Version: August 27, 2017

Lab Guide for 437L

Fall 2017

Experiments, protocols, rubrics, and guides to

writing and presenting

By Erin Lavik*
*Experiments except solar lab were adapted from previous lab guides

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CONTENTS
General Lab policies to remember..................................................................................................................................5

UNSTEADY-STATE HEAT TRANSFER..................................................................................................................................6

Introduction and Scope.......................................................................................................................................6

Experimental.........................................................................................................................................................6

Data and Analysis................................................................................................................................................7

PID CONTROL OF A DOUBLE PIPE HEAT EXCHANGER...................................................................................................12

Introduction and Scope.............................................................................................................................................12

Experimental.............................................................................................................................................................12

Data and Analysis......................................................................................................................................................13

Background Information...........................................................................................................................................13

Bibliography..............................................................................................................................................................16

FIXED AND FLUIDIZED BEDS..........................................................................................................................................19

Introduction and Scope.............................................................................................................................................19

Apparatus-.................................................................................................................................................................20

Procedure-.................................................................................................................................................................20

Data and Analysis......................................................................................................................................................21

Make your own solar cells............................................................................................................................................23

Websites worth visiting to understand more about solar cells:...............................................................................23

Introduction..............................................................................................................................................................23

How do solar cells work?......................................................................................................................................24

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 Natures solar cells................................................................................................................................................24

Silicon Based Solar Cells........................................................................................................................................25

Dye Sensitized solar cells (DSSCs).........................................................................................................................25

Experimental methods..............................................................................................................................................26

Commercial solar cells..........................................................................................................................................26

Dye-based solar cells.............................................................................................................................................27

Cleaning up...........................................................................................................................................................32

Things to consider and discuss in your paper...........................................................................................................32

References.................................................................................................................................................................32

The Joys of Paper Writing or Making your Name in the Field......................................................................................34

Abstract.....................................................................................................................................................................34

Introduction..............................................................................................................................................................34

Experimental.............................................................................................................................................................35

Materials...............................................................................................................................................................35

Results.......................................................................................................................................................................35

Discussion.................................................................................................................................................................36

References.................................................................................................................................................................36

Figure captions..........................................................................................................................................................36

Figures.......................................................................................................................................................................37

Since the Story is the Key, How do you Figure out What is the Story......................................................................37

Appendicies...............................................................................................................................................................38

So you want to publish in Science? (Honestly, this is mostly true for any publication)...............................................38

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How to Give a Presentation..........................................................................................................................................39

The Motivation..........................................................................................................................................................39

Text Stinks.................................................................................................................................................................39

The What...................................................................................................................................................................39

How: The methods....................................................................................................................................................39

When: for proposals.................................................................................................................................................39

Dont read from the slides and other important advice...........................................................................................39

The last word.............................................................................................................................................................40

Questions?................................................................................................................................................................40

Making a Poster for a Conference.................................................................................................................................40

Satistics and Analysis of DATA.......................................................................................................................................42

Summarize the Data..................................................................................................................................................42

Looking for Differences between Groups (ANOVA)..................................................................................................43

Determining Which groups are Different..................................................................................................................45

Corrections to the T test for Multiple Comparisons.................................................................................................47

Multiple Comparisons Against a single Control........................................................................................................48

Non-Parametric Data................................................................................................................................................48

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GENERAL LAB POLICIES TO REMEMBER

Were in this together. The goal is for all of us to learn as much as possible. Help each other. Help me. We
work in teams. Science is hard enough. Working together is critical to success. However, you still need to
do your own work and your own analysis to make sure you understand what is going on.

Come prepared. Make sure youve done the reading and know what youre doing

Clean up. If you leave a mess, youre messing with your lab mates. I already clean up after two dogs and a
toddler. Im not cleaning up after you. The best way to have equipment break is to leave it a mess.

