis of a
problem in two-compartment diffusion. Masters thesis, Massachusetts Institute
of Technology, Cambridge, MA.
Carruthers, A. (1984). Sugar transport in animal cells: The passive hexose trans
fer system. Prog. Biophys. Mol. Biol., 43:3369.
Colquhoun, D. and Hawkes, A. G. (1977). Relaxation and uctuations of mem
brane currents that ow through drug-operated channels. Proc. R. Soc. London,
Ser. B, 199:231262.
Colquhoun, D. and Hawkes, A. G. (1995a). The principles of the stochastic in
terpretation of ion-channel mechanisms. In Sakmann, B. and Neher, E., editors,
Single-Channel Recording, pages 397482. Plenum Press, New York, NY.
147
148
BIBLIOGRAPHY
Colquhoun, D. and Hawkes, A. G. (1995b). A Q-matrix cookbook. How to write

only one program to calculate the single-channel and macroscopic predictions
for any kinetic mechanism. In Sakmann, B. and Neher, E., editors, Single-Channel
Recording, pages 589633. Plenum Press, New York, NY.
Cox, D. R. and Miller, H. D. (1965). The Theory of Stochastic Processes. John Wiley
and Sons, New York, NY.
Einstein, A. (1906). Sur theorie der brownschen bewegung. Ann. Physik, 19:371
381. [For translation see Einstein (1956)].
Einstein, A. (1956). Investigations on the Theory of the Brownian Movement.
Dover Publications. R. Furthe and A. D. Cowper, eds. [Translation of original
publications].
Fick, A. (1855). On liquid diffusion. Philos. Mag., 10:3039.
Frankenhaeuser, B. and Hodgkin, A. L. (1957). The action of calcium on the
electrical properties of squid axons. J. Physiol., 137:218244.
Gerald, C. F. and Wheatley, P. O. (1989). Applied Numerical Analysis. AddisonWesley, Reading, MA.
Hanselman and Littleeld (1996). Mastering MATLAB. Prentice-Hall, Englewood
Hills, NJ.
Hille, B. (1992). Ionic Channels of Excitable Membranes. Sinauer Associates Inc.,
Sunderland, MA.
Hodgkin, A. L. (1964). The Conduction of the Nervous Impulse. Charles C.
Thomas, Springeld, IL.
Hodgkin, A. L. and Huxley, A. F. (1952). A quantitative description of membrane
current and its application to conduction and excitation in nerve. J. Physiol.,
117:500544.
Hodgkin, A. L. and Katz, B. (1949a). The effect of sodium ions on the electrical
activity of the giant axon of the squid. J. Physiol., 108:3777.
Hodgkin, A. L. and Katz, B. (1949b). The effect of temperature on the electrical
Huxley, A. F. (1959). Ion movements during nerve activity. Ann. N.Y. Acad. Sci.,
81:221246.
Johnston, D. and Wu, S. M. S. (1995). Foundations of Cellular Neurophysiology.
MIT Press, Cambridge, MA.
BIBLIOGRAPHY
149
Kandel, E. R., Schwartz, J. H., and Jessell, T. M. (1991). Principles of Neural

Science. Elsevier, New York, NY.
Katz, B. (1966). Nerve, Muscle and Synapse. McGraw-Hill Inc., New York, NY.
Keynes, R. D. and Aidley, D. J. (1991). Nerve and Muscle. Cambridge University
Kulik, C. C. and Kulik, J. A. (1986). Effectiveness of computer-based education
in colleges. AEDS J., pages 81108.
Neher, E. and Sakmann, B. (1976). Single-channel currents recorded from mem
brane of denervated frog muscle bres. Nature, 260:799802.
Nicholls, J. G., Martin, A. R., and Wallace, B. G. (1992). From Neuron to Brain: A
Cellular and Molecular Approach to the Function of the Nervous System. Sinauer
Associates, Sunderland, MA.
Plonsey, R. and Barr, R. C. (1988). Bioelectricity, A Quantitative Approach. Plenum
Press, New York, NY.
Press, W. H., Flannery, B. P., Teukolsky, S. A., and Vetterling, W. T. (1986). Nu
merical Recipes. The Art of Scientic Computing. Cambridge University Press,
Cambridge, Great Britain.
Press, W. H., Flannery, B. P., Teukolsky, S. A., and Vetterling, W. T. (1988). Numer
ical Recipes in C. The Art of Scientic Computing. Cambridge University Press,
Cambridge, Massachusetts.
Shah, D. M. (1990). Computer simulation of the random walk model of diffusion.
Bachelors thesis, Massachusetts Institute of Technology, Cambridge, MA.
Shampine, L. F. and Reichelt, M. W. (1997). The MATLAB ODE suite. SIAM J. Sci.
Comput., 18:122.
Stein, W. D. (1986). Transport and Diffusion Across Cell Membranes. Academic
Tasaki, I. and Hagiwara, S. (1957). Demonstration of two stable potential states
in the squid giant axon under tetraethylammonium chloride. J. Gen. Physiol.,
40:859885.
Weiss, T. F. (1996a). Cellular Biophysics. Volume 1: Transport. MIT Press, Cam
bridge, MA.
Weiss, T. F. (1996b). Cellular Biophysics. Volume 2: Electrical Properties. MIT
Press, Cambridge, MA.
150
BIBLIOGRAPHY
Weiss, T. F., Trevisan, G., Doering, E. B., Shah, D. M., Huang, D., and Berkenblit,
S. I. (1992). Software for teaching physiology and biophysics. J. Sci. Ed. Tech.,
1:259274.
Wilson, J. M. and Redish, E. F. (1989). Using computers in teaching physics.
Physics Today, pages 3441.
CELLULAR BIOPHYSICS:
TEACHING AND LEARNING
WITH COMPUTER SIMULATIONS
By
Thomas Fischer Weiss
with the assistance of
Scott I. Berkenblit, Tanmaya S. Bhatnagar, Elana B. Doering,
David Huang, David Koehler, Tommy Ng, Leela Obilichetti,
Stephanie Peek, Devang M. Shah, Giancarlo Trevisan
Massachusetts Institute of Technology
FALL 2000
Date of last modication: August 28, 2000
ii
iii
Preface
Historical perspective
During the 1980s the use of computers and information technologies began to
have an impact on higher education (Kulik and Kulik, 1986; Balestri, 1988; Wilson and Redish, 1989; Athena, 1990a; Athena, 1990b). As an integral part of
this trend, in 1983 MIT in partnership with the Digital Equipment Corporation
and the IBM Corporation launched Project Athena which was designed to make
computation available to undergraduate students through a network of computers located in public clusters on the MIT campus (Athena, 1990a; Athena,
1990b). A major objective of Project Athena was to improve undergraduate education through the use of computation and information technologies. Faculty
were encouraged to participate, and support for faculty software developers was
provided on a competitive basis.
I had been involved in teaching cellular biophysics at MIT since the 1960s.
The possibility of using software as a pedagogical aid was intriguing. With support from Project Athena, a software package on the Hodgkin-Huxley model for
nerve excitation was developed as part of an undergraduate thesis (by David
Huang), and was rst used to teach cellular biophysics in the Fall 1984 semester.
The software was designed to be easy to use so that a students attention would
be focussed on the Hodgkin-Huxley model and not on the computer. Informal
discussions with students and a survey of student views showed that the software was an enormous success. During the rst semester, the software was
used primarily in lecture demonstrations and as the basis for student projects.
Both pedagogic methods were found to be eective. The use of the software
in lecture was very eective in motivating and engaging students. The student
projects were eective in allowing students to pursue a research project of their
choice with sta assistance. For many students this was their rst experience
with a research project. The use of these projects, developed in the rst year,
was so successful that it has been used ever since.
The initial results with the Hodgkin-Huxley software were so successful educationally, that several other software development projects involving student
programmers were launched. During this phase of software development, 5
software packages were developed and, in one form or another, have been used
every year to teach the subject. All of these packages were revised extensively in
response to suggestions from students and sta. The original software runs on
UNIX workstations under MITs Project Athena and is available to the MIT community on a network of about 1000 UNIX workstations located in public clusters
on the MIT campus as well as in some living groups. All this software was written
in C and XWindows and was based on a library of graphic user interface subroutines written by one of the students (Giancarlo Trevisan). The software has been
used in lectures, in recitations held in an electronic classroom in which each
iv
student uses a workstation, in homework assignments, and in student projects.
Various modes of use of the software in teaching were developed and are described briey elsewhere (Weiss et al., 1992) and more extensively in the last
chapter of this text. The software has become an integral part of the subject,
and it is dicult to imagine teaching the subject without the software.
Several problems became apparent in the development and utilization of the
software. First, it was very expensive, in time and in money, to develop the
software with the software tools available in the late 1980s. Much of the time
was expended in the development of graphic user interfaces that make the software easy for the user but which are tedious for the programmers to specify.
These graphic user interfaces had to be written in a low-level language (XWindows). After 1991, funds from corporate sponsors were no longer available to
support the development of new software which slowed considerably. Second,
maintenance of the software became a major headache. It became dicult for
a single faculty member with research, teaching, and other academic commitments to maintain a library of software in the face of changes in the operating
systems. Third, as word spread about the existence of the software, educators
and students outside of MIT requested the software. These requests accelerated
dramatically after one of the software packages entitled Hodgkin-Huxley Model
won the 1990 EDUCOM/NCRIPTAL Higher Education Software award for Best Engineering Software. However, almost all of the requests came from students and
faculty with access to Macintosh or PC computers and not to UNIX workstations.
Thus, when these people were informed that the software ran only on UNIX
workstations, they invariably lost interest. At the time the software was written,
the computational power of workstations so exceeded that of personal computers (PCs) that it was simply not possible to provide the type of performance on
PCs that was achieved on the workstations. Furthermore, MITs Project Athena
was committed to a network of UNIX workstations. Thus, for both software and
hardware considerations, it did not make sense to port the existing software to
PCs. The high cost of software development and maintenance did not justify
further development of educational software on UNIX workstations alone, and
the development of new software was terminated in 1991.
By 1995, a number of developments made it feasible to address the problems described above and to develop software for teaching cellular biophysics
in a manner that would make it easier to maintain, easier to modify, and widely
available. Thus, all the software was rewritten to operate under MATLAB, which
is a software package produced by The MathWorks, Inc., for the following reasons:
MATLAB is a powerful interpretive computational and visualization software package with a large number of higher-level built-in functions. Thus,
it is suitable for the development of educational software packages.
MATLAB is available for most computer platforms. The vendor supports
v
changes in MATLAB that are required as changes in computer platforms
occur. With the use of software built on MATLAB, this major maintenance
job is transferred from individual faculty members to the vendor who has
both the nancial incentive and expertise to maintain the vendor software.
Large improvements in performance of PCs have made the development

of computationally intensive educational software feasible on these platforms.
MATLAB has provided increasingly sophisticated tools for building graphic

user interfaces (GUIs). These GUIs are essential for building user-friendly
educational software packages.
MATLAB has rapidly become the de facto leader in supporting educational

computational subjects at MIT and elsewhere. Thus, students are exposed
to MATLAB in other subjects and the dierent exposures are mutually reinforcing.
Here, we describe this MATLAB-based version of the software which now constitutes 6 packages. The most recent addition to the library of packages is one
devoted to the propagated action potential along an unmyelinated nerve ber.
Although the software is not linked directly to any textbook, it was developed
in parallel with textbooks in cellular biophysics (Weiss, 1996a; Weiss, 1996b).
Acknowledgement
A number of people contributed to the success of the development of this software. We thank Project Athena, especially its two directors Steven Lerman and
Earll Murman, for their support. In addition Gerald Wilson, Joel Moses, Richard
Adler, Paul Peneld, and Jerey Shapiro were unfailingly supportive of this effort. A number of students were involved in this eort. For many students
the software project constituted a portion of their undergraduate thesis requirement; others (as norws) used the software projects to satisfy SM thesis requirements. David Huang wrote the rst version of the Hodgkin-Huxley model package. David Koehler also contributed to this package. Devang M. Shah wrote
the rst version of the random-walk model package which was also revised by
Elana B. Doering. Chapter 2 is based heavily on Devangs thesis (Shah, 1990).
Scott I. Berkenblit wrote the rst version of the macroscopic diusion package.
Chapter 3 is based heavily on Scotts Master of Science thesis (Berkenblit, 1990).
Stephanie Peek and Leela Obilichetti helped to develop the carrier-mediated
transport package. Giancarlo Trevisan was a major contributor to all the packages. He wrote the rst version of the voltage-gated ion channel package. He
later rewrote the Hodgkin-Huxley package and the carrier-mediated transport
package. He wrote all the graphic user interface routines that were ultimately
used by all the packages. Generations of students beneted from his eorts. The
vi
recipients of the 1990 EDUCOM/NCRIPTAL Higher Education Software Award for
Best Engineering Software for the Hodgkin-Huxley package were Thomas Weiss,
Giancarlo Trevisan, and David Huang. More than 15 generations of the students
who took the subject helped to nd aws in the software and made valuable
suggestions for its improvements. Tanmaya S. Bhatnagar ported all the original
ve software packages to MATLAB, adding new features and improving many of
them substantially. His sense of esthetics marks all the packages. Tommy Ng
wrote the elegant propagated action potential package described in Chapter 6
which constituted his Master of Engineering thesis project. The chapter is based
heavily on Tommys thesis.
Besides the support from Project Athena, the development of the software
was supported by the Howard Hughes Medical Institute for which we are grateful. I was supported in part by the Thomas and Gerd Perkins professorship. The
porting of the software to MATLAB was supported for 3 years by the National
Science Foundation (NSF), Division of Undergraduate Education. We would particularly like to thank Dr. Herbert Levitan, Section Head of Course and Curriculum Development of NSF. Dr. Karen C. Cohen has been helpful in the evaluation
of the software. Subsequent work has been supported by the MIT Class of 51
Fund for Excellence in Education, the MIT Class of 55 Fund for Excellence in
Teaching, and the MIT Class of 72 Fund for Educational Innovation, and by a
John F. and Virginia B. Taplin Faculty Fellowship.
Contact information
Information on cellular biophysics texts, errata, changes, etc. can be found in
the study materials section.
Contents
1 INTRODUCTION
1.1 Motivation . . . . . . . . . . . . . . . .
1.2 Overview Of Software Packages . . .
1.3 Brief Introduction To MATLAB . . .
1.3.1 Jargon . . . . . . . . . . . . . .
1.3.2 Help . . . . . . . . . . . . . . .
1.4 General Operation Of The Software
1.4.1 Directory structure . . . . . .
1.4.2 Starting the software . . . . .
1.4.3 Quitting the software . . . . .
1.4.4 Printing a gure . . . . . . . .
1.4.5 Reading from and saving to a
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1
2
2
3
4
5
5
5
6
7
7
7
2 RANDOM WALK MODEL OF DIFFUSION

2.1 Introduction . . . . . . . . . . . . . . . . . . . .
2.1.1 Historical background . . . . . . . . .
2.1.2 Macroscopic and microscopic models
2.1.3 Overview of software . . . . . . . . . .
2.2 Description Of The Random-Walk Model . .
2.2.1 Particle parameters within a region .
2.2.2 Boundary conditions . . . . . . . . . .
2.3 Users Guide To The Software . . . . . . . . .
2.3.1 RW Control . . . . . . . . . . . . . . . .
2.3.2 RW Particle . . . . . . . . . . . . . . . .
2.4 Problems . . . . . . . . . . . . . . . . . . . . . .
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le
3 MACROSCOPIC DIFFUSION PROCESSES

3.1 Introduction . . . . . . . . . . . . . . . . .
3.1.1 Background . . . . . . . . . . . . .
3.1.2 Macroscopic model of diusion
3.1.3 Overview of software . . . . . . .
3.2 Methods of Solution . . . . . . . . . . . .
3.2.1 Analytic solutions . . . . . . . . .
3.2.2 Numerical Solutions . . . . . . . .
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viii
CONTENTS
3.2.3 Summary . . . . . . . . . . . . . .
3.3 Users Guide To The Software . . . . . .
3.3.1 MD Control . . . . . . . . . . . . .
3.3.2 MD Initial concentration prole
3.3.3 Numerics . . . . . . . . . . . . . .
3.3.4 Simulation results gures . . . .
3.4 Problems . . . . . . . . . . . . . . . . . . .
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40
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48
48
51
53
4 CARRIER-MEDIATED TRANSPORT
4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.2 Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.2.1 Steady-state behavior of a simple, four-state carrier that binds
one solute . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
two solutes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
carrier that binds one solute . . . . . . . . . . . . . . . . . . . .
4.3.1 Numerical methods . . . . . . . . . . . . . . . . . . . . . . . . . .
4.3.2 Choice of numerical parameters . . . . . . . . . . . . . . . . . .
4.4 Users Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.4.1 CMT Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.4.2 Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.4.3 Steady-state interactive analysis . . . . . . . . . . . . . . . . . .
4.4.4 Steady-state graphic analysis . . . . . . . . . . . . . . . . . . . .
4.4.5 Transient analysis . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.5 Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
59
60
60
5 HODGKIN-HUXLEY MODEL
5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.1.1 Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.1.2 Overview of the software . . . . . . . . . . . . . . . . . . . . . .
5.2 Description Of The Model . . . . . . . . . . . . . . . . . . . . . . . . . .
5.2.1 Voltage-clamp and current-clamp congurations . . . . . . . .
5.2.2 The membrane current density components . . . . . . . . . .
5.2.3 The membrane conductances . . . . . . . . . . . . . . . . . . . .
5.2.4 The activation and inactivation factors . . . . . . . . . . . . . .
5.2.5 The rate constants . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.2.6 Time constants and equilibrium values of activation and inactivation factors . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.2.7 Default values of parameters . . . . . . . . . . . . . . . . . . . .
5.3.1 Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
87
88
88
88
89
89
89
90
91
91
61
63
66
69
69
69
69
70
71
71
75
78
81
92
92
93
93
CONTENTS
5.3.2 Choice of integration step t . . . . .
5.3.3 Method for computing solutions . . .
5.4 Users Guide To The Software . . . . . . . . .
5.4.1 HH Control . . . . . . . . . . . . . . . .
5.4.2 HH Parameters . . . . . . . . . . . . . .
5.4.3 HH Stimulus . . . . . . . . . . . . . . .
5.4.4 Numerics . . . . . . . . . . . . . . . . .
5.4.5 Analysis . . . . . . . . . . . . . . . . . .
5.4.6 Scripts . . . . . . . . . . . . . . . . . . .
5.5 Problems . . . . . . . . . . . . . . . . . . . . . .
5.6 PROJECTS . . . . . . . . . . . . . . . . . . . . .
5.6.1 Practical considerations in the choice
5.6.2 Choice of topics . . . . . . . . . . . . .
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118
118
6 PROPAGATED ACTION POTENTIAL

6.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6.1.1 Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6.1.2 Overview of the software . . . . . . . . . . . . . . . . . . . . .
6.2 Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6.2.1 Core conductor equations . . . . . . . . . . . . . . . . . . . . .
6.2.2 Representation of stimulating electrodes . . . . . . . . . . .
6.2.3 Longitudinal currents . . . . . . . . . . . . . . . . . . . . . . . .
6.2.4 Intracellular and extracellular potential dierences . . . . .
6.2.5 The membrane current density . . . . . . . . . . . . . . . . . .
6.2.6 The membrane conductances . . . . . . . . . . . . . . . . . . .
6.2.7 Default values of parameters . . . . . . . . . . . . . . . . . . .
6.3 Numerical Method of Solution . . . . . . . . . . . . . . . . . . . . . .
6.3.1 Forward Euler method . . . . . . . . . . . . . . . . . . . . . . .
6.3.2 Backward Euler method . . . . . . . . . . . . . . . . . . . . . .
6.3.3 Crank-Nicolson method . . . . . . . . . . . . . . . . . . . . . .
6.3.4 Staggered increment Crank-Nicolson method . . . . . . . . .
6.4 Users Guide to the Software . . . . . . . . . . . . . . . . . . . . . . .
6.4.1 PAP Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6.4.2 PAP Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6.4.3 PAP Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . .
6.4.4 PAP Stimulus . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6.4.5 PAP Numerics . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6.4.6 PAP Voltage-Recorder . . . . . . . . . . . . . . . . . . . . . . . .
6.4.7 PAP Variable Summary . . . . . . . . . . . . . . . . . . . . . . .
6.4.8 PAP Space-Time Evolution . . . . . . . . . . . . . . . . . . . . .
6.4.9 PAP 3D Plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6.4.10 PAP Comparison Plots . . . . . . . . . . . . . . . . . . . . . . .
6.4.11 Step-by-step Guide To Setting Up A Customized Simulation
6.5 Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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125
126
126
126
127
127
128
129
130
130
131
131
131
132
134
136
138
140
141
142
144
149
150
152
153
153
155
156
162
163
CONTENTS
6.6 PROJECTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170
7 VOLTAGE-GATED ION CHANNELS

7.1 Introduction . . . . . . . . . . . .
7.1.1 Historical background .
7.1.2 Overview of software . .
7.2 Description Of The Model . . .
7.3 Numerical Methods . . . . . . .
7.3.1 Integration step . . . . .
7.3.2 Initial conditions . . . . .
7.4 Users Guide . . . . . . . . . . . .
7.4.1 IC Control . . . . . . . . .
7.4.2 IC Parameters . . . . . . .
7.4.3 Membrane potential . . .
7.4.4 Numerics . . . . . . . . .
7.4.5 Analysis . . . . . . . . . .
7.5 Problems . . . . . . . . . . . . . .
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8 PEDAGOGICAL METHODS
8.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . .
8.2 Uses Of The Software . . . . . . . . . . . . . . . . . . . .
8.2.1 Lectures . . . . . . . . . . . . . . . . . . . . . . . .
8.2.2 Electronic classroom and homework problems
8.2.3 Projects . . . . . . . . . . . . . . . . . . . . . . . .
8.3 Assessment . . . . . . . . . . . . . . . . . . . . . . . . . .
8.3.1 Cost of development . . . . . . . . . . . . . . . .
8.3.2 Extent of software usage . . . . . . . . . . . . . .
8.3.3 Informal assessment of impact on learning . .
8.3.4 Surveys and focus groups . . . . . . . . . . . . .
8.3.5 Impact on teaching . . . . . . . . . . . . . . . . .
8.4 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . .
8.4.1 Pedagogical matters . . . . . . . . . . . . . . . . .
8.4.2 Practical matters . . . . . . . . . . . . . . . . . . .
8.4.3 Bottom line . . . . . . . . . . . . . . . . . . . . . .
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220
220
221
221
222
222
223
223
224
226
List of Figures
1.1 Cellular biophysics software gure showing the available software
packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.2 Save gure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.1
2.2
2.3
2.4
2.5
2.6
2.7
2.8
6
8
Denition of grid of particle locations . . . . . . . . . . . . . . . . . .

Denition of simulation eld, regions, and boundaries . . . . . . . .
Motion of a particle in a homogeneous region . . . . . . . . . . . . . .
Motion of a particle at a vertical perimeter boundary . . . . . . . . .
Motion of a particle at an internal vertical boundary . . . . . . . . . .
The RW Control gure . . . . . . . . . . . . . . . . . . . . . . . . . . . .
RW Particles gure showing the initial locations of particles . . . . .
RW Particles gure showing the locations of particles after a 100
step random walk . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.9 RW Parameters gure . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.10 RW Summary gure showing a numerical summary of statistics after a 100 step random walk . . . . . . . . . . . . . . . . . . . . . . . . .
2.11 RW Histogram gure showing a histogram of particle locations after a 100 step random walk . . . . . . . . . . . . . . . . . . . . . . . . .
2.12 RW Axis gure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.13 RW Graph gures showing the mean and standard deviation of particle location versus step number . . . . . . . . . . . . . . . . . . . . .
2.14 Parameters for a random walk in 3 regions . . . . . . . . . . . . . . .
2.15 Initial locations of particles for a random walk in 3 regions . . . . .
25
29
30
3.1 Classes of initial concentration proles simulated by the software

3.2 The MD Control gure . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.3 Initial concentration prole for impulses . . . . . . . . . . . . . . . .
3.4 MD Axis scale gure . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.5 Initial concentration prole for sinusoids . . . . . . . . . . . . . . .
3.6 Initial concentration prole for discontinuities . . . . . . . . . . . .
3.7 Initial concentration using the arbitrary option . . . . . . . . . . . .
3.8 Initial concentration for the two compartments option . . . . . . .
3.9 The MD Analytic parameters and MD Numeric parameters gures
3.10 MD Plots vs. position gure . . . . . . . . . . . . . . . . . . . . . . . .
3.11 MD Plots vs. time gure . . . . . . . . . . . . . . . . . . . . . . . . . .
36
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43
43
45
46
47
49
50
50
51
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24
xii
LIST OF FIGURES
4.1
4.2
4.3
4.4
4.5
4.6
Kinetic diagram of the simple, four-state carrier . . . . . . . . . . . .

Kinetic diagram of a simple, six-state carrier that binds two solutes
Kinetic diagram of a general, four-state carrier model . . . . . . . . .
CMT Control gure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
CMT Units gure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
The CMT Parameters and CMT State gures for the simple, fourstate carrier model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.7 The CMT Parameters and CMT State gures for the simple, six-state
carrier model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.8 The CMT Parameters and CMT State gures for the general, fourstate carrier model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.9 The CMT Steady state plot gure . . . . . . . . . . . . . . . . . . . . . .
4.10 CMT Setup steady state plot gure . . . . . . . . . . . . . . . . . . . . .
4.11 The Axis scale gure . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.12 Modify line properties gure . . . . . . . . . . . . . . . . . . . . . . . .
4.13 The CMT Transient plot gure . . . . . . . . . . . . . . . . . . . . . . .
4.14 The CMT Setup transient plot gure . . . . . . . . . . . . . . . . . . . .
4.15 The CMT Transients numerics gure . . . . . . . . . . . . . . . . . . .
5.1
5.2
5.3
5.4
5.5
5.6
5.7
Voltage-clamp conguration . . . . . . . . . . . . . . . . . . . . . . . . .
Current-clamp conguration . . . . . . . . . . . . . . . . . . . . . . . .
The HH Control gure after the software is initiated . . . . . . . . . .
The HH Parameters gure after the software is initiated . . . . . . .
HH parameters vs. potential gure . . . . . . . . . . . . . . . . . . . . .
HH Setup parameters vs. potential plot gure . . . . . . . . . . . . . .
HH parameters vs. potential gure showing the eect of calcium
concentration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.8 Axis scale gure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.9 Modify line properties gure . . . . . . . . . . . . . . . . . . . . . . . .
5.10 HH Stimulus gure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.11 HH Stimulus gure showing an example of a stimulus waveform . .
5.12 HH Stimulus gure showing an example of the use of an m-le to
generate a sinusoidal stimulus . . . . . . . . . . . . . . . . . . . . . . .
5.13 HH Numerics gure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.14 HH Plots vs. time gure . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.15 HH Variable summary gure. . . . . . . . . . . . . . . . . . . . . . . . .
5.16 HH Graphics gure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.17 HH Setup plot gure. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.18 HH Graphics gure showing a parametric plot of membrane conductance versus membrane potential . . . . . . . . . . . . . . . . . . .
5.19 HH Graphics gure showing the membrane potential obtained at
dierent temperatures . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.20 Simulation results for dierent parameters that block the action
potential (Problem 5.11) . . . . . . . . . . . . . . . . . . . . . . . . . . .
61
63
66
70
70
71
72
73
76
76
77
78
79
80
80
89
90
94
96
98
98
99
100
101
101
103
103
104
105
105
106
107
108
109
116
LIST OF FIGURES
xiii
5.21 Examples of action potentials . . . . . . . . . . . . . . . . . . . . . . . . 119

5.22 Dependence of the action potential on temperature . . . . . . . . . . 120
5.23 Eect of extracellular sodium concentration on the action potential 120
6.1 Equivalent network model of incremental sections of an unmyelinated nerve ber . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6.2 Relation of stimulus electrodes to a ber . . . . . . . . . . . . . . . . .
6.3 The PAP Control gure when the software is initiated. . . . . . . . .
6.4 The PAP Workspace gure. . . . . . . . . . . . . . . . . . . . . . . . . .
6.5 Snapshots of a propagating action potential shown using Color
Space-Time Evolution in the PAP Workspace gure. . . . . . . . . . .
6.6 The PAP Parameters gure. . . . . . . . . . . . . . . . . . . . . . . . . .
6.7 The PAP Parameters vs. Potential gure. . . . . . . . . . . . . . . . . .
6.8 The PAP Stimulus gure. . . . . . . . . . . . . . . . . . . . . . . . . . .
6.9 The PAP Stimulus gure showing a stimulus that consists of two
pulses: the rst pulse is an exponential pulse and the second is a
ramp plus a rectangular pulse. . . . . . . . . . . . . . . . . . . . . . . .
6.10 The PAP Numerics gure. . . . . . . . . . . . . . . . . . . . . . . . . . .
6.11 The PAP Voltage-Recorder gure. . . . . . . . . . . . . . . . . . . . . .
6.12 The PAP Variable Summary gure. . . . . . . . . . . . . . . . . . . . .
6.13 The PAP Space-Time Evolution gure showing a snapshot of a propagating action potential. . . . . . . . . . . . . . . . . . . . . . . . . . . .
6.14 The PAP 3D Plots gure showing a propagating action potential.
Top: a surface plot. Bottom: a mesh plot. . . . . . . . . . . . . . . . .
6.15 The Setup PAP Comparison Plot gure showing the variables used
to setup Figure 6.16.). . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6.16 The PAP Comparison Plots gure showing a xed-space plot of the
membrane potential, Vm , and the ionic conductances, GNa and GK ,
with model parameters and the stimulus dened in Figures 6.6 and
6.8. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6.17 The PAP Comparison Plots gure showing a xed-time plot of the
membrane potential, Vm , and the activation factors, m and h, obtained from a simulation with model parameters and the stimulus
dened in Figures 6.6 and 6.8. . . . . . . . . . . . . . . . . . . . . . . .
6.18 The PAP Axis Scale gure. . . . . . . . . . . . . . . . . . . . . . . . . . .
6.19 The Modify Line Properties gure. . . . . . . . . . . . . . . . . . . . . .
7.1
7.2
7.3
7.4
7.5
7.6
7.7
Kinetic diagram of a channel that has 5 states . . . . . . . . . . . . .

The probability of occurrence of more than 1 event in an interval t
The IC Control gure after the software is initiated . . . . . . . . . .
IC Parameters gure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
IC Specify rate constants gure . . . . . . . . . . . . . . . . . . . . . . .
IC View rate constant gure . . . . . . . . . . . . . . . . . . . . . . . . .
IC Setup view rate constant gure . . . . . . . . . . . . . . . . . . . . .
128
129
141
143
145
146
148
149
151
151
153
154
155
157
158
159
160
161
162
175
179
180
181
183
184
185
xiv
LIST OF FIGURES
7.8 IC Membrane potential gure . . . . . . . . . . . . . . . . . . . . . . . .
7.9 IC Numerics gure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
7.10 IC State occupancy gure . . . . . . . . . . . . . . . . . . . . . . . . . .
7.11 IC Ionic current gure . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
7.12 IC Summary gure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
7.13 IC Graphics gure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
7.14 IC Setup graphics gure . . . . . . . . . . . . . . . . . . . . . . . . . . .
7.15 IC Graphics gure showing the state occupancy probabilities for a
four-state channel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
7.16 IC Graphics gure showing the ionic conductances of a two-state,
three-state, and a four-state channel . . . . . . . . . . . . . . . . . . . .
187
187
189
190
191
192
193
8.1
8.2
8.3
8.4
207
209
211
Random walk in two regions . . . . . . . . . . . . . . . . . . . . . . . .

Steady-state distribution . . . . . . . . . . . . . . . . . . . . . . . . . . .
Time constants in two-compartment diusion . . . . . . . . . . . . .
The threshold for eliciting an action potential in the Hodgkin-Huxley
model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
8.5 Sample project proposal . . . . . . . . . . . . . . . . . . . . . . . . . . .
194
195
212
216
List of Tables
2.1 The macroscopic laws of diusion . . . . . . . . . . . . . . . . . . . . .
11
3.1 Summary of computational methods. . . . . . . . . . . . . . . . . . .

3.2 Concentration well Problem 3.7 . . . . . . . . . . . . . . . . . . . . .
41
57
4.1 Modiable parameters of the carrier models . . . . . . . . . . . . . . .
74
xv
xvi
LIST OF TABLES
Chapter 1
INTRODUCTION
1.1
Motivation
I have been engaged in teaching cellular biophysics since 1965. Computer simulations were rst used to teach this material in 1984 and have been used ever
since. There is no question in my mind that the use of the software has deepened
students understanding of the subject material. All faculty who have taught the
subject, even those who started as skeptics, have been convinced of the educational ecacy of the software described here. Students have no basis of
comparison of the subject before and after use of the software, but generally
enjoy using the software and feel that it is helpful, and sometimes crucial, for
understanding the concepts. This book provides a complete description of the
software including some background material for each topic.
The rst chapter introduces the software packages and MATLAB, on which
the packages are based. The subsequent 6 chapters each describe one of the
software packages in some detail complete with problems and projects. The last
chapter is devoted to describing the pedagogical methods we have used to teach
cellular biophysics using computer simulation. It is aimed at faculty interested
in using the software for teaching but may be useful for students as well.
1.2
Overview Of Software Packages
The software for cellular biophysics consists of 6 software packages. The titles
of the software packages, with acronyms in parentheses, are described briey
below.
Random Walk Model of Diusion (RW) allows users to select parameters of the
random walks of particles in a eld and to observe the resulting spacetime evolution of particle location. This package is intended to link the
macroscopic laws of diusion to its probabilistic, microscopic basis.
Macroscopic Diusion Processes (MD) allows users to select the initial spatial
distribution of solute concentration, the diusion parameters, and to observe the resulting space-time evolution of solute concentration and ux.
This package is intended to give users intuition about macroscopic diusion processes.
Carrier-Mediated Transport (CMT) allows users to examine simple models of
carrier-mediated transport through cellular membranes. For each of three
models, the user can change any parameter and can instantly see the eect
on the state of the carrier-model. This interactive mode is intended to
build intuition about these models. In addition, there is a graphic mode
that allows display of steady-state and transient responses to changes in
any parameter.
1.3. BRIEF INTRODUCTION TO MATLAB
Hodgkin-Huxley Model Space Clamped (HH) allows users to investigate the

space-independent Hodgkin-Huxley model. Users can change parameters
of the Hodgkin-Huxley model of the space-clamped giant axon of the squid,
and perform simulation experiments in either the voltage-clamp or the
current-clamp conguration.
Hodgkin-Huxley Model Propagated Action Potential (PAP) allows users to investigate the space-dependent Hodgkin-Huxley model. Users can change
parameters of the Hodgkin-Huxley model of the giant axon of the squid,
and examine propagation of the action potential and of sub-threshold potentials as a function of space and time.
Voltage-Gated Ion Channels (IC) allows users to design a voltage-gated ion channel. The user selects the number of states, the conductance and gating
charge associated with each state, the voltage-dependence of state transition rates, and the membrane potential. The user can then perform simulation experiments on the channel model.
These packages are all designed to enhance comprehension of topics in cellular
biophysics by providing pedagogic tools that can be used as a basis for lecture
demonstration, open-ended problems that lend themselves to classes held in an
electronic classroom in which students have access to computers, homework
problems, and research projects. Although independent of any textbook, this
suite of software packages was developed in parallel with textbooks in cellular
biophysics (Weiss, 1996a; Weiss, 1996b).
1.3
Brief Introduction To MATLAB
All the software packages are written in MATLAB which is an interactive programming environment for numerical and symbolic computations and for visualization of computational results. Because MATLAB runs on most of the major
computer platforms, the cellular biophysics software operates on all platforms
supported by MATLAB. The present version of the software is written on MATLAB version 5.3 which is available under Windows and UNIX but not under MacOS. MATLAB version 5.3 is required to operate this software.1
The MATLAB environment is interpretive. That is, commands can be entered
at a prompt and interpreted within the scope of a MATLAB session. Thus, computational results generated by a simulation are available to the user for further
analysis. The software is designed to perform all the simulations with minimal
typed commands. The graphical user interface allows navigation through the
1
Although not tested extensively, the software should run on the Student Version of MATLAB. However, it may be that parameters can be chosen for these packages which will not
satisfy the limitations of the Student Version.
software using a sequence of mouse events (e.g., clicking the mouse, pulling
down a menu, dragging the mouse).
Users of the software do not need to learn MATLAB to use the software. However, knowledge of MATLAB can enhance users usage of the software. A number
of texts on MATLAB are available (Hanselman and Littleeld, 1997). In addition,
MATLAB manuals can be ordered directly from MathWorks. Section 1.3.1 is a
glossary of some useful terms in the MATLAB vocabulary. Section 1.3.2 mentions resources that can provide on-line help with MATLAB.
1.3.1
Jargon
The following terms are useful in navigating in the MATLAB environment.

axes The area in a gure containing plots and annotation. See the MATLAB
command axes.
buttons Rectangular regions allowing a sequence of commands to be executed
when they are clicked, selected, or edited. See the MATLAB command
uicontrol.
command window The window that appears when MATLAB is started. Commands entered at the MATLAB prompt (>>) in this window are evaluated in
the workspace.
gure A rectangular window containing graphical objects, such as axes, buttons,
and menu items. See the MATLAB command figure.
MAT-le A binary data le containing MATLAB variables. Each software package
uses and stores a dierent set of variables.
menubar A bar at the top of a gure (Windows and UNIX implementations) or at
the top of the monitor screen (in some implementations) associated with
the currently selected gure. When selected, the menu item expands to
show its related submenu items. Submenu items marked with a checkmark are currently active selections.
M-le A text le containing a sequence of commands to be evaluated in the
MATLAB workspace. The software contains a collection of m-les which
can be recognized by the extension .m.
parameters Numeric values that dene each model.
popup-menu A rectangular region showing the current popup-menu selection.
When clicked, the menu is expanded to show all the options. See the MATLAB command uicontrol.
1.4. GENERAL OPERATION OF THE SOFTWARE
variables Numeric values of independent variables set by the user or of dependent variables calculated from the model.
workspace A collection of variables in the current session of MATLAB. When
MATLAB is started, the workspace is empty. Variables appear in the workspace
as they are dened.
1.3.2
Help
Help on MATLAB is available through the command window using the following
commands at the MATLAB prompt (>>)
who lists the variables in the current workspace.
help function provides some help on the command function.
help help provides help on getting started using help.
lookfor word nds functions that involve word.
Additional help is available in the descriptions of individual software packages.
1.4
1.4.1
General Operation Of The Software

Directory structure
The software is designed to be run from a directory that includes the following
les/directories:
cmt is a directory that contains the carrier-mediated transport software.
hh is a directory that contains the Hodgkin-Huxley model of a space-clamped
axon software.
ic is a directory that contains the voltage-gated ion channel software.
md is a directory that contains the macroscopic diusion processes software.
pap is a directory that contains the Hodgkin-Huxley model of a propagating
action potential software.
rw is a directory that contains the random walk model software.
softcell.m is a MATLAB m-le that initializes the software and allows the user
to choose software packages from a menu.
startup.m is a MATLAB m-le that may be used to startup the software automatically.
Figure 1.1: This Cellular biophysics

software gure is displayed when
the software is started and shows
the available software packages.
The appearance of the menu bar
near the top of the gure varies
somewhat for the dierent platforms. This gure was obtained using Windows 2000 and MATLAB version 5.3.
tlib is a directory that contains a library of software routines used by all the
packages.
1.4.2
Starting the software
The software is accessible through MATLAB via a menu that allows selection
of the software packages and initializes all packages. The startup procedure is
given for the dierent platforms.
Windows, UNIX, and other operating systems that support MATLAB. Initialize
MATLAB, and type the following instruction (in the MATLAB window) at the
MATLAB prompt (>>)
>> cd directory
where directory is the name of the directory (folder) that houses the cellular biophysics software.2 Then type
>> softcell
This command displays the Cellular biophysics software gure shown in
Figure 1.1. Clicking on any package, initializes that package and hides the
Cellular biophysics software gure.
UNIX workstation on Project Athena at MIT. From the dashboard at the top of
the monitor select
Courseware
Electrical Engineering and Computer Science
6.021J/6.521J Quantitative Physiology
New MATLAB v5 Software
This procedure displays the Cellular biophysics software gure shown in
Figure 1.1. Clicking on any package, initializes that package and hides the
Cellular biophysics software gure.
2
To verify that the directory is the right one, either type pwd to indicate the name of the
present directory or type ls to list the contents of the directory. It should contain the le
softcell.m. If it does not contain this le then either the selected directory is wrong or the
cellular biophysics software is not installed on your computer.
1.4. GENERAL OPERATION OF THE SOFTWARE
If a software package is selected, a number of gures are displayed including the XX Control gure, where XX is the acronym of the software package
(RW, MD, CMT, HH, IC). Clicking on the in the upper right-hand corner of the
menubar, deletes any gure. Clicking on the in the upper right-hand corner of
the menubar of the XX Control gure exits from the software package and results
in the display of the Cellular biophysics software gure shown in Figure 1.1.
1.4.3
Quitting the software
Clicking on the in the upper right-hand corner of the menubar of the Cellular
biophysics software gure exits the cellular biophysics software. Clicking on the
in the upper right-hand corner of the menubar of the MATLAB Command
window exits MATLAB.
1.4.4
Printing a gure
Each gure associated with each package contains a Print button which if pressed
brings up a print gure that allows the user to print on any printer on the network to which the computer is connected or to store a postscript le of the
gure.
1.4.5
Reading from and saving to a le
A variety of information about the software can be saved in MAT-les using the
standard MATLAB binary le format (see MATLABs save and load commands).
For example, all the packages allow storage of simulation parameters to allow a
simulation to be repeated at a later time. In addition, results of simulations can
also be saved in les for later retrieval. However, the information stored varies
for dierent software packages, and the individual descriptions of the packages
should be consulted for more detailed information.
A le can be read by pushing the Open button in a gure. A le can be stored
by pushing the Save button. Pushing either button displays a gure (Figure 1.2)
that allows the user to navigate to the desired directory to either read or save a
le.
Figure 1.2: Save gure opened

from the HH package using Windows 2000 and MATLAB 5.3.
Chapter 2
RANDOM WALK MODEL OF
DIFFUSION
10
2.1. INTRODUCTION
2.1
2.1.1
11
Introduction
Historical background
A bolus of soluble material will gradually spread out in its solvent until a uniform
solution results. This diusion process must have been familiar to humans in
antiquity. However, a mathematical description of these macroscopic changes in
concentration was not available until the 1850s (Fick, 1855), and a microscopic
or particle-level model, not until the turn of this century (Einstein, 1906).
Diusion plays an important role in such a wide range of disciplines, that it is
important for students of science and engineering to develop an understanding
of the macroscopic laws of diusion and their microscopic basis. We will review
some important characteristics of the macroscopic laws of diusion and their
relation to random-walk models. A fuller treatment is available elsewhere (Weiss,
1996a).
2.1.2
Macroscopic and microscopic models
Macroscopic laws of diusion

The macroscopic laws of diusion for the simple case when the particles are not
subject to a body force, the medium does not convect the particles, the diusion
coecient is a constant, and the particles are conserved are summarized in one
and three dimensions in Table 2.1. These equations relate the ux of particles
Equation
Ficks rst law
Continuity equation
Diusion equation
One Dimension Three Dimensions

c
= Dc
= D
x
c
= c
=
x
t
t
2c
c
c
=D 2
= D2 c
t
x
t
Table 2.1: The macroscopic laws of diusion for a concentration of particles diusing
in a homogeneous region with a constant diusion coecient D, in the absence of a
body force on the particles or convection of the medium, and where the particles are
conserved.
(), which is the number of moles of particles transported through a unit area in
a unit time, to the concentration of particles (c), which is the number of moles of
particles per unit volume. Ficks rst law relates ux to particle concentration;
it is analogous to other laws that relate a ow to a force such as Ohms law of
electric conduction, Darcys law of convection, and Fouriers law of heat ow.
12
Ficks rst law implies that a solute concentration gradient causes a solute ux
in a direction to reduce the concentration gradient. The continuity equation
follows from conservation of particles, and the diusion equation is obtained by
combining Ficks rst law with the continuity equation.
Microscopic basis of diusion
An important notion in understanding diusion processes is to relate the macroscopic laws of diusion to microscopic models of diusing particles. The simplest microscopic model that captures the essence of diusion is the discretetime, discrete-space random walk. In a one-dimensional random walk in a homogeneous region of space, we assume a particle moves along the x-axis in a
series of statistically independent steps of length +l or l, where the time between steps is . In an unbiased walk, positive and negative steps are equally
likely, i.e., each has probability 1/2. It can be shown that statistical averages of
properties of a population of particles obey the macroscopic laws of diusion.
In particular, this simple model can be shown (Weiss, 1996a) to yield Ficks rst
law with a diusion coecient,
l2
.
D=
2
Therefore, the connection between the random walk of a particle and the laws of
macroscopic diusion can be made clear if the motion of a number of particles
(on the order of 50) can be visualized for a number of steps.
2.1.3
Overview of software
The software described here is intended to allow users to investigate the properties of the simplest microscopic model that captures the essence of diusion:
the discrete-time, discrete-space random-walk model.
In the discrete-time, discrete space random walk model described here, there
is a population of particles which execute statistically-independent, but otherwise identical two-dimensional random walks in a rectangular eld. The eld
can be divided into one, two, or three homogeneous regions whose widths are
speciable, and whose properties may dier. Each particle undergoes a random walk with parameters that include: the probability that the particle takes
a step to the left or right, and the step size. These parameters can be set independently in the three regions. The particles can be set to have a speciable
lifetime. One source and one sink of particles can be placed in the eld and the
initial concentration of particles can be specied in each of the three regions.
Characteristics of the boundary conditions between regions can also be specied. With this software package it is possible: to visualize the spatial evolution
of particle concentration from a variety of initial distributions selectable by the
user; to examine the evolution of particle concentration from a source and in the
13
1 unit
j +2
j +1
Figure 2.1: Denition of grid of particle locations. A particle

is shown at the grid location (i, j). The distance between
adjacent grid locations, in both the horizontal and vertical
directions, is the unit distance.
j
j 1
j 2
i 2 i 1 i
i +1 i +2
presence of a sink; to examine diusion in regions of diering diusion coecients; to simulate diusion of particles subjected to a body force; to simulate
diusion between two compartments separated by a membrane; to investigate
the eects of chemical reactions or recombination which consume particles at
a xed rate; and to investigate the eects of dierent boundary conditions between regions. Two diusion regimes can be run and displayed simultaneously
to allow direct comparison between the space-time evolution of two dierent
diusion processes. In addition, a variety of statistics of the spatial distribution
of particles can also be displayed.
By watching the particles move and by comparing simulation results to expectations, the user can develop an intuition for the way in which the random
motions of particles lead to their diusive spread.
2.2
Description Of The Random-Walk Model
In this simulation, the discrete-time, discrete-space random walk takes place on

a nite two-dimensional grid of locations accessible to the particles and called
the eld. The location of each particle is specied by giving its coordinates on
this grid (i, j) where i is the horizontal coordinate and ranges from 0 to 399 and
j is the vertical coordinate and ranges from 0 to 99 (Figure 2.1). The horizontal
distance between adjacent grid locations is 1 unit of distance and all spatial
dimensions of the random walk are expressed as multiples of this unit distance.
The location of the particle in the grid can change probabilistically at each step
of the random walk. Thus, successive steps represent successive times that are
separated by a unit time interval. All times are expressed in terms of the number
of steps of the random walk.
The eld can be divided into one, two or three homogeneous regions (Figure 2.2). Certain parameters of the simulation are dened for the entire eld,
others at boundaries between regions, and still others are dened independently
for each region. The latter parameters will be described rst and include: region
size, particle step size, directional probabilities, and initial particle distribution.
14

Region 1
Region 2
Region 1 size
vertical internal
boundaries
Region 2
perimeter boundary:
vertical
horizontal
Figure 2.2: Denition of simulation eld, regions, and boundaries. Solid lines delimit
the perimeter boundaries of the eld; dashed lines indicate the internal vertical boundaries that separate the regions.
2.2.1
Particle parameters within a region
The parameters that dene the random walk are identical at each location within
a region each region is homogeneous. These parameters are described below.
Region size
The width of each region can be specied, but the sum of the widths cannot
exceed 400. This allows a variety of diusion regimes to be dened. For example, if Region 1 has width of 400 then the other two regions must have width 0
and the random walk is dened for one homogeneous region. By specifying two
regions with non-zero widths, it is possible to dene a diusion process with
dierent initial conditions in the two regions. This allows a rich variety of initial
distributions to be dened. Three non-zero width regions allows simulation of
diusion between two regions separated by a third region with dierent properties. This might be used to investigate diusion between two baths separated by
a membrane.
Step size
The step size denes the distance, in multiples of unit distances, that particles
may move in each step of time. Varying the step size simulates varying the
diusion coecient. The size of a region is always set to a multiple of the step
size in that region; all particles in a region are located at integer multiples of
the step size starting from the left boundary of the region. This ensures that
particles at a boundary fall on the boundary and simplies the specication of
particle motion at a boundary.

upper left
15
upper right
step size
expired
lower left
lower right
step size
Figure 2.3: Schematic diagram of motion of a particle in a homogeneous region. The

grid of possible particle locations, separated by unit distances, are indicated by + symbols. A particle is shown in the center of the gure at one instant in time. One time
step later the particle either stays in the same location or moves to one of 4 possible
locations (indicated by the shaded particle) or it expires (is removed from the eld). If
the particle moves, it translates one step size (here shown as 2 units of distance) in
both the vertical and the horizontal direction.
Particle motion directional probabilities

At each instant in time, a particle is at some location in the region. The disposition of the particle at the next instant in time is determined by one of six
mutually exclusive and collectively exhaustive possibilities as illustrated in Figure 2.3. The particle can move one step size to the upper left, upper right, lower
left, or lower right; stay in the same location (center); or be eliminated (expire).
The probabilities for each of the six outcomes is as follows:
P[expired] = 1/L ,
P[center] = (1 1/L) (1 p q) ,
P[upper left] = 0.5 (1 1/L) q ,
(2.1)
P[lower left] = 0.5 (1 1/L) q ,

where L is the average lifetime of the particle, i.e. the average number of time
steps to expiration; p is the conditional probability that the particle moves to
the right given that it has not expired; q is the conditional probability that the
particle moves to the left given that it has not expired. Note that while the
probability of moving to the left and to the right can dier, the probability of
moving up or down is always the same. Because the six probabilities dene all
the possible outcomes at each instant in time, they sum to unity.
Dierent types of random walks are described by changing the directional
probabilities. The random walk dened by assuming p = q = 1/2 is the simple,
16
unbiased random walk described in Section 2.1. In general, if p = q the random

walk is unbiased; there is no statistical tendency for particles to move preferentially in either horizontal direction. However, if p q, the random walk is biased
so that there is a tendency for particles to move in one horizontal direction. For
a step size of S, the mean distance E[m] that the particle moves to the right in
n units of time is
E[m] = Sn(1 1/L)(p q) .
2.2.2
Boundary conditions
The eld contains three dierent types of boundaries (Figure 2.2) which are, in
order of increasing complexity, horizontal perimeter boundaries at the top and
bottom of the eld, vertical perimeter boundaries at the left and right ends of
the eld, and vertical internal boundaries that separate regions.
Horizontal perimeter boundaries
Horizontal perimeter boundaries act as perfectly reecting walls. If a particle
is located within one step size of such a boundary and takes a step toward
the boundary then the new vertical location of the particle is determined in the
following manner: the vertical distance the particle travels to reach the wall plus
the vertical distance the particle travels after reecting from the wall must sum
to the step size. This relation determines the new location given the old location
and the value of the step size.
Vertical perimeter boundaries
The vertical perimeter boundaries are also reecting walls. Because the probabilities of stepping to the left and right need not be the same, we found that
purely reecting wall of the type described for the horizontal perimeter boundaries created undesirable artefacts especially when the conditional probabilities
of moving to the left and right were not equal (p q). Therefore, we modied the boundary condition so that a particle that would have crossed a vertical
perimeter boundary at a given step was placed on the boundary and then subject
to the following boundary condition which is illustrated for the left boundary in
Figure 2.4 and whose directional probabilities are:
P[expired] = 1/L ,
P[center] = (1 1/L) (1 p) ,
i.e. the particle cannot move to the left.
(2.2)
17
upper right
step size
left vertical
perimeter
boundary
expired
lower right
Figure 2.4: Schematic diagram of motion of a particle at a vertical perimeter

boundary. For purposes of illustration
the particle motion at the left boundary
is shown. Conditions at the right boundary are the mirror-image of those shown
here.
step size
left region
right region
upper right
upper left
step size in
right region
expired
lower left
lower right
Figure 2.5: Schematic diagram of motion of a particle at an internal vertical

boundary between two regions. The
step size is 1 to the left of the boundary and 2 to the right of the boundary.
step size in step size in

left region right region
internal vertical
boundary
Vertical internal boundaries
The motion of particles at a vertical internal boundary is similar to that within

a homogenous region. The dierences are that: the step sizes in the two adjacent regions may dier; and special directional probabilities, specied by the
user, apply at the boundary. These have been provided to allow users to explore
the consequences of a rich variety of boundary conditions. To simplify boundary
conditions, the software ensures that particles do not cross this boundary in one
time step but rather they land on the boundary. This is guaranteed by forcing
the width of boundaries, initial particle locations, locations of sources and sinks
to be commensurate with the step size. Given this restriction, the possible outcomes for a particle on a boundary are shown schematically in Figure 2.5. The
directional probabilities are identical to those in a homogeneous (region given
above) except that the conditional probability of moving to the left and to the
right given that the particle did not expire (p and q in the homogeneous region)
are independently specied at each internal boundary. The step size to the left
is equal to the step size in the region to the left of the boundary; the step size
to the right is equal to the step size in the region to the right of the boundary.
18
Figure 2.6: The RW Control gure.
2.3
MATLABs command window) RW Control and RW Particle set #1.
2.3.1
RW Control
The RW Control gure controls the random walk software and is shown in Figure 2.6. The part of the RW Control gure below the menubar is divided into two
panels. The left panel indicates which of the two independent simulations are to
be displayed the choices are Particle Set #1 and/or Particle Set #2. When RW
is selected, Particle Set #1 is selected by default.
The right panel allows the simulation to be started, paused, continued, or
reset. If Reset is chosen, the step counter is set to 0 and the particle locations
are reset to their initial locations. The # steps in the random walk before the
simulation pauses can be entered in the text edit box. Clicking 1-step executes
one step of the random walk. A counter for the current number of steps in the
random walk is displayed.
2.3.2
RW Particle
The RW Particle gure shows the locations of particles in the eld as shown for
an initial distribution of particles in Figure 2.7. When the simulation is started
by clicking the Start button in the RW Control gure, the random walks of the
particles are exhibited in the RW Particle gure. A step counter indicates the
number of steps taken in the random walks. After 100 steps of the random
walks of particles, the RW Particle gure is as shown in Figure 2.8.
Several options are provided in the RW Particle gure. The user can select
Param to change the parameters of the random walk, Summ to obtain a numerical summary of statistics of the random walk, Hist to obtain a histogram of
particle positions, and Graphs to obtain plots of statistics versus step number.
These options are described in detail below. The RW Particle gure also has options to Open a le that contains a particle distribution, Save the current particle
distribution in a le, and Print the current gure. Clicking on Save saves the following: the current state of all the particles including the expected locations of
particles, the histogram binwidth, the step #, and all the parameters.
19
Figure 2.7: RW Particles gure showing the initial locations of particles. Initially there
are 50 particles located at position 200 and spread randomly with a uniform distribution in the vertical direction.
Figure 2.8: RW Particles gure showing the locations of particles after a 100 step random walk for the initial locations of particles shown in Figure 2.7.
20
Figure 2.9: RW Parameters gure showing the parameters used to dene the simulations whose particle distributions are shown in Figures 2.7 and 2.8.
RW Parameters
Choosing Param in the RW Particles gure displays the RW Parameters gure,
shown in Figure 2.9, which allows selection of the parameters of the simulation.
Region #1 is indicated in blue in both the RW Parameters gure and in the RW
Particle gure; magenta is used for region #2 and green for region #3. After new
parameters are chosen, clicking on Update resets the initial distribution to the
newly selected one and activates all the new parameters. The parameters are
described below. In addition, the parameters (alone) can be saved in a le (by
clicking on Save) or read from a le (by clicking on Open).
Region Size. The user may dene up to three regions, whose combined
width may not exceed 400. To eliminate a region, enter 0 for the region
size. Regions can also be of size k(stepsize) where k = 3, 4, 5, .... That is,
regions of size stepsize and 2(stepsize) are not allowed.
Step Size. The step size can be specied independently in each region.
Initial Distribution Of Particles. The initial distribution of particles can
be specied independently in the three regions. Particles start at locations
that are integral multiples of the step size in each region. Particles are
distributed randomly (with a uniform distribution) in the vertical direction
and have the selected distribution in the horizontal direction. The initial
distribution of particles can be selected to be one of the following.
21
Empty implies that initially there are no particles in the region.

Pulsatile implies that a specied number of particles are placed at
a specied horizontal location in the region and spaced randomly in
the vertical direction. Figure 2.7 shows an initial distribution that is
pulsatile.
Linear implies that a linear concentration prole is generated whose
slope and number of particles are specied. A uniform distribution of
particles is obtained if the slope is set to zero. Negative concentrations
are not allowed: if the parameters are chosen such that the concentration would become negative at some point in the region, these putative
negative concentrations are set to zero.
Sinusoidal implies that the spatial distribution is sinusoidal with a
specied period and number of particles.
Right Step Prob. The conditional probability of a step to the right given
that the particle has not expired can be specied independently in each
region.
Left Step Prob. The conditional probability of a step to the left given that
the particle has not expired cannot be specied. It is set automatically so
that in each region, the sum of the probabilities of all possible outcomes is
one.
Stay Prob. The conditional probability that the particle stays in the same
location given that the particle has not expired can be specied independently in each region.
Probabilities at Boundaries.
The perimeter boundaries of the eld act

as reecting boundaries; the boundaries between regions are characterized
by user-dened boundary conditions. Boundary conditions are dened as
shown in Figure 2.9: left-step-probability L, stay probability S , and rightstep-probability R at the boundary between regions. For example, if the
Region #1-#2 has the set of probabilities (L, S, R) = (0, 0, 1) then particles
at the boundary may only step to the right. Therefore, to a particle from Region #2, this looks like a reecting boundary, whereas all particles reaching
the boundary from Region #1 will cross into Region #2. As with the directional probabilities within a region, the user selects the conditional (on not
expiring) probability of a step to the right and the conditional probability
of no step; the conditional probability of a step to the left is then computed
so that probabilities of all possible outcomes sum to one.
Source. One source can be placed at a horizontal location in the eld and
covers the entire vertical height of the eld. The source must be located at
an integer multiple of the step size from the left boundary of each region
22
Figure 2.10: RW Summary gure

showing a numerical summary of
statistics after a 100 step random
walk for the same parameters as
shown in Figure 2.9 and for the initial locations of particles shown in
Figure 2.7.
in which it is located. The rate of generation of particles is specied by

giving the number of particles (specied as a two-digit number) produced
in some number of time steps (specied as a two-digit number). Thus the
rate of generation of particles can be a rational number. The particles
are generated at the horizontal location of the source and are distributed
randomly along the vertical direction using a uniform distribution. When
the source is turned on, a small + is placed at the horizontal location of
the source just above the eld.
Sink. A sink can be placed at a horizontal location in the eld and covers
the entire vertical height of the eld. The sink is located at an integer
multiple of the step size from the left boundary of each region in which it
is located. Particles that land on the sink are absorbed; hence the number
of particles at the sink is always zero. When the sink is turned on, a small
is placed at the horizontal location of the sink just above the eld.
Average Lifetime. The user may dene the average particle lifetime dened as the number of steps it takes, on average, for the particle to expire.
RW Summary
Choosing Summ in the RW Particles gure pauses the simulation and displays
numerical values of statistics in the RW Summary gure as shown in Figure 2.10.
Two sets of computations are performed simultaneously during a simulation:
statistics based on the actual locations of particle and statistics based on the
expected locations of particles. Given a particle location at one step and a set
of directional probabilities, a random number generator is used to determine
which of the possible new locations occurs at the next step. These sequence
of locations determines the locations of the particles on the screen and all the
statistics labelled actual. However, given a particle location at one time and the
23
same directional probabilities, an expected location of the particle in the next

step is also computed. Thus, during a simulation both the set of actual and
expected locations for the particles are computed and can be displayed.
The available statistics (both actual and expected) are as follows.
Mean is the mean location of the particles in the entire eld.

Standard Deviation is the standard deviation of particle location in the
entire eld.
#Generated is the cumulative number of particles generated by the source

#Absorbed is the cumulative number of particles absorbed by the sink

#Expired is the cumulative number of particles lost (due to their nite

lifetimes) since the beginning of the simulation.
Total #Particles is the total number of particles in the entire eld at each
step number.
Region 1 #Particles is the total number of particles in Region 1 at each

step number.


RW Histogram
Choosing Hist in the RW Particles gure pauses the simulation and displays the
RW Histogram gure (Figure 2.11). Histograms summarize the spatial distribution of particle locations; both the actual and the expected distribution of
particle locations are shown. Each histogram consists of a set of bins that spans
the eld in the horizontal direction; the number of bins depends upon the specication of the bin size. With a bin size of 16, there are 25 bins that span the
entire eld of 400 locations. The histogram shows the number of particles in
each bin as a function of bin location. Choice of bin size is important. A small
bin size depicts the particle distribution with high spatial resolution. However,
a small bin size implies that each bin will contain relatively few particles and the
number of particles will uctuate randomly from bin to bin. Conversely, a large
24
Figure 2.11: RW Histogram gure showing a histogram of particle locations after a 100
step random walk for the same parameters as shown in Figure 2.9 and for the initial
locations of particles shown in Figure 2.7. The histogram is for the particle locations
Figure 2.12: RW Axis gure showing options

for changing axis properties.
bin size gives a histogram with poor spatial resolution but a larger amount of
statistical averaging of the spatial distribution of particles.
The shape of the histogram is sensitive to the choice of bin size and can lead
to confusing patterns. For example, suppose the bin size is ve and the step
size is two. Suppose further that particles are located uniformly in the eld; one
particle per accessible location. However, the step size constrains the possible
locations that a particle may occupy to be separated by 2. Therefore, with a bin
size of ve, successive bins in the histogram alternate between 2 and 3 particles.
Thus the histogram will not appear uniform, but oscillatory. This problem is
cured if the bin size is an integral multiple of the step size. If the step sizes
dier in the three regions, then the bin size should be set equal to the least
common multiple of the three step sizes.
Clicking on either the ordinate or the abscissa axis label displays the RW Axis
gure (Figure 2.12) that allows the user to change the axis scale. The scale is
indicated by a vector [min max] in which min represents the minimum value and
max represents the maximum value of the range. Clicking on Log makes the axis
scale logarithmic.
25
Figure 2.13: RW Graph gures showing the mean (above) and the standard deviation
(below) of particle location versus step number for the same parameters as shown in
Figure 2.9 and for the initial locations of particles shown in Figure 2.7.
RW Graph
Choosing Graphs in the RW Particles gure pauses the simulation and displays
the RW Graph gure. The temporal evolution of any of the summary statistics
shown in Figure 2.10 can be plotted versus the step number. Figure 2.13 shows
an example of both the mean and the standard deviation of particle locations
plotted versus step number. Clicking on either the ordinate or the abscissa axis
label displays the RW Axis gure that allows the user to change the axis scale (as
in Figure 2.12).
These statistics allow a quantitative evaluation of simulation results. We give
a number of examples of the use of these statistics. A systematic change in
the mean location of the particles as a function of step number demonstrates a
drift or migration of the particles as can be achieved by a bias in the directional
probabilities. A dierence in the standard deviation of two distributions can
26
be achieved by changing the step size. The dependence on step number of the
number of particles in the eld, in a region, generated, absorbed, or expired can
be used to assess whether a particle distribution has reached steady state. The
change in the total number of particles in each region can be used to estimate
the rate of transport of particles between regions.
2.4
Problems
Problem 2.1 The purpose of this problem is to explore random walks from an
initial distribution where all particles begin from the same horizontal location.
a. Use the default simulation parameters with a pulsatile initial distribution
of particles but set the step size to 2 and 4 for Particle Sets #1 and #2,
respectively. The parameters of Particle Sets #1 and #2 should dier only
in step size. Run the simulation for 100 steps. Examine graphs of the
mean and the standard deviation of the horizontal locations of the particles
versus step number.
i. Explain quantitatively the dierences in the graphs in terms of the
dierence in step size of the two simulations.
ii. Why does the slope of the standard deviation decrease with step number? What type of dependence on step number do you expect? Explain.
[Hint You may wish to replot the graph in dierent coordinates to
check out your expectations.]
b. Now set the step size to 2 for both simulations and decrease the number
of particles in the pulsatile initial distribution for one of the simulations
to 25. Rerun the simulation. Describe how the number of particles aects
the dependence of mean location and standard deviation on step number?
Explain your results.
c. Set all the parameters at their default values and then set the step size
for both Particle Sets #1 and #2 to 2. For Particle Set #1 set the right step
probability to 0.75, the left step probability to 0.25, place an impulse of 50
particles at location 100. For Particle Set #2 set the right step probability
to 0.25, the left step probability to 0.75, place an impulse of 50 particles
at location 300. Run the simulation for at least 100 steps. Examine graphs
of the mean and the standard deviation of the horizontal locations of the
particles versus step number. Explain your results quantitatively.
Problem 2.2 The purpose of this problem is to explore the steady-state distribution of particles in the presence of a source and sink for both unbiased and biased
random walks. For all parts of this problem set the parameters for both Particle
2.4. PROBLEMS
27
Sets #1 and #2 as follows: make the size of Region #1 400; the step size 20; and
make the initial distribution of particles empty. Also place a source at location
0 and a sink at location 400 and make the histogram bin size 20.
a. Make the random walks for both Particle Sets #1 and #2 unbiased with a
right step probability of 0.5. For Particle Set #1 make a source that generates 1 particle every 2 steps and for Particle Set #2 make a source that
generates 1 particle every 1 step. Make the particle lifetime innite for both
simulations. Now run the simulation. In the steady-state, by denition the
particle distribution will not depend upon step number.
i. Before you run the simulation, estimate the form of the steady-state
particle distribution. Will it be uniform, exponential, pulsatile, linear,
Gaussian, or none of these?
ii. Using the available statistics, determine a criterion for estimating when
the particle distribution is in steady state.
iii. Now run the simulation until your criterion for steady state is met.
Look at the histograms of particle location. What is the steady-state
particle distribution? Does it t with your initial expectation? There
are dierences between the actual and expected histograms. Explain
these dierences.
iv. How can you explain the dierence in steady-state distribution for
Particle Sets #1 and #2?
v. Show that the steady-state particle distribution you have found for the
random walks is consistent with Ficks laws.
b. Use the same parameters for Particle Set #2 as in part a, but change those
of Particle Set #1 so that the source rate is also 1 particle every 1 step; and
so that the probability of a right step is 0.55. Run the simulation until it
has reached a steady state.
i. Compare the steady-state distributions for the biased and unbiased
random walks. How do they dier?
ii. Describe the shape of the steady-state distribution for the biased random walk?
iii. Modify Ficks rst law to account for not only diusion of particles but
a steady drift of particles of velocity v. Determine the steady-state
distribution of particles predicted from Ficks laws and the continuity equation in the presence of this steady drift of particles. Is this
distribution consistent with the simulation results you obtained?
c. Keep the parameters of Particle Sets #1 and #2 the same as in part b, but
change the right step probability of Particle Set #2 to 0.48. Explain the
28

dierences in the shapes of the steady-state distributions for the two simulations.
Problem 2.3 The purpose of this problem is to explore the eect of a nite particle
lifetime on the statistics of a random walk.
a. Dene a simulation with an initial particle distribution that is uniformly
distributed in space. Set the average particle lifetime to be nite. Run
the simulation until all the particles have expired. Examine a graph of #
particles versus step number. Explain the shape of this function.
b. Dene another simulation that is identical with the one in part a, but this
time with a source of particles. Do you expect a steady state to be reached
between the the source and expirations? Determine a criterion for steady
state and check out your intuition.
c. Design a combination of source rate and lifetime such that the distribution
reaches a steady state. This might correspond, for example, to a drug
concentration reaching steady state in the body, as it is both infused and
eliminated.
d. Design a combination of source rate and lifetime such that most particles
in the region have expired by the time the source injects the next batch.
This might correspond to the drug concentration when the dosing interval
is longer than the elimination half-life of the drug.
Problem 2.4 The purpose of this problem is to explore random walks in three
regions which simulates diusion through a membrane that separates two baths.
Set up the parameters as shown in Figure 2.14. For both simulations, the two end
regions contain uniform concentrations of particles; but the number of particles
diers. There is a concentration dierence between the end regions as shown
in Figure 2.15 for one of the simulations; the other is similar. The center region
can be regarded as a membrane that separates the two end regions and initially
contains no particles. The random walk in the membrane region is unbiased in
one simulation and biased in the other. Run the simulation for several hundred
steps.
a. Explain the dierences between the distributions of particles for the two
simulations.
b. Quantitatively describe the ux of particles between the two end compartments both the magnitude and sign of the ux.
c. What physical process might be represented in the simulation with Particle
Set #2?
2.4. PROBLEMS
Figure 2.14: Parameters for a random walk in 3 regions (Problem 2.4).
29
30
Figure 2.15: Initial locations of particles for a random walk in 3 regions (Problem 2.4).
Problem 2.5 The purpose of this problem is to explore random walks in three
regions which simulates diusion through a membrane that separates two baths.
Design a three region diusion regime where the center region is considered
to be a membrane. Design membrane characteristics such that the membrane
is transparent for particles moving from left to right but purely reecting for
particles moving from right to left. Test your design by running the simulation.
Problem 2.6 The purpose of this problem is to examine the steady-state particle
distribution that results in the presence of sources and sinks. Start with two identical simulations with Regions #1 and #2 that have: a region size of 400; a step
size of 2; unbiased random walks; no sources or sinks; innite particle lifetimes;
and sinusoidal initial particle distributions. Choose one simulation with a period
of 200 and the other with a period of 50. Choose an appropriate bin size for the
histograms. Run the simulation.
a. What is the shape of the equilibrium distribution of particles?
b. Which particle distribution approaches this equilibrium faster?
c. Experiment with dierent frequencies and generalize your conclusion from
part b.
Problem 2.7 The purpose of this problem is to examine the factors that inuence
the equilibrium distribution of particles and the time to reach equilibrium. This
problem deals with a random walk in two regions. Make the size of Regions #1
and #2 each 50 steps wide and set the step size to 5 in each region. Let the initial
distribution of particles in Region #1 be 50 particles distributed uniformly and
2.4. PROBLEMS
31
let the initial distribution of particles in Region #2 be empty. Run the simulation
until equilibrium is reached. Plot the number of particles in Regions #1 and #2
as a function of step number.
a. Estimate the initial Ni and nal Nf values of the number of particles in
each region and explain these values.
b. Dene the equilibrium time as the time taken for the number of particles to change from 0.1|Nf Ni | to 0.9|Nf Ni | and estimate the value of
for both Regions #1 and #2.
c. The region size aects the time course of particle number in each region.
Run simulations with the size of Regions #1 and #2 set to 25 steps and to
100 steps and measure Ni , Nf , and for each value of region size. How
do Ni , Nf , and depend upon regions size for the three sizes used in your
simulations? Explain.
d. Assume that the probabilities for steps are unchanged, which other RW
parameters will aect the time course of particle number in each region?
Indicate how the parameter will aect the time course and test your suggestion by performing appropriate simulations and measuring Ni , Nf , and
.
32
Chapter 3
MACROSCOPIC DIFFUSION PROCESSES
33
34
3.1
3.1.1
Introduction
Background
Diusion is an important transport process in physical, chemical, and biological systems. Two theoretical models of diusion capture complementary aspects of the phenomenon. The microscopic model describes the probabilistic
behavior of a population of individual solute particles which execute statistically independent, but otherwise identical, random walks. Software dealing with
such a microscopic model of diusion is described in Chapter 2. The software
described in this chapter involves macroscopic diusion which describes the
aggregate behavior of large populations of solute particles.
3.1.2
Macroscopic model of diusion
In 1855, Adolph Fick proposed a macroscopic model for passive diusion (Fick,
1855). By analogy to Fouriers law of heat conduction and Ohms law for electrical conduction, Fick proposed that the ux of solute at a point in space is
proportional to the concentration gradient at that point. Mathematically, this
relation is expressed by Ficks rst law, which, in its one-dimensional form, is as
follows:
c
,
(3.1)
= D
x
where c(x, t) is the solute concentration and (x, t) is the solute ux. The
constant of proportionality, D, is known as the diusion coecient. Conservation
of solute (in the absence of sources or sinks or of chemical reactions that create
or destroy solute) results in a second relation between concentration and ux,
the continuity equation:
c
= .
(3.2)
x
t
Dierentiating both sides of Equation 3.1 with respect to x and using the continuity equation yields Ficks second law, or the one-dimensional diusion equation:
2c
c
=D 2
(3.3)
t
x
In principle, any one-dimensional diusion process can be modelled by solving
this equation subject to the appropriate initial conditions and boundary conditions.
We next consider the same problem but with two changes: (1) a body force
acts uniformly on the solute so that it drifts (migrates) and (2) a chemical reaction occurs that removes solute. The solute ux, (x, t), is now the sum of the
diusive ux, given by Ficks law, and the ux due to drift. Thus, in this case,
= D
c
+ vc,
x
(3.4)
3.1. INTRODUCTION
35
where v is the drift velocity of the solute; i.e., the velocity of the solute in response to the body force in the absence of diusion. If r is the reaction rate at
which solute is removed, then the continuity equation becomes
c
=
r c.
x
t
(3.5)
Combining these expressions yields a modied diusion equation:

2c
c
c
=D 2 v
r c.
t
x
x
(3.6)
Thus, solute drift and a chemical reaction that removes solute contribute additional terms to the diusion equation.
If the initial concentration, c(x, 0) is known in some region of space and if the
relation between the concentration and ux is known at each boundary of this
region, then a unique solution exists for t > 0. Given an initial concentration
prole, c(x, 0), Ficks laws govern the unique evolution of the concentration
prole for all later times.
3.1.3
While macroscopic diusion has been successfully modelled by Ficks equations,

studying the equations alone provides only limited insight into the behavior of
diusion processes. The goal of this software is to help users gain intuition
about diusion in one dimension. The solutions to the diusion equation are
functions of two variables: one spatial variable, x, and time, t. These solutions
can be plotted either as a function of time at a particular point in space or as a
function of the spatial variable at a particular instant in time. Such isolated snapshots, however, do not fully convey the dynamic behavior of diusion processes.
With this software, the user can view the temporal evolution of the solute concentration and solute ux as a function of position. Thus, the software enables
the user to gain intuition about the dynamic behavior of macroscopic diusion
processes.
Furthermore, the software provides an opportunity for users to experiment
with the macroscopic diusion processes. For example, the user can explore
how changing the diusion coecient aects the time-course of the simulation.
The user can also specify transparent or reecting boundaries and can explore
how a body force acting on the solute or a chemical reaction that removes solute
inuence the diusion process. Thus, the software can be used as a tool for investigating how various parameters and boundary conditions inuence diusion
processes.
Five options for initial concentration proles, corresponding to ve characteristic diusion problems, are implemented in the software (Figure 3.1). Four
of these problems involve diusion from a specied initial concentration prole
Initial concentration
36
Impulse
Sinusoid
Discontinuity
Arbitrary
Bath 1 M
Bath 2
Position
Two compartment
Position
Figure 3.1: Schematic representation of the ve classes of initial concentration proles

simulated by the software. M designates the membrane.
in a one-dimensional region of space (which may be innite in extent), while the

fth involves diusion between two nite, well-mixed compartments separated
by a membrane.
One-dimensional diusion
In one-dimensional diusion, the initial concentration can be chosen to be one
of four options: impulses, sinusoids, discontinuities, and an arbitrary spatial
distributions. An impulse of solute concentration is a mathematical idealization
corresponding to a nite amount of solute initially concentrated at a single point
in space. In the impulses option, the user can specify the magnitude and position of up to four impulses. This option illustrates diusion from point sources.
The sinusoids option illustrate the spatial frequency response of a system governed by the diusion equation, specically, the low-pass spatial ltering eect
of diusion. By superimposing up to four sinusoids, the user can observe the dependence of the space-time evolution of concentration on its spatial frequency
content. In the discontinuities option, the initial concentration prole may be
piecewise-constant but contain discontinuities. The user can specify the magnitude and location of up to four such discontinuities. For example, this allows
simulation of the diusion that results from an initial rectangular pulse of solute concentration. The user can also explore the response for more complicated
initial conditions which can be specied by drawing an arbitrary initial concentration on the monitor screen with a mouse.
37
For these dierent initial distributions, the user can specify the boundary
type (transparent or reecting), the value of the drift velocity, and the chemical
reaction rate at which solute is removed.
Two-compartment diusion through a membrane

The baths are assumed to be well-stirred, so that the concentration within each
bath varies with time but not with position in the bath. The total amount of
solute in the system is assumed to be nite. The user can specify the width of
each bath and of the membrane, the initial concentration of each bath, and an
arbitrary initial concentration prole in the membrane.
3.2
Methods of Solution
For several of the diusion problems implemented in the software, analytic solutions of the modied diusion equation (Equation 3.6) are available in a form
that makes computation ecient. Such solutions have been used wherever possible. The remainder of the solutions were obtained by numerical methods. The
methods are described in some detail elsewhere (Berkenblit, 1990); only a brief
summary of the methods is given here.
The method used to obtain solutions depends upon the type of boundary
condition. Two types of boundary conditions for the diusion problems can be
selected by the user: transparent or reecting boundary conditions. If transparent boundaries are specied, then the region over which diusion occurs is
innite; the spatial limits of the region over which diusion is displayed are
set by the user. At a reecting boundary, on the other hand, the solute ux is
constrained to be zero, since no solute particles can cross such a boundary.
3.2.1
Analytic solutions
Analytic solutions were used to compute the response for all one-dimensional
diusion problems with transparent boundaries. These are described in this
section.
Impulse response Greens function

No drift, no chemical reaction. First, we consider the case when the drift velocity is zero and the chemical reaction rate is zero. Let the initial concentration
be a unit impulse located at position x = and delivered at time t = 0,
c(x, 0) = (x ).
(3.7)
38
The solution of the diusion equation (Equation 3.3), called the Greens function
G(x, t; , 0), is
1
2
e(x) /4Dt .
c(x, t) = G(x, t; , 0) =
4 Dt
(3.8)
Thus, the concentration prole is a Gaussian

function of the spatial variable.
The standard deviation of the concentration, 2Dt, increases with increasing
time, but the total area of the concentration remains constant because solute is
conserved.
Drift but no chemical reaction. We next consider the same problem but with
a non-zero drift velocity. In this case, the concentration satises the modied
diusion equation, Equation 3.6, with r = 0:
2c
c
c
=D 2 v
,
t
x
x
(3.9)
c(x, 0) = (x ).
(3.10)
with the initial condition

The solution can be shown to be
1
2
c(x, t) =
e(xvt) /4Dt = G(x vt, t; , 0).
4 Dt
(3.11)
Thus, the response in this case is a Gaussian function, as before, but the entire
prole drifts in the positive x-direction with drift velocity v.
Drift and chemical reaction. With a non-zero chemical rate, r , and drift velocity, v, we need to solve Equation 3.6 which has a solution
c(x, t) = er t G(x vt, t; , 0).
(3.12)
In general, if c (x, t) is the solution to Equation 3.3, with a specied initial concentration prole and transparent boundaries, then the solution to the modied
equation, 3.6, satisfying the same initial conditions, is given by
c(x, t) = er t c (x vt, t).
(3.13)
Sinusoid
First we consider the solution to Equation 3.3 with the initial condition
c(x, 0) = A (1 + sin(x + ))
(3.14)
39
for some arbitrary constant amplitude, A, spatial radian frequency, , and phase
angle, . The solution for t > 0 is given by

2
(3.15)
c(x, t) = A 1 + eD t sin(x + ) ,
which can be veried by substituting this expression into Equation 3.3. Thus,
an initially sinusoidal concentration prole remains sinusoidal for all later time,
but the amplitude decreases exponentially with time. The rate of attenuation is
proportional to the square of the spatial frequency.
With drift and a chemical reaction between solute and solvent, the solution
is

2
c(x, t) = Aer t 1 + eD t sin (x vt) + ,
(3.16)
where v is the drift velocity and r is the reaction rate.
Discontinuous initial prole
We next consider the case of an initial prole that is piecewise-constant but
contains a jump discontinuity at x = . The initial condition is that

cL , x <
,
(3.17)
c(x, 0) =
cR , x >
which can also be written as
c(x, 0) = cL + (cR cL )
(x x ) dx .
(3.18)
For t > 0, we can integrate the Greens function dened by Equation 3.8 to obtain
the solution:

G(x, t; x , 0) dx
c(x, t) = cL + (cR cL )

1
2
e(xx ) /4Dt dx
= cL + (cR cL )
4 Dt

x
1
,
(3.19)
= cL + (cR cL ) 1 erfc
2
2 Dt
where the complementary error function, erfc(x), is dened by the integral

2
2
erfc(x) =
et dt.
(3.20)
x
With a drift velocity, v, and reaction rate, r , the solution is

x vt
1
r t
r t
c(x, t) = cL e
+ (cR cL )e
1 erfc
.
2
2 Dt
(3.21)
40
3.2.2
Numerical Solutions
One-dimensional problems with reecting boundaries and the two-compartment

problem are solved using numerical methods. To solve a diusion problem numerically over some specied spatial region and some specied time interval,
the position and time variables are discretized. Denoting the time increment by
t and the position increment by x, we dene
j
ui = c(xi , tj ),
(3.22)
where
xi = x0 + ix, i = 1, . . . , N
tj = t0 + jt,
j = 1, . . . , M.
(3.23)
A general approach to solving partial dierential equations numerically is to

replace the partial derivatives by nite-dierence approximations. The nitej
dierence expressions involve the ui terms dened above and result in sets
of algebraic equations that can be solved by numerical methods for solving
matrix equations. In the software, the equation with no drift term is solved
by the implicit Crank-Nicolson algorithm, while for problems with a non-zero
drift term, this algorithm is combined with the explicit Two-Step Lax-Wendro
method (Press et al., 1988; Gerald and Wheatley, 1989). When a non-zero chemical reaction rate, r , is specied, the computed concentration is multiplied by
the attenuation factor, er t . The Crank-Nicolson and Lax-Wendro formulas involve the parameters = Dt/(x)2 and = vt/x. The numerical methods
give stable solutions provided < 0.5 and || 1. For the two compartments
option, the boundary conditions at the membrane solution interface is that the
concentration in the membrane at the interface is equal to the bath concentration.
3.2.3
Summary
A variety of techniques are used to nd analytic solutions to one-dimensional

diusion problems with transparent boundaries. The specic methods used in
the software to solve one-dimensional problems depend on the initial conditions and are summarized in Table 3.1. With two reecting boundaries and in
the absence of drift, the analytic solutions consist of innite series. Thus it is
cumbersome to compute these analytic solutions. With two reecting boundaries and with drift, analytic solutions are in general not available. Therefore,
we have chosen to solve these problems numerically using the Crank-Nicolson
and Lax-Wendro methods. The latter methods are also used to compute the
solutions to the two-compartment problem.
41
Option
Boundary Type
Computational Method
Impulse
Transparent
Analytic solution
Reecting
Crank-Nicolson
Sinusoid
Transparent
Analytic solution
Discontinuity
Transparent
Analytic solution
Reecting
Crank-Nicolson
Reecting
Crank-Nicolson
Arbitrary
Two-Compartment
Crank-Nicolson
Table 3.1: Summary of computational methods.
Figure 3.2: The MD Control

gure.
3.3
MATLABs command window) MD Control, MD Initial concentration prole,
MD Plots vs. position, and MD Plots vs. time. A typical session with the software
consists of selecting one of ve initial concentration prole options, selecting
the values of parameters, executing a simulation, and viewing the simulation
results.
3.3.1
MD Control
The MD Control gure controls the macroscopic diusion software and is shown
in Figure 3.2. The part of the MD Control gure below the menubar is divided
into three panels. The left panel controls the display of the initial concentration
and the numerical parameters of the simulation abbreviated as numerics. The
middle panel controls calculation of the simulation, and allows the simulation to
be started, paused, continued, or reset. The user can select the number of steps
in time for computing the simulation results. The interpoint time is adjustable
in the numerics gures (described later). The Time is the elapsed simulation
time since the simulation was started. Clicking on 1-step results in the computation of one step of the simulation. The simulation results and parameters
can be saved to a le and read from a le. Clicking on Save saves the follow-
42
ing items in a le: all the initial prole parameters, the numerical parameters,
concentration and ux versus position and versus time. Clicking on Open reads
these same quantities from a le. The right panel (the Simulation results panel)
controls the display of simulation results. Clicking on a selection box displays
the appropriate gure; clicking again hides it.
3.3.2
MD Initial concentration prole
The MD Initial concentration prole gure allows control of the initial concentration and all the parameters of the diusion process. The four one-dimensional
diusion problems and the two-compartment problem are implemented in the
software as ve options called: Impulses (Figures 3.3), Sinusoids (Figures 3.5),
Discontinuities (Figures 3.6), Arbitrary (Figures 3.7), and Two Compartments
(Figures 3.8). To change the prole type, the user clicks on the prole pushbutton in the MD Initial concentration prole gure. Each pushbutton has an
icon suggesting the initial prole type. Parameters can be viewed by clicking on
Parameters in the same gure which results in the display of the appropriate
parameters gure. Parameters can be changed by typing in the text edit box.
To activate the new parameters, the user must click on Update either in the MD
Parameters gure or in the MD Initial concentration prole gure; these actions
are equivalent. Information about the initial prole and parameters (alone) can
be saved in a le by clicking on Save or read from a le by clicking on Open.
These actions can be done either in the MD Parameters gure or in the MD Initial concentration prole gure; they are equivalent.
Features of initial proles and parameters common to all options
Variables. The initial concentration is plotted in the MD Initial concentration
prole gure (Figures 3.3, 3.5, 3.6, 3.7, and 3.8). Check boxes in the upper lefthand and the upper right-hand corners allow display of the initial concentration
and/or the initial ux.
Axes scales. An axis scale can be changed by clicking on its label to display the
Axis-scale gure Figure 3.4. The new axis limits can be typed into the edit boxes
to change the axis.
Markers. There are two markers that are indicated by two green triangles on
the abscissa of both the MD Initial concentration prole gure and the MD Plots
vs. position gure. These markers indicated positions at which the concentration
and ux can be displayed as a function of time in the MD Plots vs. time gure.
The positions of these markers can be controlled numerically or graphically. Numerical control is achieved by typing into the appropriate text edit box in the parameters gure (Figures 3.3, 3.5, 3.6, 3.7, and 3.8). Graphical control is achieved
43
Figure 3.3:
Initial concentration prole for impulses; MD Initial concentration prole gure
(above), MD Impulse prole parameters gure for
impulses (below). A single impulse located at position 0.5 cm of area 10 is
specied.
Figure 3.4: MD Axis scale gure when the

abscissa is chosen in the MD Initial concentration prole gure.
44
by clicking just below the abscissa axis in the MD Initial concentration prole
gure. The left marker is controlled by clicking the left button on a two-button
mouse or by clicking the button on a single-button mouse. The right marker is
controlled by clicking the right button on a two-button (or three-button) mouse
or by shift-clicking the button on a single-button mouse.
Parameters. In the MD parameters gure for each option, the user can select a
parameter by clicking on it and then modify that parameter by typing the new
value in the text edit box. This modication is terminated by a carriage return or
by selection of another parameter. One panel displays the Diusion parameters
diusion coecient, drift velocity, and chemical reaction rate which are set
independently for each option. For the two compartments option these diusion
parameters apply to the membrane and not to the baths.
After all the parameters in the gure have been changed, the user must press
Update before the new parameters are reected in both the MD Initial concentration prole gure and the MD Plots vs. position gure. All the parameters for
each option can be saved in a le and read from a le.
Descriptions of the ve options
For each option, the user can modify the values of parameters, change all graph
parameters, and run a simulation.
Impulses. When the software is initiated, Impulses is the default initial concentration prole and the MD Initial concentration prole gure is shown in Figure 3.3. The areas and positions of 4 impulses can be specied by the user as
shown in the parameters gure so that the initial concentration has the form
A1 (x x1 ) + A2 (x x2 ) + A3 (x x3 ) + A4 (x x4 ),
where (x) is the unit impulse located at x = 0, Aj and xj are the area and
position of the jth impulse. The positions of each impulse can be set only if
its area is non-zero. Since the initial ux is the spatial derivative of the initial
concentration, if the concentration contains an impulse (x xo ) at x = xo then
the ux contains a doublet (xx

o ) at x = xo which is signied by a two-headed
arrow. Either transparent boundaries or reecting boundaries can be chosen and
the locations of right (R) and left (L) reecting boundaries can be specied.
Sinusoid. In the Sinusoid option, the amplitudes, spatial frequencies, and phase
angles of four sinusoids can be specied (Figure 3.5) so that the initial concentration has the form
A1 (1 + sin(2 f1 x + 1 )) + A2 (1 + sin(2 f2 x + 2 )) +
A3 (1 + sin(2 f3 x + 3 )) + A4 (1 + sin(2 f4 x + 4 )),
45
Figure 3.5: Initial

concentration prole for sinusoids;
MD Initial concentration prole
gure (above), MD
Sinusoid
prole
parameters gure
(below). The spatial
frequencies
and
amplitudes of four
sinusoids
were
chosen to correspond to the rst
four terms in the
Fourier series of a
square wave.
where Aj , fj , and j are the amplitude, spatial frequency, and phase of the
jth sinusoid. The spatial frequency and phase of a sinusoid can be set only
if its amplitude is non-zero. Only transparent boundaries are available for the
sinusoid option.
Discontinuity. In the Discontinuity option, the magnitude and position of four