Keep up. Lab classes are terrible classes for trying to catch up. Keep up. If you are going to have to miss a
class, talk to me as soon as possible and to your team. I understand that emergencies do happen, but they
are not common. Traffic, other meetings, etc are not emergencies. Leave extra time and plan. If you are 30
minutes late for a lab without an excuse, you may be asked to leave. 2 or more unplanned absences may
lead to a deduction in your participation grade (5%) in the course.

Work carefully. Several of the pieces of equipment in the lab are fragile. Do not wear headphones. Plan.
Look where you are going.

Take care of yourselvesbe safe. Wear safety glasses, closed toe shoes, and pants in the lab. Improper
clothing may lead to your being asked to leave the lab for your own safety.

You will have a locker. Bring a lock. You can keep pants and closed toed shoes in the locker for the lab if
need be.

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UNSTEADY-STATE HEAT TRANSFER

If you have a laptop with Matlab installed, please bring to lab the day of your experiment. You
may work together to develop the code, but do not share code directly with others. In other
words, the code must be individually written and annotated.

INTRODUCTION AND SCOPE

Heat conduction is one of the fundamental mechanisms for the transfer of energy. In this
experiment, the conduction of heat through solid bars under unsteady-state conditions is
studied. Experimentally determined temperature profiles are then compared to those predicted
from Fouriers Law.

EXPERIMENTAL
The equipment consists of ice water and warm water baths, a data acquisition system, and
aluminum and Plexiglas cylinders containing thermocouples at various radial positions (see
Schematics and Specifications).

For Plexiglas: specific gravity = 1.18

thermal conductivity = 0.12 Btu/hr-ft-F

heat capacity = 0.35 Btu/lb-F

To conduct the experiment, place both cylinders in the warm water bath set to approximately
37C. (The temperature difference between the ice and water baths should be at least 30C.)
When the temperature of the cylinder is uniform at 37C, set the recording frequency to minutes
for the Plexiglas cylinder or seconds for the aluminum cylinder and quickly immerse the cylinder
in the ice water bath. The transfer between baths must be done very quickly, particularly
for the aluminum cylinder. Record the temperature distribution in the rod (using the computer)
until the rod temperature approaches the ice water bath temperature. The entire process takes
approximately 1.5 to 2 hours for the Plexiglas and 3 to 5 minutes for the aluminum. Note:
Before starting the experiment, be sure that you understand how to run the data
acquisition system on the computer.

While waiting for the cylinders to equilibrate, work on the Matlab code described below.
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When you are finished with the experiment, take the cylinders out of the baths and let dry on
paper towels on the bench. Empty the ice bath water and setup to drain into a bucket as the ice
melts. Turn off the warm water bath.

DATA AND ANALYSIS

Fouriers Law in three dimensions describes unsteady-state heat conduction [1]:

T
( 2T ) (1)
t

where = k/ C p ( s )

C p ( s ) = heat capacity of solid, J/kg-C

= solid density, kg/m3

Because the samples are cylinders with uniform wall conditions, the heat conduction is in only
two directions, radial and axial. Assuming that little heat loss out the ends of the rods and
therefore temperature remains uniform in the axial direction, heat transfer is only in the radial
direction and the temperature is a function of only time and radial position [1]:

T 2T 1 T
[ 2 ] (2)
t r r r

What is/are the heat transfer mechanism(s) a) between the ice water and the cylinder and b)
through the cylinder? If there is more than one type of heat transfer, how do the rates compare?
Is/are the controlling (rate limiting) mechanism(s) different for the two cylinders? Based on the
controlling mechanism(s), does a simplified version of Eqn (2) describe the temperature-time
behavior of either the aluminum or Plexiglas?

Solve Eqn (2) numerically using Matlab (e.g., pdepe solver), and where appropriate, use at least
one other method to arrive at a solution for Eqn (2):

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One can arrive at solutions for Eqn (2) by multiple methods:

- Use the simplified version of Eqn (2) mentioned previously

- Most heat transfer texts provide graphical solutions of Eqn (2) for multiple geometries
(Heisler charts); use these charts to analyze data from just 3 thermocouples

Compare the experimental and calculated temperature profiles. Comment on why they might be
different. Comment on the differences between the aluminum and Plexiglas samples when they
are subjected to a step change in external temperature. Where appropriate, calculate percent
differences and the statistical significance of differences between results. Provide your raw data
as plots and show all sample calculations.