discontinuities can be specied (Figure 3.6) so that the initial concentration has
the form
A1 u(x x1 ) + A2 u(x x2 ) + A3 u(x x3 ) + A4 u(x x4 ),
46
Figure 3.6: Initial concentration prole for

discontinuities;
MD
Initial
concentration
prole gure (above),
MD Discontinuity prole parameters gure
(below).
Two discontinuities were used
to generate an initial
concentration
prole
that is a rectangular
pulse.
where u(x) is the unit step function dened as
1 if x > 0,
u(x) =
0 if x < 0,
and Aj and xj are the amplitude and position of the jth step. The position of a
step can be set only if its magnitude is non-zero. The boundary type (transparent
or reecting) is selectable, and, if the boundaries are reecting, the positions of
the two boundaries can be set.
Arbitrary. In the Arbitrary option, the initial prole is drawn on the monitor
screen by moving the mouse cursor. The details are described in Section 3.3.5.
Only reecting boundary conditions are available for this option, and the positions of the two boundaries are speciable by the user (Figure 3.7).
47
Figure 3.7:
Initial concentration using the arbitrary option; MD Initial
concentration prole gure (above), MD Arbitrary
prole parameters gure
(below).
48
Two-compartment. In the Two compartment option, specication can be made

for the width and the initial concentration in each bath, the membrane width,
and the initial membrane concentration. The initial membrane concentration
prole is drawn with a mouse cursor (as described in Section 3.3.5). The user can
also choose how the two baths and the membrane are to be displayed. Selecting
the View bath option (Figure 3.8) displays the membrane and both baths to scale.
The left boundary of the membrane is located at x = 0. Hence, the left bath is
located for x < 0 and if the width of the membrane is W , the right bath is located
at x > W . Selecting the View membrane option displays the membrane and a
small portion of each bath on each side.
3.3.3
Numerics
Clicking on Analytic parameters or Numeric parameters in the MD Control gure displays the appropriate numerics gure (Figure 3.9). The numerics gures
control the spatial and temporal resolution of the simulation. The MD Analytic
parameters gure deals with those computations that make use of analytic solutions of the diusion equation (i.e., all one-dimensional diusion problems with
transparent boundaries). For this case, the user can select the number of spatial
points at which the solution is computed. The larger the number of points, the
higher the spatial resolution of the computation and the longer it will take to
complete the computation. The user can also specify the temporal resolution of
the computation by selecting the time between samples (integration time).
The MD Numeric parameters gure deals with those computations that use
numerical integration of the diusion equation (i.e., all one-dimensional diusion problems with reecting boundaries and the two-component diusion problem). The user can choose to select the number of points in space at which the
solution is computed. The user has a choice in how the temporal resolution is
to be determined. The numerical method is stable provided an inequality that
relates the temporal and spatial resolutions is satised. If Link is selected, the
simulation determines the integration time to satisfy the inequality and to guarantee a stable integration method which results in an accurate solution. If this
choice is not selected, the user can choose the temporal resolution (integration
time) and spatial resolution independently. However, with this choice there is
no guarantee that the solution will be accurate.
3.3.4
Simulation results gures
There are two gures that display the solute concentration and ux during a
simulation. The MD Plots vs. position gure displays the concentration and/or
the ux as a function of position at each instant in time during the simulation
(Figure 3.10). The current simulation Time is displayed in the upper left part
of the gure. Axes limits can be changed by clicking on the axes labels to dis-
49
Figure 3.8:
Initial concentration for the two
compartments
option;
MD Initial concentration
prole gure for the two
compartments option for
the bath view (top) and the
membrane view (center),
MD
Two-compartment
prole parameters gure
(bottom). The bath view
shows the left bath located between 1 and 0
cm, the membrane located
between 0 and 1 cm, and
right bath located between
1 and 3 cm.
50
Figure 3.9: The MD Analytic parameters and MD Numeric parameters gures.
Figure 3.10: MD Plots vs. position gure.
51
Figure 3.11: MD Plots vs. time gure.
play the Axis-scale gure. The two green triangular markers mirror the markers
shown in the MD Initial concentration prole gure. With the Two compartments
option, the user can also chose how the two baths and the membrane are to be
displayed in the MD Plots vs. position gure. Selecting the View membrane option displays the membrane and a bit of each bath on each side. Selecting the
View baths option displays the membrane and both baths to scale.
The MD Plots vs. time gure (Figure 3.11) displays the concentration and/or
the ux as a function of time during the simulation for two positions selected by
the markers found in both the MD Initial concentration prole gure and the MD
Plots vs. position gure (Figure 3.10). The locations of the markers are indicated
at the top of the gure. Axes limits can be changed by clicking on the axes labels
to display the Axis-scale gure.
3.3.5
Arbitrary concentration proles
For the MD Arbitrary and MD Two compartment options, the user can draw
an arbitrary initial concentration prole by clicking on the Reset/Draw button
which will also erase an existing prole. Drawing a prole consists of generating
a list of concentration values at a corresponding array of positions. The user
selects these points by moving the mouse and clicking any mouse button. After
the rst point is selected by the user, the word Incomplete is displayed over the
prole indicating that the prole is incomplete and does not span the horizontal
52
dimension of the plotting eld. As the pointer moves within the plotting eld in
the MD Initial concentration prole gure, a line joins the last point which was
selected to the current pointer position. When a button is pressed, the position
and concentration that are added to the coordinate arrays depend on the pointer
location:
1. If a mouse button is pressed within the graph axes and to the right of the
previous point, then the coordinates of the pointer location are added to
the list.
2. A mouse button pressed at a position that does not lie to the right of the
previous point is ignored, in order to ensure that the user-drawn concentration prole is a single-valued function of position.
3. If a mouse button is pressed outside the boundaries of the graph (but still
within MD Initial concentration prole gure), then the point that is added
to the list is the point of intersection between the graph boundary and a
line from the previous point to the current position. Thus, while a prole
is being drawn, it is constrained to lie entirely within the boundaries of the
graph.
4. In the arbitrary initial prole, the concentration at the left-hand point of
the prole is set to a default value. The user can change the value of this
point by pressing the mouse button for rst point at the desired vertical
location but to the left of the concentration axis. In the two components
option, the concentration at the left-hand point of the prole is set equal
to the concentration in the left bath (bath #1), and the concentration at the
right-hand point of the prole is set equal to the concentration in the right
bath (bath #2).
5. If the mouse button is pressed outside the MD Initial concentration prole
gure, e.g., on another gure, then the prole is incomplete.
6. An incomplete prole can be completed by pressing Update. In the arbitrary initial prole, a horizontal line segment is drawn from the last chosen point to the right boundary. In the two-compartment option, the last
chosen point is connected to the concentration in the right bath.
7. An incomplete prole can be completed by clicking the mouse button with
the cursor located just to the right of the right boundary of the region. Item
3 (above) gives the rule that indicates the location of the right boundary
point.
Clicking on Update after completion of the prole, activates the initial prole.
3.4. PROBLEMS
3.4
53
Problems
Problem 3.1 The purpose of this problem is to explore the relation between molar
solute concentration and molar solute ux. The diusion coecient is D = 105
cm2 /s.
a. For an initial, spatial sinusoidal solute concentration with an amplitude
of 10 mol/cm2 and a frequency of 1 cm1 , determine the initial spatial
distribution of the molar solute ux.
b. Determine an initial spatial distribution of molar solute concentration such
that the initial spatial distribution of molar ux is a constant of value 1
mol/(cm2 s).
Problem 3.2 The purpose of this problem is to explore the space-time evolution of
solute diusion from a point source. For all parts of this problem use a single impulse and transparent boundaries. Set the impulse strength to 100 moles/cm2 ,
place the impulse at position 0.5 cm, and set the drift velocity and the reaction
rate to zero. Set the marker positions to 0.55 and 0.6 cm unless indicated otherwise. Set the diusion coecient to 105 cm2 /s and run the simulation for 1000
seconds. Obtain a plot of the concentration and ux on appropriate ordinate
scales. You should obtain the spatial distribution of the concentration and the
ux at 1000 seconds and both variables as a function of time at the two marker
positions. Repeat these two steps for a diusion coecient of 4 105 cm2 /s.
a. Briey describe qualitatively the eect of the change in diusion coecient
on the spatial distribution of concentration.
b. For both values of the diusion coecient, determine the maximum amplitude of the concentration versus position and the width of the spatial
distribution of concentration at an amplitude that is e1 of its peak value.
Explain the numerical values of all four measurements. Be brief and precise; state your assumptions explicitly.
c. For the diusion coecient at 105 cm2 /s, examine the concentration versus time at the two positions 0.55 and 0.6 cm. Briey describe, in a qualitatively manner, the dierences in concentration versus time at the two
positions.
d. For the diusion coecient at 105 cm2 /s, measure the maximum concentration as a function of time at the two positions and the time of occurrence
of this maximum. Explain the values of all four measurements. Be brief and
precise; state your assumptions explicitly.
e. Explain the shape of the spatial distribution of ux for a diusion coecient of 105 cm2 /s.
54

f. Explain the relation between the ux and concentration versus time at location 0.55 cm for a diusion coecient of 105 cm2 /s.
g. Rerun the simulation for a diusion coecient of 105 cm2 /s at positions
0.45 and 0.55 cm. Explain the dierences in the ux as a function of time
for these two locations.
Problem 3.3 The purpose of this problem is to explore the space-time evolution
of solute diusion from a point source in the presence of drift. Set the impulse
strength to 100 moles/cm2 ; place the impulse at position 0.5 cm; set the diffusion coecient to 105 cm2 /s, and the reaction rate to zero. Set the marker
positions to 0.75 and 0.9 cm unless indicated otherwise. The parts of this problem that deal with reecting boundaries are solved numerically. To decrease the
time taken for these computations, consider decreasing the spatial resolution of
the computation to 10 points.
a. Set the boundary conditions to transparent and the drift velocity to zero
and run the simulation for 1000 s. Now set the drift velocity to 104 cm/s
and run the simulation again for 1000 s. Describe the eect of the drift
on the spatial distribution of concentration. Account quantitatively for the
position of the peak of the spatial distribution at 1000 s.
b. Set the boundary conditions to reecting and the drift velocity to zero.
Run the simulation until the spatial distribution is no longer a function of
time. This is the equilibrium distribution. What is the spatial distribution
at equilibrium? Explain your answer.
c. Set the boundary conditions to reecting, the drift velocity to 104 cm/s,
and run the simulation. Describe the eect of drift on the spatial distribution of concentration. Illustrate your description with printed copies of the
distribution at characteristic times.
d. With the boundary conditions still set to reecting and the drift velocity
104 cm/s, determine the equilibrium spatial distribution of concentration.
Account quantitatively for this distribution.
e. It is known that the density of air decreases exponentially with distance
above the earths surface. Explain this phenomenon, taking the above simulation results into account.
Problem 3.4 The purpose of this problem is to explore some of the assumptions
that underlie two-compartment diusion. As shown elsewhere (Weiss, 1996a,
Chapter 3), two-compartment diusion is based on 4 assumptions:
1. The two compartments are well-mixed so that the concentrations of solute
n are uniform and have values at time t of cn1 (t) and cn2 (t).
3.4. PROBLEMS
55
2. Solute particles are conserved, e.g., there is no chemical reaction present

that either creates or destroys particles.
3. The membrane is suciently thin and the number of solute particles contained in the membrane at any time is negligibly small.
4. The membrane is suciently thin that at each instant in time the concentration prole in the membrane is in steady state.
This problem concerns the conditions for the validity of assumptions 3 and 4.
Specically, you will explore the eect of bath dimensions on two-compartment
diusion without making these two assumptions.
In all parts of the problem, use the Two compartments option of the software.
Set the membrane width to 0.01 cm, and the concentration of bath #1 to 70 and
bath #2 to 10 mol/cm3 . Leave the drift velocity and reaction rate at 0 and the
diusion coecient at 105 cm2 /s. Set the parameters of the plot of concentration versus position so that the membrane and a little of each bath are visible on
the screen select membrane view. Note that the left edge of the membrane is
at a position of 0 cm. Draw some initial concentration in the membrane. Make
sure all ordinate scales on all plots are 0 to 100 mol/cm3 . Keep these parameters
xed throughout this problem. To reduce the time taken for the computation reduce the spatial resolution in the membrane to 10 points in space. The software
will determine the time increment (DELTA_T). Initially set the number of steps so
that the end time is 5 s.
For each of the pairs of bath widths Bath #1 = 1 cm, Bath #2 = 1 cm; Bath #1
= 0.1 cm, Bath #2 = 0.1 cm; Bath #1 = 0.01 cm, Bath #2 = 0.01 cm; Bath #1 = 0.01
cm, Bath #2 = 0.05 cm; Bath #1 = 0.001 cm, Bath #2 = 0.001 cm; answer the
following questions.
a. Assess the validity of assumption 4.
i. Make rough estimates of both the steady-state (ss ) and equilibrium
(eq ) time constants from the computations.
ii. Estimate the same two time constants based on theoretical considerations (Weiss, 1996a, Chapter 3).
iii. What is your conclusion based on your computations and your estimates of time constants?
b. Assess the validity of assumption 3.
i. Before you do the computation, make an estimate of the nal concentration in each bath. Then do the computation, and check your initial
estimates against the computed values
ii. If they dier, explain the basis of the dierence.
56

iii. How good is the assumption that the quantity of solute in the membrane is negligible? If you decide that the quantity of solute in the
membrane is not negligible, design a simulation experiment to test
your conclusion.
e. Are the bath concentrations exponential functions of time? Explain.
Problem 3.5 The purpose of this problem is to explore the successes and pitfalls of
the method of images for solving diusion problems in the presence of a reecting
boundary. Some problems in diusion with a reecting boundary can be solved
by using the solution for a transparent boundary and the method of images to
match the reecting boundary condition.
In all parts of this problem, set the drift velocity to zero, the reaction rate
to zero, and the diusion coecient to 105 cm2 /s unless state otherwise. The
parts of this problem that deal with reecting boundaries are solved numerically. To decrease the time taken for these computations, consider decreasing
the spatial resolution of the computation to 10 points.
a. Use reecting boundaries, and an initial impulse of concentration of strength
100 moles/cm2 located at 0.2 cm. Run the simulation for 1000 s and obtain
a print of the spatial distribution of concentration at time 1000 s and the
concentration versus time at locations 0 and 0.3 cm.
b. At a reecting boundary, the ux must be zero. Change the boundary
condition to transparent and determine the parameters of two impulses:
one to match the left boundary condition and another to independently
match the right boundary condition. Run the simulation again and compare
with the results in part a. Does this method of images work exactly?
Explain.
Problem 3.6 The purpose of this problem is to explore the space-time evolution of
diusion from an initial sinusoidal concentration prole. Diusion from an initial
sinusoidal concentration distribution gives important insights into the spacetime evolution of diusion processes. In all parts of this problem, use a drift
velocity of zero, a reaction rate of zero, and a diusion coecient of 105 cm2 /s
unless state otherwise.
a. Use an initial concentration that is sinusoidal with amplitude 50 moles/cm2
and a spatial frequency of 1 cycle/cm. Run the simulation for 1000 s and
print the spatial distribution of concentration at 1000 s and the concentration versus time at 0.25 and 0.75 cm. Repeat this procedure for sinusoids
with the same amplitudes but the following spatial frequencies: 3, 5, and 7
cycles/cm. Summarize your results both qualitatively (in words) and then
quantitatively (with suitable calculations).
3.4. PROBLEMS
57
Amplitude
Position
(mol/cm2 )
(cm)
10
100
10
0.4
10
0.6
10
100
Table 3.2: Concentration well Problem 3.7.
b. Construct a periodic waveform from four sinusoids with the following amplitudes (moles/cm2 ) and spatial frequencies (cycles/cm): 105, 1; 35, 3;
21, 5; 15, 7. Run the simulation and observe the spatial distribution of
concentration. Summarize your results and relate them to results of part
a.
c. Switch to the arbitrary initial distribution option and set the boundary conditions to reecting. Using the mouse draw an arbitrary, preferably jagged,
initial prole. This part of this problem uses a numerical solution method
that is time consuming. To decrease the time taken for these computations, consider decreasing the spatial resolution of the computation to 10
points. Run the simulation and watch the spatial distribution of concentration change. Summarize your results. What is the eect of diusion on the
spatial distribution?
Problem 3.7 The purpose of this problem is to explore the time it takes for diusion to take place in a concentration well. We examine the following two estimates
of diusion time.
1. A crude estimate of the time t1 it takes for 1/2 the particles to diuse over
a distance x is t1 = x 2 /D (Weiss, 1996a, Sections 3.2 and 3.3).
2. The time for equilibration of a slab of dimensions 2a so that the average
concentration in the slab is half its nal value corresponds to the condition
Dt2 /a2 = 0.21 (Weiss, 1996a, Figure 3.18).
Dene a concentration well as shown in Table 3.2 and let the diusion coecient
be D = 105 cm2 /s.
a. Run the software and measure the concentration in the center of the well
as a function of time. Estimate the time t3 it takes for this concentration to
reach 1/2 its nal value.
b. Quantitatively compare the estimates t1 , t2 , and t3 .
58

c. Briey discuss the bases of the dierences you found between these three
estimates.
c. Suggest a new method to estimate an equilibration time that will be close to
t2 using the concentration well dened in Table 3.2. Test your suggestion
by performing the computations and making the comparison.
d. Why are there discontinuities in the well at 100? What eect do they have
on the estimates of equilibration time.
Chapter 4
CARRIER-MEDIATED TRANSPORT
59
60
4.1
Introduction
Transport of many solutes including important metabolites (e.g. monosaccharides, amino acids, mononucleotides, phosphates, uric acid, etc.) through cellular membranes is accomplished by membrane-bound carrier molecules that
combine with the solute molecule on one face of the membrane, then translocate in the membrane and uncombine at the other face. Thus, transport involves
chemical reactions in which the solute binds and unbinds with a carrier. This
type of transport is called carrier-mediated transport. Carrier-mediated transport has distinctive properties. For example, the relation of ux to concentration saturates, i.e., it does not obey Ficks law for membranes. In addition, different molecules compete for the carrier. For example, glucose and sorbose (two
monosaccharides) compete for the sugar carrier. Hence, transport of one sugar
can inhibit transport of another simply by occupying a site to which both can
bind.
There are canonical models of carrier-mediated transport that capture important properties of the transport of metabolites through cellular membranes. It
is important to understand these canonical models in order to understand how
metabolites are transported across these membranes. Derivations of predictions
of these models are not particularly dicult to follow; the individual steps are
simple. However, the models typically result in messy algebraic expressions that
relate ux to concentration and transport parameters. Thus, it is easy to get lost
in algebraic manipulation as well as in a sea of parameters so that an intuitive
grasp of the models becomes illusive. The intent of this software is to allow the
user to develop intuition for these models.
4.2
Description Of The Models
Descriptions of carrier-mediated transport as well as models of such transport

processes can be found elsewhere (Stein, 1986; Weiss, 1996a). Here we consider
three models and list both the assumptions and the important results. First,
we consider the steady-state behavior of a simple, four-state carrier that binds
one solute Then, we consider the steady-state behavior of a simple, six-state
carrier that binds two solutes with dierent anities. Finally, we consider both
the transient and the steady-state behavior of a general, four-state carrier model
4.2. MODELS
61
Membrane
S +
Intracellular
cSi
noE
ES
Eo
ES
KSi
ES i
niES
4.2.1
KSo
E
E
S = ES
+ So
cSo
Extracellular
niE
Figure 4.1: Kinetic diagram of

the simple, four-state carrier
ES o
noES
Steady-state behavior of a simple, four-state carrier that

binds one solute
Assume that the membrane contains NET moles of carrier per unit area of membrane.1 Each of these carriers exist in one of four states labeled ES i , ES o , E i , and
E o (Figure 4.1). In the ES states, the solute S is bound to the carrier E; in the
E state the carrier is unbound. In the ES i and E i states, the carrier, bound and
unbound, communicates with the solution on the inner side of the membrane.
In the ES o and E o states, the carrier, bound and unbound, communicates with
the solution on the outer side of the membrane. The densities of carrier in the
four states are niES , noES , niE , and noE moles per unit area of membrane. The uxes
of bound and unbound carrier are ES and E and the ux of solute is S . The
ux is dened as positive when the ux is in the outward direction; the units
are in moles per unit area per second. The model is dened by the following
assumptions:
of the carrier density over all of its states equals the total density of carrier
in the membrane
(4.1)
NET = niES + noES + niE + noE .

ES + E = 0.
(4.2)
1
Because the kinetic equations for binding of the carrier to the solute are analogous to
those of the binding of an enzyme to its substrate, the carrier is denote by E which stands for
enzyme.
62

the form ES i . The unbound carrier is assumed to undergo a similar reaction between the two conformations E i and E o . These two reactions are assumed to be rst-order reactions with forward and reverse rate constants,
E , ES , E , and ES , so that the uxes are dened as follows:
ES = S = ES niES ES noES ,
E =
E niE
E noE .
(4.3)
(4.4)
In the simple model, the binding reactions at the membrane interfaces are
assumed to be so rapid, compared to the rate of transport of solute across
the membrane, that the membrane interface reactions are assumed to be
at equilibrium, i.e.,
cSi niE
cSo noE
o
=
K
and
= KSi ,
(4.5)
S
noES
niES
where KSo and KSi are the dissociation constants on the two membrane interfaces.
These equations can be solved to determine the ns in terms of the concentrations and transport parameters. Equations 4.3 and 4.4 can be used to determine
the s. Combining Equations 4.2, 4.3, and 4.4 yields
(ES niES ES noES ) + (E niE E noE ) = 0.
(4.6)
Equations 4.1, 4.5, and 4.6 can be expressed as a matrix equation as follows:
i
nES
KSi
0 cSi 0
o
0 KSo
0 cS noES
ES ES E E ni
E
1
1
1
1
noE
0
0
=
0 .
NET
(4.7)
The rst two rows correspond to the two relations in Equation 4.5. The third
row results from Equation 4.6, and the fourth row corresponds to Equation 4.1.
This set of simultaneous equations has the following solutions (Weiss, 1996a):
cSi (E KSo + ES cSo )
,
D1
(4.8)
cSo (E KSi + ES cSi )

= NET
,
D1
(4.9)
KSi (E KSo + ES cSo )

,
D1
(4.10)
KSo (E KSi + ES cSi )

= NET
,
D1
(4.11)
niES = NET
noES
niE = NET
noE
4.2. MODELS
ES i
Intracellular
cSi
Ri
cRi
Ei
ES o
ES
KSo
E
E
E
KRi
ER i
niER
noES
ES
KSi
niE
Si
Membrane
S = ES
noE
Eo
KRo
ER
ER
R = ER
cSo
So
Ro
Extracellular
niES
63
Figure 4.2: Kinetic diagram of a simple,

six-state carrier that binds two solutes (S
and R).
cRo
ER o
noER
where
D1 = (E KSo + ES cSo )(KSi + cSi ) + (E KSi + ES cSi )(KSo + cSo ).
(4.12)
S and E can be obtained from Equations 4.3 and 4.4.

as
S =S S ,
where
S = ES niES and S = ES noES .
4.2.2
Steady-state behavior of a simple, six-state carrier that binds

two solutes
The simple, four-state carrier shown in Figure 4.1 can be extended to account
for the binding of two solutes that compete for binding sites on the carrier (Figure 4.2). In this scheme, solutes S and R combine with carrier E but with dierent
anities. The binding to solute S has dissociation constants KSi and KSo and the
binding to R has dissociation constants KRi and KRo .
The kinetic equations are analogous to those derived for the simple, fourstate carrier except that the carrier now has 6 states:
64
of the carrier density over all of its six states equals the total density of
carrier in the membrane
NET = niES + noES + niER + noER + niE + noE ,
(4.13)
where NET is the total density of carrier in the membrane.
Since the carrier remains in the membrane, the net ux of carrier must be
zero
ES + ER + E = 0.
(4.14)
The uxes are related to the carrier densities so that

ES = S = (ES niES ES noES ).
(4.15)
ER noER ).
E noE ).
(4.16)
ER = R =
E =
(ER niER
(E niE
(4.17)
In the simple model, the reactions at the membrane interfaces are assumed
to take place so rapidly, compared to the rate of transport of solute across
the membrane, that the membrane interface reactions are assumed to be
at equilibrium, i.e.,
i i
cSo noE
c o no
c i ni
o cS nE
= KS , i = KSi and R o E = KRo , R i E = KRi ,
o
nES
nER
nES
nER
(4.18)
where KSo , KSi , KRo and KRi are the dissociation constants for solutes S and
R, respectively at the two membrane interfaces.
Combining Equations 4.14 and 4.15, 4.16, and 4.17 yields
(ES niES ES noES ) + (ER niER ER noER ) + (E niE E noE ) = 0.
(4.19)
It is of interest to obtain the ux of solutes S and R as a function of both concentrations and the transport parameters KSi , KSo , KRi , KRo , ES , ER , E , ES , ER ,
E , and NET . Therefore, it is useful to regard the system of algebraic equations
given by Equations 4.14 through 4.19 as a set of 6 equations in the 6 unknowns
niES , noES , niER , noER , niE , and noE . These can be written in matrix form as follows:
Ki
0
0
0 cSi 0 niES
S
o
0 KS
0 cSo noES
0
0
i
0
0 KRi
0 cRi 0
nER
o
o
0
o
0
0 cR
0
KR
nER
i
nE
ES ES ER ER E E
1
1
1
1
1
1
noE
0
0

0
=
0

0
NET
(4.20)
4.2. MODELS
65
The rst four rows correspond to the four relations in Equation 4.18. The fth
row results from Equation 4.19, and the sixth row corresponds to Equation 4.13.
This set of simultaneous equations has solutions (Weiss, 1996a):
niES = NET
cSi KRi (E KSo KRo + ES cSo KRo + ER KSo cRo )

,
D2
(4.21)
noES = NET
cSo KRo (E KSi KRi + ES cSi KRi + ER KSi cRi )

,
D2
(4.22)
niER = NET
KSi cRi (E KSo KRo + ES cSo KRo + ER KSo cRo )

,
D2
(4.23)
cRo KSo (E KSi KRi + ES cSi KRi + ER KSi cRi )

= NET
,
D2
(4.24)
niE = NET
KSi KRi (E KSo KRo + ES cSo KRo + ER KSo cRo )

,
D2
(4.25)
noE = NET
KSo KRo (E KSi KRi + ES cSi KRi + ER KSi cRi )

,
D2
(4.26)
noER
where
D2 = KSi (cRi ER + KRi E )(KSo KRo + cSo KRo + KSo cRo ) +
KSo (cRo ER + KRo E )(KSi KRi + cSi KRi + KSi cRi ) +
cSi KRi ES (KSo KRo + cSo KRo + KSo cRo ) +
cSo KRo ES (KSi KRi + cSi KRi + KSi cRi ).
(4.27)
The uxes can be computed using Equations 4.15-4.17.

The solute uxes can also be expressed in terms of the uni-directional uxes
as
S = S S ,
R = R R ,
where
S = ES niES and S = ES noES ,

R = ER niER and R = ER noER .
66

Membrane
S + E
Intracellular
cSi
ai
ao
niES
noE
Eo + S o
ho go cSo
g i hi
ES i
4.2.3
bi
bo
S = ES
Extracellular
niE
Figure 4.3: Kinetic diagram of a general,

four-state carrier model that binds one solute.
ES o
noES
Transient and steady-state behavior of a general, four-state

carrier that binds one solute
Transient solution
Suppose that in the simple, four-state carrier model shown in Figure 4.1, the assumption that the interfacial binding reactions are fast is dropped. The model
which results is called the general, four-state carrier model and the kinetic diagram for this model is shown in Figure 4.3.
This model is dened by the following assumptions:
The total amount of carrier, bound and unbound, is constant, i.e. at each
instant in time the sum of the densities of carrier over all of its states
equals the total density of carrier
NET = niES (t) + noES (t) + niE (t) + noE (t).
(4.28)
Since both transient and steady-state values will be considered, the notation will be to specify a variable that changes in time as, for example, niES (t)
and its steady-state value as niES ().

ES (t) + E (t) = 0.
(4.29)
the form ES i . The unbound carrier is assumed to undergo a similar reaction between the two conformations E i and E o . The kinetic equations for
the general, four-state carrier model can be written for the rate of change
4.2. MODELS
67
of carrier in each of the four states by a matrix dierential equation which

is
i
nE (t)
o
d
nE (t) =
i
dt nES (t)
noES (t)
nE (t)
gi
0
ai hi cSi
ao
noE (t)
ai
ao ho cSo
0
go
i
ni (t) . (4.30)
hi c S
0
bo
bi gi
ES
0
bi
bo go
ho cSo
noES (t)
The binding reactions are not assumed to be arbitrarily fast. Since the
binding reactions are assumed to be second-order kinetic equations, the
solute concentrations enter the binding reactions.
The four kinetic equations are not independent; e.g., the fourth can be derived
from the rst three equations. Thus, the fourth equation can be eliminated and
noES (t) can be eliminated using the conservation of carrier relation,
noES (t) = NET niE (t) noE (t) niES (t),
(4.31)
to yield the matrix equation
i
nE (t)
d o
nE (t) =
dt
niES (t)
i
ai hi cSi
nE (t)
ao
gi
ai go ao go ho c o
no (t) +
go
(4.32)
E
S
i
i
hi cS bo
bo
bi gi bo
nES (t)
0
go NET .
(4.33)
bo
This matrix equation can be solved for the three carrier densities and Equation 4.31 can be used to solve for the fourth density. The solution for each of
the carrier densities has the form
nj (t) = Aj1 e1 t + Aj2 e2 t + Aj3 e3 t ,
(4.34)
where the nj s are the four carrier densities, the s are the three non-zero eigenvalues of the system, and the As are the residues. This solution is valid when
the eigenvalues are distinct. All 4 carrier densities have the same 3 eigenvalues,
but in general, the residues dier. Since the rate constants and concentrations
are all positive quantities, it can be shown that all the eigenvalues have negative
real parts. Both the eigenvalues and residues are functions of the rate constants
and the solute concentrations. Hence, the solutions yield the carrier densities
(niES (t), noES (t), niE (t), and noE (t)) as functions of time for any values of the concentrations of solute S and of the transport parameters ai , ao , bi , bo , gi , go , hi ,
ho , and NET .
68
Steady-state solution
In the steady state, the density of carrier in each of its four states is constant and
the derivative terms on the left-hand side of Equation 4.30 are zero. As noted
previously, the four equations are not independent. Thus, one of the equations
can be eliminated. However, conservation of carrier leads to an independent
constraint which can be added to the three independent steady-state equations
to yield the following four steady-state equations
i

ao
nE ()
0
gi
(ai + hi cSi )
0

o
go
(ao + ho cSo )
0
ai
nE () = 0 . (4.35)
i
i
hi cS
0
(bi + gi ) bo nES () 0
1
1
1
noES ()
1
NET
The solutions (Weiss, 1996a) are ratios of sums of products of rate constants
M i no ()
Mo
M i no ()
M o ni ()
niE ()
= E, E
= E , ES
= ES , ES
= ES ,
NET
D
NET
D
NET
D
NET
D
(4.36)
where
MEi = ao bi go + ao gi go + ao bo gi + bo gi ho cSo ,
MEo = ai bi go + ai gi go + ai bo gi + bi go hi cSi ,
i
= ai bo ho cSo + ao go hi cSi + ao bo hi cSi + bo hi ho cSi cSo ,
MES
o
MES
D =
ai bi ho cSo + ai gi ho cSo +
i
o
+ MES
.
MEi + MEo + MES
ao bi hi cSi
(4.37)
bi hi ho cSi cSo ,
The steady-state ux is found elsewhere and equals (Weiss, 1996a)

bi go hi cSi niE () bo gi ho cSo noE ()
.
E () = S () = ES () =
(4.38)
These equations yield the values of the n()s and the ()s in steady state as
a function of the concentrations of solute S and of the transport parameters ai ,
ao , bi , bo , gi , go , hi , ho , and NET .
as
S () =S () S (),
where
S () =
S () =
bi go hi cSi niE ()
,
bo gi ho cSo noE ()
.
4.3
4.3.1
69
Numerical Methods And Parameters

Numerical methods
The steady-state values of the carrier densities and the carrier uxes are algebraic functions of the solute concentrations and of the parameters. They could
have been computed directly from the steady-state matrix equations for each
carrier model. However, it proved to be faster to compute these quantities directly from the solutions of these matrix equations which are: Equations 4.3-4.4
and Equations 4.8-4.11 for the simple, four-state carrier, Equations 4.15-4.17 and
Equations 4.21-4.26 for the simple, six-state carrier, and Equations 4.36-4.38 for
the general, four-state carrier.
The transient solution for the general, four-state carrier was obtained by solving Equation 4.33 numerically using MATLABs ode15s routine for solving sets
of ordinary dierential equations. The solution for 3 of the 4 carrier densities
were computed; the fourth was computed from Equation 4.31. Eigenvalues of
the matrix of rate constants (Equation 4.33) were computed to aid the user in
choosing a time scale for displaying transient responses. Eigenvalues were computed using MATLABs eig function.
4.3.2
Choice of numerical parameters
The software enables the user to compute the ns and s for any values of the
parameters, the s, s, Ks, NET , and the concentrations of solute, the cs. For
the simple models, the software is initiated with default parameters chosen to
approximate hexose transport in human erythrocytes (Carruthers, 1984; Stein,
1986) assuming a symmetric transport scheme. The density of carriers was set
to NET = 10 pmoles/cm2 . The dissociation constant of solute S was set to approximate that of D-glucose, KSi = KSo = 2 moles/cm2 , and that of R was set
to that of a solute to which the carrier binds with lower anity, approximating
that of D-xylose, so that KRi = KRo = 200 moles/cm2 . All the rate constants
were set equal with a value that made the maximum ux 100 pmoles/cm2 -s so
that ES = ES = ER = ER = E = E = 20 s1 . For the general model, the parameters were chosen somewhat arbitrarily except that rate constants of binding
reaction were chosen to be much greater than those of translocation reactions.
All the parameters were chosen to be approximately consistent with the simple
models. The concentrations of solute were chosen arbitrarily as follows: cSi = 2,
cS0 = 1, cRi = 2, cRo = 1 moles/cm3 .
4.4
Users Guide
When the program is selected, 3 gures are displayed (in addition to MATLABs
command window): CMT Control, CMT Parameters, and CMT State. The CMT
70
Figure 4.4: CMT Control gure.
Figure 4.5: CMT Units gure showing the

units of all the variables in the carrier models.
Control gure controls the software. The remaining gures are for steady-state
interactive analysis of the simple, four-state carrier. In the interactive mode, any
parameter of the carrier model can be changed and the resulting steady-state values of carrier densities and uxes are displayed immediately. The same steadystate interactive analysis is available in all three models: the simple symmetric,
four-state carrier; the simple symmetric, six-state carrier; and the general, fourstate carrier. Additional modes of analysis allow plotting the steady-state values
of carrier densities and uxes as functions of a user-specied model parameter.
In addition, for the general, four-state carrier, the user can observe transient
changes in carrier densities in response to a change in parameters. All of these
modes of analysis are selected using the CMT Control gure.
4.4.1
CMT Control
The part of the CMT Control gure (Figure 4.4) below the menubar is divided
into three panels. The Model panel allows the user to choose a particular model
for analysis. The Analysis panel allows the user to choose among the available
modes of analysis in the software by clicking on the appropriate button. The
miscellaneous panel allows the user to display the units for all variables used by
the software (Figure 4.5).
4.4. USERS GUIDE
71
Figure 4.6: The CMT Parameters gure (left) and CMT State gure (right) for the simple,
4.4.2
Model
The CMT Control gure allows selection of three models of carrier-mediated

transport. Selecting a dierent model will initiate the steady-state, interactive
analysis for that model. The models are:
Simple, four-state: refers to the simple, four-state carrier that binds one solute.
This is the default model that is displayed when the software is initialized.
The parameters and state gures associated with this model are shown in
Figure 4.6.
Simple, six state: refers to the simple, six-state carrier that binds two solutes
General, four-state: refers to the general, four-state carrier that binds one solute
4.4.3
Steady-state interactive analysis
Interactive, steady-state analysis involves two gures the CMT Parameters and
the CMT State gures. Any parameter (independent variable) can be changed in
the CMT Parameters gure and the resulting changes in the steady-state values
72
Figure 4.7: The CMT Parameters gure (left) and CMT State gure (right) for the simple,
six-state carrier model that binds two solutes.
4.4. USERS GUIDE
73
Figure 4.8: The CMT Parameters gure (left) and CMT State gure (right) for the general,
of the carrier state densities and carrier uxes (dependent variables) are displayed in the CMT State gure. The parameters for all three carrier models are
listed in Table 4.1. In both the CMT Parameters and CMT State gures, clicking
on any variable (parameter, carrier density, or carrier ux) displays information
about that variable.
CMT Parameters
The numerical value of each parameter is displayed in the button located either
above or below each parameter. Parameter values can be changed en masse
by clicking the appropriate buttons in the upper part of the parameters gure.
Parameters can be Reset to their default values or read from a le. Parameters
may also be saved to a le.
Parameters may be changed individually in three ways.
A value may be changed arbitrarily by clicking on the button for each parameter. The button is changed to a text-edit box which allows editing the
parameter value. After typing RETURN, the new values of carrier densities
and carrier uxes are computed and displayed in the CMT State gure. A
non-numeric entry or a negative entry is not accepted and the prior value
is restored.
74

Simple
Simple
General
four state
six state
four state
Total carrier density
NET
NET
NET
Rate constants
E , E ,
E , E , ES , ES ,
ai , ao , bi , bo
ES , ES
ER , ER
gi , go , hi , ho
Solute concentrations
cSi , cSo
cSi , cSo , cRi , cRo
cSi , cSo
Dissociation constants
KSi , KSo
KSi , KSo , KRi , KRo
Table 4.1: Modiable parameters of the carrier models the independent variables.

decremented by clicking on or in the upper right in the CMT Parameters
gure. The state gure is updated with each incremental change in the
parameter.

or to the left of the , respecdecremented repeatedly by clicking on
tively. The CMT State gure is updated with each incremental change in
the parameter. Clicking on a repeat button again stops the repetitive process.
In the general, four-state carrier, passive transport of solute (also called the
principle of detailed balance) requires that (Weiss, 1996a)
ai ho bo gi = ao hi bi go .
When this condition is violated, a warning messages is displayed in the CMT
Parameters gure, and the ratio
r =
ao hi bi go
ai ho bo gi
is displayed. To avoid warning messages for small dierences in r caused by the

limited precision with which parameters are specied, messages are displayed
only if r diers from 1 by more than 5%.
CMT State
The steady-state values of carrier densities and carrier uxes are displayed in
the CMT State gure below each quantity for the particular set of parameters
4.4. USERS GUIDE
75
shown in the CMT Parameters gure. These quantities are also displayed graphically. Carrier densities are displayed with bar graphs that represent the relative
densities of carrier in each states. Both four-state carriers display niE , noE , niES ,
and noES . The six-state carrier displays niE , noE , niES , noES , niER , and noER . The carrier uxes are displayed with thick arrows in the center of the gure. No arrow
is displayed when the ux is zero. The direction of the arrow indicates the direction of the ux. The color of the arrow indicates the relative magnitude of
the carrier ux; a small magnitude ux has a black arrow, a large magnitude ux
has a bright red arrow. The color coding is irrelevant for the four-state models
since there are only two uxes and they must have the same magnitude, but is
useful for the six-state model.
4.4.4
Steady-state graphic analysis
Selection of Graphic analysis in the CMT Control gure, displays the CMT Steady
state plot gure (Figure 4.9). This gure allows the user to plot any variable
versus any of the parameters of the carrier-mediated transport model. This
gure contains a number of panels.
described below.
Setup. Clicking on Setup results in the display of the CMT Setup steady
state plot gure (Figure 4.10) which allows selection of one independent variable which determines the abscissa of the plot and multiple
dependent variables which determine the ordinates.
Variables. Clicking on an independent variable selects it for the abscissa (X) variable and deselects a previously selected variable.
Clicking on an unselected dependent (Y) variable adds it to the
collection of selected variables. Clicking on a selected dependent
variable deselects it. A maximum of four types of dependent variables can be selected for plotting. The range over which the independent variable is swept can be selected in the text edit box.
Values of parameters of the model (those not being changed) can
be selected from a le or taken from the interactive environment
by clicking on the appropriate button in the upper left panel of
the gure.
Graph. Clicking on Graph results in a plot of the selected data. The
new plot replaces the old plot.
Overlay. Clicking on Overlay results in the next plot being overlayed
over the current plot.
Open. Clicking this button allows plotting of results stored in a le.
76
Figure 4.9: The CMT Steady state plot gure showing a plot of carrier densities versus
cSi on linear ordinate and abscissa scales.
Figure 4.10: CMT Setup steady

state plot gure showing a plot
of uxes and carrier densities
versus cSi on linear ordinate
and abscissa scales.Note that cSi
(which is highlighted in blue)
was selected as the independent variable that denes the
abscissa (horizontal axis) in the
plot. The variables niE , noE , niES ,
and noES were selected as the dependent variables and plotted
as the ordinates (vertical axis).
4.4. USERS GUIDE
77
Figure 4.11: The Axis scale gure after the

abscissa was selected in Figure 4.9.
Save. Clicking this button allows the information in the plot to be saved in
a le. All lines, labels, and annotations are saved.
Print. Clicking on Print prints the gure.
displays a vertical line, the cross line, in the plot
Cross-line. Clicking on
eld at the location of the pointer cursor. The line follows the cursor
as it moves across the plot eld. The values of all plotted variables at
the intersection with the cross line are displayed in the legend. Clicking on cross-line button again removes the cross-line values from the
legend and removes the cross line from the plotting eld.
Annotate. Clicking on A and then on a desired location in the plot area
displays a text edit box at that location. Click in the text edit box, type
the annotation followed by a <RETURN> when the annotation is completed. Clicking on the annotation and dragging the mouse moves the
annotation to a desired location in the plot eld. The text string can
be formatted into mathematical notation by using a LATEX like notation,
e.g., to get niES type n_{ES}i.
Zoom. Clicking on + allows the user to magnify a region of the plotting
eld by clicking on it. Additional magnication can be achieved by
zooming again.
Unzoom. Clicking on
undoes the eects of all prior zooms.
Axes control. The plot axes can be changed by clicking on any of the axis labels
either the abscissa or any of the ordinates which results in the display
of the CMT axis scale gure (Figure 4.11). The axis scale can be chosen to
be linear, logarithmic, and/or reciprocal. If none of the options is chosen,
the scale is linear. If log scale is chosen, the scale is the logarithm of the
magnitude of the variable. If invert is chosen then the reciprocal of the
abscissa variable is plotted either on a linear or on a logarithmic scale.
Clicking on Apply results in a change in the axis. The title of the axis label
can also be edited and the plot range can be changed.
recorded.
78
Figure 4.12: Modify line properties

gure. The user can select the line
color, style, and the marker.
Line properties. The color, line style, and symbol type are used to encode
a particular variable; this marker is shown in the legend. Clicking on
the marker displays a gure that allows the user to edit all the line
and marker properties (Figure 4.12).
Variable name. The name of the variable that was plotted is shown. Clicking on the variable name alternately displays and hides the curve associated with this entry. When variables are added or deleted, the axis
the axis gure.
Cross-line If the cross-line is used the cross-line values are displayed.
Data-set. The time when the curves were generated are indicated. Clicking on the time stamp alternately displays and hides all the curves
associated with this legend item.
4.4.5
Transient analysis
Transient analysis is available only for the generalized, four-state carrier by

clicking on Transient in the CMT Control gure. This action displays the CMT
Transient plot gure (Figure 4.9). The display control features of this gure are
similar to those of the CMT Graphics Figure described above (Figure 4.9). We
describe the dierences only.
Setup. Clicking on Setup displays the CMT Setup transient plot gure shown in
Figure 4.14. The rst column of this gure shows all the 11 independent
variables for the general, four-state carrier. The initial values are shown in
the second column and the nal values are shown in the fourth column.
The initial values can be changed individually by typing in the new value
in the appropriate text edit box. The third column gives several options
for changing any particular variable. Several independent variables can be
changed at once. The transient parameters can be saved in a le and read
from a le. The bottom of the gure gives several additional options for
changing variables.
Numerics. Clicking on this item displays the CMT Transients numerics gure
which gives information to the user and allows for control of the time scale
4.4. USERS GUIDE
79
Figure 4.13: The CMT Transient plot gure showing the transient response to the
change in parameters shown in Figure 4.14 and using the numerical data shown in
Figure 4.15.
80
Figure 4.14: The CMT Setup transient plot gure.
of the transient response (Figure 4.15). The CMT Transients numerics gure displays the eigenvalues (as rate constants or time constants) of the
transient response. These eigenvalues can be computed for the initial or
the nal values of all parameters by clicking on the appropriate button in
this gure. The eigenvalues have the dimensions of rate constants (RC).
But the software allows the equivalent time constants (TC = 1/RC) to be
displayed. In addition, the user can choose to show the absolute value of
either the rate constant or the time constant. The nal value of the time in
the plot is determined by the bottom panel which has several options.
Figure 4.15: The CMT Transients numerics gure.
4.5. PROBLEMS
81
Absolute scale. Selecting this item displays plots of all carrier densities on the
same absolute scale.
Relative scale. Selecting this item displays plots of all carrier densities on individual scales so that all the carrier densities are discernible.
4.5
Problems
Problem 4.1 The purpose of this problem is to explore the steady-state behavior
of the simple, symmetric, four-state carrier model. You will observe the eects of
changes in parameters on both the ux and the carrier densities. Use the simple,
four-state carrier model and start with all the parameters at their default values.
a. What is the relation of S and E ? Explain.
b. What is the relation of the direction of S to the sign of cSi cSo ? Explain.
c. How does the state of the carrier depend on solute concentration?
i. Do changes in cSi change niES and niE ? If so, how? If not, why not?
ii. Do changes in cSi change noES and noE ? If so, how? If not, why not?
iii. Do changes in cSo change niES and niE ? If so, how? If not, why not?
iv. Do changes in cSo change noES and noE ? If so, how? If not, why not?
Problem 4.2 The purpose of this problem is to explore the eect of asymmetry of
the parameters of the simple, four-state carrier model on the relation between ux
and concentration dierence across the membrane. Use the simple, four-state
carrier model and start with all the parameters at their default values. Note the
symmetry of the default parameters, i.e., E = ES , E = ES , and KSi = KSo .
a. Using the default parameters, plot S versus cSi .
i. Determine the value of cSi at which the sign of S changes. Explain
this sign change.
ii. On this plot indicate the region for which cSi cSo > 0. Is S > 0 for
this range?
iii. On this plot indicate the region for which cSi cSo < 0. Is S < 0 for
this range?
iv. What can you conclude from parts i-iii?
b. Use the interactive environment, and change ES from its default value
of 20 s1 to 60 s1 . At these values what is the relation of the solute
concentration gradient to the ux of solute?
82

c. Use the default parameters except that ES = 60 s1 . Plot S versus cSi .
i. Determine the value of cSi at which the sign of S changes. Explain
this sign change.
ii. On this plot indicate the region for which cSi cSo > 0. Is S > 0 for
this range?
iii. On this plot indicate the region for which cSi cSo < 0. Is S < 0 for
this range?
iv. What can you conclude from parts i-iii?
d. In part c is the ux always down the chemical potential gradient of the

solute? If not, from where does the energy for transporting the solute
come?
Problem 4.3 The purpose of this problem is to explore the eect of asymmetry
of the parameters of the simple, four-state carrier model on the relation between
unidirectional ux and concentration.
a. Use the simple, four-state carrier model and start with all the parameters
at their default values. Note the symmetry of the default parameters, i.e.,
E = ES , E = ES , and KSi = KSo .
i. Plot 1/ S versus 1/cSi . [The unidirectional eux S is called euxS

in the software.]
ii. Plot 1/ S versus 1/cSo . [The unidirectional inux S is called inuxS
in the software.]
iii. To make direct comparisons between results you may wish to overlay
the plots. What do you conclude from parts i and ii? Explain these
results.
b. Use the simple, four-state carrier model with all the parameters at their
default values except change KSi from its default value of 2 to 4 mol/cm3 .
Note that the parameters are no longer symmetric.
i. Plot 1/ S versus 1/cSi . [The unidirectional eux S is called euxS

in the software.]
ii. Plot 1/ S versus 1/cSo . [The unidirectional inux S is called inuxS
in the software.]
iii. To make direct comparisons between results you may wish to overlay
the plots. What do you conclude from parts i and ii? Explain these
results.
4.5. PROBLEMS
83
c. Compare the results in part a with those obtained in part b. What can you
conclude from these results?
Problem 4.4 The purpose of this problem is to explore the functional relation
between solute ux and solute concentration when expressed in dierent coordinates. Use the simple, four-state carrier model and start with all the parameters
at their default values, except set cSo = 0. In parts a through c your job is to estimate the values of (S )max and KSi from the graphs specied, where (S )max is
the maximum ux of S with cSo = 0.
a. Obtain a graph of S versus cSi in linear coordinates.
b. Obtain a graph of S versus cSi in double logarithmic coordinates.
c. Obtain a graph of 1/S versus 1/cSi .
d. Determine the values of (S )max and KSi from the model parameters.
e. Compare the 4 sets of values you have obtained for (S )max and KSi .
Problem 4.5 The purpose of this problem is to explore the eect of solute concentration on carrier state. Use the simple, four-state carrier model and start with
all the parameters at their default values, except set cSo = 0. Obtain a graph of
all four carrier states as a function of cSi . Some of the these ns increase, others
decrease, while others remain constant. Summarize and explain the results you
found.
Problem 4.6 The purpose of this problem is to explore some of the conditions
for which a plot of ux versus concentration in reciprocal coordinates results in
a straight line. Use the simple, four-state carrier model and start with all the
parameters at their default values.
a. Set cSo = 0 and plot 1/S versus 1/cSi .
b. Set cSo to its default value, cSo = 1 mol/cm3 , and plot 1/S versus 1/cSi .
c. Compare the results in parts a and b and explain the dierences.
d. With cSo = 1 mol/cm3 , plot 1/ S versus 1/cSi . [The unidirectional eux
S is called euxS in the software.] Compare the results of parts b and d

and explain the dierence.
Problem 4.7 The purpose of this problem is to explore the process of exchange
diusion. Use the simple, four-state carrier model and start with all the parameters at their default values.
84

a. In the interactive environment, set E = E = 0. Explain the values of the
variables in the state diagram.
b. In the graphics environment, plot S versus cSi . What do you conclude?
c. In the graphics environment, plot 1/ S and 1/ S versus 1/cSi . What do

you conclude?
d. Reconcile the results of parts b and c.
e. The process dened in this problem has been called exchange diusion.
Critique this choice of name for this process. Why is this name appropriate? Why is this name inappropriate?
Problem 4.8 The purpose of this problem is to compare properties of simple and
general, four-state carriers.
a. Use the simple, four-state carrier model and start with all the parameters
at their default values. For both cSo = 1 and cSo = 10 mol/cm3 , plot 1/ S
versus 1/cSi . [The unidirectional eux S is called euxS in the software.]