Bibliography

1. Welty, J.R., Wicks, C.E., Wilson, R.W., and Rorrer, G. Fundamentals of Momentum, Mass
and Heat Transfer. 4th ed. New York: John Wiley & Sons. 2001. Chapter 18: Unsteady-
State Heat Conduction.

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Schematic of Plexiglas Bar

Left: end view, Right: side view

a = the x distance between thermocouples

b = the r distance between thermocouple radii

c = the x distance from the end of the bar to the closest thermocouple

Plexiglas Bar Specifications

OD = 3" a = " c = 2"

Length = 24" b = "

Thermocouple x distance from the end of r radius of the thermocouple from the bar
# the bar (in) centerline (in)

1 3.25 0.00

2 3.00 0.25

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 3 2.75 0.50

4 2.50 0.75

5 2.25 1.00

6 2.00 1.25

Schematic of Aluminum Bar

Left: end view, Right: side view

a = the x distance between thermocouples

b = the r distance between thermocouple radii

c = the x distance from the end of the bar to the closest thermocouple

Aluminum Bar Specifications

OD = 3" a = " c = "

Length = 24" b = "

Thermocouple x distance from the end of r radius of the thermocouple from the bar
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 # the bar (in) centerline (in)

1 1.75 1.25

2 1.50 1.00

3 1.25 0.75

4 1.00 0.50

5 0.75 0.25

6 0.50 0.00

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PID CONTROL OF A DOUBLE PIPE HEAT EXCHANGER

INTRODUCTION AND SCOPE

Heat exchangers are commonly used in the chemical process industries and an experimental
double pipe heat exchanger is available in the laboratory. The purpose of this experiment is to
investigate the dynamics of the heat exchanger to develop an appropriate process control
scheme. The dynamics of the exchange in either counter or parallel flow are to be investigated.
By changing the desired temperature of the outlet of the exchanger, process control parameters
for PID control will be determined and implemented.

The experiment is based upon the measurement of temperature over data and inlet and outlet
fluid temperatures and flow rates. Given these data, estimates for the proportional gain, interval
time, and derivative time for the inlet flow rate may be computed.

EXPERIMENTAL

Apparatus- The heat transfer unit consists of five parts: a heat exchanger, hot and cold water
circuits, controls and instrumentation. The exchanger is two concentric copper pipes (outside
pipe: 0.500-in OD, 0.430-in ID; inside pipe: 0.250-in OD, 0.190-in ID) with hot water flowing
through the inner pipe and cold water in the outer; the effective length of the exchanger is 1.07
m. Thermocouples at various locations are used to measure the fluid temperatures. (See the
Appendix for more information about the thermocouple locations.)

Two different methods will be used to determine control parameters for this heat exchanger. The
first is the open-loop Cohen-Coon method, which requires implementing a single change to the
system inputs and analyzing the system outputs. The second is the closed-loop Ziegler-Nichols
method, which requires adjusting a control parameter directly until the system output seems to
uniformly oscillate instead of achieving a steady state.

Procedure- Start by connecting the quick-connect plugs on the exchanger to give either co-
current or counter current flow. (Consult with the instructor on the choice for your experiments.)
Open the valves for both cold and hot water and start the water pumps. Set the cold water flow
rate at 0.3 gpm, and then choose a hot water flow rate close to the maximum value possible.
The temperature of the hot water should be kept at 110F. Once the system has reached steady
state, record all temperatures and flow rates. (After a change in flow rate, it takes about 20 min
for the system to reach steady state.)

Next, to gather data for the Cohen-Coon method, use LabVIEW to vary the hot water flow rate 2
or 3 additional times. For each data run, be sure to click the white Run arrow at the top left of
LabVIEW to record your data, then click the red Stop button when finished. LabVIEW will
automatically write an Excel file to the location and name specified in the textbox. Be sure to
rename or copy this Excel file between runs, or else LabVIEW will write over the same file each

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time the Run button is clicked! Between data runs, make the appropriate adjustments, then click
the Run arrow to start a new trial.