You may wish to overlay the plots to compare the results directly.
b. Use the general, four-state carrier model and start with all the parameters
at their default values. For both cSo = 1 and cSo = 10 mol/cm3 , plot 1/ S
versus 1/cSi . [The unidirectional eux S is called euxS in the software.]

You may wish to overlay the plots to compare the results directly.
c. What do you conclude from parts a and b.
Problem 4.9 The purpose of this problem is to explore properties of six-state carriers. Use the simple, six-state carrier model and start with all the parameters
at their default values. Set the solute concentrations of S and R to zero on both
sides of the membrane.
a. Explain the initial carrier states and ux values.
b. Increase cSi and observe both the carrier states and the ux. What is the
relation of the ux of S to cSi ?
c. Now set cSi = 10 mol/cm3 and increase cRi . How do the uxes of S and R
depend upon cRi ?
d. Set cSi = 10 and cSo = 5 mol/cm3 . Now increase cRi from an initial value of
0. How do the uxes of S and R depend upon cRi ? Pay particular attention
to the direction of the ux of S.
4.5. PROBLEMS
85
Problem 4.10 The purpose of this problem is to explore properties of the simple,
six-state carrier model; in particular, the relation between the solute ux and
the parameters of the model. Use the simple, six-state carrier model and start
with all the parameters at their default values. Choose any parameter of the
model (a rate constant or a dissociation constant). Try to think of a change in
that parameter that will lead to an increase in S . Change the value of this
parameter accordingly and determine if this change results in an increase in S .
If S does not change the way you predicted, nd out why. If it does change
as you predicted, then try another parameter and repeat the process. Do this
for at least 5 parameters to make sure that you have developed some intuition.
Describe what you did and the outcome.
Problem 4.11 The purpose of this problem is to explore elementary properties of
the transient response of the general, four-state carrier. Use the general, fourstate carrier model and start with all the parameters at their default values.
a. In the interactive environment, record the values of all states of the carrier
niE , niES , noE , and noES . Now change cSi from its default value of 2 to 20
mol/cm3 and record the values of all the states of the carrier.
b. Switch to the transient environment and compute the transient response
as cSi is stepped from its default value of 2 to 20 mol/cm3 .
i. Determine the initial and nal values of the transient response and
compare these results with the results obtained in part a.
ii. From plots of the transient response, estimate the time it takes the
response to go from its initial value to 0.63 of its nal value.
c. Examine the CMT Transients numerics gure.
i. Explain why there are multiple time constants listed?
ii. Do the time constants listed in this gure explain the transient response seen in part b? Explain.
Problem 4.12 The purpose of this problem is to explore eigenvalues of the general, four-state carrier model. Use the general, four-state carrier model and start
with all the parameters at their default values. Switch to the transient response
and click on Setup in the CMT Transient plot gure. This displays the CMT
Setup transient plot gure. Select Numerics in the latter plot to display the CMT
Transient numerics gure. Make sure that the eigenvalues are calculated from
the nal parameter values and that rate constants are displayed instead of time
constants. In this problem, you will change the nal values and calculate the
eigenvalues expressed as rate constants.
a. Record the eigenvalues (as rate constants) for the default settings.
86

b. Change the value of cSi from its default value of 2 to 20 mol/cm3 . Record
the eigenvalues (as rate constants) corresponding to cSi = 20 mol/cm3 .
c. Compare the eigenvalues (as rate constants) for cSi = 2 to that for cSi = 20
mol/cm3 .
d. Explain why the eigenvalues (as rate constants) depend upon the concentration.
e. Suppose you regard the general, four-state carrier as a system that relates
the solute concentrations (as inputs) to the uxes (as outputs). Is that
system linear?
Problem 4.13 The purpose of this problem is to explore the eigenvalues of the
general, four-state carrier model. Use the general, four-state carrier model and
start with all the parameters at their default values. Switch to the transient
response and click on Setup in the CMT Transient plot gure. This displays the
CMT Setup transient plot gure. Select Numerics in the latter plot to display the
CMT Transient numerics gure. Make sure that the eigenvalues are calculated
from the nal parameter values and are expressed as time constants. In this
problem, you will change the nal values and calculate the eigenvalues (as time
constants).
a. Record the eigenvalues (as time constants) for the default settings.
b. For each of the values given below, plot the transient response and record
the eigenvalues (as time constants).
i. Change the binding/unbinding rate constants gi , go , hi , ho to 0.1 of
their default values.
ii. Change the binding/unbinding rate constants gi , go , hi , ho to 0.01 of
iii. Change the binding/unbinding rate constants gi , go , hi , ho to 0.001 of
iv. Change the binding/unbinding rate constants gi , go , hi , ho to 0.0001
of their default values.
c. Plot the locations of the eigenvalues (as time constants) versus the factor
by which the binding/unbinding rate constants were multiplied in double
logarithmic coordinates.
d. Examine the transient responses and the results of part c. Discuss the
implication of these results.
Chapter 5
HODGKIN-HUXLEY MODEL SPACE
CLAMPED
87
88
5.1
5.1.1
Introduction
Background
Electrically excitable cells produce action potentials which are important for
transmission of information in neurons, for contraction of muscle cells, and for
secretion of chemical substances by neurosecretory cells (Aidley, 1989; Hodgkin,
1964; Katz, 1966; Kandel et al., 1991; Keynes and Aidley, 1991; Nicholls et al.,
1992; Weiss, 1996b). The macroscopic mechanisms of production of action potentials can be understood in terms of the nonlinear electrical characteristics of
cellular membranes rst described by Hodgkin and Huxley for the membrane
of the giant axon of the squid (Hodgkin and Huxley, 1952). Since the nonlinear properties of the membranes of electrically excitable cells are controlled by
the membrane potential, it is relatively simple to understand these mechanisms
when the membrane potential is constant, but vastly more dicult when the
membrane potential is not constant such as occurs during an action potential.
Of course, it is the properties of electrically-excitable cells under the latter conditions that are the most important for the function of these cells.
5.1.2
Overview of the software
The purpose of this software package is to allow users to enhance their comprehension of the Hodgkin-Huxley model by providing a complete simulation of
the model under space clamped conditions. Thus, this software package allows
users to explore the dependence on time of the space-independent HodgkinHuxley model. This software package is complementary to the the software
package described in Chapter 6 which examines the dependence of the HodgkinHuxley model on space and on time. In the software described in the current
chapter, the user can specify the mode of stimulation (either voltage or current
clamp), model parameters (such as the membrane capacitance, the maximum
membrane conductances for membrane ionic channels, kinetic parameters for
each of these membrane conductances, the concentrations of all relevant ions,
the temperature, etc.), run the simulation, and display the results (such as the
membrane potential, membrane-current components, membrane-conductance
components, and channel activation and inactivation variables). The results
can be saved in les, and the contents of multiple les can be plotted on the
same axes. Hence, any of the parameters of the Hodgkin-Huxley model can be
changed by the user and simulation experiments can be done to examine the
consequences of the parameter changes. Extensive graphics utilities allow the
user to plot any variable versus any other variable in the model, to zoom on any
part of the plot, to annotate the plot, and to determine the coordinates of any
point on a plot using a mouse-driven cursor.
89
Jm (t)
+
V (t)
m
Jm (t)
JK
JC
JN a
GK (Vm , t)
GN a (Vm , t)
+
VK
+
VN a
JL
GL
+
V (t)
m
Cm
5.2

in the voltage-clamp conguration.
+
VL
Descriptions of the Hodgkin-Huxley model are available elsewhere (Aidley, 1989;

Hodgkin, 1964; Katz, 1966; Plonsey and Barr, 1988; Johnston and Wu, 1995;
Weiss, 1996b). A summary of this model is given in this section. The model that
is the basis of this software is a one-compartment model that represents a spaceclamped axon stimulated by means of two electrodes so that the membrane
current density and membrane potential are uniform along the length of the
axon.
5.2.1
Voltage-clamp and current-clamp congurations
Two simple and mutually exclusive stimulus congurations can be used to investigate the model: the voltage-clamp and current-clamp congurations. In the
voltage-clamp conguration (Figure 5.1), the simulated space-clamped axon is
driven by a voltage source and the membrane current density is computed. In
the current-clamp conguration, the simulated space-clamped axon is driven by
a current source and the membrane potential is computed.
5.2.2
The membrane current density components
The total membrane current density, Jm , is the sum of the capacitance current
density plus the ionic current density
Jm = JC + Jion ,
(5.1)
where the capacitance current density is

JC = Cm
dVm (t)
,
dt
(5.2)
90
+
Vm (t)
JK
JC
GK (Vm , t)
JN a
GN a (Vm , t)
JL
Jm (t)
GL
Vm (t)
Cm
+
VK
+
VN a
Jm (t)

in the current-clamp conguration.
+
VL
where Cm is the capacitance of a unit area of membrane and Vm is the membrane

potential. The ionic current density can be expressed in terms of its components
Jion = JNa + JK + JL ,
(5.3)
where the ionic current densities due to sodium, potassium and leakage are
JNa = GNa (Vm , t)(Vm (t) VNa ),
(5.4)
JK = GK (Vm , t)(Vm (t) VK ),
(5.5)
JL = GL (Vm (t) VL ),
(5.6)
and where the Nernst equilibrium potential for the nth ion is dened in terms of
the concentrations as follows

cno
RT
ln
,
(5.7)
Vn =
zn F
cni
expressed as

cno
(mV),
(5.8)
Vn = 0.08616 (Tc + 273.16) ln
cni
5.2.3
The membrane conductances
The sodium and potassium conductances are dened as

GNa (Vm , t) = GNa m3 (Vm , t)h(Vm , t),
GK (Vm , t) = GK n (Vm , t).
4
(5.9)
(5.10)
5.2.4
91
The activation and inactivation factors
The rst-order kinetic equations for the activation and inactivation factors are
written in terms of the rate constants as follows:
dm
dt
dh
dt
dn
dt
= m m(m + m ),
(5.11)
= h h(h + h ),
(5.12)
= n n(n + n ),
(5.13)
where the s and s depend upon Vm .
5.2.5
The rate constants
The dependence of the rate constants on membrane potential has been generalized from the original Hodgkin-Huxley model to allow control of the potential
dependence of individual rate constants and to represent approximately the effects of changes in calcium concentration and temperature.
The rate constants are
0.1(35 + Vm + VCa + Vm )
K T Km ,
e0.1(35+Vm +VCa +Vm ) 1
= 4e(Vm +VCa +Vm +60)/18 KT Km ,
m =
m
h = 0.07e
h =
n
n
0.05(Vm +VCa +Vh +60)
KT Kh ,
KT Kh ,
1 + e0.1(Vm +VCa +Vh +30)
0.01(Vm + VCa + Vn + 50)
KT Kn ,
=
e0.1(Vm +VCa +Vn +50) 1
= 0.125e0.0125(Vm +VCa +Vn +60) KT Kn ,
(5.14)
(5.15)
(5.16)
(5.17)
(5.18)
(5.19)
where KT is a temperature factor, that is dened as

KT = 3(T c 6.3)/10 .
(5.20)
KT multiplies all the rate constants; this eect approximates the eect of temperature on the electrical properties of the membrane of the squid giant axon
(Huxley, 1959). The factors Km , Kh and Kn have been added to the original
Hodgkin-Huxley model to allow changes to be made in the individual rate constants of m, h, and n. The factor VCa is used to approximate the dependence
of rate constants on calcium concentration and is

o
cCa
VCa = 0.03335 (Tc + 273.16) ln
12.995 (mV).
(5.21)
i
cCa
92
At the normal calcium concentration, the potential VCa has the value 0. For calcium concentration ratios that dier from the normal value, VCa diers from 0
and the dependence of the rate constants on the membrane potential is shifted
by a term that is proportional to the calcium equilibrium potential. This approximates the eect of a change in calcium concentration on the parameters of squid
giant axon membrane (Frankenhaeuser and Hodgkin, 1957). The potentials Vm ,
Vm , Vh , Vh , Vn , and Vn have the value 0 in the original Hodgkin-Huxley
model. These potentials can be used to shift the dependence of individual rate
constants on membrane potential.
5.2.6
Time constants and equilibrium values of activation and

inactivation factors
Equations 5.11-5.13 are expressed in terms of rate factors, but it is also useful
to express these equations in terms of time constants and equilibrium values, as
follows
dm
dt
dh
dt
dn
dt
=
=
=
m m
,
m
h h
,
h
n n
.
n
(5.22)
The time constants and equilibrium values can be dened in terms of the rate
constants by comparing Equations 5.11-5.13 to Equation 5.22.
m =
h =
n =
5.2.7
1
m + m
1
h + h
1
n + n
and
m =
and
h =
and
n =
m
,
m + m
h
,
h + h
n
.
n + n
(5.23)
Default values of parameters
The default numerical values for the Hodgkin-Huxley model are: GNa = 120,
o
i
GK = 36, and GL = 0.3 mS/cm2 ; Cm = 1 F/cm2 ; cNa
= 491, cNa
= 50, cKo =
o
i
= 44, cCa
= 0.00011 mmol/L; VL = 49 mV; temperature is
20.11, cKi = 400, cCa
6.3 C.
5.3
5.3.1
93
Numerical Methods
Background
In order to compute the membrane potential for a given set of parameters, the
equations describing the Hodgkin-Huxley model (listed in Section 5.2) must be
approximated in a form that is appropriate for numerical solution on a digital
computer. A variety of methods exist for the numerical integration of a set of
coupled dierential equations (Press et al., 1986). The simplest methods, called
the forward and backward Euler methods, is to approximate all derivatives by
rst dierences, and to solve the resulting collection of algebraic equations at
a series of discrete times separated by a time increment t. Although simple
in concept, the Euler methods are not particularly accurate or ecient. Because
the Hodgkin-Huxley software is built on MATLAB which includes a variety of
methods of numerical integration, the user can choose the method of integration
from a number of choices.
5.3.2
Choice of integration step t
The accuracy of all numerical methods is dependent on the choice of the integration step t. Simulation users will need to concern themselves with the choice
of t. If t is decreased, the accuracy of a single step increases but the time it
takes to compute the solution increases. Furthermore, if computations are continued for a large number of steps, the accumulation of round-o errors, due
to the limited precision for representing numbers in a computer, can become
appreciable. Conversely, if t is increased, the accuracy of the computation
decreases and the solution may even diverge. This divergence can lead to spurious phenomena that may mistakenly be attributed to the Hodgkin-Huxley model
when they are really artifacts of the numerical methods. A plausible empirical
test of whether or not a solution is suciently accurate is to test the sensitivity
of the solution to changes in t. If increasing the value of t does not appreciably change the solution, then the value of t used initially is too small and
time was wasted in performing the computation. If decreasing the value of t
does not appreciably change the computational result, then the larger value is
preferable. The simulation of the Hodgkin-Huxley model is set initially with default numerical parameters. For changes in parameters of the model that do not
appreciably change the various time constants of the model, the default numerical parameters are adequate. However, if changing a model parameter (such as
the temperature, membrane capacitance, etc.) appreciably decreases some time
constant of the system, then a smaller value of t should be used. Therefore, it
is advisable to explore briey the eects of varying t on simulation results.
94
Figure 5.3: The HH Control gure

after the software is initiated.
5.3.3
Method for computing solutions
In the voltage clamp simulation, the solution is obtained as follows: Suppose the
solution is known at time tp t and the solution at time tp is desired. The value
of the membrane potential Vm (tp ) at tp is determined from specication of the
stimulus (see Equations 6.23 and 6.24 on Page 149). This value is substituted
into Equations 5.14 and 5.19 to determine the rate constants at tp . Using these
rate constants, and given the values of m, h, and n at time tp t, the values of
m, h, and n are determined at tp by solving Equations 5.11-5.13 numerically by
an integration method that can be chosen by the user. The values of these factors
are used to compute the values of the conductances and current densities from
Equations 5.1-5.6. The computation is begun with initial values of m, h, and n
that are determined from Equation 5.23 for a membrane potential equal to the
source voltage for t < 0.
In the current clamp simulation, the initial values of m, h, n, and Vm are computed rst. This is done by using MATLABs fzero function to solve the set of
Equations 5.1, 5.3-5.21 and a specication of the source current (Equation 6.23
on Page 149) with the derivatives of all the variables set to zero. Starting with
these initial values, the time-varying equations are solved numerically by an integration method that can be chosen by the user.
5.4
When this software is selected, 3 gures are displayed (in addition to MATLABs
command window): HH Control, HH Parameters, HH Stimulus. The HH Control
gure controls the software (Figure 5.3). The HH Parameters gure allows the
user to change any of the parameters of the model. The HH Stimulus gure
allows the user to specify the stimulus. Once the parameters and the stimulus
are specied, clicking the Start pushbutton results in the computation of the
response as a function of time. A variable is plotted as a function of time during
the computation. Upon completion of the computation, the user can examine
the results graphically and numerically.
5.4.1
95
HH Control
The part of the HH Control gure (Figure 5.3) immediately below the menubar
allows the user to choose between voltage-clamp and current-clamp congurations. Below this choice of conguration, there are three panels. In the left panel,
the user can choose to view the HH Parameters gure (which is used to specify
the parameters), the HH Stimulus gure (which is used to specify the stimulus as
a function of time), and/or the HH Numerics gure (which control the numerical
methods and numerical parameters). In the center panel, the user can start the
simulation by clicking on the Start button. The user can also save the simulation (including a specication of all the model and numerical parameters, the
stimulus, and simulation results) in a le and open a previously stored le (that
includes a specication of all the model and numerical parameters, the stimulus, and simulation results). The right (analysis) panel becomes active after the
simulation is completed and allows the user to select three options for analysis
of the results. The rst option allows the user to plot any model variable as a
function of time. This gure is displayed automatically as the computation proceeds. The second option displays a numerical summary of simulation variables.
The third option allows the user to access a quite general plotting facility that
not only plots any of the model variables versus any other model variable, but
allows plotting results stored in les.
5.4.2
HH Parameters
Changing parameter values

The HH Parameters gure contains three columns for each parameter: the rst
column identies the parameter, the second gives its default value, and the third
column shows the value of the parameter if it is modied from its default value.
Parameters are selected for modication by clicking on the entry in the third
column of the parameter eld. When a parameter is selected, its third column
entry is replaced by an edit box. Clicking any mouse button inside the edit box
allows the parameter to be changed. The new value of the parameter is entered
from the keyboard; < RETURN > terminates the parameter entry. If the new
value diers from the default value, then the new value will appear in the third
column. With this method of display, the parameter list can be scanned quickly
to indicate which parameters dier from their default values.
Cm 0, cs > 0, Ks > 0, and the temperature must be above absolute zero. The
derived parameters cannot be changed but are derived from the other parameters and are displayed for the convenience of the user. For example, the sodium
equilibrium potential VNa cannot be changed directly by the user, but changes
automatically when the sodium concentrations or temperature are changed.
96
Figure 5.4: The HH Parameters gure after

the software is initiated.
97
Reading, saving, printing, reseting the parameters

Parameters (only) can be read from a le by clicking on Open and can be saved
by clicking on Save. Saving and reading in the HH Parameters gure deals only
with the model parameters; e.g., simulation results are not read or saved. The HH
Parameters gure can be printed by clicking the Print button. The parameters
can be reset to default values by clicking on Reset.
Viewing the voltage dependent parameters
The Hodgkin-Huxley model contains several parameters that are instantaneous
functions of the membrane potential. Plots of these parameters are available
as a function of Vm for the following: m (Vm ), m (Vm ), m (Vm ), m (Vm ),
h (Vm ), h (Vm ), h (Vm ), h (Vm ), n (Vm ), n (Vm ), n (Vm ), n (Vm ) (see Sections 5.2.5 and 5.2.6). These can be accessed by clicking on the button marked
, , , h, m, n which results in the display of the HH parameters vs. potentialgure (Figure 5.5). This gure contains a number of panels.
described below.
Setup. Clicking on Setup results in the display of the HH Setup parameters vs. potential plot gure (Figure 5.6) which allows selection of the
voltage-dependent parameters as a function of the membrane potential.
Variables. The abscissa is the membrane potential. Clicking on any
variable adds it to the collection of selected ordinate variables.
Clicking on it again deselects it. Values of parameters of the
model can be selected from a le or taken from the parameters
by clicking on the appropriate button in the upper right panel of
the gure.
Overlay. Clicking on Overlay results in the next plot being overlayed
over the current plot. Since the voltage-dependent parameters
depend upon additional parameters and variables, overlaying the
plots allows a display of the eect of these additional parameters
and variables on the voltage dependence parameters. For example, a plot of m versus Vm for dierent calcium concentrations
reveals the eects of calcium concentration on the voltage dependence of sodium activation (Figure 5.7).
98
Figure 5.5: The HH parameters vs. potential gure after selection of parameters as in
Figure 5.6.
Figure 5.6: The HH Setup parameters vs. potential plot

gure that was used to produce the plot shown in Figure 5.5.
99
Figure 5.7: The HH parameters vs. potential gure showing the eect of calcium concentration on the voltage dependence of the sodium activation parameter m . The
calcium concentration was varied from 0.000011 to 0.11 mmol/L by factors of 10.
100
Figure 5.8: The Axis scale gure.

e.g., to get m type m_{\infty}.
zooming again.
Unzoom. Clicking on
of a gure that allows changing the axis (Figure 5.8). The axis scale can be
chosen to be linear, logarithmic, and/or reciprocal. If neither the Log nor
the Inverse (1/) options is chosen, the scale is linear. If Log is chosen, the
scale is the logarithm of the magnitude of the variable. If Inverse (1/) is
chosen then the reciprocal of the variable is plotted either on a linear or on
a logarithmic scale. Clicking on Apply results in a change in the axis. The
plot range can be changed, but the axis labels cannot be edited.
recorded.
Line properties. The color, line style, and symbol type are used to encode a
particular variable; this marker is shown in the legend. Clicking on the
101
Figure 5.9: The Modify line properties gure.
Figure 5.10: HH Stimulus gure with the default stimulus waveform

for a current-clamp conguration.
marker allows the user to edit the attributes of the plot line/symbol
(Figure 5.9).
the axis gure.
5.4.3
HH Stimulus
Selecting Stimulus in the controls gure displays the HH Stimulus gure as shown
in Figure 5.10. The stimulus is the membrane potential in the voltage-clamp con-
102
guration and the membrane current density in the current-clamp conguration.

The duration of the stimulus can be set and, as described below, the user can
also select a le that will dene the stimulus arbitrarily.
Use of the m-le hhpulse.m
By default, the stimulus is generated by the MATLAB m-le hhpulse.m which
uses the parameters listed in the lower part of the stimulus gure. The stimulus is the sum of a constant plus two independently speciable pulses. Each
pulse can be a rectangular pulse, a ramp pulse or an exponential pulse or a combination of these. If the slope and the time constant are set to zero, then the
remaining parameters specify the amplitude, duration and onset time of a rectangular pulse. If the slope has a non-zero value, a ramp of that slope is added to
the rectangular pulse for the duration of the pulse. Similarly, if the time constant
has a non-zero value, then an exponential pulse with the selected time constant
is added to the waveform. The time constant can be positive or negative.
The stimulus, s(t), is dened as follows
s(t) = s o + s 1 (t) + s 2 (t),
(5.24)

i
s (t) =
(5.25)
0
otherwise,
where pulse i (i = 1 or 2) starts at to and has a duration tdur . The amplitude
of the pulse is Ai , the slope is mi , and the time constant is i . With this specication, a rich variety of stimuli can be produced; an example is shown in Figure 5.11.
The stimulus parameters alone can be read from or saved to a le by selecting
either Open or Save in the HH Stimulus gure.
Use of stimulus m-les
This specication of the stimulus by hhpulse.m is quite rich. However, a user
who wishes to dene a stimulus that diers from the one provided can write a
MATLAB m-le to generate that stimulus. That le can then be selected in the
HH Stimulus gure, and the stimulus it generates will be displayed in the gure.
However, the parameters will have to be set by the user in the m-le. The script
for the available m-les can be used as templates to dene new user-specied mles. For example, the simple m-le shown in Figure 5.12 generates a sinusoidal
stimulus.
103
Figure 5.11: HH Stimulus

gure showing an example of a stimulus current
waveform consisting of a
constant plus two pulses:
the rst pulse is a ramp
plus rectangular pulse; the
second is an exponential
pulse.
Figure 5.12: HH Stimulus

gure showing an example
of the use of an m-le to
generate a sinusoidal stimulus.
104
Figure 5.13: HH Numerics gure.
5.4.4
Numerics
Selecting Numerics in the controls gure displays the HH Numerics gure (Figure 5.13). This gure allows selection of the numerical method used to solve
the ordinary dierential equations (or ode solver) as well as the numerical parameters of the simulation. The dialog-box that appears at the top allows direct
selection of one of seven ode solvers called: ode45, ode23, ode113, ode23t,
ode15s, ode23s, and ode23tb. The MATLAB manuals or MATLABs help facility
should be consulted for further information about these methods. For example, to learn about ode15s type Help ode15s at MATLABs command line in
the MATLAB Command Window. More detailed descriptions are available elsewhere (Shampine and Reichelt, 1997). By default, the software uses the ode15s
ode solver. The integration methods require that the following parameters be
dened: Initial step-size, Maximum step-size, Relative Tolerance.
The relative tolerance is an estimate of the accuracy of the solution, i.e., a tolerance of 0.001 implies that the error in the solution is less than 0.1% of the
correct value. Decreasing the tolerance will increase the accuracy of the solution, but will increase the computation time.
The numerical parameters alone can be saved in a le or read from a le by
clicking on Save or Open, respectively, in the HH Numerics gure.
5.4.5
Analysis
The software provides one numeric and two graphic displays of simulation results. These three displays are selected and deselected in the controls gure.
Analysis is available after a simulation has been run if the parameters have not
been changed after the simulation was run.
Plots versus time
Selecting Plots vs. time in the Analysis panel of the HH Control gure displays
the HH Plots vs. time gure as shown in Figure 5.14. During a computation, this
gure displays the following variables: Vm in current clamp conguration and
m in voltage-clamp conguration. When the computation is completed, any vari-
105
Figure 5.14: The

HH
Plots
vs.
time gure with
Vm chosen for
plotting.
Figure 5.15: The HH Variable

summary gure after the simulation has been completed
using the default parameters
for a current-clamp conguration.
able can be selected by clicking on the dropdown menu at the top of the gure
and then dragging the mouse to the variable of interest. This gure provides a
simple and rapid means of plotting any of the simulation variables versus time.
Clicking on an axis label displays the Axis scale gure (see Figure 5.8) which
allows the axis to be changed.
Variable summary
Selecting Variable summary in the HH Control gure displays the HH Variable
summary gure as shown in Figure 5.15. This gure contains ve columns of
text. The rst column identies the simulation variable. The second shows
the units for the variable. The third contains the initial value of the variable.
The fourth and fth columns contain the minimum and maximum values of the
106
Figure 5.16: HH Graphics gure showing the membrane potential and ionic conductance obtained from a simulation with model parameters and the stimulus dened in
Figures 5.4 and 5.10.
variables during the course of the simulation. The dropdown menus located
below the menubar allow the user to control the precision and formatting of the
numerical values.
Graphics
Selecting Graphics in the HH Control gure displays the HH Graphics gure as
shown in Figure 5.16. This gure allows plotting any result of the simulation
against any other in coordinates chosen by the user. The control of this gure is
virtually identical to that for the HH Parameters vs. potential gure (Figure 5.5).
Hence, we describe only the dierences. The main dierence occurs if Setup is
selected in the HH Graphics gure which results in display of the HH Setup plot
gure (Figure 5.17). Several dependent variables can be plotted simultaneously.
107
Figure 5.17: HH Setup plot gure showing the variables used

to setup Figure 5.16.
In addition, results saved in les can be plotted so that results for dierent
parameters can be compared. In addition, results of consecutive simulations
can be overlayed. We give a few examples of the types of graphics that are
readily available with the HH Graphics gure.
As shown in Figure 5.18, parametric plots of one variable versus another
with time as the parameter are easily obtained. Figure 5.19 shows the membrane
potential obtained at several dierent temperatures. This gure was obtained by
overlaying successive computations. It could also have been created by saving
the results of simulations performed for dierent temperatures in les and then
plotting the results from these les.
5.4.6
Scripts
Scripting commands alleviate the burden of being present while repetitive, time
consuming simulations are computed. The set of commands available to the
software user can be found by issuing the command help hhscr.
Although the set of scripting commands is not exhaustive enough to allow
operating all aspects of the software from the command-line, it is sucient to
carry out some of the time-consuming elements of the simulation.
The following is an example of a script used to perform current clamp simulations at dierent temperatures.
%A Hodgkin-Huxley script demonstration
%(contents are in HHDEMO1.M)
%This script can be used to generate simulation data using the
%current-clamped configuration. The temperature is varied while
%all other parameters remain unchanged.
%For each value of the temperature, the simulation is run
%and the resulting data are saved to data files which can then
108
Figure 5.18: HH Graphics gure showing a parametric plot of membrane conductances

versus membrane potential during an action potential. All the parameters were the
default parameters shown in Figure 5.4 and the stimulus was the same as shown in
Figure 5.10 except that the duration was increased to 20 ms.
109
Figure 5.19: HH Graphics gure showing the membrane potential obtained at dierent
temperatures. All the parameters were the default parameters shown in Figure 5.4
except for the temperature and the stimulus was the same as shown in Figure 5.10.
110
%be used to display the results in the Graphics figure.

%Before using the script, make sure that the Hodgkin-Huxley
%software has been started.
%If it hasnt been started, start the software using SOFTCELL.M
%as follows softcell(hh);
%hhscr(set) will list the parameters that can be changed
%The parameter names are case-sensitive, so make sure that
%you type them exactly as shown.
%Insure that the current clamped configuration is being used.
hhscr(set,Configuration,Current clamped);
%Since a lot of files will be created, it is best to store them
%in a separate folder. Examples of foldername are
%foldername = C:\data\temp; %Windows
%foldername = /user/tsb/data/temp; %UNIX
foldername = pwd;
%Set up a loop that increments through a temperature range.
%In this case, we use the range T = [0 10 20 30] Celsius
for temp = 0:10:30
%set the models temperature parameter
newtemp = hhscr(set,T_C,temp);
%perform simulation
hhscr(start);
%For feedback, display the temperature in the console
disp([Temperature is set to num2str(newtemp)]);
%create a unique filename that contains the simulation data
filename = [temp num2str(temp) .mat];
%save the simulation data to the file
hhscr(save,simulation,foldername,filename);
end
%Thats it -- all the data have been saved.
%Now, display the data simultaneously by following these steps:
5.5. PROBLEMS
111
%1. call up the "Graphics" figure,

%2. using "Setup", select which variable(s) to plot,
%3. still inside "HH Setup plot" figure, select the source of "Get
%
values from" to be the "Files with parameters".
% 3a. using "Select files", add the files to the list "Use these
%
files".
% 3b. select "Overlay" to view the selected variable(s) in all
%
the datafiles.
Scripting can also be used to create customized plots of variables. For example, after running a simulation, the time dependance of the sodium conductance
can be plotted on a separate gure using the following commands:
u_gna = hhscr(get,G\{ Na\}); %get the sodium conductance vector
u_time = hhscr(get,t); %get the vector of sampled time values
figure; %create a new figure
plot(u_time,u_gna); %plot sodium conductance vs. time
Once the values of these variables are so obtained, they can be manipulated,
modied, and saved to les.
5.5
Problems
Problem 5.1 The purpose of this problem is to explore the Hodgkin-Huxley model
in the voltage-clamp conguration. Use the default parameters of the HodgkinHuxley model under voltage-clamp conditions to complete the following problems. You may change only the stimulus parameters.
a. The potassium conductance
potential such that the potassium conductance reaches its nal of
GK (Vm , ) = 9 0.2 mS/cm2 .
ii. What is the value of the time constant of n, n , during this pulse?
b. The sodium conductance
potential such that the peak sodium conductance is 15 0.2 mS/cm2 .
Make sure that the pulse duration is sucient so that there is a peak
in the sodium conductance before the pulse terminates.
ii. What are the values of m and h at the time of the peak value of the
sodium conductance?
112

iii. Increase the amplitude of the pulse 20 mV from the value you found
iv. Decrease the amplitude of the pulse 20 mV from the value you found
Problem 5.2 The purpose of this problem is to explore the dierences in time
dependence of the [in]activation factors in voltage-clamp and current-clamp experiments.
a. Run the simulation in the voltage-clamp conguration using the default
parameters, except delay the onset of the pulse of voltage by 1 ms to make
the on and o transients more readily visible. Examine the results of the
simulation and answer the following questions.
iv. Plot the voltage dependence of m , h , n , m , h , and n . Check the
numerical values of these variables against those obtained in parts i,
ii, and iv.
b. Run the simulation in the current-clamp conguration using the default parameters. Examine the results of the simulation and answer the following
questions.
c. Succinctly summarize the dierences in the time dependence of all these
variables in voltage-clamp and current-clamp congurations.
Problem 5.3 The purpose of this problem is to explore a useful aspect of performing simulation experiments on a model; the model can be used to test ideas
concerning proposed measurements on cells.
Assume that the membrane of neuron X has voltage-current characteristics
as described by the Hodgkin-Huxley model except that the voltage dependences
of the parameters of the factors n, m, and h are unknown. In this problem
you are asked to develop methods to estimate the voltage dependence of some
of these parameters and to assess the accuracy of your methods. To make the
5.5. PROBLEMS
113
simulations realistic, in all parts of the problem you may only change the following parameters: the concentrations of sodium, potassium, and calcium either
inside or outside the cell, and the temperature. You may use either voltageclamp experiments or current clamp experiments. You can choose any stimulus
waveform that you can construct with the simulation. However, you must base
your estimation method on the membrane current in voltage clamp experiments
and/or on the membrane potential in current-clamp experiments. For example,
you cannot base your estimation method on a direct measurement of m(t).
a. Develop a method to estimate the voltage dependence of m . Use the
simulation to assess the accuracy of your method by comparing the results
of your estimation of m with a direct computation of m .
b. Develop a method to estimate the voltage dependence of h . Use the simulation to assess the accuracy of your method as in part a.
Problem 5.4 The purpose of this problem is to explore the threshold for eliciting an action potential for a model of a space-clamped axon. By changing the
amplitude of the stimulus pulse, while keeping all other parameters at their default values, determine the thresholdof the action potential to a precision of 4
signicant digits.
a. Describe the changes in action potential waveform as a function of current
amplitude.
b. Does the change in waveform of the action potential as a function of stimulus amplitude violate the all-or-none principal? Explain.
c. Investigate the basis of the change in waveform of the action potential by
examining the behavior of variables in addition to the membrane potential
as the current amplitude is varied.
Problem 5.5 The purpose of this problem is to explore the refractory properties
of the Hodgkin-Huxley model. Apply two current pulses, each of amplitude 30
A/cm2 and duration 0.5 ms, separated by 12 ms in time. Set the simulation
duration to 20 ms. Run the simulation. You should observe two action potentials. Reduce the inter-pulse interval to 10 ms. What happens? Now change the
amplitude of the second pulse to 50 A/cm2 and observe the response. Change
the inter-pulse interval to 5 ms and observe the outcome.
a. Have you observed properties of the absolute or the relative refractory period?
b. By examining the behavior of the factors m, n, and h during these twopulse simulations, determine which of these factors are most inuential in
refractory properties.
114
Problem 5.6 The purpose of this problem is to explore the phenomena of repetitive activity and depolarization block of the Hodgkin-Huxley model. Perform
a sequence of simulations with the following parameters. Use a single current
pulse of duration 40 ms, a simulation duration of 50 ms, and stimulus amplitudes of 10, 25, 50, 100, and 200 A/cm2 .
a. Note that both the number of action potentials and their amplitudes vary
with the current amplitude. Sketch the relation between the number of
action potentials and current amplitude and between action potential amplitude and current amplitude.
b. By examining the behavior of the factors m, n, and h determine which of
these factors are most inuential in determining repetitive activity. Explain
your reasoning.
Problem 5.7 The purpose of this problem is to explore the phenomenon of anodebreak excitation. The phenomenon can be demonstrated by applying a pulse
of current of duration 20 ms and amplitude 20 A/cm2 . Use a simulation
duration of 40 ms.
a. Why is this phenomenon called anode-break excitation?
b. By exploring the model variables explain this phenomenon.
Problem 5.8 The purpose of this problem is to explore the phenomenon of accommodation. Accommodation can be illustrated by applying a ramp of current of
slope 0.4 A/(cm2 ms) starting at an amplitude of 0 for a duration of 6 seconds (also set the simulation duration to 6 seconds). The model does not show
Na = 120 mS/cm2 but does for a value
accommodation for the default value of G
2
of 80 mS/cm . When the simulation is completed, plot the sodium, potassium
and membrane current versus the membrane potential.
a. Perhaps no action potential has occurred in response to the ramp of current because the reduced value of the sodium conductance prevents action
potential from being generated for any stimulus. Test this hypothesis.
b. Explain the underlying basis of accommodation.
c. What does the phenomenon of accommodation suggest about the notion
of the threshold for eliciting an action potential?
Problem 5.9 The purpose of this problem is to explore sub-threshold oscillations
in the Hodgkin-Huxley model. Sub-threshold oscillations can be observed by using the default parameters with current pulses of 50 ms duration and simulation
durations of 100 ms. Use current amplitudes of .01, .1, 1, 2, and 2.5 A/cm2 .
5.5. PROBLEMS
115
a. Describe your observations.

b. Can the response of the model to a step of current be represented by the
response of a network consisting of a constant resistance in parallel with a
constant capacitance. Explain.
c. If your answer to part b was no, then devise a current stimulus such that
the models response will approximate that of a network consisting of a
constant resistance in parallel with a constant capacitance. Explain your
method.
Problem 5.10 The purpose of this problem is to explore the strength-duration relation of the Hodgkin-Huxley model. Determine the threshold current amplitudes
(to three signicant gures) for eliciting action potentials for current pulses of
duration 0.01, 0.05, 0.1, 0.5, 1, 2, 5, 10, and 20 ms.
a. How does the threshold depend on current duration for low durations?
b. How does the threshold depend on current duration for long durations?
Problem 5.11 The purpose of this problem is to explore the interplay of factors
that determine the excitation of an action potential in the Hodgkin-Huxley model.
The Hodgkin-Huxley model with the default parameters stimulated by a pulse of
membrane current of amplitude 20 A/cm2 and of duration 0.5 ms produces an
action potential as shown in Figure 5.20. In each of the following computations,
one membrane parameter only diers from the default parameters, and for each
of these computations no action potential occurs. The parameter changes are:
i. A change in the temperature from 6.3 C to 35 C blocks the action potential
as shown in Figure 5.20.
ii. A change in the maximum potassium conductance from 36 to 72 mS/cm2
iii. A change in the internal calcium concentration from 0.0001 to 0.0002
mmol/l blocks the action potential. [Results not shown.]
iv. A change in the membrane capacitance from 1 F/cm2 to 20 F/cm2 blocks
the action potential as shown in Figure 5.20.
v. A change in the external calcium concentration from 44 mmol/l to 22
mmol/l blocks the action potential. [Results not shown.]
116
Figure 5.20: Results of simulation with all model parameters at their default values
except where indicated (Problem 5.11). The curve labelled Default was obtained with
the default parameters. The curve labeled Tc = 35 was obtained with the default parameters except that the temperature was set to 35 C. The curve labeled Cm = 20 was
obtained with the default parameters except that the membrane capacitance was set to
20 F/cm2 .
5.5. PROBLEMS
117
Examination of the results for the above computations (e.g., Figure 5.20) reveals that there is no large change in membrane potential, i.e., no action potential
has occurred. For each of the computations:
a. Explain why no action potential occurred. You may wish to base your explanation on the results obtained with each of the above computations. For
example, you may wish to examine the membrane currents, conductances,
and activation variables that occurred for each computation. You may also
wish to perform additional computations using dierent model parameters. For example, to see why no action potential occurs for a large temperature change, it might be instructive to examine the eects produced by
smaller changes in temperature. Since for many of the parts of this problem, there are large changes in parameters you may wish to explore the
role of the numerical methods in arriving at the solutions.
b. Determine a set of parameters so as to produce an action potential with a
waveform that is identical, except for a change in time scale and a change
in resting potential, to the action potential obtained with the default parameters. However, for each of the above parts, you may not change the
parameter that diers from its default value. For example, for computation
in part i, you may not change the temperature. Your task is to change some
other parameter or group of parameters such that the action potential is
restored. For computation in part ii, you may not change the maximum
potassium conductance. For computations in parts iii and v, you may not
change either the internal or the external calcium concentration, etc. REMEMBER the objective is not just to produce an action potential, that
is too easy, but to obtain an action potential whose waveform is identical to that obtained with the default parameters. To determine whether
or not the action potential is identical to that obtained with the default
parameters, you can superimpose plots and/or look at the variables summary gures from the responses. You should use the computer as a tool
to check your ideas and not as a substitute for thinking. You should avoid
a strictly trial-and-error approach. There are simply too many parameters
in the Hodgkin-Huxley model for you to explore them all randomly. When
you have arrived at a satisfactory solution, print a hard copy of the model
parameters gure showing the parameters you used to solve the problem
and include this with your solution. Explain why your parameter change
produces the desired result. [HINT: simulations are not required to solve
these problems, but they are helpful for checking ideas quickly.]
118
5.6
PROJECTS
The simulation software lends itself to more extensive study than that included
in the Problems. These more extensive studies are called Projects and these are
described here.
5.6.1
Practical considerations in the choice of a topic
Projects can involve almost any of the properties of the Hodgkin-Huxley model.
However, to avoid projects whose aims are vague (e.g., I would like to understand how the Hodgkin-Huxley model works) the proposed project should be in
the form of a specic and testable hypothesis. Projects that involve months of
computation should obviously be avoided. Experience should indicate the duration required to run simulations of the Hodgkin-Huxley model. These durations
should be taken into account explicitly in planning a project. For example, any
project that involves measuring the threshold of occurrence of an action potential for many dierent parameter values is bound to be very time consuming,
because determining the threshold for a single set of parameters itself involves
many computations. The task is to choose a physiological property of the excitation of the action potential that is of interest, and then to dene a specic,
feasible project.
5.6.2
Choice of topics
Topics can involve comparing predictions of the Hodgkin-Huxley model with

measurements on cells. For example, the eects of changes in sodium ion
concentration on the action potential have been measured (Hodgkin and Katz,
1949a; Baker et al., 1961). A project might involve reading the original papers
that describe such measurements (some were made before the Hodgkin-Huxley
model was formulated), and testing the hypothesis that these measurements
are (or are not) consistent with the Hodgkin-Huxley model. Similarly, a project
might involve examining the eect of some pharmacological substance on measurements of the action potential and testing the hypothesis that the substance
produces its eect by changing one or another parameter of the model. These
projects will require some reading of original literature which is often dicult
and usually time consuming. However, such a project can lead to a very rewarding educational experience. Alternatively, the project might involve a purely
theoretical topic in which some property of the model is explained in terms of
the underlying structure of the model. This type of project does not necessarily
involve reading the original literature. To make the process of project denition more tangible, we shall discuss one property of the Hodgkin-Huxley model
of a space-clamped axon, the shape of the action potential, and suggest some
appropriate projects based on this property.
5.6. PROJECTS
119
+50
+50
Squid giant
axon
50
50
100
100
0
+50
4
Time (ms)
8
+50
Cat
motoneuron
50
100
100
4
Time (ms)
+50
3
6
Time (ms)
Frog sartorius
muscle fiber
50
Electric eel
electroplaque
10
20
Time (ms)
30
+50
Cat myelinated
fiber
50
-50
100
100
0
1
Time (ms)
Sheep purkinje
fiber
0.5
1
Time (s)
1.5
Figure 5.21: Examples of action potentials measured in a variety of cell types (Keynes
and Aidley, 1991, adapted from Figure 2.4).
Background
The waveform of the action potential is dierent in dierent types of electricallyexcitable cells. As demonstrated in Figure 5.21, while the action potential waveform has a peak-to-peak amplitude of about 100 mV, the duration and time
course vary greatly. It is also known that the action potential waveform of a
cell can be changed by changing a number of experimental variables. For example, increasing the temperature tends to decrease the duration of the action
potential (Figure 5.22), and reducing the external sodium concentration reduces
the amplitude and increases the duration of the action potential (Figure 5.23).
Since action-potential waveforms vary from cell to cell and vary for one cell if
environmental variables are changed, this raises a question To what extent
are changes in action-potential waveforms seen in dierent cells due to inherent
dierences in the membrane mechanisms rather than to dierences in membrane
parameters with identical membrane mechanisms? For example, the action po-
Vm(t) Vmo (mV)
120
100
20.2
3.6
32.5
50
6.3
9.8
13.3
0
0
1
2
Time (ms)
Figure 5.22: Dependence of the action potential on temperature for measurements

obtained from a giant axon of the squid (Hodgkin and Katz, 1949b).
40
1
3
-40
-80
0
2
Time (ms)
Figure 5.23: Eect of extracellular sodium concentration on the membrane potential of

a giant axon of a squid (Hodgkin and Katz, 1949a, adapted from Figure 4). Traces 1 and
3 are the action potentials obtained in normal sea water before and after trace 2 which
was obtained in sea water with 50% sodium content. Isotonic solutions were obtained
by using mixtures of sea water and a glucose solution.
5.6. PROJECTS
121
tentials of the squid axon and the frog and rat nodes of Ranvier shown in Figure 5.21 were measured at dierent temperatures. In fact, the briefest action potentials were obtained at the highest temperatures. Since Figure 5.22 indicates
that the duration of the action potential does become shorter at higher temperatures in squid axon, it may be that the temperature dierences in the measurements could explain the dierences in the waveforms of the action potentials
of these three preparations. It is clear that temperature changes alone cannot
explain all the variations seen in Figure 5.21 since the long-duration action potential of frog cardiac muscle was obtained at a higher temperature than was the
action potential of the squid giant axon. However, perhaps some combination
of changes of parameters in addition to temperature (e.g., ion concentrations,
ion conductances, membrane capacitance, etc.) might explain the long-duration
action potential of cardiac muscle.
The list of projects given below includes a number that deal with the waveform
of the action potential generated by the Hodgkin-Huxley model as well as a few
that deal with other topics.
1. Hypothesis The dierence in waveform of the action potential of a frog
node of Ranvier and of a squid giant axon (Figure 5.21) can be reproduced
by the Hodgkin-Huxley model of a squid giant axon by a change in temperature.
2. Hypothesis The membrane capacitance determines the time course of
the rising phase of the action potential. Increasing the membrane capacitance decreases the rate of increase of the rising phase of the action potential.
3. Hypothesis The falling phase of the action potential (repolarization) can
occur in the absence of a change in potassium conductance.
4. Hypothesis Increasing the temperature suciently blocks the occurrence of the action potential because the membrane time constant limits
the rate at which the membrane variables can change and prevents the difference in time course of the sodium and potassium activation which is
responsible for initiation of the action potential.
5. Hypothesis The initiation of the action potential is independent of the
potassium conductance.
6. Hypothesis The prolonged plateau of the cardiac muscle action potential can be accounted for by the Hodgkin-Huxley model with a potassium
conductance that has a slow activation.
122
7. Hypothesis The eect of tetraethylammonium chloride (TEA) on the action potential of the squid giant axon can be modelled with the HodgkinHuxley model by decreasing Kn and increasing Kh . Articles in the literature
should be consulted for this project (Armstrong, 1966; Armstrong and Binstock, 1965; Tasaki and Hagiwara, 1957).
8. Hypothesis The shape of the action potential in the presence of tetraethylammonium chloride (TEA) can be accounted for by the Hodgkin-Huxley
model with a reduced maximum value of the potassium conductance. Articles in the literature should be consulted for this project (Armstrong, 1966;
Armstrong and Binstock, 1965; Tasaki and Hagiwara, 1957).
9. Hypothesis Increasing the external calcium concentration will block the
occurrence of the action potential because this will reduce the dierence in
the time constant of sodium and potassium activation which is responsible
for the initiation of the action potential.
10. Hypothesis Increasing the external concentration of potassium will decrease the refractory period; decreasing this concentration will lengthen
the refractory period.
11. Hypothesis Increasing the external concentration of sodium will decrease the refractory period; decreasing this concentration will lengthen
the refractory period.
12. Hypothesis Absolute and relative refractory periods are decreased by
increasing the rate constants for sodium inactivation and for potassium
activation.
13. Hypothesis Repolarization cannot occur if the potassium activation rate
constant is zero.
14. Hypothesis The threshold of the action potential to a brief pulse of current decreases as the external potassium current is increased.
15. The Hodgkin-Huxley model with default parameters does not exhibit accommodation (Weiss, 1996b). Hypothesis Accommodation occurs if the
leakage conductance is increased.
16. The Hodgkin-Huxley model with default parameters does not exhibit accommodation (Weiss, 1996b). Hypothesis Accommodation occurs if the
potassium conductance is increased.
17. Hypothesis Increasing the leakage equilibrium potential will block the
action potential.
5.6. PROJECTS
123
18. Hypothesis The eect of the changes in concentration of sodium ions on

the action potential of the giant axon of the squid can be accounted for by
the Hodgkin-Huxley model. Articles in the literature should be consulted
for this project (Hodgkin and Katz, 1949a; Baker et al., 1961).
19. Hypothesis In response to rectangular pulses of current, the rheobase of
the strength-duration relation increases as temperature increases.
20. Hypothesis An increase in temperature results in a decrease in the duration of the refractory period.
21. Hypothesis The threshold membrane potential at which the HodgkinHuxley model produces an action potential in response to a brief pulse
of current is equal to the membrane potential for which the linearized
Hodgkin-Huxley equations have unstable eigenvalues.
22. Application of a long-duration constant current to the Hodgkin-Huxley
model produces a train of action potentials. Hypothesis The frequency
of the action potentials increases with increasing current amplitude.
of action potential increases as the parameter Kn is increased.
of action potential increases as the temperature is increased.
25. Hypothesis An increase in the external concentration of potassium increases the threshold potential at which an action potential is elicited.
26. Hypothesis Increasing Kh will result in an increase in the steepness of
the repolarization phase of the action potential.
Caveats
Any of these (or other) hypotheses can be the starting point for a project. Most
of the hypotheses given above are simplistic, and a careful investigation will
reveal their shortcomings. The Hodgkin-Huxley model is suciently complex
that investigation of any of the hypotheses will most likely lead to unexpected
results. It is informative to pursue these unexpected results and to try to understand their bases. For example, you may nd that in pursuing some hypothesis
you choose to change some parameter of the model that you expect to result
in some change in action potential waveform. The resulting computation might
reveal, much to your surprise and chagrin, that no action potential has occurred
124
or that multiple action potentials occur. Investigation of these unexpected ndings will usually be instructive. The aim should be not simply to reject or accept
the hypothesis but to delve into the topic in sucient depth so as to a deepen
understanding of the model. One outcome of the project might be to restate the
original hypothesis in a new and more sophisticated form.
In pursuing these projects, it is important to keep in mind that it is not nerve
membrane that is being investigated but rather a model of nerve membrane; in
fact, a very specic model the Hodgkin-Huxley model for the membrane of
the squid giant axon. Explanations of all phenomena seen with the model must
involve the primitive concepts of this model e.g., the ionic conductances, ionic
concentrations, ionic currents, the capacitance, and the variables m, n, and h.
Explanations in terms of molecular channel mechanisms or electrodiusion of
ions in the membrane or ion pumps are irrelevant in so far as they are not contained in the Hodgkin-Huxley model! Finally, it is important to remember that
the software performs a numerical integration of the Hodgkin-Huxley equations.
Thus, the user will have to contend with the inherent approximations involved
in numerical solutions of equations.
Chapter 6
HODGKIN HUXLEY MODEL
PROPAGATED ACTION POTENTIAL
125
126
6.1
6.1.1
CHAPTER 6. PROPAGATED ACTION POTENTIAL
Introduction
Background
An electrically excitable cell produces a dierence of potential across its cell

membrane, called an action potential. The dierence in membrane potential is
accompanied by a ow of current longitudinally through the intracellular and
extracellular media, as well as current ow across the cell membrane along its
entire length. The spatial coupling of current ow through neighboring segments of the membrane results in the propagation of the action potential along
the cell surface.
In the 1950s, Hodgkin and Huxley derived a partial dierential equation that
eectively describes the electrical properties of the giant axon of the squid
(Hodgkin and Huxley, 1952). This partial dierential equation consists of the
core conductor equations, that describe the relation of current and voltage for
an electrical cable, plus a characterization of the electrical properties of the cell
membrane. The cell is assumed to be cylindrical and the inner and outer conductors are assumed to be equipotentials at each longitudinal position. Numerical
solutions to the partial dierential equation were originally computed tediously
by hand (Hodgkin, 1977; Huxley, 1964). With the introduction of the digital computer in the 1950s, solutions to these equations were computed more rapidly
(Fitzhugh and Antosiewicz, 1959). By the 1960s computer speeds had increased
to allow the rst comprehensive study of the solutions to the partial dierential
equations (Cooley and Dodge, 1966). Further increases in computer speeds and
the development of improved numerical methods (Moore et al., 1975; Joyner
et al., 1978; Hines, 1984), have allowed solutions to be obtained on personal
computers. The software package described here yields numerical solutions of
the partial dierential equation that describe the propagation of the action potential along a model of the squid giant axon.
6.1.2
Overview of the software
This software deals with the time and space dependent Hodgkin-Huxley model
and is complementary to the software described in Chapter 5. The software
described in the current chapter is comprised of a number of setup and analysis gures that are launched from a main control gure. Using the setup gures, the user can specify the physical characteristics of the axon (length, radius,
etc.) and parameters of the membrane (capacitance, conductances of membrane
ionic channels, kinetic parameters, etc.) and bath (concentration of all relevant
ions, temperature, etc.). A stimulus source can be customized to the users
specications, and graphic icons of a pair of stimulus electrodes can be visually placed along a schematic representation of an axon. In addition, graphic
icons representing a pair of recording electrodes can be placed along the axon
6.2. THEORY
127
schematic to compute and display the dierence in potential. When a simulation is started, solutions are calculated using one of four user selectable numerical methods, and the time-evolution of the membrane potential is shown color
coded to convey the space-time evolution of potentials on the axon schematic.
After a simulation is completed, the user can display any of the computed solution variables (such as membrane potential, membrane-current components,
membrane-conductance components, channel activation and inactivation variables, etc.) using dierent interactive analysis gures which include: a gure
that displays the space-time evolution of any solution variable, a gure that generates three-dimensional plots to show the dependence on time and on space of
any solution variable, and a gure that generates comparison plots between the
solution variables at xed times or at xed positions.
6.2
Theory
The theory of the propagation of an action potential along an unmyelinated axon

was rst described for the squid giant axon (Hodgkin and Huxley, 1952). We
briey review this theory here; a more detailed description is available elsewhere
(Weiss, 1996b).
6.2.1
Core conductor equations
An incremental portion of the core conductor model of a cylindrical unmyelinated nerve ber is shown in Figure 6.1. Kirchhos laws relate the variables of
this incremental model. The core conductor equations result (Weiss, 1996b) if
the limit of these equations is taken as the incremental length of the ber goes
to zero, z 0,
Ii (z, t)
z
Io (z, t)
z
Vi (z, t)
z
Vo (z, t)
z
Vm (z, t)
Vm (z, t)
z
= Kei (z, t) Km (z, t),
(6.1)
= Km (z, t) Keo (z, t),
(6.2)
= ri Ii (z, t),
(6.3)
= ro Io (z, t),
(6.4)
= Vi (z, t) Vo (z, t),
(6.5)
= ri Ii (z, t) + ro Io (z, t).
(6.6)
These equations can be combined to obtain a relation between the membrane

potential Vm and the membrane current density Jm at time t and location z along
128
ri z
Kei (z, t)z
Ii (z, t)
ri z
Ii (z+z, t)
Vi (z+z, t)
Vi (z, t)
Inner conductor
Km (z, t)z
Kei (z+z, t)z r z

i
Km (z+z, t)z
+
Vm (z+z, t)
Vm (z, t)
Membrane
Outer conductor
ro z
Vo (z, t)
Vo (z+z, t)
ro z
Io (z, t)
Io (z+z, t)
Keo (z, t)z
ro z
Keo (z+z, t)z
z + z
Figure 6.1: Equivalent network model of incremental sections of an unmyelinated nerve

ber showing the reference directions for all the voltage and current variables. The Ks
are currents per unit length of the ber: Km is the membrane current; Keo and Kei are
extrinsic currents applied (by electrodes) externally and internally, respectively. Ii and
Io are the internal and external longitudinal currents. Vm is the potential across the
membrane and Vi and Vo are the internal and external potentials, respectively. The
internal and external resistance per unit length of the ber are ri and ro .
a cylindrical, unmyelinated nerve ber, often called the core-conductor equation

1
2 Vm (z, t)
1
(ro Keo (z, t) + ri Kei (z, t)),
= Jm (z, t)
2
2 a(ro + ri )
z
2 a(ro + ri )
where a is the radius of the cylindrical cell and Km = 2 aJm , where Jm is the
membrane current per unit area. In addition, the resistance per unit length of
cytoplasm can be expressed in terms of the resistivity as follows
ri =
i
4 a2
where i is the resistivity of cytoplasm.
6.2.2
Representation of stimulating electrodes
An arrangement of stimulating electrodes is shown in Figure 6.2. From Kirchhos current law we have that at any position along the ber
Ii (z, t) + Io (z, t) + Is (z, t) = 0,
(6.7)
6.2. THEORY
129
I1 (t)
I2 (t)
Figure 6.2: The relation of two

pairs of stimulus electrodes to a
ber is shown. The stimulus electrodes are shown as extracellular
but any of the electrodes can be
intracellular or extracellular.
Extracelllular
Intracellular
Extracellular
z11
z12
z21
z22
where Is (z, t) is the stimulus current in the positive z-direction which can be
written as

Is (z, t) = I1 (t) u(z z11 ) u(z z12 ) + I2 (t) u(z z21 ) u(z z22 ) ,
(6.8)
where u(z) is the unit step function dened as
1 if z > 0,
u(z) =
0 if z < 0.
The electrode conguration shown in Figure 6.2 also imparts current components to Equations 6.1 and 6.2. With all the electrodes external, the currents per
unit length are as follows

Keo (z, t) = I1 (t) (z z11 ) (z z12 ) + I2 (t) (z z21 ) (z z22 ) ,
Kei (z, t) = 0,
where (z) is the unit impulse function.
If all four of the electrodes were intracellular then the currents per unit length
would be
Keo (z, t) = 0,

Kei (z, t) = I1 (t) (z z11 ) (z z12 ) I2 (t) (z z21 ) (z z22 ) ,
With careful attention to signs, any combination of intracellular and extracellular

stimulating electrodes can be accommodated. The algorithm is that extracellular
electrodes supply positive impulses at the cathode and negative impulses at
the anode; intracellular electrodes supply negative impulses at the cathode and
positive impulses at the anode.
6.2.3
Longitudinal currents
By using the core conductor equations (Equation 6.6) and the KCL equation for
the current (Equation 6.7), we can solve for the longitudinal currents as follows
Ii (z, t) =
ro
1 Vm (z, t)
Is (z, t),
ri + ro
z
ri + ro
130

Io (z, t) =
6.2.4
ri
1 Vm (z, t)
Is (z, t).
ri + ro
z
ri + ro
Intracellular and extracellular potential dierences
The expressions for the longitudinal currents can be combined with Equations 6.3
and 6.4 and the result integrated on z to yield the potential dierences of a
recording electrode at zr 2 minus that at zr 1 as follows
ri
(Vm (zr 2 , t) Vm (zr 1 , t))
ri + ro
zr 2
ri ro
+
Is (z, t) dz,
ri + ro zr 1
ro
Vo (zr 2 , t) Vo (zr 1 , t) =
(Vm (zr 2 , t) Vm (zr 1 , t))
ri + ro
zr 2
ri ro
Is (z, t) dz,
+
ri + ro zr 1
Vi (zr 2 , t) Vi (zr 1 , t) =
where use of Equation 6.8 results in

zr 2

Is (z, t) dz = I1 (t) (z z11 )u(z z11 ) (z z12 )u(z z12 )
zr 1

+I2 (t) (z z21 )u(z z21 ) (z z22 )u(z z22 ) .
6.2.5
The membrane current density
The membrane current density consists of a capacitance current density and an

ionic current density Jion as follows,
Jm (z, t) = Cm
Vm (z, t)
+ Jion (z, t),
t
where Cm is the specic membrane capacitance, i.e., the capacitance of a unit

area of membrane. For purposes of numerical solution of the core conductor
equation, it is helpful to combine the ionic current density with the external
currents so that
J(z, t) = Jion (z, t)
1
(ro Keo (z, t) + ri Kei (z, t)),
2 a(ro + ri )
(6.9)
and, therefore, the core conductor equation can be expressed as

1
2 Vm (z, t)
Vm (z, t)
+ J(z, t).
= Cm
2
2 a(ro + ri )
z
t
(6.10)
The ionic current density can be expressed in terms of its ionic components
Jion (z, t) = GK (Vm , t)(Vm VK ) + GNa (Vm , t)(Vm VNa ) + GL (Vm VL ), (6.11)
6.3. NUMERICAL METHOD OF SOLUTION
131
where Vn is the Nernst equilibrium potential of ion n

cno
RT
Vn =
ln
,
zn F
cni
expressed as

cno
(mV),
Vn = 0.08616 (Tc + 273.16) ln
cni
6.2.6
The membrane conductances
A full description of the Hodgkin-Huxley model of the ionic conductances is

given beginning with Section 5.2.3.
6.2.7
Default values of parameters
The default numerical values for the Hodgkin-Huxley model are: GNa = 120,
o
i
GK = 36, and GL = 0.3 mS/cm2 ; Cm = 1 F/cm2 ; cNa
= 491, cNa
= 50, cKo =
o
i
= 44, cCa
= 0.00011 mmol/L; VL = 49 mV; external
20.11, cKi = 400, cCa
resistance per unit length, ro = 0 Ohm/cm; resistivity of axoplasm, i = 35.4
Ohmcm; axon radius, a = 238 m; temperature is 6.3 C.
6.3
Numerical Method of Solution
There are several ways to obtain a numerical solution to the equations describing the membrane potential in a cylindrical cell. In the nite-element method, the
cylindrical axon is segmented into small cylinders over each of which the membrane potential is assumed to be constant. Ordinary dierential equations (with
time as the independent variable) can be written to describe the membrane potential and membrane current for each segment and the set of ordinary dierential equations can be solved numerically with appropriate boundary conditions
linking the electrical variables in adjoining segments. In the nite-dierence
method, the partial dierential equations are discretized directly by discretizing
the membrane potential and membrane current and approximating the spatial
and temporal derivatives with nite dierences. We use the second method
which is described in a number of texts on numerical methods of solution of
partial dierential equations (Smith, 1985; Press et al., 1986; Gerald and Wheatley, 1989) and in research papers on the solution of the Hodgkin-Huxley model
132
(Hines, 1984; Hines and Carnevale, 1998; Mascagni and Sherman, 1998; Pearlmutter and Zador, 1999).
The rst step is to discretize the membrane potential and current density
variables as follows,
Vin = Vm (iz, nt) = Vm (z, t)|z=iz,t=nt ,
Jin = J(iz, nt) = J(z, t)|z=iz,t=nt ,
where z and t are the increments in z and t. The second spatial derivative
is approximated by the centered dierence (also known as the method of lines),
n
n
Vi+1
2Vin + Vi1
2 Vm (z, t)
.
z2
(z)2
All of the numerical methods implemented use the above centered dierence
approximation to the second spatial derivative. The methods dier only in the
approximation of the temporal derivative. There are two simple ways to approximate the temporal derivative at time t. In the forward Euler approximation,
V n+1 Vin
Vm (z, t)
i
,
t
t
whereas in the backward Euler approximation
V n Vin1
Vm (z, t)
i
.
t
t
The temporal approximation used in the Crank-Nicolson method essentially averages the forward Euler and the backward Euler approximations. The staggered
increment Crank-Nicolson method is a variant of the Crank-Nicolson method
with desirable numerical characteristics.
6.3.1
Forward Euler method
With the forward Euler approximation, the discretized core conductor equation
(Equation 6.10) is
n

n+1
n
Vi+1 2Vin + Vi1
Vi
Vin
1
+ Jin .
= Cm
(6.12)
2 a(ro + ri )
(z)2
t
By collecting terms, the forward Euler approximation leads to the following difference equations
n
n
Vin+1 = Vi+1
+ (1 2)Vin + Vi1
Jin ,
where
=
t
t
and =
.
2 a(ro + ri )(z)2 Cm
Cm
133
Note that the forward Euler approximation results in an explicit method of solution since it gives an explicit formula for computing the Vin+1 given both Vin and
Jin , i.e., the values of variables at time n + 1 are computed directly from their
values at at time n.
In order to solve the equations numerically, we require initial conditions
along the length of the ber plus boundary conditions at the two ends of the
ber. Initial conditions are simply that the membrane potential is at its resting
value and that the membrane current is zero. The method for computing the
resting potential is described in Section 5.3.3. A variety of boundary conditions
are plausible. We shall use the boundary condition that the ber is closed at
both ends so that the longitudinal current is zero at the two ends of the ber.
Equation 6.12 essentially expresses Kirchhos current law which can be modied at the closed end to set the appropriate longitudinal current to zero. Using
this method for i = 1 and setting the longitudinal current from node 0 to node
1 to zero yields
1
2 a(ro + ri )
V2n V1n
(z)2

= Cm
V1n+1 V1n
t

+ J1n ,
which, after collecting terms, results in the dierence equation

V1n+1 = V2n + (1 )V1n J1n .
A similar equation results at the other end of the ber model so that the matrix
equation can be written as
V1n+1
V n+1
2
V n+1
3
V n+1
I1
n+1
VI

0

0

=
.

.

.

0

0
1 2
1 2
0
.
.
.
.
.
.
.
.
.
0
.
.
.
0
.
.
.
0
.
.
.
1 2
1 2
V1
Vn
2
V3n
n
VI1
VIn
J1n
Jn
Jn
Jn
I1
JIn
The matrix equation can be written compactly as

Vn+1 = AF E Vn Jn .
To obtain a solution, we need to compute Jin . This current is linked to the
ionic currents (Equation 6.9) which themselves depend upon factors that are
solutions to dierential equations (Equations 5.11-5.13). Let x stand for m, n,
and h then we have
dx
= m x(m + m ),
dt
134
where and are instantaneous functions of membrane potential. We discretize this equation with the forward Euler algorithm as follows

xin xin1
= x Vin1 xin1 x Vin1 + x Vin1 ,
t
and collect terms to obtain

xin = xin1 1 t x Vin1 + x Vin1
+ tx Vin1 .
(6.13)
With the factors m, n, and h substituted for x, the ionic current can be computed as follows
n 4
n
n 3 n
n
n
(Jion )n
i = GK (ni ) (Vi VK ) + GNa (mi ) hi (Vi VNa ) + GL (Vi VL ),
n
where each of the factors min , nn
i , and hi are computed according to Equation 6.13. The total current is
Jin = (Jion )n
i
n
ro (Keo )n
i + ri (Kei )i
.
2 a(ro + ri )
Although the Forward Euler method is relatively easy to understand, its numerical properties are undesirable. The forward Euler method is stable provided
0.5 which implies that to achieve stable solutions, the discretization in space
and in time cannot be chosen independently. Specically, a stable solution requires t a(ro + ri )(z)2 Cm (Mascagni and Sherman, 1998). Thus, a choice
of x limits the choice of t required to achieve stable solutions. If t is too
large, the solution will diverge. Thus, for example, the forward Euler algorithm
cannot be used to eciently compute the response for large values of t such as
would be desirable to determine steady-state responses. Furthermore, the error
resulting from temporal and spatial discretization behaves as O(t)+O((x)2 ).
Thus, although the method of solution using the forward Euler algorithm is simple to understand, the numerical properties of the method are not desirable.
6.3.2
Backward Euler method
With the backward Euler approximation (advanced one point in time), the discretized core conductor equation is
n+1

n+1
n+1
Vi+1 2Vin+1 + Vi1
Vi
Vin
1
+ Jin+1 ,
= Cm
(6.14)
2 a(ro + ri )
(z)2
t
which, after collecting terms and changing signs, yields the dierence equation
n+1
n+1
Vi+1
+ (1 + 2)Vin+1 Vi1
= Vin Jin+1 .
135
Note that the backward Euler method is an implicit method of solution since it
gives an implicit formula for computing the Vin+1 given both Vin and Jin . Thus,
the solution can only be obtained by solving a set of coupled algebraic equations.
We use the same initial and boundary conditions as for the forward Euler
algorithm. By modifying Equation 6.14 with a closed end condition at i = 1 and
collecting terms, the dierence equation is
V2n+1 + (1 + )V1n+1 = V1n J1n .
A similar equation results at the other end of the ber model so that the incorporation of the closed-end boundary conditions results in the following matrix
equation
1+
1 + 2
1 + 2
0
.
.
.
.
.
.
.
.
.
0
.
.
.
0
.
.
.
0
.
.
.
1 + 2
1 + 2
1+
V1n+1
V2n+1
V3n+1
.
.
.
n+1
VI1
VIn+1
V1n

V2n

Vn

3

=
.

.

.

n
VI1

VIn
J n+1
n+1
J2
n+1
n+1
JI1
n+1
JI
The matrix equation can be written compactly as

ABE Vn+1 = Vn Jn+1 ,
which has the solution

Vn+1 = ABE 1 Vn Jn+1 .
(6.15)
Similar to the procedure with the forward Euler algorithm, Jin+1 can be computed from the factors that determine the ionic conductances. Once again, we
let x stand for m, n, and h, and we discretize this equation, this time with the
backward Euler algorithm as follows

xin+1 xin
= x Vin+1 xin+1 x Vin+1 + x Vin+1 ,
t
xin+1

xin + tx Vin+1

.

=
1 + t x Vin+1 + x Vin+1
(6.16)
K (nn+1
Na (min+1 )3 hn+1
=G
)4 (Vin VK ) + G
(Vin VNa ) + GL (Vin VL ),
(Jion )n+1
i
i
i
136
where each of the factors min+1 , nn+1

, and hn+1
are computed according to Equai
i
tion 6.16. The total current is
Jin+1
(Jion )n+1
i
ro (Keo )n+1
+ ri (Kei )n+1
i
i
.
2 a(ro + ri )
One dierence is that the factor xin+1 depends upon the potential Vin+1 so
that the four equations Equation 6.15 and three equations (one for each of
the factors m, n, and h) of the form of Equation 6.16 need to be solved simultaneously. To obtain accurate solutions, the set of 4 equations are iterated until
, and hn+1
converge to within some specied
the 4 variables V n+1 , min+1 , nn+1
i
i
limit. For example, Equation 6.15 can be solved for the value of V n+1 using the
values of the factors at time increment n to compute new values of the factors.
These are then used to compute the new value of V n+1 which is used to compute
new values of the factors, etc.
The backward Euler algorithm is stable for all values of t and x. Thus t
and z can be chosen independently. Large values of t can be used to determine approximate steady-state values of the solution. Just as for the forward
Euler algorithm, the error resulting from temporal and spatial discretization using the backward Euler algorithm behaves as O(t) + O((x)2 ).
6.3.3
Crank-Nicolson method
In the Crank-Nicolson method, the forward Euler and backward Euler approximations are averaged to yield the following dierence equation
n+1

n+1
n
n
Vi+1 2Vin+1 + Vi1
Vi+1
2Vin + Vi1
1
=
+
4 a(ro + ri )
(z)2
(z)2

n+1
Vi
Vin
1
+ (Jin + Jin+1 ).
(6.17)
Cm
t
2
Alternatively, this equation can be regarded as satisfying the partial dierential
equation at the discrete time n + 12 with central dierences used for all derivatives. This interpretation is exploited in the next section on the Staggered increment Crank-Nicolson method.
Equation 6.17 can be rearranged and simplied so that all the voltage variables evaluated at time step n + 1 are on the left and all those at time step n are
on the right as follows
J n+1 + Jin
n+1
n
n
n+1
.
+ (1 + )Vin+1 Vi1
= Vi+1
+ (1 )Vin + Vi1
i
Vi+1
2
2
2
2
2
As can be seen from the above equations, the Crank-Nicolson method is also an
implicit method.
137
We use the same initial and boundary conditions as for the forward and backward Euler algorithms. By modifying Equation 6.17 at the closed end at i = 1
and collecting terms, the dierence equation is
V2n+1 + (1 + )V1n+1 = V2n + (1 )V1n (J1n + J1n+1 ).

2
2
2
2
2
A similar equation results at the other end of the ber model so that with the
incorporation of the closed-end boundary conditions, the matrix equation for
the Crank-Nicolson method is
1+ 2
1 2
1+
1+
0
.
.
.
.
.
.
.
.
.
0
.
.
.
0
.
.
.
0
.
.
.
1+
1+
1+ 2
0
.
.
.
.
.
.
.
.
.
0
.
.
.
0
.
.
.
0
.
.
.
V1n+1
V2n+1
V3n+1
.
.
.
n+1
VI1
VIn+1
n
V1
Vn
V3n
n
V
I1
VIn
n
J1
J2n
J n
3

.
2
.
JI1
JIn
J n+1
1

n+1
J2

n+1
J
3

+
.

.

.

n+1
JI1

n+1
JI
The matrix equation can be written as

ACN1 Vn+1 = ACN2 Vn

n
J + Jn+1 ,
2

Vn+1 = ACN1 1 ACN2 Vn

ACN1 1 Jn + Jn+1 .
2
Similar to the procedure with the forward and backward Euler algorithms,
we need to compute Jin from the factors that determine the ionic conductances.
Once again, we let x stand for m, n, and h, and we discretize this equation, this
time with the trapezoidal rule, so as to preserve the O((t)2 ) error in time, as
follows

n+ 12
n+ 12
n+ 12
n+1
x Vi
xi
x Vi
+ x Vi
xin+1 xin
=
t

2

n+ 12
n+ 1
n+ 1
n
x Vi
xi x Vi 2 + x Vi 2
+
,
2
138
xin+1 =
1+
t
2
+xin
t
x
2
t
2
1+
t
2
n+
Vi 2
n+ 12
Vi

1

+ x

1
n+ 1
Vi 2

n+
n+ 1
x Vi 2 + x Vi 2

n+ 12
n+ 12
x Vi
+ x Vi
(6.18)
K (nn+1
Na (min+1 )3 hn+1
=G
)4 (Vin VK ) + G
(Jion )n+1
i
i
i
where each of the factors min+1 , nn+1
, and hn+1
are computed according to Equai
i
tion 6.16. The total current is
Jin+1 = (Jion )n+1

i
ro (Keo )n+1
+ ri (Kei )n+1
i
i
.
2 a(ro + ri )
As with the backward Euler algorithm, the factor xin+1 depends upon the pon+ 1
tential Vi 2 through the parameters and so that iteration must be used to

arrive at a solution of the 4 simultaneous equations.
For linear, parabolic partial dierential equations, the Crank-Nicolson method
yields stable solutions although not as stable as the backward Euler method,
i.e., spurious bounded amplitude oscillations may appear for large values of increments. In contrast to both the forward and backward Euler algorithms, the
error resulting from temporal and spatial discretization for the Crank-Nicolson
method behaves as O((t)2 ) + O((x)2 ) provided appropriate boundary conditions (such as those shown above) are used. Thus, with the Crank-Nicolson
method it is possible to achieve more accurate solutions for large time intervals
than for the backward Euler method.
6.3.4
Staggered increment Crank-Nicolson method
A computationally ecient method (Hines, 1984) that avoids iteration of the solution is based on the observation that the Crank-Nicolson dierencing scheme
1
satises the partial dierential equation at the discrete time n+ 2 . This property
can be seen by writing out the expression as follows
n+ 12
n+ 12
n+ 12
n+ 12
n
+ Vi1
Vi
1
n+ 12
Vi+1 2Vi
Vi
+
J
=
2C
, (6.19)
m
i
2 a(ro + ri )
(z)2
t
139
which results in the following dierence equation

n+ 1
n+ 1
n+ 1
n+ 1
Vi+1 2 + (1 + )Vi 2 Vi1 2 = Vin Ji 2 .
2
2
2
Note that starting with the membrane potential at discrete time n, the dierence
1
equation computes (by an implicit method) the potential at n + 2 . Then the
potential at discrete time n + 1 is computed by the explicit method
n+ 12
Vin+1 = 2Vi
Vin .
(6.20)
We use the same initial and boundary conditions as for the other algorithms.
By modifying Equation 6.19 at the closed end at i = 1 and collecting terms, the
dierence equation is
n+ 1
n+ 1
n+ 1
V2 2 + (1 + )V1 2 = V1n (J1 2 .
2
2
2
A similar equation results at the other end of the ber model so that the matrix
equation is
1+ 2
1+
1+
0
.
.
.
.
.
.
.
.
.
0
.
.
.
0
.
.
.
0
.
.
.
1+
1+
1+
n+
V1 2
n+ 1
V2 2
1
n+
V3 2
.
.
.
n+ 1
VI1 2
1
n+ 2
VI
V1n

V2n

Vn

3

=
.

.

.

n
VI1

VIn
1
n+ 2
J1
n+ 12
n+ 1
J3 2

.
2
.
n+ 12
I1
n+ 1
JI 2
The matrix equation can be written as

1
ACN Vn+ 2 = Vn
n+ 1
J 2,
2

n+ 12
= ACN

n+ 1
2
.
V J
2

(6.21)
This scheme requires that the current be evaluated at the time n + 12 which
can be done by iteration as described previously or by having two computing
1
time grids staggered by 2 units of time. To maintain the error due to time
quantization at O((t)2 ), we need to compute the factors with second-order
accuracy by a centered dierence as follows
n+ 12
xi
n 12
xi
t

n
= x Vi

n
x Vi
n+ 12
xi
n
+ x Vi
n 12
+ xi
2
140

tx Vin
n+ 12
n 12 1
xi
+
x
=

i
t
1 + 2 x Vin + x Vin
1+
t
2
t
2

x Vin + x Vin

x Vin + x Vin
(6.22)
n+ 12
(Jion )i
2 4
2
K (nn+
Na (min+ 2 )3 hn+
=G
) (Vin VK ) + G
i
i
n+
n+ 2
where each of the factors mi 2 , ni

Equation 6.22. The total current is
n+ 1
Ji 2
n+ 1
(Jion )i 2
n+ 2
, and hi
n+
are computed according to
n+ 2
ro (Keo )i 2 + ri (Kei )i
2 a(ro + ri )
The method is outlined as follows:

n 12
Start with the value of Vin and the value of xi
which allows a computa-
tion of
n
Ji 2 ;
n+ 12
Compute xi
using Equation 6.22 which then allows a computation of
n+
Ji 2 ;
1
n+ 2
Compute Vi
using Equation 6.21;
Compute Vin+1 using Equation 6.20;

n+ 12
The solution has now been advanced to Vin+1 and the value of xi
The process can be initiated by calculating either Vi or xi for a
increment to stagger the variables.
6.4
1
2
time step
Users Guide to the Software
When the software is selected from the Softcell menu, two gures are displayed
(in addition to MATLABs command window): PAP Control, and PAP Workspace;
the PAP Workspace is distinct from MATLABs workspace. The PAP Control gure allows the user to display other gures for setup and analysis, and to start
a simulation. The PAP Workspace gure is (as the name suggests) a workspace
where a schematic representation of an axon, a stimulus source, and a voltage
recorder are displayed. In the PAP Workspace gure, the user can choose to display the stimulus setup gure (PAP Stimulus), the parameter setup gure (PAP
141
Figure 6.3: The PAP Control gure when the software is

initiated.
Parameters), the voltage recorder gure (PAP Voltage-Recorder), and place the
electrodes of the stimulus source and recorder using the mouse cursor on the
axon schematic. Clicking on the Start pushbutton in the PAP Control gure results in the computation of the response as a function of time and space. Upon
completion of the computation, the user can choose to view the space-time evolution of the membrane potential (which is one of the computed solution variables) by means of a color code along the axon schematic in the PAP Workspace
gure. The user can also examine the space-time evolution of other response
solution-variables to gain insight to the models dynamic behavior or use 3D and
comparison plots for static analyses of the models behavior.
6.4.1
PAP Control
There are three panels in the PAP Control gure (Figure 6.3). With the left panel,
the user can display the PAP Workspace gure (See Section 6.4.2) and the PAP
Numerics (See Section 6.4.5). In the center (Simulation) panel, the user can specify the simulation duration and start the simulation by clicking on the Start
pushbutton. The right (Analysis) panel allows the user to do post simulation
analysis of the results. The rst (Variable summary) option allows the user to
display a numerical summary of all the solution variables. The second (Spacetime evolution) option allows the user to view the dynamics of a solution variable (such as membrane potential, membrane current-components, etc.) as a
function of space with running time. The third (3D plots) option allows the user
to view three-dimensional graphs of any solution variable as a function of time
and space. The fourth (Comparison plots) option allows the user to compare
multiple solution variables as a function of a solution variable of choice (or as a
function of time or space) in two dierent modes: xed-time or xed-space.
142
Starting, pausing, and stopping a simulation

Clicking on the Start pushbutton starts the computation of the solution variables. While a computation is in progress, the status-bar located along the bottom of the gure shows the name of the numerical method being used and the
percentage of completion. The Start pushbutton changes to a Pause pushbutton. Clicking on the Pause pushbutton pauses the computation and causes the
status-bar to display Paused. When the simulation is paused, the Pause pushbutton changes to a Continue pushbutton. Clicking on the Continue pushbutton
resumes the computation and the two states (pause/continue) toggle with each
click of the pushbutton until the computation is completed. Upon completion,
the pushbutton changes back to Start and the status-bar acknowledges successful completion along with a time stamp. Next to Start is the Stop pushbutton
which allows the user to abort a computation that is currently in progress or
paused. Clicking on the Stop pushbutton causes the status-bar to display Simulation Aborted.
Loading, saving, and re-initializing