To gather data for the Ziegler-Nichols method, allow the system to approach a steady-state,
then use the proportional gain to induce an oscillation in the outlet temperature. LabVIEW will
continue to collect data and write to an Excel spreadsheet, but it will not record the proportional
gain, so make sure to note this data point.

In week two, enter appropriate PID control schemes, one at a time, and run the system to reach
the set points prescribed by the instructor. The time/temperature data will be collected and
written to an Excel spreadsheet to the location specified in the LabVIEW window.

DATA AND ANALYSIS

Cohen-Coon Method: For each data run, examine the time versus temperature data to fit a first-
order response function to this data (see the background information for more help). Once the
time constant, delay time, and process gain are determined, the table of tuning parameters can be
used to compute appropriate control scheme parameters.

Ziegler-Nichols Method: For each data run, control scheme parameters can be computed based
on two items: the period of observed oscillations in temperature versus time, and the proportional
gain that induced this oscillation.

Based on the background information, which control scheme appears to be more stable? Which is
more aggressive?

In week two, examine the data to determine which control scheme was more effective. Which
scheme allowed the temperature to reach the set point more quickly? Which scheme had less
overshoot? Which scheme had fewer oscillations? Suggest reasons for the different results. Is
there an even better control scheme that is close to those suggested by the two methods here?
Use the rest of your time to tweak your scheme in search of even better control.

BACKGROUND INFORMATION

A control system is used to automate a process to achieve a desired output. Control systems
exist in a number of places in chemical systems to achieve a specific level in a tank, flow rate
in a pipe, or temperature in a reactor, just to name a few. The experiment performed here could
be along any of those lines, but the determining of tuning parameters would be virtually the
same in every situation!

The controller is tuned to reach a desired steady-state as quickly as possible. The Cohen-Coon
and Ziegler-Nichols methods were established early in process control theory to provide such a
response with a decay ratio (Seborg et al., p. 225) this means that the controller
overshoots the steady state, then overcorrects, but each overcorrection results in a maximum
offset that is about 25% or less than the previous overshoot (see Figure 1). These methods
make it easy to compute control parameters, but because of their overshoot and oscillations, not

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always practical to implement. The decay ratio is an important way to compare different control
schemes.

1
process variable
desired setpoint
process output

0.5

-0.5
0 2 4 6 8 10 12 14 16 18 20
time

Figure 1. Example of a process with a decay ratio of . The amplitude of the second peak
in this damped oscillation is the amplitude of the first peak.

There are three tuning parameters in PID control: the proportional (P) gain, Kp; the integral (I)
time, I; and the derivative (D) time, D. In general, the larger Kp is, the more aggressive the
control scheme is it will manipulate the system to get to the steady-state as fast as possible,
but if set too high, the system will overshoot the desired steady-state. Further, when used alone,
proportional control results in offset the steady-state value of the output does not match the
desired set point. The integral time is used to correct this offset. The larger this value, the less
often the system oscillates. Finally, the derivative time (D ) is used to dampen the oscillations,
ideally resulting in less overshoot. As D increases, the amplitude of overshoot tends to
decrease.

The Cohen-Coon method prescribes PID tuning parameters based on fitting data to a first-order
exponential decay curve. This fitted curve then results in three critical parameters: the process
gain (K), the process time constant (, and the delay time (tdelay), all computed by Equations 1-3.

x ss x0
K
u1 u 0 [1]

t t ln 2
t 0.632 0.5 0.632
1 ln 2 [2]

t t ln 2
t delay 0.5 0.632 t0
1 ln 2 [3]

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where x represents the value of the process variable (in this case, the outlet water temperature),
the subscript ss representing the final steady-state value and 0 representing the initial value,
prior to any changes to the system; u represents the manipulated variable (in this case, the hot
water flow rate), with 0 being the value before it is manipulated and 1 being the value after; t
represents a specific time for the data, with each subscript corresponding to the time at which
the process variable is that fraction of the way between its initial and final states. See Figure 2
for a graphical representation of these values.

x_1
process variable

x0.632=x0+0.632(x1-x0)
experimental data
x0.5=x0+0.5(x1-x0) first-order fit
finding t0.5

x_0 finding t0.632

-20 0 20 40 60 80 100 120
manipulated variable

u_1

u_0

-20 0 20 40 60 80 100 120

time

Figure 2. Example for finding t-values necessary to compute Cohen Coon parameters. In
this example, t0=0, t0.5=60, t0.632=65.4.

The Ziegler-Nichols method determines PID tuning parameters based on the proportional gain
Ku that nearly results in an unstable system. For a secret value of the gain, to be determined
experimentally, there will be an output that oscillates with a set period Pu (and does not dampen
or grow).

For both methods, the heuristics for computing the PID control parameters are given in the
Appendix.

BIBLIOGRAPHY

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1. Bequette, B.W. Process Control: Modeling, Design, and Simulation 1st ed. Upper Saddle
River, NJ: Prentice-Hall. 2003. Chapter 6: PID Controller Tuning.
2. Seborg, D.E., Edgar, T.F., Mellichamp, D.A., Doyle III, F.J. Process Dynamics and Control
3rd ed. Hoboken, NJ: Wiley. 2011. Chapter 12: PID Controller Design, Tuning, and
Troubleshooting.

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Appendix

Figure A1. Double Pipe Heat Exchanger Thermocouple Locations

The variables expressed in the table below are all described in the text of this document.

Table A1. PID Tuning Heuristics (from Bequette, pp. 198-203)

Method Proportional Gain, Kp Integral Time, I Derivative time, D

Cohen-Coon 4 t delay t delay 4t delay

t delay 32 6
K c t delay 3 4 t delay
11 2
t delay
13 8

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Ziegler-Nichols 0.6 K u Pu Pu
2 8

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FIXED AND FLUIDIZED BEDS

INTRODUCTION AND SCOPE

Processes involving contact of fluids and solids such as heat transfer, chemical reaction and
mass transfer are carried out in both fixed and fluidized beds (examples provided in Table 1). At
low velocities, the solid particles will form a fixed bed, while at higher velocities the bed is
changed to an almost fluid-like state (fluidized). Fluidization initially occurs at a velocity where
the pressure drop over the bed counterbalances the weight of the bed.

Table 1. Applications of Fixed and Fluidized Beds

Application Examples

Transportation of solids Slurry pipeline for coal

Heat exchange Energy recovery from hot catalyst particles

Drying Hot air drying of grains

Catalytic reactions Catalytic cracking of hydrocarbons

Biotechnology Chromatographic separation of proteins

You will observe the bed height and pressure drop through the provided fixed and fluidized bed
systems as a function of fluid velocity, and then compare the experimentally determined values
with literature predictions. The pressure drop-velocity curves for increasing and decreasing
increments of fluid velocity will be determined in 3 separate trials and means and standard
deviations will be calculated.

You will also comment on the appearance of the bed at different points of fluidization.
Depending on the difference in density between the fluid and the bed packing (or ballotini), the
size of the particles, column diameter and the fluid velocity, the bed will behave differently
(Figure 1).

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 Figure 1. Types of flow in fluidized beds

APPARATUS-

The equipment consists of two 5-cm ID Plexiglas columns. Both contain ballotini. One column,
containing 485 m diameter ballotini (density = 3 g/cm3), is connected to a pump which allows
circulation of water through the column. Fine ballotini (density = 2.875 g/ cm3), 267 m diameter,
is used in the other column to which air is supplied. Each column is equipped with a pressure
gauge to measure pressure change across the column, and the bed height can be read from a
scale on the side of the column. The total mass of the ballotini in the water system is 1 kg, while
the column used with air contains 500 g.