The user can save all simulation parameters and results in a le as well as load
a previously saved le by clicking on the Save and Open button, respectively.
The data stored includes the parameter values of the axon, the membrane, the
bath, the stimulus, the conguration of the electrodes, and solution variables.
When a le is loaded, the lename (along with its directory path) is shown in
this gures status-bar as well as in the status-bar of other setup gures such
as PAP Parameters, PAP stimulus, and PAP numerics. This is useful for keeping
track of the source of the parameter values used during a session.
When the software is launched, the gures status-bar displays Ready. This
indicates that no simulation has been run and that there are no results. This is
the initial state of the software and all parameters are set to their default values.
After parameters have been changed they can be reset to their default values by
clicking on the Default pushbutton.
6.4.2
PAP Workspace
Selecting Workspace in the PAP Control gure displays the PAP Workspace gure
(Figure 6.4). The PAP Workspace gure consists of a window and a control region. The window contains from top to bottom: a ruler, an interactive display
area (showing a schematic of an axon, a stimulus-source icon, and a voltagerecorder icon), another ruler, a status-bar, and a horizontal scrollbar. The default length of the axon is three centimeters and ts in the windows display
area. The schematic representation of a longer axon model stretches beyond
the display areas right edge. The user can use the horizontal scrollbar to scroll
143
Figure 6.4: The PAP Workspace gure.
to the hidden portion. By default the top ruler is set to show number of discretized segments, and the bottom ruler is set to show distance in centimeters.
Clicking on either ruler will toggle its unit of measurement between number of
discretized segments and distance. The status-bar shows the simulation time.
Clicking on the Help button located in the lower right corner of the PAP
Workspace gure displays the PAP Workspace Help gure. This gure shows
a step-by-step guide to setting up a customized simulation as described in Section 6.4.11.
Positioning electrodes
Stimulus electrodes (yellow) are located above the axon schematic and voltagerecorder electrodes (grey) are located below the axon schematic. The user can
control the position of an electrode either by pointing and clicking near the
electrode or by clicking and typing in the Electrode Positions panel.
To change electrode locations by the point-and-click method, rst select the
electrode by clicking on the appropriate radiobutton in the Electrode Positions
panel. Note that the positive and negative electrodes of the stimulus (S+ and
S) are selected independently from the positive and negative electrodes of the
recorder (R+ and R). After the appropriate radiobutton is selected, clicking
anywhere outside of the axon schematic within the interactive display area (e.g.,
the black region) sets the electrodes longitudinal position to the mouse-click location. Clicking in the black region above the axon schematic moves the stimulus
electrodes, and clicking in the black region below the axon schematic moves the
144
recorder electrodes. Both stimulus and recording electrode positions can also be
changed by typing in the relevant text edit boxesin the Electrode Positions panel.
Clicking on an electrode will toggle the electrode position between intracellular
and extracellular. Clicking on the check boxes in the Electrode Positions panel
also allows control of the intracellular/extracellular locations of electrodes. The
check box on the right part of the Electrode Positions panel controls the display of
the voltage recorder and its electrodes. Distances between stimulus electrodes
and between voltage recording electrodes are indicated below the lower ruler.
Displaying other setup gures
Clicking on the stimulus-source icon (yellow) will bring up the PAP Stimulus gure where the user can specify the characteristics of the desired stimulus (See
Section 6.4.4). Clicking on the voltage-recorder icon (green and grey) will display the PAP Voltage-Recorder gure where a real-time potential curve is plotted
during a simulation run (See Section 6.4.6). Clicking on the axon schematic will
display the PAP Parameters gure where the user can change the parameters of
the axon, the membrane, and the bath (See Section 6.4.3).
Showing discretization and color-coded space-time evolution
The option (Show discretization) to the right of the Color Space-Time Evolution
panel allows the user to toggle on/o the spatial discretization display on the
axon schematic. In the Color Space-Time Evolution panel, the pushbutton Start
allows the user to playback the space-time evolution of the membrane potential
on the axon schematic by using a color code to convey the range of potential
levels. The playback can be stopped using the Stop button. During playback,
the Start becomes a Pause button which allows the user to pause the playback.
The speed of the playback can be adjusted in the Speed eld located under the
pushbutton. For example, if the simulation data contains membrane potential
values for every 0.01 ms, changing the eld value to ten will playback simulation
data of every 0.1 ms.
Note that a voltage curve is plotted in the Voltage-Recorder gure during
playback (See Section 6.4.6). Figure 6.5 shows a series of snapshots taken from
a time-evolution color code visualization of the membrane potential of a threecentimeters long axon model.
6.4.3
PAP Parameters
Clicking on the axon schematic in the PAP Workspace gure displays the PAP
Parameters gure (Figure 6.6). The PAP Parameters gure is divided into three
sections: Membrane Characteristics, Bath Characteristics, and Axon Characteristics. In each section, there are three columns for each parameter: the rst col-
Figure 6.5: Snapshots of a propagating action potential shown

using Color Space-Time Evolution in the PAP Workspace gure.
145
146
Figure 6.6: The PAP Parameters gure.
147
umn identies the parameter, the second gives its default value, and the third
column shows the value of the parameter if it is modied from its default value
(Note that the PAP Parameters gure data entry method is based on that of the
HH Parameters gure).
Changing parameter values
Parameters can be modied by clicking on the entry in the third column of the
parameter eld. When the parameter is selected, its third column entry is replaced by an edit box. Clicking any mouse button inside the edit box allows the
parameter to be changed. The new value of the parameter is entered from the
keyboard; < RETURN > terminates the parameter entry. If the new value diers
from the default value, then the new value will appear in the third column. With
this method of display, the parameter list can be scanned quickly to indicate
which parameters dier from their default values.
Cm 0, cs > 0, Ks > 0, i 0, ro 0 (ro cannot be zero when i = 0),
the axons radius and length must be greater than zero, and the temperature
must be above absolute zero. The derived parameters cannot be changed but
are derived from the other parameters and are displayed for the convenience of
the user. For example, the sodium equilibrium potential VNa cannot be changed
directly by the user, but changes automatically when the sodium concentrations
or temperature are changed.
Loading, saving, resetting, and printing
The parameters can be loaded from a le by clicking on Open and can be saved
by clicking on Save. Saving and loading in the PAP Parameters gure deals only
with the models axon, membrane and bath parameters; e.g., simulation results
are not loaded or saved. When a parameters le is loaded, the status-bar of the
PAP Parameters gure displays the lename (with the directory path) and the
parameter values loaded from the le become the default values. For example,
if the user changes the temperature value and clicks the Reset pushbutton, the
temperature value resets to the value stored in the loaded le. To reset the
parameter values to their software-default values, use the Default pushbutton in
the PAP Control gure. If no le is loaded, clicking the Reset pushbutton resets
the parameter values to the software-default values. The PAP Parameters gure
can be printed using the Print button.
The Hodgkin-Huxley model of a propagated action potential as well as the HodgkinHuxley model of a membrane action potential of a space-clamped axon contains
several parameters that are instantaneous functions of the membrane potential.
148
Plots of these parameters are available as a function of Vm for the following:

m (Vm ), m (Vm ), m (Vm ), m (Vm ), h (Vm ), h (Vm ), h (Vm ), h (Vm ), n (Vm ),
n (Vm ), n (Vm ), n (Vm ) (see Section 5.2.3). These can be accessed by clicking
on the button marked , , , h, m, n which results in the display of the PAP
Parameters vs. Potential gure (Figure 6.7).
Figure 6.7: The PAP Parameters vs. Potential gure.
Note that the PAP Parameters vs. Potential gure is similar to the PAP Comparison Plots gure described in Section 6.4.10. Please refer to that section for
more information about the available plot manipulation functions. The PAP Parameters vs. Potential gure has its own setup gure which diers from the one
of the PAP Comparison Plots . Clicking on the Setup button displays this setup
gure. The user can select one or more variables and click on either Graph
or Overlay to make the plot. The Graph and Overlay buttons are described in
Section 6.4.10.
149
Figure 6.8: The PAP Stimulus gure.
6.4.4
PAP Stimulus
Clicking on the stimulus-source icon (yellow) in the PAP Workspace gure displays the PAP Stimulus gure (Figure 6.8). Note that the layout of the PAP Stimulus gure is similar to that of the HH Stimulus gure. The upper-half of the
gure shows a graph of the stimulus pulse(s) specied in the parameter-entry
columns: Pulse 1 and Pulse 2. The duration of the stimulus depends on the duration of the simulation specied in the PAP Control gure. For example, if the
simulation duration is four milliseconds, then the abscissa of the stimulus graph
is also of length four milliseconds.
Specifying a pulse
A maximum of two pulses can be dened using a set of parameters for each
pulse. In addition, a holding DC current can be specied in the Holding current
eld. Thus, the overall stimulus is the sum of a constant plus two independently speciable pulses. In mathematical terms, the stimulus, s(t), is dened
as follows
s(t) = s o + s 1 (t) + s 2 (t),
(6.23)
150

i
s (t) =
0
otherwise,
(6.24)
where pulse i (i = 1 or 2) starts at to and has a duration tdur . The amplitude

of the pulse is Ai , the slope is mi , and the time constant is i . If the slope and
the time constant are set to zero, then the remaining parameters specify the
amplitude, duration and onset time of a rectangular pulse. If the slope has a
non-zero value, a ramp of that slope is added to the rectangular pulse for the
duration of the pulse. Similarly, if the time constant has a non-zero value, then
an exponential pulse with the selected time constant is added to the waveform.
The time constant can be positive or negative.
i
, Ai , mi , and i that denes a pulse in the form of EquaThe variables toi , tdur
tion 6.24 are specied in the PAP Stimulus gure by the parameter elds Start,
Duration, Amplitude, Slope, and Time constant in the Pulse i column, respectively. By adjusting these parameters, the user can generate rectangular pulses,
ramp pulses, exponential pulses or a combination of these. An example is shown
in Figure 6.9.
Loading, saving, and resetting

The parameters can be loaded from a le by clicking on Open and can be saved
by clicking on Save. Saving and loading in the PAP Stimulus gure deals only with
the stimulus parameters; e.g., simulation results are not loaded or saved. When
a le with stimulus parameters is loaded, the status-bar of the PAP Stimulus
gure displays the lename (with the directory path) and the parameter values
loaded from the le become the default values. For example, if the user changes
the holding current value and clicks the Reset pushbutton, the holding current
value resets to the value stored in the loaded le. To reset the parameter values
to their software-default values, use the Default pushbutton in the PAP Control
gure. If no le is loaded, clicking the Reset pushbutton resets the parameter
values to the software-default values.
6.4.5
PAP Numerics
Selecting Numerics in the PAP Control gure displays the PAP Numerics gure
(Figure 6.10). The PAP Numerics gure allows the user to select the numerical
method used to solve the partial dierential equations described in Section 6.2.
151
Figure 6.9: The PAP Stimulus gure showing a stimulus

that consists of two pulses: the rst pulse is an exponential pulse and the second is a ramp plus a rectangular
pulse.
Choosing a numerical method and specifying discretization parameters

The list-box located at the top of the gure allows the user to select one of four
available numerical methods: forward Euler, backward Euler, Crank-Nicolson,
and staggered Crank-Nicholson (staggered C-N). These numerical methods are
described in detail in Section 6.3. By default, the software uses the staggered C-N
numerical method. All numerical methods employ the nite dierence method
which requires two discretization parameters: a time step, t, and a spatial
step, z. Decreasing the time step produces a smoother time evolution of the
solution variables (for example, a smoother action potential propagation), but
computation time and memory usage increases. Decreasing the space step produces an axon schematic with more discrete elements hence a smoother spatial
Figure 6.10: The PAP Numerics gure.
152
evolution of the solution variables (for example, a smoother membrane-potential

curve as a function of space when viewed in a snapshot), but computation time
and memory usage increases. In order to obtain a reasonably accurate solution
using a particular numerical method, the discretization parameters have to be
chosen appropriately.
Loading, saving, resetting, and printing
The parameters can be loaded from a le by clicking on Open and can be saved by
clicking on Save. Saving and loading in the PAP Numerics gure deals only with
the numerics parameters; e.g., simulation results are not loaded or saved. When
a numerics parameters le is loaded, the status-bar of the PAP Numerics gure
displays the lename (with the directory path) and the parameter values loaded
from the le become the default values. For example, if the user changes the time
step and clicks the Reset pushbutton, the time step resets to the value stored in
the loaded le. To reset the parameter values to their software-default values,
use the Default pushbutton in the PAP Control gure. If no le is loaded, clicking
the Reset pushbutton resets the parameter values to the software-default values.
The PAP Numerics gure can be printed using the Print button.
6.4.6
PAP Voltage-Recorder
Clicking on the voltage-recorder icon (grey and green) in the PAP Workspace
gure displays the PAP Voltage-Recorder gure (Figure 6.11). The PAP VoltageRecorder gure shows a graphing region where a voltage curve is plotted when
the user clicks on the Start button located in the PAP Workspace gure. When
plotting a curve, the graphing area can display only a portion 3 ms long. If
the plot extends beyond 3 ms, the scrollbar under the graphing area becomes
active, so the user can scroll to see any section of the curve. Also, a Show entire
plot option is enabled, so the user can choose to display the whole curve on
the graphing area. For example, shrink the abscissa to t the entire plot in the
graphing region.
The voltage plot corresponds to the voltage recorded at the location of the
recording electrodes located beneath the axon schematic. The user can reposition the recording electrodes as described in Section 6.4.2 and click on Start
to obtain the corresponding voltage plot. Clicking on the Grid option displays a
grid on the graphing region.
Markers can be set to measure the times of occurrence of features in the
waveform. Clicking on the t1 marker and clicking on the plot, results in a red,
vertical line; clicking again xes the time of occurrence of that line. The same
can be done with the t2 marker. The time of occurrence of each of the markers
and the dierence in time between the two markers are displayed at the top of
the gure.
153
Figure 6.11:
The
age-Recorder gure.
6.4.7
PAP
Volt-
PAP Variable Summary
Selecting Variable summary in the Analysis panel of the PAP Control gure displays the PAP Variable Summary gure as shown in Figure 6.12. This gure
allows the user to display the initial, minimum, and maximum value of any solution variable. The user can either select to view these summary values obtained
from the spatial dimension at a specied time, or from the temporal dimension
at a specied location. The time and location are specied in units of milliseconds and centimeters, respectively. The largest valid time value is equal to the
simulation duration, and the largest valid location value is equal to the length of
the axon model.
6.4.8
PAP Space-Time Evolution
Selecting Space-time evolution in the Analysis panel of the PAP Control gure
displays the PAP Space-Time Evolution gure as shown in Figure 6.13. This gure
only appears if there are simulation results (i.e. after a simulation has been run).
The PAP Space-Time Evolution gure provides a means of viewing the dynamics
of any solution variable along the axon as time changes.
Viewing the space-time evolution of a solution variable
When the gure is rst displayed, Vm (membrane potential) is selected in the
list-box located at the top of the gure. Use the list-box to view any desired
solution variable. After a selection is made, the graph under the list-box shows
154
Figure 6.12: The PAP Variable Summary gure.
155
Figure 6.13: The PAP Space-Time Evolution gure showing

a snapshot of a propagating action potential.
the selected solution variable as a function of space at time = 0 ms. To view

the selected solution variable as a function of space at progressing time starting
from 0 ms, click on the Start pushbutton. The process can be stopped and
paused using the appropriate buttons. The Start button changes to a Pause
button when a process is running. Clicking on an axis label displays the Axis
conguration gure (Figure 6.18) which allows the user to change the properties
of the axis.
6.4.9
PAP 3D Plots
Selecting 3D plots in the Analysis panel of the PAP Control gure displays the
PAP 3D Plots gure (Figure 6.14). This gure only appears if there are simulation
results (i.e. after a simulation has been run). The PAP 3D Plots gure provides a
means of visualizing the space-time dependence of any solution variable.
Viewing a 3D plot of a solution variable
When the gure is rst displayed, Vm (membrane potential) is selected in the
list-box located at the top of the gure. Use the list-box to view any desired
solution variable. After a selection is made, the surface plot beneath the listbox shows the selected solution variable as a function of space and time. The
colorbar on the right indicates the magnitude of the colored surface plot. To
change the view angle use the horizontal scrollbar located at the bottom and the
vertical scrollbar located on the left of the plot. The vertical scrollbar controls
156
the viewing elevation (i.e. rotates the plot up and down), and the horizontal
scrollbar controls the viewing azimuth (i.e. rotates the plot left and right). In
addition, the user can switch between mesh and surface plot by toggling the
mesh option on/o . Since the mesh plot samples the surface of the variable as
a function of space and time, care must be taken with evaluating 3D mesh plots
of discontinuous functions.
Clicking on the box option toggles on/o an axes-bounding box. Clicking on
a solution variables axis label displays the Axis conguration gure (Figure 6.18)
which allows the user to change the properties of that axis.
6.4.10
PAP Comparison Plots
Selecting Comparison plots in the Analysis panel of the PAP Control gure displays the PAP Comparison Plots gure as shown in Figure 6.16. The PAP Comparison Plots gure allows the user to plot any solution variable against any other.
The gure displays a group of pushbuttons on the upper-left corner, a legend
panel on the upper-right corner, and a graphing region.
Using the Comparison Plots Setup gure to generate plots
Clicking on the Setup button in the PAP Comparison Plots gure displays the
Comparison Plots Setup gure (See Figure 6.15) where the user can choose: xedspace plots (Figure 6.16) or xed-time plots (Figure 6.17). Fixed-space plots
require the user to specify a longitudinal location of the axon, zo , in units of
centimeters. The user can use this mode to generate solution-variable-A vs. solution variable-B at location, zo , plots. Fixed-time plots require the user to specify a
time, to , in units of milliseconds. This mode is used to generate solution-variableA vs. solution-variable-B at time, to , plots.
Follow these steps to make a plot:
Choose a plotting mode: xed-space plots or xed-time plots.

For xed-space plots specify the Distance parameter: enter a value in units
of centimeters. Note that the maximum allowable value is the length of the
axon model. Multiple distance values can also be entered in MATLAB array
format (i.e. [1.0 1.5 3.5], [1.0 : 0.05 : 2.0]). Please refer to the MATLAB
users manual for more information.
For xed-time plots specify the Time parameter: enter a value in units
of milliseconds. Note that the maximum allowable value is equal to the
simulation duration. Multiple time values can also be entered in MATLAB
array format.
Choose a solution variable in the X-Variable panel: this is the independent

variable and it corresponds to the the values along the abscissa.
Figure 6.14: The PAP 3D Plots gure showing a propagating action potential. Top: a surface plot. Bottom: a mesh
plot.
157
158
Figure 6.15: The Setup PAP Comparison Plot gure showing the variables used to setup Figure 6.16.).
Choose one or more solution variables in the Y-Variable panel: multiple

dependent variables can be plotted for comparison. They are all plotted as
a function of the solution variable selected in the X-Variable panel. Dependent variables that have same unit of measurements share one ordinate
axis. Both sides of the plotting area may show distinct ordinate axes to accomodate distinct units of the variables selected. For example, the user can
choose to plot the membrane potential, Vm , and the sodium conductance,
GNa , both as a function of time, t. In this case, the user would select t in
the X-Variable panel, and both Vm and GNa in the Y-Variable panel. Since
Vm is in units of millivolts and GNa is in units of mS/cm2 , the plot should
show two ordinate axes. The abscissa, in this case, should be in units of
milliseconds.
Click on Graph to graph the selections on a cleared plotting region. The

Graph pushbutton clears all previous plots. Click on Overlay to graph the
selection on the plotting region without clearing any previous plots. This
feature allows the user to overlay the solutions obtained from dierent
simulations. For example, suppose the user wants to plot the membrane
potential, Vm , as a function of time, t, at the axon longitudinal location,
zo = 2 cm, for temperature values of 6.5 , 18 , and 20 Celsius. The user
would need to run a simulation with the temperature parameter set to 6.5,
plot Vm vs. t at zo = 2 using the Graph button. Then do the subsequent
simulation runs with the the other two temperature values and plot using
the Overlay button so that all three plots are retained in the plotting region.
In addition, the user can make plots using data stored in les. To do this,
Figure 6.16: The PAP Comparison Plots gure showing a

xed-space plot of the membrane potential, Vm , and the
ionic conductances, GNa and GK , with model parameters
and the stimulus dened in Figures 6.6 and 6.8.
159
160
Figure 6.17: The PAP Comparison Plots gure showing a

xed-time plot of the membrane potential, Vm , and the activation factors, m and h, obtained from a simulation with
model parameters and the stimulus dened in Figures 6.6
and 6.8.
161
Figure 6.18: The PAP Axis Scale gure.
select the Files with Parameters option and click on the Select les pushbutton.
A le-loading dialog box appears which allows the user to select the data le(s).
The user can then plot the loaded solution variables.
Annotating, zooming, and other functions
The PAP Comparison Plots gure has a few functions that facilitates the analysis
of the plots.
Clicking on the Cross-line pushbutton
displays a vertical line in the plot

region at the location of the pointer cursor. The line follows the cursor as
it moves across the plot region. The values of all plotted variables at the
intersection with the cross-line are displayed in the Legend panel, under
the column labeled Cross-line . Clicking on the Cross-line button again
removes the cross-line values from the legend and removes the cross line
from the plotting region.
Clicking on the A button allows the user to make annotations on the plot.
With this button set to on, click on a desired location in the plot to display a text edit box at that location. Click in the text edit box, type the
annotation followed by a <RETURN> when the annotation is completed.
Clicking on the annotation and dragging the mouse moves the annotation
to a desired location in the plot eld. The text string can be formatted into
mathematical notation by using a LATEX like notation, e.g., to get m type
m_{\infty}.
Clicking on the
button next to the annotation button allows the user

to magnify a region of the plotting region by clicking on it. Clicking again
causes further magnication. Clicking on the - button causes the plot to
change to its original magnication.
In the plotting region, clicking on any of the axis labels (i.e. either the
abscissa or any of the ordinates) displays an axis scale gure (Figure 6.18)
which allows the user to change parameters of the chosen axis. The range
of the axis can be specied in MATLAB array format (i.e. [-200 200]) in the
162
Figure 6.19: The Modify Line

Properties gure.
Range eld. The range is set to rescale automatically by default. To inhibit

auto-scaling, unselect the Auto option. Selecting the Log option changes
the axis scale to a logarithmic scale (i.e. the logarithm of the magnitude
of the variable is plotted). Selecting the Inverse [1/] option produces a
reciprocal scale axis. (i.e. the reciprocal of the magnitude of the variable is
plotted). A combination of the two is allowed.
In the Legend panel, clicking on any entry under the column labeled Marker
displays a modify line properties gure (Figure 6.19) which allows the user
to customize the color, line style, line width, marker type, and marker size
of the selected plot curve. The color eld is specied in RGB values in a
MATLAB array (i.e. to specify the primary color, red, use [1 0 0]).
In the Legend panel, clicking on any entry under the column labeled Name
causes the curve associated with that entrys variable to alternately display
and hide. Hiding and displaying curves causes the axes to rescale automatically unless the auto-scaling function of the particular axis is disabled by
means of the axis scale gure described above.
Loading, saving, and printing
The user can save the plots by clicking on the Save pushbutton. All lines, axis
scale and annotations are saved. The Open pushbuttons loads a previously saved
le. The plots can be printed using the Print button.
6.4.11
Step-by-step Guide To Setting Up A Customized Simulation
Launch the software from the Softcell menu. Once the application has started,
two gures will be displayed: the PAP Control gure, and the PAP Workspace
gure. All model parameters are started in their default values. To start setting
up a simulation with customized parameter values, complete all or any of the
following steps:
6.5. PROBLEMS
163
1. Change the membrane, axon, and bath parameter values: in the PAP Workspace
gure, click on the axon schematic. The PAP Parameters gure is displayed.
Adjust any parameter as described in Section 6.4.2. Clicking on the axon
schematic again closes the PAP Parameters gure.
2. Change the stimulus-pulse parameter values: in the PAP Workspace gure,
click on the stimulus-source icon (yellow lled-circle with an arrow inside).
The PAP Stimulus gure is displayed. Adjust any parameter as described
in Section 6.4.4. Clicking on the stimulus-source icon again closes the PAP
Stimulus gure.
3. Position the stimulus electrodes: in the PAP Workspace gure, select the appropriate radiobutton in the Electrode Positions panel (i.e. cathode/anodeelectrode). To position the selected electrode longitudinally along the axon
schematic, click on the black region between the top ruler and the schematic.
The desired electrode moves to the position of the mouse cursor. Click on
the electrode to toggle its position between intracellular and extracellular.
Note that the icon of an intracellular electrode touches the axon schematic,
whereas an extracellular electrode does not.
4. Position the voltage-recording electrodes: in the PAP Workspace gure, select the appropriate radiobutton in the Position Electrode panel. Click on
the black region between the bottom ruler and the axon schematic to move
the desired electrode to the position of the mouse cursor. Click on the
electrode to toggle its position between intracellular and extracellular.
5. Change the numerics values: in the PAP Control gure, click on the Numerics option. The PAP Numerics gure is displayed. Adjust any parameter as
described in Section 6.4.5.
6. Change the simulation duration: in the PAP Control gure, enter the simulation duration in milliseconds.
7. Start simulation: in the PAP Control gure, click on the pushbutton Start.
Note that when a simulation has started, the Start pushbutton changes to
a Pause pushbutton. Clicking on Pause pauses the simulation. Click on
Continue to resume. Click on the Stop pushbutton anytime to abort.
6.5
Problems
Problem 6.1 The purpose of this problem is to estimate the conduction velocity of
the action potential. Using the default parameters of the Hodgkin-Huxley model,
devise a method to estimate the conduction velocity of the action potential. Describe your method carefully and give a numerical estimate of the conduction
velocity for the default parameters.
164
Problem 6.2 The purpose of this problem is to investigate the dependence of the
propagated action potential on resistance per unit length of the inner and outer
conductors and the relation of these results to the notion of a space clamp.
a. Run the simulation using the default parameters. Examine the membrane
potential as a function of space and time. You may wish to use the threedimensional plots or to use the comparison plots to plot the membrane
potential as a function of time for locations from 0.5 cm to 2.5 cm every
0.2 cm.
b. Reduce the resistivity of the intracellular conductor i to 10 Ohmcm. Run
the simulation again and examine the membrane potential as a function of
space and time.
c. Reduce the resistivity of the intracellular conductor i to 1 Ohmcm. Run
space and time.
d. Reduce the resistivity of the intracellular conductor i to 0.1 Ohmcm. Run
space and time.
e. Keep the resistivity of the intracellular conductor i to 0.1 Ohmcm but
increase the resistance per unit length of the outer conductor ro to 10,000
Ohm/cm. Run the simulation again and examine the membrane potential
as a function of space and time.
f. What do you conclude about the dependence of the membrane potential on
space and on time as the internal and external resistance per unit length
are decreased?
g. How are these results related to the notion of a space clamp? How are these
results related to the notion of an electrically large cell and an electrically
small cell.
h. Explain how you could reduce the eective resistivity of the inner conductor i in an experiment on an axon.
Problem 6.3 The purpose of this problem is to investigate the step response of
the Hodgkin-Huxley model with the nonlinear elements removed. Determine the
stimulus and numerical parameters required to examine the step response of
the Hodgkin-Huxley model when stimulated at z = 1.5 cm with the nonlinear
elements removed, i.e., set GNa = GK = 0. Perform simulations with i = 35.4
Ohmcm and for i = 0.001 Ohmcm. Save the results in les. In the various
parts of this problem, you will examine the solutions that you have already computed and saved.
6.5. PROBLEMS
165
a. For i = 35.4 Ohmcm, examine the dependence of the membrane potential on space at various times by plotting Vm versus z at dierent times.
Describe the results as precisely as possible.
b. For i = 0.001 Ohmcm, examine the dependence of the membrane potential on space at various times by plotting Vm versus z at dierent times.
Describe the results as precisely as possible. Compare these results with
those of part a.
c. For i = 35.4 Ohmcm, examine the dependence of the membrane potential
on time at various positions by plotting Vm versus t at dierent positions.
Describe the results as precisely as possible.
d. For i = 0.001 Ohmcm, examine the dependence of the membrane potential on time at various positions by plotting Vm versus t at dierent
positions. Describe the results as precisely as possible. Compare these
results with those of part c.
Problem 6.4 The purpose of this problem is to investigate the relations among the
membrane potential, the intracellular potential, and the extracellular potential.
a. Run the simulation with the default parameters.
i. Examine the space-time evolution of Vm , Vi , and Vo . Describe the relation among these three variables. Explain these results.
ii. Using the comparison plots, plot Vm , Vi , and Vo versus position at the
time t = 0.4 ms and at the time t = 1 ms. Describe the relation among
these three variables at the two times and explain these results.
b. Set ro to equal the default value of ri and repeat part a.
c. Compare the results in parts a and b and explain the dierences.
Problem 6.5 The purpose of this problem in to relate the membrane potential
as a function of space to the membrane potential as a function of time during a
propagated action potential.
a. Run the simulation using the default parameters. Compare the membrane
potential as a function of time at 2 cm with the membrane potential as a
function of position at 1 ms. Determine the relation between these two
waveforms.
b. Move the electrode S+ (keeping it intracellular) to position 2.9 cm and run
the simulation again. Once again compare the membrane potential as a
function of time at 2 cm with the membrane potential as a function of
position at 1 ms. Determine the relation between these two waveforms.
166
c. The relation between the membrane potential as a function of time and of

position for part a diers from that in part b. Explain the dierence.
Problem 6.6 The purpose of this problem in to examine the relation between the
membrane potential as a function of time and the longitudinal current as a function of time during a propagated action potential.
a. Run the simulation using the default parameters.
i. Compare the membrane potential as a function of time with the external longitudinal current Io as a function of time at the position 2 cm.
Determine the relation between these two waveforms.
ii. Compare the external longitudinal current Io as a function of time with
the internal longitudinal current Ii as a function of time. Pay particular
attention to t < 0.5 ms and to t > 0.5 ms. What is the relation of these
two variables in these two time ranges. Explain these results.
b. Move the intracellular electrode (S+ ) to position 2.9 cm and run the simulation again.
i. Once again compare the membrane potential as a function of time
with the external longitudinal current as a function of time at the position 2 cm. Determine the relation between these two waveforms.
ii. Compare the results of parts a-i and b-i. Explain the dierences.
Problem 6.7 The purpose of this problem in to examine the relation among the
membrane potential, the longitudinal currents, the membrane current density
and the capacitance current all as functions of time during a propagated action
potential.
Run the simulation using the default parameters.
a. Using the comparison plots, compare Vm and Ii as a function of time at a
location of 1.5 cm. What is the relation and why?
b. Using the comparison plots, compare Vm and JC as a function of time at a
c. Using the comparison plots, compare Ii and JC as a function of time at a
d. Using the comparison plots, compare Ii and Jm as a function of time at a
e. Using the comparison plots, compare Vm and Jm as a function of time at a
6.5. PROBLEMS
167
f. Using the comparison plots, compare Ii and Io as a function of time at a

Problem 6.8 The purpose of this problem is to examine the waveform of the propagated action potential at various locations along the axon. Use the default parameters of the model except arrange the stimulating electrodes as follows: S
is extracellular and located at position 1 (discrete segment 1 located at 0 cm)
and S+ is intracellular and located at position 20 (1 cm). The stimulus current
provided by the current source (which can be seen by clicking on the current
source) ows from S to S+ and is 0.05 mA with a duration of 0.5 ms. Run the
simulation and compare Vm at the locations 1, 1.5, 2, 2.5 cm by plotting all 4
traces on one axis using the Comparison Plots.
a. Does the all-or-none principal apply at all the positions along the axon?
b. Explain the dierences in waveshape at the dierent locations along the
axon. You may wish to plot additional variables on your plot of Vm .
Problem 6.9 This problem concerns the direction of a current stimulus that elicits
a propagating action potential. The parameters of the model are the default values as indicated. Throughout this problem, the stimulus electrodes are located
as follows: S is located at position 1 (discrete segment 1) and S+ is located at
position 30.
a. Simulations with one intracellular and one extracellular electrode.
i. Set S to be extracellular and S+ to be intracellular. The stimulus
current provided by the current source (which can be seen by clicking
on the current source) ows from S to S+ and is 0.05 mA with a
duration of 0.5 ms. Run the simulation and determine whether an
action potential occurs and, if so, at which electrode(s) it arises.
ii. With all other parameters the same as in part a-i, make S intracellular
and S+ extracellular. Run the simulation and determine whether an
action potential occurs and, if so, at which electrode(s) it arises.
iii. Draw a diagram of current ow about the axon and through the current source for the two cases considered in parts a-i and a-ii. Describe
the conditions for the occurrence of an action potential and explain
the polarity of Vm when an action potential does not occur.
b. Simulations with two extracellular electrodes.
i. Set the stimulating electrodes and the stimulating current identical
to that in part a-i except make both current electrodes extracellular.
Run the simulation and determine whether an action potential occurs
168

and, if so, at which electrode(s) it arises. Examine the two longitudinal
currents Ii and Io and and the membrane current Jm and explain these
results.
ii. With the default settings in part b-i, ro = 0 which crudely simulates
an axon in a large volume of sea water. This assumption is reasonable
for computing whether or not an action potential occurs since only
the sum ro + ri occurs in these equations and for an axon in a large
volume of sea water ro ri . But assuming that ro = 0 does not
give a good approximation for determining longitudinal currents, for
example. Therefore, in this part of the problem, increase ro to 20,000
Ohm/cm so that it is roughly comparable to ri . This value of ro can be
achieved experimentally by putting an axon in an insulating medium
(oil, air, deionized sucrose) so that only a thin layer of sea water clings
to the axon. Run the simulation and determine whether an action
potential occurs and, if so, at which electrode(s) it arises. Examine Ii ,
Io , and Jm . What do you conclude?
iii. Keep all the stimulus parameters the same as in b-ii except make both
stimulating electrodes intracellular. Run the simulation and determine
whether an action potential occurs and, if so, at which electrode(s) it
arises.
iv. Return to the conditions of part b-ii except reverse the polarity of the
stimulus current, i.e., make its amplitude 0.05 mA. Run the simulation and determine whether an action potential occurs and, if so, at
which electrode(s) it arises.
c. Integrate the results you have obtained in parts a and b to come to a general
conclusion about the key properties of an electric current stimulus that
elicits an action potential.
Problem 6.10 The purpose of this problem is to investigate what happens when
two action potentials travelling in opposite directions collide.
a. Start with the default parameters, and adjust the stimulus electrodes so
that an action potential is produced both at 0 cm and at 3 cm. You will need
to understand the direction of a current stimulus that elicits and action
potential. You may wish to explore Problem 6.9 to aid you to understand
this matter. [HINT: Note also that the default value for ro = 0 so that little
of the stimulus current from an extracellular electrode enters the axon.
Therefore, you may wish to adjust the value of ro .]
b. By plotting the results using the various plotting tools, determine what has
happened. Did the action potentials pass through each other or did they
annihilate each other? Suggest an explanation for your results.
6.5. PROBLEMS
169
Problem 6.11 The purpose of this problem is to explore the bases of the subthreshold oscillatory response of the model to a step of current. Start with the
default parameters except as follows: set the duration of the current pulse to
10 ms and its amplitude to 0.0001 mA. Set the duration of the simulation to
10 ms in the PAP Control gure. Run the simulation and examine the results.
You should nd that the membrane potential contains a highly damped slow
oscillation at the onset which constitutes the step response. The purpose of this
problem is to determine the basis of the oscillation.
a. Devise an experiment to determine whether the relation of the stimulus
current to the membrane potential is a linear relation for current stimulus
parameters near those given above. What do you nd?
b. Investigate whether the variation in membrane potential with position is
somehow responsible for the shape of the step response, in particular, the
presence of the oscillations.
i. Devise a simulation experiment that will eliminate the spatial variation
of the membrane potential and run a simulation.
ii. Demonstrate that the spatial variation you set out to eliminate is in
fact eliminated.
iii. Are the oscillations eliminated?
iv. Which aspects of the step response are changed and why?
c. If oscillations are still present in the step response, devise simulation experiments to determine their origin.
d. Discuss how the results you have obtained in the previous parts are related
to the cable model of an axon?
Problem 6.12 The purpose of this problem is to explore the variables associated
with a propagated action potential near the end of the model axon.
Use the
default parameters to compute the propagated action potential.
a. Using the comparison plots, plot Ii and Io versus time at positions of 2.9
and 3 cm. Explain the dierences in longitudinal currents with position.
b. Using the comparison plots, plot Jm versus time at positions of 2.9 and 3
cm. Explain the dierences in membrane current densities with position.
Problem 6.13 The purpose of this problem is to investigate the space constant of
the Hodgkin-Huxley model of the giant axon of the squid.
170
a. Design a simulation experiment in order to estimate the space constant of

the Hodgkin-Huxley model of the giant axon of the squid for the default
parameters. Determine the value of the space constant.
b. Keeping all other parameters the same, set the radius of the axon to 0.0952
cm and repeat part a.
c. Compare the estimated space constants in parts a and b and explain the
dierence.
6.6
PROJECTS
This simulation software lends itself to more extensive study than that included
in the Problems. These more extensive studies are called Projects. A description
of the practical considerations in the choice of a project are contained in Section 5.6. Specic topics for projects with the software described in this Chapter
are listed here.
1. Hypothesis The eect of temperature on the conduction velocity of the
squid giant axon can be t by the Hodgkin-Huxley model. Articles in the
literature should be consulted for this project (Chapman, 1967; Easton and
Swenberg, 1975).
2. Hypothesis When two action potentials are elicited, the velocity of the
second is slower than the velocity of the rst action potential. This phenomenon is predicted by the Hodgkin-Huxley model. Articles in the literature should be consulted for this project (George et al., 1984).
3. Hypothesis The threshold current for eliciting an action potential with an
intracellular electrode is higher for a space-clamped than for an unclamped
model of an axon.
4. Hypothesis Increasing the membrane capacitance will decrease the conduction velocity.
5. Hypothesis Increasing the membrane conductance (by scaling all the
ionic conductances) will increase the conduction velocity.
6. Hypothesis Increasing the external concentration of sodium will increase
the conduction velocity.
7. Hypothesis Increasing the external concentration of potassium will increase the conduction velocity.
6.6. PROJECTS
171
8. Hypothesis Increasing the external concentration of calcium will increase

the conduction velocity.
9. Hypothesis Increasing the temperature will increase the conduction velocity.
10. Hypothesis The solution using the forward Euler method is stable provided t a(ro + ri )(z)2 Cm .
11. Hypothesis The backward Euler algorithm is stable for all values of t
and x.
12. Hypothesis The Crank-Nicolson method and the staggered increment
Crank-Nicolson method are stable for all values of t and x.
13. Hypothesis Using the forward Euler approximation, the error resulting
from temporal and spatial discretization behaves as O(t) + O((x)2 ).
14. Hypothesis Using the backward Euler approximation, the error resulting
from temporal and spatial discretization behaves as O(t) + O((x)2 ).
15. Hypothesis Using the Crank-Nicolson method and the staggered increment Crank-Nicolson method, the error resulting from temporal and spatial discretization behaves as O((t)2 ) + O((x)2 ).
172
Chapter 7
VOLTAGE-GATED ION CHANNELS
173
174
7.1
7.1.1
Introduction
Historical background
Passive transport of ions through cellular membranes is mediated by membranebound channel proteins that form selectively permeable ion channels. Although
their existence was long suspected, the rst direct physiological evidence for
these channels became available in 1976 (Neher and Sakmann, 1976). Subsequently, many dierent types of channels have been identied (Hille, 1992).
Channels can be categorized on the basis of the physical/chemical variable that
opens or gates the channel. For example, the channels that underlie the properties of electrically excitable cells are gated by the membrane potential and are
called voltage-gated channels. These channels are opened by a change in membrane potential. Other channels are gated by the binding of specic chemical
substances, mechanical deformation of the membrane, etc. In all of these cases,
the channels behave as if they have a discrete number of states, of which a few
(usually only one) are conducting or open states and the others (usually more
than one) are non-conducting or closed states. The channel switches rapidly and
randomly among its allowable states, and the probability that a transition occurs
at a particular time depends on the value of the gating variable.
Models of the gating of single ion channels were developed almost immediately after single-channel data were obtained (Colquhoun and Hawkes, 1977).
Descriptions of these models can be found elsewhere (Colquhoun and Hawkes,
1995a; Weiss, 1996b).
7.1.2
This software package enables users to enhance their understanding of models

of the gating of single voltage-gated ion channels. The software allows the user
to design a channel by choosing the number of states, the voltage dependence
of transitions between states, the conductance and gating charge of each state,
and the equilibrium potential for the channel. After the channel is designed, the
user can analyze the behavior of the channel to a change in membrane potential. Any of the variables associated with the channel can be displayed including
the state occupancy probability, ionic conductance, ionic current, gating charge,
and gating current. Both random variables and their expected values can be displayed as a function of time. The software is suciently powerful and exible
to allow users to synthesize realistic, state-of-the-art models for the gating of
voltage-gated ion channels.
7.2
175
A brief description of the channel model is given here; a more complete description is given elsewhere (Weiss, 1996b). We assume that a channel has N states
and that at each instant in time t, the channel is found in one of its states (Figure 7.1). The states are enumerated as {S1 , S2 , S3 , . . . SN }. Each state has state at-
S1
1 , Q1
12
21
15
S2
2 , Q2
23
32
51
S3
3 , Q3
45
34
43
S4
4 , Q4
54
S5
5 , Q5
Figure 7.1: Kinetic diagram of a channel that has 5 states. The states are shown linked
by rate constants for transitions between states, where ij is the rate of transition from
state i to state j. When the channel is in state j the conductance of the channel is j
and the gating charge of the channel is Qj .
tributes: the state conductance and the state gating charge. The state attributes
for these states are denoted as {1 , 2 , 3 , . . . N } for the state conductances and
{Q1 , Q2 , Q3 , . . . QN } for the state gating charges. Given the membrane potential Vm
and the equilibrium potential Veq , the state ionic currents are {I1 , I2 , I3 , . . . IN }.
Thus, when the channel is in state Sj , the state conductance is j , the state ionic
current is Ij = j (Vm Veq ), and the state gating charge is Qj . Gating currents
occur at the transitions of the gating charge.
The temporal evolution of the electrical properties of a channel depend upon
the state occupancy probabilities which we discuss briey. Dene the probability
that the channel is in state j at time t as xj (t), and the transition probability that
the channel is in state j at time t + t given that it was in state i at time t as
yij (t + t). The fundamental assumption of the model for state transitions is
that the transition probabilities depend on the present state of the channel and
not on previous states. Such a probabilistic process is called a Markov process.
Formally, we assume that
yij (t + t) = ij t + o(t) ,
where o(t) has the property that limt0 o(t)/t = 0 and ij is a rate constant for transitions from state i to state j. The rst term is the probability of
176
occurrence of a single transition in the interval of duration t when this interval

is short and the rate of transitions is ij . The second term takes into account
the probability of the occurrence of multiple transitions in the interval. For intervals t that are suciently small so that no more than one transition is likely
to occur in the interval, the o(t) term is negligible; we will ignore this term in
the development that follows. The probability that the channel is in state j at
time t + t and in state i at time t is yij (t + t)xi (t) ij xi t.
The increase in probability that the channel is in state j in the time interval
(t, t + t) is xj (t + t) xj (t). In this time interval, this probability increases
as a result of transitions from states i into state j and decreases as a result of
transitions from state j into state i. By collecting all such terms we obtain,
xj (t + t) xj (t)
N

ij xi (t)t
i=1,i=j
N

ji xk (t)t ,
i=1,i=j
where the rst summation is due to transitions into state j and the second summation is due to transitions out of state j. If we rearrange the terms and take
the limit as t 0, we obtain the dierential equation
N
N

dxj (t)
=
ij xi (t)
ji xj (t).
dt
i=1,i=j
i=1,i=j
This equation can be written in matrix form by

probabilities to be
11 12
21 22
=
N1 N2
(7.1)
dening the matrix of transition
1N
2N
.
NN
where ij is the transition rate from state i to state j when i = j, and ii is

N
chosen so that i=1 ij = 0. The state occupancy probability satises the matrix
dierential equation
dx(t)
= x(t),
(7.2)
dt
where x(t) is a row matrix of state occupancy probabilities. In addition, since
the channel is in one of its N states at each instant in time,
N

xj (t) = 1 .
j=1
The equilibrium state occupancy probability can be obtained directly from Equation 7.2 by setting dx(t)/dt = 0 to yield
0 = x(),
(7.3)
177
to obtain the equilibrium state occupancy probability x().