PROCEDURE-

With either the air or water system, note the initial bed height. Make sure the pressure is zero
with no fluid flow. (If the pressure reading is not zero, check with the instructor.) Then start the
flow of the fluid and measure the pressure drop through the bed and the bed height as a
function of fluid velocity over as wide a range of velocities as possible. Record the data both
with increasing and decreasing flow rates. At each fluid velocity, note the state of the bed
(describe appearance of bed in a few words). With the water system, make sure the pressure
has stabilized before taking the reading.

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After completing observations for the air or water system, repeat the experiment with the other
fluid. For each fluid system, collect the pressure drop-velocity data and the bed height-velocity
data in at least 3 separate trials. In other words, collect 3 sets of data with increasing increments
of velocity and 3 sets of data for decreasing increments of velocity.

DATA AND ANALYSIS

Based on dimensional analysis and laboratory data, a relationship has been developed to
predict the pressure drop in fixed beds [1]. The relationship is called the Ergun Equation:

2
P 150Vs (1 ) 2 1.75Vs (1 )

L 2
Dp 3 D p 3
(1)

where Dp = particle diameter (equation 1 assumes spherical particles), m

L = bed height, m

P = pressure drop across bed, N/m2

Vs = superficial velocity (velocity in empty tube), m/s

= void fraction, dimensionless

= 1 - (volume of solid particles) / (total bed volume)

= fluid viscosity, Pa-s

= fluid density, kg/m3

(NOTE: A small change in has a large effect on the predicted P.)

In fluidized beds, an equation for the pressure drop is obtained by equating the bed weight per
unit area of cross section to the pressure drop [1]:

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 P
(1 )( s ) g (2)
L

where g = acceleration due to gravity, m/s2

s = particle density, kg/m3

The velocity at the onset of fluidization is called the minimum fluidization velocity, Vmf, and is
generally determined from a plot of P versus velocity at the velocity where the P line
determined under fixed bed conditions crosses the P line determined under fluidization
conditions. For small, spherical particles (Re based on Dp < 1), the minimum fluidization velocity
may be predicted from [1]:

3
g (s ) m 2
Vmf Dp (3)
150 (1 m )

where m = void fraction at Vmf

Prepare one graph of the mean pressure drop versus fluid velocity for each fluid; show separate
lines for increasing and decreasing fluid velocity. Show the mean and standard deviations
calculated from the 3 trials.* How do the data for increasing and decreasing fluid velocity differ?
Discuss. For both fluids, compare predicted and actual pressure drops and minimum fluidization
velocities and discuss reasons for any discrepancies. Where appropriate, calculate percent
errors and the statistical significance of differences between results.

Examine graphs of the bed height versus fluid velocity for each system. Are the data with water
and air different? Discuss. Report your observations on the state of the bed in both systems. Are
they the same or different? Describe qualitatively what is happening for the water versus air
systems and explain why any differences occur in how each fluid impacts the bed behavior.

* If you have any questions about how to calculate or plot standard deviations, see the instructor
before submitting your report.

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MAKE YOUR OWN SOLAR CELLS

Much of the information for this lab is drawn from two excellent papers in the Journal of Chemical Education [1, 2]:

1. Anunson, P.N., et al., Involving students in a collaborative project to help discover inexpensive, stable
materials for solar photoelectrolysis. Journal of Chemical Education, 2013. 90(10): p. 1333-1340.

2. Cost, A.L., High-Efficiency Solar Cell Based on Dye-Sensitized Colloidal TiO2 Film, Brian OReagan and
Michael Gretzel. Nature, 1991. 353: p. 737-746.

They provided the foundation for the lab as well as some of the background and protocols. I am beyond grateful.
Dr. Lavik

WEBSITES WORTH VISITING TO UNDERSTAND MORE ABOUT SOLAR CELLS:

http://www.ucsusa.org/clean-energy/renewable-energy/how-solar-panels-work#.WYtBPVGGPLZ

https://www.scientificamerican.com/article/solar-cells-prove-cleaner-way-to-produce-power/

http://solararmy.org

http://www.pveducation.org/pvcdrom/characterisation/electronics

https://web.stanford.edu/group/mcgehee/publications/MT2007.pdf

INTRODUCTION

Richard Smalley, a Nobel Prize winner, coined the term Terrawatt Challenge in 2004 to describe the call to have 14
TW of renewable energy by 2050 [3]. Renewable energy comes in all sorts of packages, but one that has drawn
substantial interest in the last decade has been solar cells and solar panels.