If the matrix is constant, then the solution to the matrix equation for the
state occupancy probability is (Colquhoun and Hawkes, 1995a)
x(t) = x(0)et ,
where x(0) is the matrix of the initial value of x(t). Evaluation of the exponential
matrix yields the result
N

S j e j t ,
(7.4)
x(t) = x(0)
j=1
where j is the jth eigenvalue of and S j is the jth spectral matrix of . Therefore, we see that the state occupancy probabilities are weighted sums of exponentials whose exponents are the eigenvalues of the transition rate matrix.
Because the matrix is singular, one eigenvalue has value zero. All other eigenvalues have negative real parts (Cox and Miller, 1965). Thus, the non-zero eigenvalues lead to solution exponentials that decay with time.
For a voltage-gated channel, the transition rates depend explicitly on the
membrane potential which in turn may vary with time. If the rate constants are
assumed to satisfy the theory of absolute reaction rates (Weiss, 1996a; Weiss,
1996b), then they depend exponentially on the membrane potential,
Aij eaij Vm if i j,
ij (Vm ) =
0
if i = j,
where Aij is a rate factor and aij is an exponential factor. ij (Vm ) depends
on the membrane potential which in turn depends upon time. Therefore, the
rate constants will in general depend upon time. A more physical representation
follows by linking the rate constants to the state gating charges. In this formulation, the rate constants that link states i and j (where i j) can be written
as
ij (Vm ) = Ae
ji (Vm ) = Ae
(0.5+)
Qj Qi

(Vm Vij )/kT

(0.5) Qi Qj (Vm Vji )/kT
,
,
where k is Boltzmanns constant, T is the absolute temperature, is an asymmetry factor, Qi and Qj are the state gating charges in states i and j, Vij and Vji
are the membrane potentials at which the rate constants equal A.
During intervals of time when the membrane potential is a constant, Equation 7.2 is a linear, rst-order matrix dierential equation with constant coecients. The solution determines the state occupancy probabilities, the {xj (t)}s.
The expected values of the channel conductance, channel current, and gating
charge are computed directly from the state occupancy probabilities. If the conductance of the channel is j when the channel is in state j, then the expected
178
value of the conductance of the channel, g(t), is

g(t) =
N

j xj (t).
(7.5)
j=1
If we assume that the current through the channel when the channel is in state
j is j (Vm Veq ), the expected value of the single-channel current, i(t), is
i(t) =
N

j xj (t)(Vm Veq ) = g(t)(Vm Veq ).
(7.6)
j=1
Similarly, if the gating charge of the channel when the channel is in state j is Qj ,
the expected value of the single-channel gating charge, qg (t), is
qg (t) =
N

Qj xj (t).
(7.7)
j=1
The expected value of the single-channel gating current, ig (t), is

ig (t) =
7.3
7.3.1
dqg (t)
.
dt
(7.8)
Numerical Methods
Integration step
The dierential equation for the state occupancy probability (Equation 7.2) is
solved numerically using methods described elsewhere (Colquhoun and Hawkes,
1995b). The accuracy and eciency of the numerical solution depends upon the
value of the integration step, t. The value of t needs to be chosen small
enough so that the time rate of change in the occupancy probabilities can be resolved accurately and so that the random variables are represented accurately.
The choice of an adequate value of t depends upon the eigenvalues of the state
transition rate matrix. Typically, t should be chosen so that t 1/|max |,
where max is the eigenvalue with the largest magnitude. The smaller t is chosen the more accurate the integration in any one step, but the longer the computation will take. In addition, long computations can result in the accumulation of
round-o errors. Thus, the choice of t is a compromise between the speed and
accuracy of the simulation. Solution of the matrix equation (Equation 7.4) determines the occupancy probabilities of each state. From these probabilities, the
expected values of the conductances, currents and gating charge are computed
using Equations 7.5-7.8.
179
0.2
E(t)
0.1
Figure 7.2: The probability of occurrence of

more than 1 event in an interval t where
the rate of events is and the events are distributed according to a Poisson distribution.
0.05
0.02
0.01
0.005
0.1
0.2
0.5
Random variables are computed from state transition probabilities. Transitions probabilities from state i to state j are computed from the relation
yij (t + t) ij t at each instant in time. The time interval for computing
random variables is set equal to the integration step t. The occurrence of a
transition is determined by a random number generator. The sequence of state
transitions determines the sequence of conductance values and gating charges
since each state has a unique conductance and gating charge. The conductance
values determines the current since this current is determined by specifying the
conductance, the membrane potential, and the channel equilibrium potential.
The gating current random variable is represented by impulses at the times of
transition of the gating charge and whose areas equal the discontinuities in gating charge.
In order to accurately represent the random variables, the time interval must
be chosen suciently brief that the probability of occurrence of more than 1
change in state in the interval is negligible. The probability of occurrence of
k events in an interval t with an average rate of events of is given by the
Poisson distribution
(t)k t
e
.
(7.9)
Pr(k, t) =
k!
Hence, the probability of occurrence of more than 1 event in an interval is
E(t) = 1 Pr(0, t) Pr(1, t) = 1 (1 + t)et .
(7.10)
The probability of more than one event in an interval E(t) is shown plotted
versus t in Figure 7.2. Note that for t 0.2, E(t) 0.018.
7.3.2
Initial conditions
In order to obtain a solution to Equation 7.2, initial conditions must be specied. There are several plausible choices for the initial conditions, i.e., the initial
states of the channel. One choice is simply to specify the initial state deterministically. A second choice is to choose the most probable state as the initial state.
The most probable state can be obtained by solving Equation 7.3 and choosing the initial state as the one with the highest probability. A third choice is
180
Figure 7.3: The IC Control gure after the software is initiated.
to choose the initial state probabilistically according to the equilibrium probability for state occupancy as determined by Equation 7.3. All three choices are
implemented in the software.
7.4
When the software is initiated, 2 gures are displayed (in addition to MATLABs
command window): the IC Control and the IC Parameters gures. The IC Control
gure controls the software (Figure 7.3). The IC Parameters gure allows the
user to design a single channel. Once the channel is designed, the membrane
potential is specied as a function of time, and the numerical variables chosen,
the simulation can be run, and the statistical properties of the channel variables
can be analyzed.
7.4.1
IC Control
The portion of the IC Control gure (Figure 7.3) below the menubar is divided
into three panels. The setup panel allows the user to: select Channel parameters which is used to design the channel, Membrane potential which is used to
specify the membrane potential as a function of time, and Numerics which is
used to specify the initial conditions and the integration of the computation. A
panel just below the setup panel controls the simulation. The simulation can
be started, stopped, paused, or continued. Clicking on Open allows results saved
in les to be read. Clicking on Save allows the user to save the results of the
simulation in a le; all parameters of the channel design are saved as well as the
7.4. USERS GUIDE
181
Figure 7.4: The IC Parameters gure.
simulation results. The analysis panel allows display of the results of a simulation.
7.4.2
IC Parameters
The IC Parameters gure displays the default channel kinetic diagram as shown
in Figure 7.4. The user can either read a previously stored channel model from
a le or construct a channel model by editing the default channel model. Editing entails adding new states, adding or modifying rate constants that link the
states, assigning ionic conductances and gating charges to states, and assigning
an equilibrium potential to the channel model.
Each box in the channel parameters gure (Figure 7.4) represents a particular
state of the channel and is given a number from 1 to 8 (a maximum of 8 states is
possible). The arrows connecting these states depict the transition rates between
states. Each box also contains the ionic conductance of the channel when the
channel is in that state, i.e., the state ionic conductance. The ionic conductance
can be changed by clicking on its value and typing the new value into the text
182
edit box. The ionic conductance is expressed in picosiemens (pS). A value of

zero denotes a non-conducting state. Each box also contains the gating charge
valence z of the channel when the channel is in that state; the gating charge
valence can be changed by clicking on its value and typing the new value into
the edit box. The gating charge valence can be positive or negative and need not
be an integer. The gating charge is ze, where e = 1.602 1019 C. The value of
the channel equilibrium potential can be changed by clicking in the text edit box
in the upper right hand corner of the IC Parameters gure and typing the new
value in the text edit box. A single click on a rate constants displays its voltage
dependence in the IC Parameters gure.
Add new state
A new state can be added to the diagram by clicking on New. A new state will be
created and positioned in the upper left corner of the eld. A new state or any
existing state can be repositioned in the window by clicking on the grey region
at the top of the state boxes and dragging the state box to a new position. To
delete a state the user clicks on the red delete box in the upper left-hand portion
of the state box.
Add rate constant
To add rate constants linking state i to state j, the user rst clicks on Add in the
IC Parameters gure, then clicks in the state box for state i, and then clicks in
the state box for state j. During this operation, the cursor becomes a cross hair.
A pair of default rate constants is added to link these two states.
IC Specify rate constants
To modify the rate constants that link two states, the user double clicks on the
selected rate constants to obtain the IC Specify rate constants gure (Figure 7.5).
The user selects which rate constant to modify or to create by clicking on the
appropriate pushbutton. The voltage dependence of the rate constant, can be
specied numerically by typing numbers into the appropriate text edit boxes or
graphically by using the mouse. Clicking on two locations in the plot of rate constant versus potential puts an exponential function through those two points. A
formula for the dependence of the rate constant on membrane potential is displayed in the lower left-hand corner of the IC Parameters gure. This formula is
also displayed by clicking on a rate constant in the IC Parameters gure.
Clicking on Delete deletes the pair of rate constant from the IC Parameters
gure. Clicking on the two curved linked arrows exchanges the two rate constants. Clicking on Revert resets the rate constant to the previously stored value.
7.4. USERS GUIDE
183
Figure 7.5: The IC Specify rate constants gure after the user has double clicked on the
rate constants linking states 1 and 2 in Figure 7.4 and changed the parameters of the
the rate constant so that 12 = 2.5e0.01Vm (1/ms) and 21 = 3e0.04Vm (1/ms), where
Vm is in mV..
184
Figure 7.6: IC View rate constant gure after the rate constants have been dened as in
Figure 7.5.
Miscellaneous features
If Reset Diagram is selected the current channel kinetic diagram is erased and
the default channel kinetic diagram is drawn. A previously stored diagram can
be retrieved by selecting Open. The current diagram can be saved to a le by selecting Save. Clicking on Save in the IC Parameters gure saves all the channels
parameters but not the simulation results.

The voltage dependent rate constants can be displayed by clicking on the button
marked V iewRC in the IC Parameters gure which results in the display of
the IC View rate constants gure (Figure 7.6). This gure contains a number of
panels.
7.4. USERS GUIDE
185
Figure 7.7: The IC Setup view rate constant gure.
described below.
Setup. Clicking on Setup in the IC View rate constants gure displays the
IC Setup view rate constants gure (Figure 7.7) which allows selection
of the voltage-dependent parameters as a function of the membrane
potential.
Variables. The abscissa is the membrane potential. Shift clicking on
any variable adds it to the collection of selected ordinate variables. Clicking on any variable, selects that variable and deselects
all others. The variables associated with each pair of rate constants are: ij , ji , ij = 1/(ij + ji ), xij = ij /(ij + ji ), and
xji = ji /(ij + ji ). ij is the time constant for transition between states i and j provided there are only two states; if there
are more than two states, then ij has no particular signicance.
Similarly, xij is the probability that the channel will be in state j at
equilibrium provided there are only two states; if there are more
than two states, then xij has no particular signicance.
186

e.g., to get 12 type \alpha_{12}.
zooming again.
Unzoom. Clicking on
of a gure that allows changing the axis (see Figure 5.8). The axis scale can
be chosen to be linear, logarithmic, and/or reciprocal. If neither the Log
nor the Inverse (1/) options is chosen, the scale is linear. If Log is chosen,
the scale is the logarithm of the magnitude of the variable. If Inverse (1/) is
chosen then the reciprocal of the variable is plotted either on a linear or on
a logarithmic scale. Clicking on Apply results in a change in the axis. The
plot range can be changed, but the axis labels cannot be edited.
recorded.
Line properties. The color, line style, and symbol type are used to encode a
particular variable; this marker is shown in the legend. Clicking on the
marker allows the user to edit the attributes of the plot line/symbol
(see Figure 5.9).
the axis gure.
7.4.3
Membrane potential
Selection of Membrane Potential in the controls gure displays the IC Membrane

potential gure (Figure 7.8). The membrane potential can be a rectangular pulse
of potential superimposed on a steady holding potential. The user can select
7.4. USERS GUIDE
187
Figure 7.8: IC Membrane potential gure after selection of a

pulse of potential.
Figure 7.9: IC Numerics gure appropriate for

rate constants shown in
Figure 7.6 and membrane
potential shown in Figure 7.8.
the holding potential, the duration of the stimulus, the onset time of the pulse
starts, the pulse duration, and pulse amplitude. The parameters of the membrane potential can be read from and saved to a le.
7.4.4
Numerics
The IC Numerics gure (Figure 7.9) controls the choice of the integration step
and initial conditions for the simulation. The gure consists of ve panels. The
two upper panels deal with the eigenvalues of the transition rate matrix. The
middle panes deal with the method for choosing the integration step size. The
bottom panel deals with the choice of initial conditions (initial states).
188
Eigenvalues
For a given choice of membrane potential and voltage-dependent rate constants,
the software computes the eigenvalues of the transition rate matrix and displays these results to the user. These eigenvalues have the dimensions of rate
constants (RC). The user can also choose to display the time constants (TC =
1/RC) corresponding to these eigenvalues. In addition, the absolute value of
these rate and time constants can also be displayed.
Integration step
The smallest time constant is computed from the fastest eigenvalue and the user
can choose, by editing the text edit box, to make the integration step a fraction
(or a multiple) of this smallest time constant. Alternatively, the user can choose
a xed integration time. The integration time that results from the users choice
is displayed as is the probability of more than one transition during an interval
of time that equals the integration step.
Initial state
The initial state for a simulation can be chosen deterministically to be any of
the allowable states or the most probable state for the given initial values of the
membrane potential. By default, the initial state is chosen probabilistically by
computing the state occupancy probabilities for the chosen initial value of the
membrane potential and choosing the initial state randomly using these probabilities.
7.4.5
Analysis
Clicking on the analysis panel of the IC Control gure allows access to a variety
of displays of simulation results including such variables as: the state occupancy, the state occupancy probability, the ionic conductance, the ionic current,
the gating charge, and the gating current. Both the random variables and their
expected values can be displayed. Ten channels with similar characteristics can
be examined simultaneously to allow users to relate macroscopic to microscopic
variables. Results of multiple simulations can also be plotted on a single set of
axes for the sake of direct comparison.
Three dierent types of graphs are available. The rst type allows plotting
a single variable as a function of time in xed coordinates. An example is the
IC State occupancy gure shown in Figure 7.10. The top panel shows the simulation for 10 independent channels, the middle panel shows the results for
channel 1 alone, and the bottom panel shows the state occupancy probabilities
for both states of the channel. A second example of this type of graph is the
IC Ionic current gure shown in Figure 7.11. Selected for plotting are the ionic
7.4. USERS GUIDE
Figure 7.10: IC State occupancy gure with all variables selected for display.
189
190
Figure 7.11: IC Ionic current gure showing the relation between the random variable
and its expected value of the ionic current.
current random variable, its expected value, and the average ionic current of 10
identically distributed but statistically independent channels. Similar plots are
available for the ionic conductance, gating charge, and gating current. These displays are helpful for relating macroscopic to microscopic variables and random
variables to their expected values.
A second type of graph is the IC Summary gure which allows comparison
of the time dependence of channel variables to each other in xed coordinates
(Figure 7.12). Most of the variables are self-evident from the display. However,
the representation of the gating current random variable requires some comment. The gating charge random variable is a random rectangular wave. Hence,
the gating current random variable, which is dened as the derivative of the
gating charge random variable, is a random impulse train (train of Dirac delta
functions). We represent these impulses with vertical arrows. The time of occurrence of an arrow equals the time of occurrence of an impulse and the height of
the arrow equals the area of the impulse. On the scale of visibility of the gating
current random variable, the expected value is often too small to see. Hence, in
the plot of the gating current, deselecting the random variable will allow its expected value to be observed. Clicking on the radio button for Cross line displays
a vertical line that tracks the position of the mouse cursor. The values of the
intersection of the line with each variable is displayed.
The above graphs have limited capability for control of scales. The ordinate
7.4. USERS GUIDE
Figure 7.12: IC Summary gure with all variables selected for display.
191
192
Figure 7.13: IC Graphics gure showing the expected value of the ionic current and of
the gating charge for the channel dened in Figures 7.4-7.8.
scale is autoscaled automatically. This is convenient but can be misleading in

that errors inherent in numerical calculations become autoscaled and can appear large if the scale is not read. For example, if for some set of parameters
some current variable is in principle zero, its numerical value may be limited
by the numerical accuracy of the computations to be 1023 pA, a small current.
However, if autoscaled in the above graphs, this current may appear large. The
type of graph described below yields more control over plotting scales and can
help the user to interpret such small currents.
The third type of graph allows comparison of results obtained in dierent
simulations in coordinates dened by the user. Clicking on Graphics in the em
IC Control gure displays the IC Graphics gure (Figure 7.13).
This gure allows plotting most of the results of the simulation; the random
variables are not plotted with the IC Graphics gure but all the expected values
and probabilities of all variables are plotted. For the allowable variables, any
7.4. USERS GUIDE
193
Figure 7.14: The IC Setup graphics gure showing the variables

used to setup Figure 7.13.
variable can be plotted against any other in coordinates chosen by the user. The
control of this gure is virtually identical to that for the IC View rate constants
gure (Figure 7.6). Hence, we describe only the dierences. The main dierence
occurs if Setup is selected in the IC Graphics gure which results in display
of the IC Setup graphics gure (Figure 7.14). Several dependent variables can
be plotted simultaneously. In addition, results saved in les can be plotted so
that results for dierent parameters can be compared. In addition, results of
consecutive simulations can be overlayed. We give two examples of the type
of graphics that are readily available with the IC Graphics gure. Figure 7.15
shows the state occupancy probabilities of all four states as a function of time.
Figure 7.16 shows the ionic conductances of three dierent channel models a
two-state, a three-state, and a four-state model.
194
Figure 7.15: IC Graphics gure showing the state occupancy probabilities for a
four-state channel whose successive states are linked by rate constant such that
12 = 23 = 34 and 21 = 32 = 43 where 12 and 21 are identical to those in
Figure 7.5.
7.4. USERS GUIDE
195
Figure 7.16: IC Graphics gure showing the ionic conductances of a two-state,

three-state, and a four-state channel where the last state in each of these
three channel models is a conducting channel with a conductance of 20 pS.
12 = 23 = 34 = 4e0.04Vm and 21 = 32 = 43 = 0.2e0.05Vm (ms1 ). The membrane potential had at a holding potential of 80 mV and stepped to +40 mV.
196
7.5
Problems
Problem 7.1 The purpose of this problem is to explore the properties of a channel
that has one two-state gate that is not voltage gated. This two-state channel has
rate constants that are not a function of membrane potential; this channel is not
voltage-gated. Dene a two-state channel for which state 1 is closed (nonconducting) and state 2 is open (conducting),
12
1 2.
21
Use rate constants that are constant (independent of membrane potential). In all
parts of this problem use rate constants such that 12 + 21 = 10 ms1 .
a. Determine opening and closing rate constants such that the channel is
equally likely to be in state 1 or state 2.
b. Determine opening and closing rate constants such that the channel is
three times as likely to be in state 2 than in state 1.
c. Use the same rate constants as in part b. Set the membrane potential so
that it is 50 mV for t < 0.5 ms and +50 mV for t > 0.5 ms. The objective
of this part is to design a channel that has a single-channel current when
the channel is open (I) of 1.2 pA when the membrane potential is 50
mV and +0.8 pA when it is +50 mV.
i. Determine the equilibrium potential and single-channel conductance
when the channel is open (). Check your answer by running the simulation using the values of the equilibrium potential and single-channel
conductance you determined.
ii. What is the average single-channel current (i) for t < 0.5 ms? What is
the average single-channel current for t > 0.5 ms?
Problem 7.2 The purpose of this problem is to explore the properties of a channel that has a two-state gate that is voltage gated. This two-state channel has
rate constants that are functions of membrane potential; the channel is voltagegated. Dene a two-state channel for which state 1 is closed (nonconducting)
and state 2 is open (conducting),
12
1 2.
21
Set the membrane potential to 60 mV for t < 0.2 ms and to +40 mV for t > 0.2
ms.
7.5. PROBLEMS
197
a. Determine voltage-dependent rate constants such that: the channel is closed

(with probability > 0.8) for t < 0.2 ms; the channel is open (with probability > 0.8) for t 0.2 ms; and the channel opens with a time constant of
about 0.2 ms.
b. Determine parameters of the channel such that when the channel is open,
the single-channel current (I) is +0.5 pA at a membrane potential of +40
mV and is zero when the membrane potential is 10 mV.
c. Is this an activation gate or an inactivation gate?
d. Change the equilibrium potential to 70 mV. Repeat the simulation. Could
this channel describe the kinetics of the potassium channel in the HodgkinHuxley model? In what ways does it resemble the potassium channel? In
what ways does it dier from the potassium channel?
e. Change the equilibrium potential to +50 mV. Repeat the simulation.
i. Is the average channel conductance a continuous function of time?
Explain!
ii. Is the average channel current a continuous function of time? Explain!
iii. Could this channel describe the kinetics of the sodium channel in the
Hodgkin-Huxley model? In what ways does it resemble the sodium
channel? In what ways does it dier from the sodium channel?
Problem 7.3 The purpose of this problem is to explore the properties of two twostate voltage-gated channels that dier only in their state conductances. This
problem deals with two channels that each have two states with the same kinetic
diagram, namely
12
1 2,
21

12 = 4e0.04Vm and 21 = 2e0.01Vm .
Each channel is subject to a membrane potential prole that is 60 mV from
t = 0 to t = 1 ms after which the membrane potential is +10 mV for 2 ms. The
equilibrium potential for each channel is +40 mV. The channels dier only in
the conductance assigned to each state. Channel 2 has 1 = 0 and 2 = 20 pS;
Channel 2 has 1 = 20 pS and 2 = 0.
a. Which channel opens in response to a depolarization? Explain.
b. Which channel closes in response to a depolarization? Explain.
198
c. Does the time-dependence of the probability that the channel is in state 1

dier for these two channels? Explain.
Problem 7.4 The purpose of this problem is to explore the eect of scaling the
rate constants on the kinetic properties of a channel. The kinetic diagram has the
form
12
1 2.
21
The membrane potential is 60 mV from t = 0 to t = 1 ms and +10 mV for 2

ms. The equilibrium potential is +40 mV. The channel conductances are 1 = 0
and 2 = 20 pS.
a. Set the voltage dependence of the rate constants as
12 = 4e0.04Vm and 21 = 2e0.01Vm ,
and run the simulation. Plot the ionic conductance and ionic current.
Record the values of eigenvalues.
b. Next double the rate constants so that the voltage dependence of the rate
constants becomes
12 = 8e0.04Vm and 21 = 4e0.01Vm .
Run the simulation again. Plot the ionic conductance and ionic current.
c. Next halve the rate constants so that the voltage dependence of the rate
constants becomes
12 = 2e0.04Vm and 21 = 1e0.01Vm .
Run the simulation again. Plot the ionic conductance and ionic current.
d. Examine the results and draw conclusions about the eect of scaling the
rate constants without otherwise changing their voltage dependence. Focus
both on the random variables and on the expected values of both the ionic
conductance and the ionic currents. Be as quantitative as possible.
Problem 7.5 The purpose of this problem is to explore the eect of the choice of
initial state on the properties of a channel with a simple, two-state gate.
a. Start the simulation with the default parameters. Examine the Summary
plot and the State occupancy plot.
7.5. PROBLEMS
199
b. Now display the IC Numerics gure. Note that the default initial state is
Random. Now change the initial state to be state 1. Start the simulation.
i. Describe the dierences between the results obtained with a random
initial state and an initial state of 1. What accounts for this dierence.
ii. Carefully display the time course of the state occupancy probability
using the Graphics gure and determine the time constant of the time
course of the state occupancy probability.
iii. Compare the time constant you estimated in part ii with the eigenvalue
(expressed as a time constant) from the Numerics gure.
Problem 7.6 The purpose of this problem is to explore the gating charge of a
channel that has one two-state gate. The rate constants of the channel are 12 = 1
and 21 = 2 ms1 . The gating charge of state 1 is 0 and that of state 2 is 2eC.
a. Run the simulation and determine the expected value of the gating charge.
Explain its value.
b. Without changing any other parameter, determine a value of 12 such that
the expected value of the gating charge is 1eC.
c. Set both 12 = 21 = 2 ms1 and set the gating charge of both state 1 and 2
to 2eC. Run the simulation. Explain the expected value of the gating charge.
[Hint you may nd it convenient to use the Graphics plots (which you
can select from the IC Control gure. This option allows a great deal of
control over axes scales which may be important to interpret the results.]
Problem 7.7 The purpose of this problem is to explore the relation among ionic
conductance, ionic current, gating charge, and gating current for a channel that
has one two-state gate. The rate constants are 12 = 1 and 21 = 2 ms1 . The
gating charge of state 1 is 0 and that of state 2 is 2eC. The ionic conductance
of state 1 is 0 and that of state 2 is 20 pS. Run the simulation. [Hint for
some parts of this problem, you may nd it convenient to use the Graphics plots
(which you can select from the IC Control gure). This option allows a great deal
of control over axes scales which may be important to interpret the results. The
other plots have autoscaled axes in which small errors, inherent in numerical
calculations, are autoscaled to appear large.]
a. Examine the expected value of the ionic conductance.
i. Describe the ionic conductance.
ii. Explain its value.
b. Examine the expected value of the ionic current.
200

i. Describe the ionic current.
ii. Explain its values.
c. Examine the expected value of the gating charge.

i. Describe the gating charge.
d. Examine the expected value of the ionic current.
i. Describe the ionic current.
e. Note that the expected value of the ionic conductance and gating charge are
non-zero constants, the expected value of the gating current is zero, and
the expected value of ionic current is not constant. Explain these results.
Problem 7.8 The purpose of this problem is to explore the physical properties of
the gating charge. The kinetic diagram for the channel has the form
12
1 2,
21
where
12 = 4e0.04Vm and 21 = 2e0.01Vm ,
The membrane potential is 60 mV from t = 0 to t = 1 ms and +10 mV for 2

ms. The stimulus duration is 3 ms. The equilibrium potential is +40 mV. The
channel conductances are 1 = 0 and 2 = 20 pS.
a. Perform simulations using the following state gating charges. Plot both the
expected value of the gating charge and the expected value of the gating
current.
i. Q1 = 0 and Q2 = 2eC.
ii. Q1 = 0 and Q2 = 2eC.
iii. Q1 = 2eC and Q2 = 0.
iv. Q1 = 2eC and Q2 = 0.
b. Give a quantitative account of the key properties of the gating charge and
gating current waveforms the initial values, nal values, and time constants.
c. Of the results obtained in part a, which are physically plausible results.
Explain.
7.5. PROBLEMS
201
Problem 7.9 The purpose of this problem is to explore the eigenvalues of channel
models.
a. Consider a two-state channel with the rate constants 12 = 1 and 21 = 2
(ms1 ) and the default membrane potential shown in Figure 7.8.
i. What are the eigenvalues for the two values of the membrane potential?
ii. Why are the eigenvalues at the two membrane potentials the same?
Check your explanation by changing the membrane potential and determining the eigenvalues.
iii. What is the relation of the eigenvalue to the rate constants? Check
your relation by changing the rate constants and determining the eigenvalue.
iv. Design a simulation experiment that computes the temporal change
of some variable of the two-state model to reveal the signicance of
the eigenvalue.
b. Consider a two-state channel with the rate constants 12 = 1.6818e0.008664Vm
and 21 = 2 (ms1 ) where Vm is in mV and the default membrane potential
is shown in Figure 7.8.
ii. Why are the eigenvalues at the two membrane potentials dierent?
iii. What is the relation of the eigenvalues to the rate constants? Check
your relation by changing the rate constants and determining the eigenvalue.
iv. Design a simulation experiment that computes the temporal change
of some variable of the two-state model to reveal the signicance of
the eigenvalue. Which eigenvalue determines the temporal response?
c. Consider a three-state channel with the default rate constants 12 = 1,
21 = 2, 23 = 2, and 32 = 1 (ms1 ) and the default membrane potential
ii. Why are the eigenvalues at the two membrane potentials the same?
202

iii. Determine a relation that computes the eigenvalues from the rate constants? Check your relation by changing the rate constants and determining the eigenvalues.
Problem 7.10 The purpose of this problem is to explore the properties of a threestate channel whose rate constants are not a function of membrane potential; this
channel is not voltage-gated. Dene a three-state channel with the following
kinetic scheme
23
12
1 2 3,
21
32
where states 1 and 2 are closed and state 3 is open. In all parts of this problem, make the rate constants independent of membrane potential, and use rate
constants in the range 0.1-10 ms1 .
a. Determine a set of rate constants such that the channel is equally likely to
be in any one of its three states.
b. Try a set of rate constants such that ij = ji . What are the probabilities
of occupying each state? Try another such set having this property. What
are the probabilities of occupying each state with this new set? What can
you conclude about this case?
c. Determine a set of rate constants such that the probabilities that the channel is in states 1:2:3 are approximately 0:0.5:0.5.
d. Determine a set of rate constants such that the probabilities that the channel is in states 1:2:3 are approximately 0:0.25:0.75.
e. Determine a set of rate constants such that the probabilities that the channel is in states 1:2:3 are approximately 0.2:0.3:0.5.
Problem 7.11 The purpose of this problem is to explore the properties of voltagegated channels with two, three, and four states. Assume that the equilibrium
potential of each channel is 40 mV and that the membrane potential starts at
60 mV and switches to +10 mV at 1 ms and is maintained at this value for 2
ms. The three channels are dened as follows:
The two-state voltage-gated channel has a kinetic diagram

12
1 2,
21

12 = 4e0.04Vm and 21 = 2e0.01Vm .
7.5. PROBLEMS
203
The three-state voltage-gated channel has a kinetic diagram

12
23
21
32
1 2 3,
12 = 23 = 4e0.04Vm and 21 = 32 = 2e0.01Vm .
The four-state voltage-gated channel has a kinetic diagram

12
23
34
21
32
43
1 2 3 4,
12 = 23 = 34 = 4e0.04Vm and 21 = 32 = 43 = 2e0.01Vm .
In exploring the following issues, it is instructive to examine graphs that show
the membrane potential as well as both the random variables and mean values or
probabilities associated with the record of state occupancies, the conductance,
and the current through the channel.
a. For each of the channels, make the last state (the state with the highest
state number) the conducting state with a conductance of 20 pS and make
all other states non-conducting. Compare the mean conductance of the
two-state, the three-state, and the four-state channels. What can you say
about the eect on channel conductance of increasing the number of closed
states that precede the open state?
b. Now consider the four-state channel. Compute the mean conductance
when state 1 has a conductance of 20 pS and all other states are nonconducting. Repeat this computation except make state 2 the conducting
state with all others nonconducting. Repeat again with state 3 and then
state 4. Compare the mean conductance for these four conditions. Which
of these conductances most closely resembles the sodium conductance of
squid axon? Explain.
Problem 7.12 The purpose of this problem is to design a three-state channel that
activates and then inactivates. The channel activates at about 0 mV at a rate that
is three times as fast as it inactivates.
a. Consider a channel that must open before it inactivates, e.g.
12
23
21
32
1 2 3,
where both states 1 and 3 are closed and state 2 is open.
b. Consider a channel that need not open before it inactivates.
204
Chapter 8
PEDAGOGICAL METHODS
205
206
CHAPTER 8. PEDAGOGICAL METHODS
8.1
Introduction
This chapter describes the pedagogical methods that were developed to teach
cellular biophysics using the software described in this text. The chapter is
aimed primarily at instructors who wish to use this material in teaching although
students may nd the material helpful. The description given here expands that
available previously (Weiss et al., 1992).
8.2
Uses Of The Software
The software has become an integral part of teaching cellular biophysics. It is

used throughout the subject, wherever it can be didactically eective. The software is used in lecture to motivate, engage, and inform students. The software is
helpful to visualize and to intuit dynamic processes. Use of the software in special classes held in an electronic classroom is an eective way to get students
away from solving problems by pattern recognition (Mazur, 1997) and forcing
them to confront the material in a dierent way. Use of the software in projects
can deepen students understanding of the subject material and can be used to
teach students how to go about a research project.
8.2.1
Lectures
We have used a lecture room with a large screen (13.618) for projecting a
computer monitor screen. Thus, students are able to see all the interactions of
the lecturer with the computer. We have used the software in a variety of ways:
to help students to visualize concepts, to build intuition, to motivate, and to
engage the students intellect. We illustrate some of these techniques.
Some concepts are grasped instantly when presented graphically. The intuition that results is complementary to that which results from a mathematical
exposition. The combination of an intuitive, visual grasp of a concept and the
precise, abstract mathematical description is powerful. Computer simulations
can be especially helpful with building intuition.
Example 8.1 In the random-walk model of diusion with an unbiased random walk, each particle moves one step to the left or to the
right with equal probability; the particle has no preferred direction of
motion. Yet a population of diusing particles tends to move down
the particle concentration gradient. Thus, there is an apparent paradox between the undirected motion of individual particles and the
directed motion of a population of particles. This apparent paradox
is resolved in an instant by viewing a population of particles undergoing random walks (Figure 8.1). By watching the simulation, the user
8.2. USES OF THE SOFTWARE
207
Figure 8.1: Random walk in two regions. The initial distribution of particles (upper left)
shows 50 particles in the left region and none in the right region. After 35001 steps,
the particles have been dispersed in the two regions (upper right). The number of
particles in the right region (lower) zero when the step number is zero and approaches
25 at a large step number. The rate of increase of particles in the right region is a
measure of the ux of particles from the left to the right regions. This simulation also
demonstrates how long it takes for the two regions to come to equilibrium.
208

develops an intuition for the way in which the random motions of particles lead to their diusive spread. Furthermore, this demonstration
sets the stage for a precise derivation of Ficks rst law (which relates
particle ux to concentration gradient) starting from a random-walk
model of diusion (Weiss, 1996a, Section 3.2.1).
Some models of biological phenomena are dicult to teach not because the
mathematics is dicult, but because the mathematics is messy with a large number of parameters. Thus, students can get lost in the notation and in the messiness of the description. A software package that allows manipulation of the
model parameters can cut through the messy description and build intuition
very quickly to expose the inherent simplicity of the underlying model.
Example 8.2 Even the simplest models of carrier-mediated transport
involve a number of parameters and several physical processes. In
our experience in teaching this topic, there is a great tendency for
students to get lost. The derivations of the relations of ux to concentration are simple, but take some time and do not give a great deal
of insight into the workings of this class of models. We have found
that time spent in lecture using the carrier-mediated transport package gives students an immediate intuition into the workings of these
models. Students are then motivated to follow the derivations and to
appreciate the precise description that results.
Simulations are especially helpful to motivate students to grapple with concepts that may be dicult and to foster a sense of intellectual engagement. Properly used in lecture, the simulations promote an active participation in learning
rather than the more passive participation that comes from simply listening to
a lecture (Mazur, 1997). Asking students question in lecture gets them to participate intellectually.
Example 8.3 The simplest diusion processes result when both particle ux and concentration are time independent. To motivate students to think about such processes it is helpful to ask them to predict the steady-state spatial distribution of particles when the ux is
a constant in space and time. Is the distribution constant? Is it exponential? Is it Gaussian? After the students have made their guesses
and perhaps after a tally of all the guesses has been made the
simulation of the random-walk model can be begun with a constant
source of particles at one end of a rectangular eld and a sink at the
other. The derivation of the steady-state distribution can proceed on
the blackboard while the simulation is in progress. The parameters
of the simulation can be chosen so that the spatial distribution of
particles approaches its steady-state distribution in about the time it
209
Figure 8.2: Steady-state distribution for random walks in a single compartment. The
compartment was initially empty as shown in the upper left panel and the step size was
set to 5. There was a source at 0 and a sink at 195. One particle per step was generated
by the source. After 4001 steps, the particles were distributed as shown in the upper
right panel with the histogram shown in the lower left panel. Except right near the
source, the spatial distribution is linear. The number of particles is plotted versus
step number in the lower right panel. The results show that the number of particles is
approaching a constant for this number of steps indicating that the distribution is near
its steady-state distribution.
takes to complete the derivation. From time to time during the derivation, the lecturer can check the progress of the simulation by examining the dependence of the number of particles in the eld on time.
This number approaches an asymptotic steady-state value. Hence,
this plot gives a quantitative estimate of whether the spatial distribution has reached its steady state (Figure 8.2). When the derivation is
complete and the simulation is complete the two can be compared.
This usage of the computer is fun and motivates students to follow
the derivation which solves this problem rigorously.
Example 8.4 Diusion between two nite compartments through a
separating membrane is an important transport process in biological
systems. It can model, for example, diusion between the cytoplasm
of a cell and the extracellular uid, across the plasma membrane.
There are two important time scales for two-compartment diusion
through a membrane: the time for the concentration in the membrane
to reach its steady-state distribution and the time for equilibration of
the two compartments. For thin membranes, the spatial distribution
210

of concentration in the membrane reaches its steady-state distribution much more rapidly than the time it takes the two compartments
to equilibrate. Thus, it is adequate to relate ux and concentration
by a steady-state relation even though concentrations in the two compartments are changing in time; a point that can be somewhat tricky
for students to understand. This conceptual diculty is removed if
the solution to the two-compartment diusion problem can be displayed for a membrane of arbitrary thickness. Simulation experiments make these two time scales clear (Figure 8.3). Furthermore,
there is a general lesson to be learned about the nature of approximations to be made for a system with many kinetic processes, but where
one process is rate-limiting.
Example 8.5 A dening characteristic of electrically excitable cells is
their sharp threshold for excitation. Sub-threshold current stimuli
produce no action potential; super-threshold currents do. The dierence in current level between sub- and super-threshold stimuli can
be very small. The Hodgkin-Huxley model possesses such a sharp
threshold which can be demonstrated (Figure 8.4) by showing that a
small increase in a subthreshold stimulus current can result in an action potential. The mathematical basis for the threshold is subtle. We
have found that demonstrating the sharp threshold in the HodgkinHuxley model in a dramatic fashion will motivate students to examine the mathematical basis of sharp thresholds in such dierential
equations (Weiss, 1996b, Section 4.4.1). By preparing in advance, the
threshold can be bracketed so that an increase of one unit in the
least signicant digit changes a sub-threshold stimulus to a suprathreshold stimulus. This raises the students curiosity about the nature of a threshold in a dierential equation and motivates them to
follow the lecture devoted to this property.
Another use of computers in lecture is to perform What if experiments as

a way to build intuition. A typical and obvious use is to ask the class to predict what will happen if some system under study is perturbed in some way.
This type of audience participation breaks the formality of the lecture, puts
students at ease, and engages their intellect. A simulation can be run and the
outcome of the experiment can be obtained instantly. There is then an opportunity to discuss the relation between the outcome of the simulation experiment
and the students expectations. Changing almost any parameter of any of the
simulations can lead to valuable discussions and deeper insights.
Example 8.6 Suppose we have two solutes that can bind to a transporter in a chemically-mediated transport mechanism. What if ... we
change the dissociation constant for the second solute on the inside
211
Figure 8.3: Time constants in two-compartment diusion. The left bath initial concentration was 10 mol/cm3 with a width of 0.5 cm; the right bath initial concentration
was 5 mol/cm3 with a width of 1 cm; the membrane width was 0.01 cm and the initial concentration was drawn as shown in the upper left plot. The upper three plots
show the spatial distribution of concentration (membrane view with a bit of each bath
on each side) at three times: 0, which shows the initial distribution; 15 seconds, which
shows the distribution is linear in the membrane but the two baths are not equilibrated;
3705 seconds, which shows the baths and membrane near equilibration. The lower two
plots show the concentration as a function of time. The left plot vs. time shows the
concentration as a function of time in the left bath and for a point in the membrane.
The concentration in the membrane has not changed appreciably over a time span for
which the concentration in the membrane has nearly reached steady-state. The right
plot shows the concentration as a function of time in the two baths over a time scale
that shows the concentration equilibrating.
212
Figure 8.4: The threshold for

eliciting an action potential
in the Hodgkin-Huxley model.
The stimulus is a current pulse
of 1 ms duration; the subthreshold amplitude is 14.3820
and the suprathreshold amplitude is 14.3821 A/cm2 .
of the membrane? How will the uxes of the rst and second solutes change? How will the fraction of transporters bound to the rst
and second solutes on the inside of the membrane change? How will
the fraction of transporters bound to the rst and second solutes on
the outside of the membrane change? Such questions are answered
quickly by use of the chemically-mediated transport package and the
answers invite further discussion.
As will be described in further detail below, lectures can also be used to
perform a research project live with audience participation. Thus, the lecturer
and the students are working on the project together. This lends a quite dierent
atmosphere to lectures.
The uses of computation described above have become integral, and now
essential, parts of lectures and are performed live in the lecture room. It has
proved both an eective and an enjoyable part of teaching and learning.
8.2.2
Electronic classroom and homework problems
We hold several classes in an electronic classroom in which each student has

access to a computer workstation and is free to work either from prepared homework problems or in a self-directed manner. We have found that most students
prefer to work on the homework problems and only a few will work independently. Some students nish that portion of the homework assignment in the
session in the electronic classroom. Others start on the problems and nish
them at a later date.
213
Students and sta members work together in this setting. The objective is
for everyone to arrive at the solution to the problems, each of which is chosen
to illustrate some important issue in the subject matter. This mode of work is
noncompetitive, cooperative, and self-paced. It also provides a good opportunity
for students and sta to interact in a more informal setting than is possible in a
lecture or a recitation.
Some of the problems we have frequently assigned for homework and used
successfully in an electronic classroom are described below.
Example 8.7 In connection with two-compartment diusion, we use
Problem 3.4 to make sure students understand the dierence between
the time constant to reach steady state in a membrane and the time
constant to reach equilibrium between the two baths that are separated by the membrane (see Example 8.4).
Example 8.8 We often assign Problem 4.1 to give students some feeling for the relation between ux and concentrations for the simple,
symmetric, four-state carrier model. This is the simplest of the models for carrier-mediated transport through membranes and it is a
stepping stone for understanding more complex models.
Example 8.9 The Hodgkin-Huxley model is dicult for undergraduate students to comprehend. Therefore, we start students thinking about the model in the voltage-clamp conguration by assigning
Problem 5.1. Part a is straightforward but part b requires that students perform simulations iteratively to arrive at a solution. They
learn about the interaction of activation and inactivation to yield the
sodium conductance in a voltage-clamp conguration.
Example 8.10 We usually assign one part of Problem 5.11 to get students thinking about the Hodgkin-Huxley model in the current-clamp
conguration. The assignment is in the form of a puzzle. Students
enjoy the challenge of guring out the puzzle. With a set of default
model parameters and stimulus current parameters, the HodgkinHuxley model gives rise to an action potential. A change in one of
many dierent parameters of this model leads to no action potential
in response to the same current stimulus. Students are given problems in each of which one parameter (e.g., temperature, membrane
capacitance, an ion conductance, and ion concentration) has been
changed to block the occurrence of the action potential. Students are
asked to nd a compensatory change in parameters that will restore
the action potential to be identical (within certain bounds) to that
obtained with the default parameters. This type of problem forces
students to examine the interactions of internal model variables in a
critical manner.
214

Example 8.11 Understanding the kinetic behavior of single channels
is challenging for students. We usually assign Problem 7.1, which
deals with a two-state channel that is not voltage gated, and Problem 7.2, which deals with a two-state channel that is voltage gated.
Both of these problems ask students to design a channel that opens
at a particular value of the membrane potential and has prescribed kinetic properties. Students learn about the dierences between voltagegated and ungated channels. Also, these problems exercise the students intellect in a very dierent manner than do the traditional
problem sets that are a routine part of homework assignments. In
a traditional homework assignment, students are asked to analyze
problems that are completely dened. The software problems can be
less well dened so that the denition of the problem is part of the
assignment.
8.2.3
Projects
We have found it educationally eective to require that students complete a

project of their choice using the Hodgkin-Huxley model software. The exercise
aords students an opportunity to formulate a hypothesis about a theoretical
topic, to write a proposal, to test the hypothesis, to reach a conclusion, and
to communicate their results in writing. Although these projects can be quite
time consuming (for both students and faculty), they have been very popular
with the vast majority of students. For many of the students, this is the rst
learning activity that has the avor of a research project. To emphasize the
importance of this educational activity, performance on the project is graded
and accounts for 15% of the grade in the subject, a percentage that is comparable
to the importance of one of the examinations in the subject.
During one semester when enrollment in the subject was unusually high, it
was necessary to pair up students to make the management of projects acceptable.1 Perhaps not surprisingly, we found that the quality of the work seemed
to improve. Thus, we have asked students to work in teams of two ever since
although we do not require it.
We also found that as the years went by, reports got longer and longer. Thus,
to encourage the students to be concise we placed limits on the lengths of report.
We give the following instructions to students about the rules for the project.
Students may do projects individually or in pairs. If a pair of students collaborate on a project they should submit a single proposal
and a single report which identies both members of the team and
gives both email addresses. Proposals will be returned as soon as
1
Interacting with students to help them write acceptable proposals and to conduct these
projects takes considerable time. Assessing a single nal project report takes over one hour.
215
possible so that students may revise them. Only the nal, accepted
proposal will be given a grade.
The demonstration project performed in lecture cannot be the basis
of a student project. The report should be at most 10 pages of text
and at most 10 gures and tables.
We describe the steps involved in the project in detail.
The proposal
Students are required to write a proposal, which must be approved before they
start the project. Sometimes students write as many as 4 proposals before an
adequate project is dened. Interestingly, the impetus for rewriting proposals
comes as often from the student wanting to get it right as it does from the instructor. The main task for the instructor is to help students to dene a project
that is challenging but still feasible taking into account the students interests
and knowledge. The project involves formulating and testing a hypothesis about
some property of the Hodgkin-Huxley model, preferably one that has physiological signicance. It is desirable, although not necessary, that students read papers
in the literature concerning their topic.
Students are given the following instructions:
The proposal should contain a brief statement of the hypothesis you
propose to test, as well as your proposed method of procedure. Include a list of the computations you will perform and the measurements you plan to make. Indicate how the measurements will be used
to help you come to a conclusion. The proposal should be written on
one 8 1/2 11 sheet of paper. A sample proposal is shown in Figure 8.5.
Demonstration project
We have found it helpful to give a one-hour lecture on how to do a research
project, by doing a project live in the lecture room. An acceptable proposal for
the project is distributed at the beginning of the lecture (such as the one in Figure 8.5). The lecture involves two members of the instructional sta who act as
a student pair working on a project. To make it run smoothly, the sta members rehearse briey. Simulations are performed in front of the class and the
two instructors argue about what is to be done next and on how to interpret the
results. They worry out loud about their grade on the project, etc. The project
is chosen so that results obtained in an initial range of parameters are plausible
and simple to interpret, but something unexpected happens when the parameter
is outside this range. One project that has been used successfully is based on
216