The traditional solar panels of my youth were silicon-based systems. The pro is that the energy density of these
systems is relatively high. The con is that they are insanely expensive and can break relatively easily. A focus on
processing and scale has brought the price down, but they continue to be expensive and their cost coupled to their
lifetime issues limits their application.

Meanwhile, organic solar cells have gained great interest. In 1991, ORegan and Graetzel published High efficiency
solar cell based on dye-sensitized colloidal TiO2 films in Nature [2], and a world was born. Cheap, flexible,
disposable but were they functional? Their energy densities havent exactly been tremendous. So, what now?

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HOW DO SOLAR CELLS WORK?
Solar cells are photovoltaics. They are essentially the reverse of light emitting diodes. In a photovoltaic, a
semiconducting material is used. The materials is doped to create a negative side (n-type) and a positive side (p-
type). (With silicon that bonds to 4 atoms, a dopant that bonds to 3 like boronwow that periodic table is useful
creates a hole, a positive spot. A dopant that bonds to 5 atoms like phosphorous has an extra electron.) When the n
type and p type are joinednot actually how they are made, but it is easier to think of it this waythe electrons
from the n type move to the holes in the p type. This movement creates an electric field in a portion of the device
called the depletion region or depletion zone.)

Figure 1: Borrowed from the American Chemical Society, Chemical Matters.

(https://www.acs.org/content/acs/en/education/resources/highschool/chemmatters/past-issues/archive-2013-2014/how-a-solar-cell-
works.html?cq_ck=1396892718960)

Photons with energy greater than the bandgap of the material cause electrons to move from the valence to the
conduction band. If the electron is created in the depletion region, the electric field will drive it and create a
current.

One would like to capture as much of the energy from the sun as possible, so, often solar cells are designed with a
range of bandgaps or, luminescent material is used to step down the high energy photons to energies consistent
with the bandgap of the solar material.

If you attach electrodes to the solar cell or array of solar cells, you can collect the energy from the system. Ta dah!
Of course, the moment you do this, you have to find a place to use or store the energy. Well worry about that in a
bit. First, we need to make some solar cells.

NATURES SOLAR CELLS

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Solar cells are often compared to plants that undergo photosynthesis. In photosynthesis, chlorophyll converts light
into sugars or chemical energy. Solar cells convert light into electrical energy.

SILICON BASED SOLAR CELLS

The earliest solar cells (photovoltaics) were single crystal silicon p-n junction systems (Figure 1). The beauty of
single crystal structures is that one doesnt have many defects which act as places were charges can get quenched.
Single crystal systems are extremely efficient, but they are also very expensive. In the 1990s, a 1 foot by 2.5 ft solar
panel would cost well over $1000. People were definitely not putting them on their roofs. It is cheaper to make
polycrystalline silicon systems, and as we moved into this century, researchers developed methods to make them
efficient enough and cheap enough that the trade off was worth it.

Not to be left behind, the rest of the materials world started asking if their favorite materials could be suitable for
photovoltaics.

DYE SENSITIZED SOLAR CELLS (DSSCS)

These solar cells borrow from nature in that they use a molecule that can absorb light just as chlorophyll does, but
the device converts the light to a current. The conversion of the absorbed light is one of the most challenging
aspects of these types of solar cells.

The molecules used to absorb light tend to involve ring structures which isnt terribly surprising. We need
molecules that absorb well in the visible and, potentially, UV parts of the spectrum. Two of the most common
include the ruthenium-based systems including cis-Bis(isothiocyanato)(2,2-bipyridyl-4,4-dicarboxylato)(4,4-di-
nonyl-2-bipyridyl)ruthenium(II).