PROPOSAL: HODGKIN-HUXLEY MODEL PROJECT
Name: Hy I.Q. Student

Email address: hiqstudent
Hypothesis: The dierence in observed action potential shape between
the giant axon of the squid and the node of Ranvier of the rat is due to a
dierence in temperature.
Background: The rate constants that determine the variables m, n, and

h in the Hodgkin-Huxley model increase as the temperature is increased.
Hence, I would expect that with increased temperature the time course
of the action potential would be briefer. The observed action potential
of the rat node of Ranvier measured at 37 C. is briefer than the action
potential of the squid giant axon measured at 16 C. Hence, I will determine
whether this dierence in temperature is adequate to explain the dierence
in action-potential waveform. In this study, I will assume that the HodgkinHuxley model accounts for action potentials in both preparations. Since the
intracellular and extracellular ionic concentrations of sodium, potassium
and calcium also dier in these two preparations, if time permits I will also
investigate the eect of this dierence.
Procedure: I will obtain the intracellular and extracellular concentrations

of sodium and potassium ions for the rat node of Ranvier from the literature. I will perform a series of simulation studies with a single pulse of
membrane current whose amplitude will be set at a constant suprathreshold value. I propose the following series of simulations
#
Temp.
Ion Concentrations
16
37
16
37
The waveforms of the action potentials obtained under the various conditions will be compared on the graphics display and the summary statistics
for each condition will be examined. If condition 4 yields an action potential that resembles that which is measured on the rat node of Ranvier, then
the hypothesis will be supported by these calculations. If they dier, then
I will investigate the bases of the dierences.
Figure 8.5: Sample proposal for a project.
217
the hypothesis Increasing the temperature increases the rate of change of the
action potential at its onset. Simulations are performed rst for a range of temperature that support this hypothesis. Using the blackboard, one member of the
sta plots the maximum rate of change of the potential (obtained conveniently
by measuring the peak of the capacitance current) for each temperature after
each simulation is performed. However, at a suciently high temperature, the
action potential is blocked. The sta members argue about whether to ignore
this eect or to go on and to confront this unexpected nding. They consider the
possibility that they have found a bug in the software or that this phenomenon
results from problems of numerical integration. By performing further simulation experiments, it is made clear that these explanations are not plausible. The
instructors propose various circular arguments of the type students frequently
propose. The action potential is blocked because the sodium conductance is
small. Of course, the sodium conductance depends upon the membrane potential. Hence, the sodium conductance is small because the membrane potential
is small. Pursuit of this circular argument (on which some students get stuck
each year in their own projects) can have the class in hysterics. In any case, the
analysis of the basis of thermal block now becomes the focus of the project.
Simulation experiments performed for small changes in temperature below the
temperature at which the action potential is blocked, reveals the interplay of
kinetic processes that result in thermal block. Since these same processes are
involved in the excitation of the action potential, the analysis can give great
insight into the mechanism of initiation of an action potential (Weiss, 1996b,
Section 4.4.8).
The computations
Students are given the following instructions on how to perform the computations.
After carefully dening the computations needed to determine the
validity of your hypothesis, you should perform the necessary computations. You should keep careful track of the computations you
perform by entering relevant information in a notebook. The notebook should indicate the date of each computational session as well
as the identity of the computer you used (make and model). Keep
an accurate record of each computation so that you can reconstruct
what you did at a later date. Save your results in les. Make composite plots to summarize a series of measurements. For example, to
show the eect on the action potential of some parameter, plot the
action potentials for selected values of the parameter on one set of
axes. Arrange you work so that you have time for some nal computations after you begin writing the report. You may nd that new
questions will arise as you write the report. If you leave adequate
218

time, you may be able to resolve these questions.
The report
Many undergraduate students have never read a scientic paper and do not
know how to write a project report. Hence, we devised the following description of the report.
The Project Report is an opportunity for you to work on your ability
to express yourself concisely. Do not repeat material that is easily
referenced. For example, there is no need to reproduce any gure
from readily-available texts: simply refer to it. Technical writing is
necessarily directed at some particular intended audience. Write the
Project Report as though it were to be published in a journal that is
read primarily by students who have taken this subject. Thus, you
may assume that your audience has some working knowledge about
the subject matter, but no detailed knowledge of your specic project.
The Project Report should contain the following sections.
Cover Page. On the cover page include the title of the project and the
authors/authors names, and the date.
Abstract. The abstract is a one paragraph (< 100 words) summary
of the report including the hypothesis investigated, the methods
used, and the principal results and conclusions. This section
should be written last.
Introduction. This is a brief section (about 1 page) designed to motivate the reader to read your report. Include background information on the problem, hypotheses to be tested, signicance of
the work, etc. You may give citations to texts where appropriate. The introduction should be directly relevant to your report
and should not discuss neurophysiology or the brain in general
terms.
Methods. Explain any methodological or procedural issues that are
not obvious. For example, if you measured the time of the peak
of the action potential as a function of some parameter, explain
how you measured the time of the peak and how you dened
when an action potential occurred, i.e., how did you separate the
action potential from the local response.
Results. Describe your computational results (whether or not they t
with expectations) in the results section. Generally, results can
be communicated more eciently and accurately with pictures,
graphs, and tables than with words alone (e.g., see Figures 5.16,
5.18, 5.19, and 8.4). However, a collection of printed graphs
219
without a written description of their relevance is unacceptable

as a Results section. Students frequently err on the side of including a large number of graphs and little description of their
relevance. The Results section should be organized to lead the
reader through a logical sequence of results that terminates inexorably in a conclusion. Your objective is to construct an airtight
case for some conclusion whether or not it supports or rejects
your original hypothesis. This is not the place to interpret or to
discuss the results.
Discussion and conclusions. State your conclusions concisely and point
out how your results support your conclusions. You might also
suggest additional computations to further test your hypothesis.
Your conclusions and discussion should be focussed on the relation between your results and your hypothesis. The discussion
section can include relevant speculations.
Appendix. The appendix should include a copy of the protocol taken
during the computational sessions.
Grade for the project

Grading of the project reports has evolved since its inception in 1984. After
using these project for a few years, we noted that many, but still less than a
majority, of the projects focussed on a relatively small number of topics. The
quality of these reports also improved markedly with time. We felt that the
graded reports from previous years were available through student archives. To
encourage students to choose new topics and to reward originality we added
an assessment for originality. In addition, we found that a hard deadline for
accepting reports was hard to enforce so we made the deadline somewhat soft
assessing a numerical penalty for lateness by a formula that the students knew
ahead of time. The following grading scheme has emerged by trial and error and
is satisfactory.
The grade will not depend on whether the project was an individual
or a team project. Both members of the team will get the same grade
on the project. The grade for the computer project will be based on
the proposal and on the report using the following criteria:
Proposal (10%) The proposal should be concise and clearly dene the
project in the form of a hypothesis. It should include a brief
description of the methods to be employed. A late proposal will
get a grade of 0.
Report Structure (15%) All the sections of the report should be present
and each should contain the relevant information.
220

Clarity/Conciseness (20%) A good report is easy to read. The content of each paragraph and each graph should be clear. Everything included in the report should be there for a reason. Points
will be deducted for extraneous material such as a large number
of graphs without explanation in the text.
Conceptual Correctness (30%) Correctness will be judged by the answers to several questions. Are there clear conceptual errors?
Are the results confused? Are the results (i.e. which follow directly from the simulations) confused with the interpretations
(which rely on information other than the simulations)?
Originality (25%) This grade will assess the degree of diculty, novelty, and imagination of the project. The simpler projects, such
as many of those suggested in Section 5.6 and used by many
students in the past, will receive 10%, more intellectually challenging, novel projects will receive 25%.
Reports that are not turned in on time will be penalized by the following formula the grade of the report will be multiplied by a lateness
factor L, where L = 0.3et/4 + 0.7et/72 and t is the number of hours
late.
Electronic interactions
Students are invited to interact with the teaching sta via electronic mail. This
has been an increasingly eective means of teaching and learning. For example,
some students prefer to submit proposals for projects electronically. The sta
responds to these electronically, sometimes within minutes but certainly by the
next morning. The rapid turnaround time between submission, critique, and resubmission can make writing an acceptable proposal, which some students nd
challenging, more ecient. Students use electronic messages to seek help on
independent projects as they are conducting them. They send queries electronically and receive responses electronically. This type of interaction, in which
the individuals involved may be located at opposite ends of the campus, is an
eective way to achieve individualized instruction.
8.3
8.3.1
Assessment
Cost of development
We estimate that it has taken about 5 person-years to develop the software.

Although harder to estimate, it has taken perhaps an additional person year of
faculty time to design software packages, thoroughly test each software package,
8.3. ASSESSMENT
221
design problems and projects, write documentation, and to investigate pedagogical methods.
8.3.2
Extent of software usage
Our use of the software in teaching has increased over the years. Our current
usage is summarized as follows: There are 37 lectures (classes attended by all
the students simultaneously) in the subject and the software is used in about
8-10 lectures. There are 24 recitations (classes attended by students in groups
of about 25) and the software has not been used in any of these; in part due
to the lack of availability of appropriate classrooms with network connections
in the past. This has now been rectied and we expect in the future to use the
software routinely in recitation classes. Several recitations devoted to using the
software are held in electronic classrooms. Typically, there are 13 problem sets
assigned during a semester; ve or six problem sets include parts that involve
the software. There is one laboratory session, which requires a formal laboratory
report but does not involve the software. There is one project that involves the
software which requires a formal report. There are about 9 short quizzes and
two long examinations; none use the software.
This assessment shows that use of the software represents a small but appreciable fraction of the teaching and learning in this subject. Since we have found
that use of the software is labor intensive both for the sta and the students, we
have been reluctant to increase the use of the software.
8.3.3
Informal assessment of impact on learning
We have not conducted a careful experiment with controlled groups to test objectively the eectiveness of the software in promoting students comprehension of the material. Subjectively, it was clear at the outset that the students
enjoyed using the software and that the sta felt that use of the software was
pedagogically eective. Thus, it did not seem fair to exclude some students
from the software for the sake of conducting a scientic experiment. Surveys of
student opinions on the ecacy of the software have been predominantly very
positive with opinions ranging from those who thought we should develop software packages for every topic in the subject to a few who found the software
confusing. Each year, several students make valuable suggestions on software
improvements or on methods for software use. These student inputs have been
important for the evolution of the software. This subject matter was taught for
20 years before the software became available and for 15 years after it became
available. The sta has little doubt that students learn the material more eciently and to a greater depth with the use of the software than they had before
the software became available.
222
There are other signs of student interest in the software. Students clearly
enjoy working on the software, especially on their own projects, despite the
great eort that is required. The impressions of the sta are that while most
students get some benet from using the software, the very best students have
an experience that most resembles a small research project. This can be seen
in the reports students write to complete their projects. Some of these reports
resemble undergraduate theses in scope and in content. Another indication of
student interest is that several students have written software on their personal
computers to emulate some of the software we have provided. This was done
just for their own interest. There is a nal and most important indication of
student interest. As a result of using the software in this subject, students
have been interested to work on the development of educational software. Since
1984, nine undergraduate and three graduate students have been involved in
this eort. They have written all the software packages.
8.3.4
Surveys and focus groups
Since 1984, surveys of students who have used the software have been conducted routinely. Sometimes these surveys were done at the end of the semester
and sometimes immediately after students completed an assignment that involved the software. Surveys were done by having students ll out forms as well
as via email. In recent years, an independent evaluator conducted the surveys
and ran focus groups. The feedback we have received has been valuable and
has helped us focus on problems students were having with the software. In
general, assessments of student have been very positive. Most students nd the
software pedagogically eective and some nd the software critical to understanding complex topics such as the Hodgkin-Huxley model. Students felt they
received the most educational benet from those software packages with which
they spent the most time. In particular, the projects were universally praised as
educationally eective.
8.3.5
Impact on teaching
It has often been assumed that one benet of the use of computers in teaching
is to conserve faculty time, and that a cost was isolation of students from each
other and from the faculty. In our experience, neither the presumed benet
nor the cost have materialized. Our use of computers in teaching has increased
contact between students and faculty and among students. The main benet has
been more eective teaching and learning. The main cost has been an increased
work load for both students and faculty.
8.4. CONCLUSIONS
8.4
223
Conclusions
We have used computers to teach biophysics and physiology since 1984. Our use
has been exclusively to develop software that simulates some physical, chemical, and biological process that is reasonably well understood. We have invented
no new models, but we have explored extant models that underlie our understanding of transport and electrical processes in cells. In teaching this material,
we have learned some lessons both pedagogical and practical which are
summarized below.
8.4.1
Pedagogical matters
Development of educational software must be driven by pedagogy

We have evolved a simple strategy for educational software development. We
identify important topics in biophysics and physiology that pose some conceptual diculties for students and examine whether comprehension could be improved by the use of computational methods. Once we identify such topics, we
design and then implement the software.
Software complements other pedagogical vehicles
Software cannot replace a good lecturer or an incisive derivation in a lucid textbook. A simulated experiment cannot replace a real laboratory experience. However, software represents an additional pedagogic vehicle that can, if appropriately used, complement other vehicles.
Students should have access to the software
While lecture demonstrations can be pedagogically eective, the potential for
learning is greatly enhanced when students use the software themselves. The
educational benets of student usage of the software as opposed to exposure to
it in lecture are similar to the benets derived when students solve problems in
homework as opposed to watching a problem solved in class.
The software must be integrated into the subject
The software should be an integral part of lectures, recitations and homework
and used only where it enhances learning and never used simply because it is
available and because the sta has invested a great eort in its production. Software homework and projects must be assigned and graded with the grade contributing to the students grade in the subject. If the grades on software assignments do not count toward the students nal grade in the subject, the student
224
will correctly conclude that the software is secondary in importance to those

assignments that do count toward the nal grade.
The software should have layers of complexity
Students approach the software with dierent levels of sophistication in their
understanding of the subject matter. It is essential to devise the software so
that all students can receive some educational benet. This requires that the
software be simple to use at the outset but contain sucient depth to challenge
the more sophisticated students and even the sta.
8.4.2
Practical matters
Even slightly awed software should be avoided

The software must aid students to learn the material and should not impede
that objective. Software with aws, even minor aws, is a distraction. Students
will remember even a minor aw in the software and will forget the point of the
demonstration. Undergraduate students, in particular, will lose condence in an
assignment that involves software with even inconsequential aws. Since they
are quite busy, it is easy to rationalize avoiding a dicult assignment by reporting that the software doesnt work even if the aws should not distract them
from the main point of the assignment. The more mature graduate students
seem more tolerant of minor aws and are willing to endure them to derive educational benet. But bugs, no matter how minor, should be avoided so that
students can concentrate fully on the didactic material.
Expect some complications
A computer in the classroom increases the range of pedagogical tools available
to the instructor. But it also complicates the instructors task. If the instructor
is prepared and competent and both a blackboard and chalk are available, not
much can go wrong with a lecture. With a computer in the classroom, things can
go wrong although the number of episodes has actually been extremely low. It
is necessary to be prepared for the possibility of a computer problem so that
valuable class time is not lost. The availability of overhead transparencies that
cover the relevant material that would have been covered with the computer is a
good backup strategy.
Design of the user interface is critical
Most of our time spent in software development is devoted to the design of user
interfaces that allow students to focus on the subject material and avoid arcane
computerese. A great deal of the students time can be conserved if the user
8.4. CONCLUSIONS
225
interface is graphic, intuitive, and common to all the software. The user interface
cannot be too transparent!
Good documentation is important
We have placed a great deal of emphasis on writing comprehensive documentation for all the software. The documentation gives some background information on the subject matter and contains a detailed users manual for the software
plus a list of suggested problems and projects. Remarkably, some students learn
to use the software by reading the manual; others experiment with the software.
There are dierent learning styles for using software. To reach a maximum
number of students, a variety of modalities are helpful.
Development of good educational software is time-consuming and iterative
All our successful packages have been rewritten many times in response to sta
and student input. There is no shortcut to the development of good educational
software.
Use of educational software increases contact with students
Early advocates of the use of computers in teaching suggested that one benet
was a saving in faculty time. Eective use of computers could replace faculty
in certain tasks. Some educational theorists worried about the isolation of student from faculty resulting from this use of computers. Our experience with
our method of use of computers has given the opposite result. It has greatly increased contact with students to the mutual advantage of students and faculty;
the interactions have been very rewarding.
Maintenance of software
Changes in operating systems or in higher level languages on which the software is based will continue to require some maintenance. In addition, student
suggestions can help to improve the software if the resources for maintenance
are available.
Projection systems
Projection systems for use of computers in the classroom have until quite recently been only marginally adequate. However, the technology is improving
rapidly and the cost is decreasing rapidly as well. However, this is not a place
to skimp. An inadequate display system, where the students cannot really see
what is being depicted, defeats all the eort required to develop the software.
226
8.4.3
Bottom line
Our experience indicates that the development, usage, and maintenance of a successful educational software package is a dicult and time-consuming process
several iterations have been required to bring our most successful packages to
their current level of performance. However, we have also found that computers
are a powerful vehicle for teaching. They can be used to: engage the students
intellect, to motivate learning, to allow students to test their understanding of
a topic, to make learning self-paced and fun. With the aid of software, students
take intellectual ownership of a topic rather than experiencing it vicariously.
Once eective software has been used in teaching and learning, it becomes an
indispensable tool.
Bibliography
Aidley, D. J. (1989). The Physiology of Excitable Cells. Cambridge University
Armstrong, C. M. (1966). Time course of TEA+ -induced anomalous rectication
in squid giant axons. J. Gen. Physiol., 50:491503.
Armstrong, C. M. and Binstock, L. (1965). Anomalous rectication in the squid
giant axon injected with tetraethylammonium chloride. J. Gen. Physiol., 48:859
872.
Athena (1990a). Computation and Educational Community: A Background Paper. Committee on Academic Computation for the 1990s and Beyond, Massachusetts Institute of Technology.
Athena (1990b). Computing for Education at MIT: Final Report. Committee on
Academic Computation for the 1990s and Beyond, Massachusetts Institute of
Technology.
Baker, P. F., Hodgkin, A. L., and Shaw, T. I. (1961). Replacement of the protoplasm of a giant nerve bre with articial solutions. Nature, 190:885887.
Balestri, D. (1988). Ivory towers, silicon basements. Infor. Tech. Quaterly, 7:5
17.
Berkenblit, S. I. (1990). Design of a software diusion simulator and analysis
of a problem in two-compartment diusion. Masters thesis, Massachusetts
Institute of Technology, Cambridge, MA.
Carruthers, A. (1984). Sugar transport in animal cells: The passive hexose transfer system. Prog. Biophys. Mol. Biol., 43:3369.
Chapman, R. A. (1967). Dependence on temperature of the conduction velocity
of the action potential of the squid giant axon. J. Physiol., 213:11431144.
Colquhoun, D. and Hawkes, A. G. (1977). Relaxation and uctuations of membrane currents that ow through drug-operated channels. Proc. R. Soc. London,
Ser. B, 199:231262.
227
228
BIBLIOGRAPHY
Colquhoun, D. and Hawkes, A. G. (1995a). The principles of the stochastic interpretation of ion-channel mechanisms. In Sakmann, B. and Neher, E., editors,
Single-Channel Recording, pages 397482. Plenum Press, New York, NY.
Colquhoun, D. and Hawkes, A. G. (1995b). A Q-matrix cookbook. How to write
only one program to calculate the single-channel and macroscopic predictions
for any kinetic mechanism. In Sakmann, B. and Neher, E., editors, SingleChannel Recording, pages 589633. Plenum Press, New York, NY.
Cooley, J. W. and Dodge, F. A. (1966). Digital computer solutions for excitation
and propagation of the nerve impulse. Biophys. J., 6:583599.
Cox, D. R. and Miller, H. D. (1965). The Theory of Stochastic Processes. John
Wiley and Sons, New York, NY.
Easton, D. M. and Swenberg, C. E. (1975). Temperature and impulse velocity in
giant axon of squid loligo pealei. Am. J. Physiol., 229:12491253.
Einstein, A. (1906). Sur theorie der brownschen bewegung. Ann. Physik, 19:371
381. [For translation see Einstein (1956)].
Einstein, A. (1956). Investigations on the Theory of the Brownian Movement.
Dover Publications. R. Furthe and A. D. Cowper, eds. [Translation of original
publications].
Fick, A. (1855). On liquid diusion. Philos. Mag., 10:3039.
Fitzhugh, R. and Antosiewicz, H. A. (1959). Automatic computation of nerve
excitation detailed corrections and additions. J. Soc. Indust. Appl. Math.,
7:447458.
Frankenhaeuser, B. and Hodgkin, A. L. (1957). The action of calcium on the
electrical properties of squid axons. J. Physiol., 137:218244.
George, S. A., Mastronarde, D. N., and Dubin, M. W. (1984). Prior activity inuences the velocity of impulses in frog and cat optic nerve bers. Brain Res,
304:121126.
Gerald, C. F. and Wheatley, P. O. (1989). Applied Numerical Analysis. AddisonWesley, Reading, MA.
Hanselman and Littleeld (1997). Mastering MATLAB 5: A Comprehensive Tutorial and Reference. Prentice-Hall, Englewood Hills, NJ.
Hille, B. (1992). Ionic Channels of Excitable Membranes. Sinauer Associates Inc.,
Sunderland, MA.
BIBLIOGRAPHY
229
Hines, M. (1984). Ecient computation of branched nerve equations. Int. J.

Bio-Med. Comput., 15:6976.
Hines, M. and Carnevale, N. T. (1998). Computer modeling mehtods for neurons.
In Arbib, M. A., editor, The Handbook of Brain Theory and Neural Networks,
pages 226230. MIT Press, Cambridge, MA.
Hodgkin, A. L. (1964). The Conduction of the Nervous Impulse. Charles C.
Thomas, Springeld, IL.
Hodgkin, A. L. (1977). Chance and design in electrophysiology: An informal
account of certain experiments on nerve carried out between 1934 and 1952.
In The Pursuit of Nature, pages 121. Cambridge University Press, Cambridge,
England.
Hodgkin, A. L. and Huxley, A. F. (1952). A quantitative description of membrane
current and its application to conduction and excitation in nerve. J. Physiol.,
117:500544.
Hodgkin, A. L. and Katz, B. (1949a). The eect of sodium ions on the electrical
Hodgkin, A. L. and Katz, B. (1949b). The eect of temperature on the electrical
Huxley, A. F. (1959). Ion movements during nerve activity. Ann. N.Y. Acad. Sci.,
81:221246.
Huxley, A. F. (1964). Excitation and conduction in nerve: Quantitative analysis.
Sci., 145:11541159.
Johnston, D. and Wu, S. M. S. (1995). Foundations of Cellular Neurophysiology.
MIT Press, Cambridge, MA.
Joyner, R. W., Westereld, M., Moore, J. W., and Stockbridge, N. (1978). A numerical method to model excitable cells. Biophys. J., 22:155170.
Kandel, E. R., Schwartz, J. H., and Jessell, T. M. (1991). Principles of Neural
Science. Elsevier, New York, NY.
Katz, B. (1966). Nerve, Muscle and Synapse. McGraw-Hill Inc., New York, NY.
Keynes, R. D. and Aidley, D. J. (1991). Nerve and Muscle. Cambridge University
Kulik, C. C. and Kulik, J. A. (1986). Eectiveness of computer-based education
in colleges. AEDS J., pages 81108.
230
BIBLIOGRAPHY
Mascagni, M. V. and Sherman, A. S. (1998). Numerical methods and neuronal

modeling. In Koch, C. and Segev, I., editors, Methods in Neuronal Modeling,
pages 569606. MIT Press, Cambridge, MA.
Mazur, E. (1997). Peer Instruction: A Users Manual. Prentice Hall, Upper Saddle
River, NJ.
Moore, J. W., Ramon, F., and Joyner, R. W. (1975). Axon voltage-clamp simulations. Biophys. J., pages 1124.
Neher, E. and Sakmann, B. (1976). Single-channel currents recorded from membrane of denervated frog muscle bres. Nature, 260:799802.
Nicholls, J. G., Martin, A. R., and Wallace, B. G. (1992). From Neuron to Brain: A
Cellular and Molecular Approach to the Function of the Nervous System. Sinauer
Associates, Sunderland, MA.
Pearlmutter, B. A. and Zador, A. (1999). Sparse matrix methods for modeling
single neurons. In Koch, C., editor, Biophysics of Computation, pages 487502.
Oxford Univ. Press, New York, NY.
Plonsey, R. and Barr, R. C. (1988).
Plenum Press, New York, NY.
Bioelectricity, A Quantitative Approach.
Press, W. H., Flannery, B. P., Teukolsky, S. A., and Vetterling, W. T. (1986). Numerical Recipes. The Art of Scientic Computing. Cambridge University Press,
Cambridge, Great Britain.
Press, W. H., Flannery, B. P., Teukolsky, S. A., and Vetterling, W. T. (1988). Numerical Recipes in C. The Art of Scientic Computing. Cambridge University
Press, Cambridge, Massachusetts.
Shah, D. M. (1990). Computer simulation of the random walk model of diusion.
Bachelors thesis, Massachusetts Institute of Technology, Cambridge, MA.
Shampine, L. F. and Reichelt, M. W. (1997). The MATLAB ODE suite. SIAM J. Sci.
Comput., 18:122.
Smith, G. D. (1985). Numerical Solution of Partial Dierential Equations: Finite
Dierence Methods. Clarendon Press, Oxford, Great Britain.
Stein, W. D. (1986). Transport and Diusion Across Cell Membranes. Academic
Tasaki, I. and Hagiwara, S. (1957). Demonstration of two stable potential states
in the squid giant axon under tetraethylammonium chloride. J. Gen. Physiol.,
40:859885.
BIBLIOGRAPHY
231
Weiss, T. F. (1996a). Cellular Biophysics. Volume 1: Transport. MIT Press, Cambridge, MA.
Weiss, T. F. (1996b). Cellular Biophysics. Volume 2: Electrical Properties. MIT
Press, Cambridge, MA.
Weiss, T. F., Trevisan, G., Doering, E. B., Shah, D. M., Huang, D., and Berkenblit,
S. I. (1992). Software for teaching physiology and biophysics. J. Sci. Ed. Tech.,
1:259274.
Wilson, J. M. and Redish, E. F. (1989). Using computers in teaching physics.
Physics Today, pages 3441.
Index
Absolute reaction rate, 177
Absolute temperature, 90, 131
Accommodation, 114
Action potentials
eect of sodium concentration, 120
eect of temperature, 120
electrically excitable cells, 88, 126
examples, 119
Activation factor, 91
All-or-none principal, 113
Analytic solutions, 37, 40, 48
Anode, 129
Anode-break excitation, 114
Backward Euler approximation, 93, 132,
134136, 171
Binding reaction, 6163, 66, 67, 86
Boundary conditions, 135, 137, 139
Hodgkin-Huxley model, 133, 169
random walk model, 13, 1617,
21
reecting, 37, 40, 48, 54, 56
transparent, 37, 40, 48, 54
Cable properties, 164
Capacitance current density, 89, 130,
166
Carrier-mediated transport
axis scale, 77
binding reaction, 6163, 66, 67,
86
carrier density, 61
chemical reaction, 60
CMT Control gure, 69, 70, 70
CMT Parameters gure, 69, 71, 71
73, 7374
232
CMT Setup steady state plot gure, 76

CMT Setup transient plot gure,
80
CMT State gure, 69, 71, 7173,
7475
CMT Steady state plot gure, 76
CMT Transient plot gure, 79
CMT Transients numerics gure,
80
CMT Units gure, 70
comparison of simple and general
carriers, 84
competitive inhibition, 63
dissociation constant, 62, 63
eigenvalues, 67, 69, 80, 85, 86
exchange diusion, 83
le handling, 73, 75, 78
ux, 61, 63, 65, 68
ux arrows, 75
general, four-state carrier, 6668,
71
schematic diagram, 66
steady-state equations, 68
transient equations, 67
transient response, 85, 86
intereactive steady-state analysis,
71
kinetic equations, 61, 63, 66
matrix dierential equation, 67
matrix equation, 62, 64, 68
modiable parameters, 74
Modify line properties gure, 78
numerical solutions, 69
overview, 2
parameter values, 69
INDEX
principle of detailed balance, 74
problems, 8186
properties, 60
simple, four-state carrier, 6163,
71, 8184
eect of asymmetry, 81, 82
ux vs. concentration, 83
simple, six-state carrier, 6365, 71
dependence of ux on concentrations, 84
dependence of ux on parameters, 85
users guide, 6981
Cathode, 129
Cell radius, 128
Centered dierence, 132
Chemical reaction, 35, 3840, 44, 60
CMT, see Carrier-mediated transport
Collision of action potentials, 168
Competitive binding, 63
Complementary error function, 39
Concentration, 11, 34, 90, 131
Conductance, 175, 178
Conduction velocity, 163, 170, 171
Continuity relation, 12, 34
Control gure
CMT, 69
HH, 94
IC, 180
MD, 41
PAP, 140
RW, 18
Core conductor equations, 126
Core conductor model, 127128
Crank-Nicolson algorithm, 40, 136
138, 171
Current clamp, 89, 95, 112
Current per unit length, 128
Cytoplasm resistivity, 128
233
Darcys law, 11
Depolarization block, 114
Diusion, see Random walk model of
diusion, see Macroscopic diffusion processes
concentration, 11, 34
continuity, 34
equilibration time, 5758
equilibrium, 30, 54
equilibrium time constant, 55
Ficks rst law, 11, 34
ux, 11, 34
macroscopic laws, 11, 12
microscopic laws, 12
steady state distribution, 26, 55
steady state time constant, 55
two compartments, 28, 30, 37, 54
56
Diusion coecient, 11, 13, 34, 44,
53
Diusion equation, 34
Diusion in a well, 57
Dirac delta function, see Unit impulse
function
Directional probabilities, 15
Discretization, 131, 132
Dissociation constant, 62, 63
Drift velocity, 34, 38, 39, 44, 54
EDUCOM/NCRIPTAL, iv, v
Eigenvalues, 67, 69, 80, 85, 86, 177,
188, 201
Electrically excitable cells, 88, 126
Equilibration time, 5758
Equilibrium, 54, 213
Equilibrium potential, 175, 181, 196,
197
Equilibrium time constant, 55, 209
Exchange diusion, 83
Expected value, 174, 177, 178, 188,
190, 192, 198, 199
Explicit method, 133
External potential, 128, 130
External resistance, 128
234
Extracellular potential, 165
Faradays constant, 90, 131
Ficks rst law, 11, 34, 208
File handling, 7, 18, 20, 41, 42, 44,
73, 75, 78, 95, 97, 102, 104,
107, 142, 147, 150, 152, 180,
181, 184, 185, 187, 193
Finite dierences, 40
Finite-dierence method, 131
Finite-element method, 131
Flux
carrier mediated, 61, 63, 65, 68
diusive, 11, 34
Forward Euler approximation, 93, 132
134, 171
Fouriers law, 11
Gating charge, 174, 175, 177, 178,
182, 188, 199
Gating current, 174, 175, 178, 188,
199, 200
Gating variable, 174
Gaussian function, 38
General, four-state carrier, see Carriermediated transport
Giant axon of the squid, 88, 126
Greens function, 38, 39
HH, see Hodgkin-Huxley model space
clamped
Histogram, 23
Hodgkin-Huxley model
accommodation, 114
activation factor, 91
all-or-none principal, 113
anode-break excitation, 114
cable properties, 164
calcium concentration, 115
capacitance current density, 89,
130, 166
collision of action potentials, 168
conduction velocity, 163, 170, 171
conguration
INDEX
current clamp, 89, 94, 95
relation of voltage to current clamp,
112
space clamp, 89
voltage clamp, 89, 94, 95, 111
112
default parameters, 92, 131
depolarization block, 114
eect of calcium concentration, 91
equilibrium values, 92
extracellular potential, 165
inactivation factor, 91
ion concentrations, 90
ionic current density, 89, 130
kinetic equations, 91
leakage current density, 90
local response, 167
longitudinal current, 166
measurement method, 112113
membrane capacitance, 90, 115,
130
membrane current density, 89, 130,
166
membrane potential, 90, 128, 165
Nernst equilibrium potential, 90,
131
polarity of excitatory current, 167
potassium conductance, 90, 115
potassium current density, 90
rate constants, 91
refractory period, 113
repetitive activity, 114
sodium conductance, 90
sodium current density, 90
space and time waveforms, 165
space clamp, 164
space constant, 169
step response, 164
strength-duration relation, 115
sub-threshold oscillations, 114, 169
temperature, 90, 91, 95, 107, 113,
115117, 119, 121, 123, 147,
170, 171
INDEX
temperature factor, 91
threshold, 115, 122, 123, 210
time constants, 92
valence, 90
voltage dependent parameters, 91,
97101, 147148
Hodgkin-Huxley model propagated
action potential
backward Euler approximation, 132,
134136, 171
boundary conditions, 169
capacitance current density, 166
cell radius, 128
color-coded space-time evolution,
144
conduction velocity, 163, 170, 171
core conductor equations, 126128
Crank-Nicolson algorithm, 136138,
171
current per unit length, 128
derived parameters, 147
external potential, 128, 130
external resistance, 128
extracellular potential, 165
le handling, 142, 147, 150, 152
forward Euler approximation, 132
134, 171
history, 126
internal potential, 128, 130
internal resistance, 128
longitudinal current, 128, 129, 166
membrane current density, 166
membrane potential, 165
numerical solution, 131140
overview, 3, 126127
PAP 3D Plots gure, 155156
PAP Comparison Plots gure, 156
162
PAP Control gure, 140142
PAP Numerics gure, 141, 150
152
PAP Parameters gure, 144
235
PAP parameters vs. potential gure, 147148
PAP Space-Time evolution gure,
153155
PAP Stimulus gure, 149150
PAP Variable summary gure, 153
PAP Voltage recorder gure, 152
PAP Workspace gure, 140, 142
144
positioning electrodes, 143
problems, 163170
projects, 170171
resistivity of cytoplasm, 128
restrictions on parameters, 147
space constant, 169
spatial resolution, 132, 144, 151
specifying numerics, 151
staggered increment Crank-Nicolson
algorithm, 138140, 171
stimulating electrodes, 128129
sub-threshold oscillations, 169
temperature, 171
temporal resolution, 132, 151
users guide, 140163
Hodgkin-Huxley model space clamped
accommodation, 114
action potential waveform, 113
anode-break excitation, 114
axis scale, 100, 105
calcium concentration, 115
default parameters, 95
depolarization block, 114
derived parameters, 95
le handling, 95, 97, 102, 104,
107
HH Axis gure, 100
HH Control gure, 9495
HH Graphics gure, 106107
HH Numerics gure, 95
HH Parameters gure, 9495
HH Parameters vs. potential gure, 97101
HH Plots vs. time gure, 104105
236
HH Stimulus gure, 94, 101102
HH Variable summary gure, 105
106
membrane capacitance, 115
model description, 8992
numerical solution, 9394
overview, 3, 88
potassium conductance, 115
problems, 111117
projects, 118124
refractory period, 113
repetitive activity, 114
scripts, 107111
software history, iii
strength-duration relation, 115
sub-threshold oscillations, 114
temperature, 115117
threshold, 113115
users guide, 94107
IC, see Voltage-gated ion channels
Implicit method, 135
Inactivation factor, 91
Inactivation gates, 203
Initial conditions, 133, 135, 137, 139
Integration time, 48, 93, 178, 187, 188
Internal potential, 128, 130
Internal resistance, 128
Ion concentration, 90, 131
Ionic conductance, 174, 181, 188, 193,
198, 199
Ionic current, 174, 175, 178, 188, 190,
198, 199
Ionic current density, 89, 130
Kinetic equations, 61, 63, 66, 91
Kirchhos laws, 127, 128, 133
Leakage current density, 90
Longitudinal current, 128, 129, 166
Macroscopic diuision processes
steady state, 213
Macroscopic diusion processes
INDEX
axis scale, 43, 51
bath view, 51
boundary conditions
reecting, 37, 40, 48, 54, 56
transparent, 37, 40, 48, 54
chemical reaction, 35, 3840, 44
concentration, 34
continuity relation, 34
diusion coecient, 34, 53
diusion equation, 34, 44
diusion parameters, 44
drift velocity, 34, 38, 39, 44, 54
equilibration time, 5758
equilibrium, 54
equilibrium time constant, 55, 209
Ficks rst law, 11, 34, 208
le handling, 41, 42, 44
ux, 34
Greens function, 38, 39
initial distribution
arbitrary, 36, 46, 5152
discontinuity, 36, 39, 4546
impulse, 3638, 44, 5354
sinusoid, 36, 3839, 4445, 53,
5657
markers, 42, 51
MD Analytic parameters gure, 48
MD Control gure, 4142
MD Initial concentration prole,
4142
MD Numeric parameters gure, 48
MD Parameters gure, 44
MD Plots vs. position gure, 41,
48
MD Plots vs. time gure, 41, 51
membrane view, 51
method of images, 56
modied diusion equation, 35
numerical solutions, 40, 48
analyic parameters, 48
numeric parameters, 48
overview, 2, 3537
problems, 5358
INDEX
reaction rate, 35
spatial resolution, 40, 48
steady state distribution, 55
steady state time constant, 55, 209
two compartments, 37, 48, 51, 54
56, 209210
users guide, 4152
Markov process, 175
MATLAB, iv, v, 35
Matrix dierential equation, 67, 176
Matrix equation, 62, 64, 68
MD, see Macroscopic diusion processes
Mean, 23
Membrane capacitance, 90, 115, 130
Membrane current density, 89, 130,
166
Membrane potential, 90, 128, 175, 177,
182, 185, 186, 201
Method of images, 56
Modied diusion equation, 35
Molar gas constant, 90, 131
Multiple-state gates, 202
National Science Foundation, vi
Nernst equilibrium potential, 90, 131
Numerical solutions, 37, 40, 48, 69,
9394, 131140, 178179, 187
188
Ohms law, 11
PAP, see Hodgkin-Huxley model propagated action potential
Particle lifetime, 15
Pedagogy
audience participation, 210
extent of software usage, 221
impact on learning, 221
impact on teaching, 222
intellectual engagement, 208
intuition, 206, 210
lessons learned, 223226
237
motivation, 210
research project, 212
surveys, 222
visualization, 206
what-if experiments, 210
Plotting
annotate, 77, 100, 161, 185
axis scale, 24, 43, 51, 77, 100,
105, 186
cross-line, 78, 100, 101, 161, 186
customized plots, 111
legend, 77
line properties, 78, 101, 186
overlay, 75, 97, 107
specic software
CMT, 7581
HH, 97101, 104107
IC, 184186, 188193
MD, 4851
PAP, 147148
RW, 2326
zoom, 77, 100, 186
zooom, 161
Potassium conductance, 90
Potassium current density, 90
Principle of detailed balance, 74
Project Athena, iiiv
Projects, 118124, 170171, 214220
demonstration, 215217
electronic interactions, 220
grade, 219220
hypotheses, 118, 121123, 170
171
proposals, 215
report, 218219
teams, 214
Random variable, 174, 179, 188, 190,
198, 203
Random walk model of diusion
axis scale, 24
boundary conditions, 1617, 21
diusive spread, 208
directional probabilities, 15, 21
238
equilibrium, 30
Ficks rst law, 208
eld, 13
le handling, 18, 20
grid, 13
initial distribution, 20
overview, 2, 1213
particle lifetime, 15, 22, 28
problems, 2631
region, 13
region size, 14, 20
RW Control gure, 18
RW Graph gure, 2526
RW Histogram gure, 2324
RW Parameters gure, 2022
RW Particle gure, 18
RW Summary gure, 2223
sink, 22
sinusoidal, 30
source, 2122
statistics, 25
steady state, 208
steady state distribution, 26
step size, 14, 20
three regions, 28, 30
unbiased random walk, 16
users guide, 1826
Rate constants, 91
Rate-limiting processes, 210
Refractory period, 113
Repetitive activity, 114
Resistivity of cytoplasm, 128
RW, see Random walk model of diffusion
Scripts, 107111
Simple, four-state carrier, see Carriermediated transport
Simple, six-state carrier, see Carriermediated transport
Sodium conductance, 90
Sodium current density, 90
Software
directories, 5
INDEX
le handling, 7
printing, 7
startup, 67
Software history, iii
Software overview
Carrier-mediated transport, 2
Hodgkin-Huxley model propagated action potential, 3, 126
127
Hodgkin-Huxley model space
clamped, 3, 88
Macroscopic diusion processes,
2, 3537
Random walk model of diusion,
2, 1213
Voltage-gated ion channels, 3, 174
Software usage
electronic classroom, 212214
lectures, iii, 206212
problems, 2631, 5358, 8186,
111117, 163170, 196203,
212
projects, iii, 118124, 170171, 214
220
Space clamp, 89, 164
Space constant, 169
Spatial frequency, 44
Spatial radian frequency, 39
Spatial resolution, 40, 48, 132, 144,
151
Staggered increment Crank-Nicolson
algorithm, 138140, 171
Standard deviation, 23, 38
State, 174, 175, 181
Steady state, 26, 55, 208, 213
Steady state time constant, 55, 209
Sub-threshold oscillations, 114, 169
Temperature, 90, 91, 95, 107, 113,
115117, 119, 121, 123, 147,
170, 171
Temperature factor, 91
Temporal resolution, 40, 48, 93, 104,
132, 151, 178, 187
INDEX
Thin membrane approximation, 55,
209
Three-state gates, 202
Threshold, 113115, 122, 123, 210
Trapezoidal rule, 137
Two-state gates, 196201
Unit impulse function, 37, 44, 129
Unit step function, 46, 129
Users guide
carrier-mediated transport, 6981
Hodgkin-Huxley model propagated action potential, 140
163
Hodgkin-Huxley model space
clamped, 94107
macroscopic diusion processes,
4152
random walk model of diusion,
1826
voltage-gated ion channels, 180
193
Valence, 90, 131
Voltage clamp, 89, 95, 111112
Voltage-gated ion channels
absolute reaction rate, 177
axis scale, 186
conductance, 178
eigenvalues, 177, 188, 199, 201
equilibrium potential, 175, 181,
196, 197
equilibrium state occupancy probability, 176
expected value, 174, 177, 178, 188,
190, 192, 198, 199
le handling, 180, 181, 184, 185,
187, 193
gating charge, 174, 177, 178, 182,
188, 199
gating current, 174, 175, 178, 188,
199
gating variable, 174
IC Control gure, 180181
239
IC Graphics gure, 192
IC Ionic current gure, 190
IC Membrane potential gure, 187,
188
IC Parameters gure, 180182
IC Specify rate constants gure,
182
IC State occupancy gure, 189
IC Summary gure, 191
IC View rate constants gure, 184
186
inactivation gates, 203
initial conditions, 179180
initial state, 188, 198
integration time, 178, 188
ionic conductance, 174, 181, 188,
193, 198, 199
ionic current, 174, 175, 178, 188,
198, 199
line properties, 186
Markov process, 175
matrix dierential equation, 176
membrane potential, 175, 177, 182,
185, 186, 201
model description, 175178
multiple-state gates, 202
numerical solutions, 178179, 187
188
overview, 3, 174
problems, 196203
random variable, 174, 179, 188,
190, 198, 203
state, 174, 175, 181
state conductance, 175
state gating charge, 175
state ionic current, 175
state occupancy probability, 175
three-state gates, 202
transition probability, 175
two-state gates, 196201
activation and inactivation gate,
197
240
eect of scaling rates, 198
gating charge, 199
gating current, 200
relation of ionic and gating variables, 199
ungated, 196, 199
users guide, 180193
INDEX

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MASSACHUSETTS INSTITUTE OF TECHNOLOGY

Department of Electrical Engineering and Computer Science,

Department of Mechanical Engineering,

Division of Bioengineering and Environmental Health,

Harvard-MIT Division of Health Sciences and Technology

Quantitative Physiology: Cells and Tissues

Issued: September 8, 2004

the cytoplasm is 150 mmol/L.

Part d. Estimate the average distance between water molecules in cytoplasm.

Part e. Determine the ratio of water molecules to potassium ions in cytoplasm.

Is xa > xb or is xa < xb ? Explain.

MASSACHUSETTS INSTITUTE OF TECHNOLOGY

Department of Electrical Engineering and Computer Science,

Department of Mechanical Engineering,

Division of Bioengineering and Environmental Health,

Harvard-MIT Division of Health Sciences and Technology

Quantitative Physiology: Cells and Tissues

Issued: September 16, 2004

Figure 1: Two compartments separated by a membrane.

Figure 2: Schematic diagrams of thin and thick membranes.

Part a. Is the following logic True or False?

Part c. Which curve (dashed or solid) represents fA ? Explain.

MASSACHUSETTS INSTITUTE OF TECHNOLOGY

Department of Electrical Engineering and Computer Science,

Department of Mechanical Engineering,

Division of Bioengineering and Environmental Health,

Harvard-MIT Division of Health Sciences and Technology

Quantitative Physiology: Cells and Tissues

Issued: September 23, 2004

= A(t)LV RT Co (t) Ci (t) .

(e.) c1CaCl2 (0) = 20; c2N aCl (0) = 30; x(0) = 3.

MASSACHUSETTS INSTITUTE OF TECHNOLOGY

Department of Electrical Engineering and Computer Science,

Department of Mechanical Engineering,

Division of Bioengineering and Environmental Health,

Harvard-MIT Division of Health Sciences and Technology

Quantitative Physiology: Cells and Tissues

Issued: October 8, 2004

Problem 1. Two compartments of a uid-lled chamber are separated by a membrane as shown in

the following gure.

MASSACHUSETTS INSTITUTE OF TECHNOLOGY

Department of Electrical Engineering and Computer Science,

Department of Mechanical Engineering,

Division of Bioengineering and Environmental Health,

Harvard-MIT Division of Health Sciences and Technology

Quantitative Physiology: Cells and Tissues

Issued: October 14, 2004

Resting potential (mV)

Figure 1: Measurements and model of electrical responses of a glial cell.

Resting potential (mV)

Resting potential (mV)

Figure 2: Effect of sodium injection and ouabain on resting potential.

concentrations shown in the following table.

The cell resting potential depends on GCl .

The cell resting potential depends on both GCl and VCl .

The cell resting potential does not depend on GCl .

The cell resting potential does not depend on VCl .