Figure 2: cis-Bis(isothiocyanato)bis(2,2-bipyridyl-4,4-dicarboxylato)ruthenium(II)

25 | P a g e
One can also use anthrocyanin which comes from blackberries and exist in a number of purple-colored fruits and
plants.

Figure 3: Anthrocyanin

Conversion is key with these systems. To convert the energy from the absorbed light into electricity one needs a
material with the appropriate bandgap. TiO2 has a bandgap at 3.2 eV which works well for these molecules. We
need as many interfaces as possible between the TiO2 and the dye molecules, so nanocrystalline TiO2 particles are
preferred with their high surface to volume ratio.

Light excites an electron in the dye. The electron is transferred to the titania. If we use an electrolyte solution and
connect the system with a circuit, the electron reduces triiodide which then oxidizes and releases the electron to
the dye molecule.

EXPERIMENTAL METHODS

COMMERCIAL SOLAR CELLS

SOLAR CELLS USED IN THIS LAB

1. Jiang transparent flexible solar cell.

From Description: Packaging assembly using UV curable polymer, to ensure a high durability. The package includes
EVA polymers and fluoropolymers ETEE (high endurance ETEE is highly light-transmissive polymer); Portable PV
components field work and travel to meet the supplemental power requirements.

2. Single crystalline solar cell

3. Polycrystalline solar cell

YOULL CONNECT AND TEST A RANGE OF SOLAR CELLS BASED ON THE PROTOCOLS BELOW. DETERMINE
THE FOLLOWING:
1. I-V curves.
2. Weight of the systems
3. Area of the solar panels.
4. Cost. (Estimate from panels available commercially)

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 5. Reported efficiency from the literature.
6. Estimate efficiency based on the IV curves you obtain. The following website is extremely helpful in doing
this:

http://www.pveducation.org/pvcdrom/solar-cell-efficiency

7. Lifetimes of these cells. Look in the literature. How long to the last? What are the mechanisms by which
they fail?

DYE-BASED SOLAR CELLS.

This is taken directly from the protocols at the solararmy.org

You will do this procedure with both the traditional DSSC molecule, the ruthenium-based compound as well as with
the blackberry juice (the anthrocyanin.)

PREPARING THE TIO 2 ELECTRODE

1. Take one piece of the FTO glass and use the multimeter to find the conductive side. Set the multimeter to
the resistance setting denoted by the symbol ohm (). If using the model included in the kit, the multimeter
dial should just be pointing straight down pointing to 200 ohm.
2. Press the points of the two metal probes onto the surface of the glass, careful that the metal points dont
touch. The conductive side will have a reading around 30 ohms. If you dont get a reading (i.e. still see the
overflow value of 1), flip the glass over and try the other side.
3. Once you have found the conductive side of the glass (the side with a resistance reading), set that side face
up on the table. Take a piece of scotch tape and cover approximately 1/8 of the surface of the glass as
shown here. The remaining open surface area will be covered with the TiO2 paste. The taped off strip will
be blank glass which is necessary for assembly in the end.
4. Using the plastic pipette, drip a couple drops of the TiO2 solution in the center of the exposed glass. Dont
add too much!
5. Use the smooth side of the pipette (i.e. no engraved numbers or seam) and immediately squeegee the
solution down and up once or twice with the side of the pipette. Aim for a thin, even coating of the paste. If
the TiO2 does not coat the entire exposed surface, quickly add another drop of TiO2 paste and re-squeegee
the whole plate. It should be a slightly transparent white color. Allow the paste to dry, undisturbed, for a
minute or two. Once dry, remove the tape from the glass.
6. Transfer the glass to a hotplate and leave the TiO 2 film face up. The exact temperature of the hotplate is
not important. Simply the hotter the plate, the faster it will be done. The surfactant and solvent in the
paste will evaporate while on the hotplate, leaving behind just the TiO2 nanoparticles. The glass will
appear to turn brown or burned, and then white again.
7. When the glass is done (i.e. the slide turned brown and then back to white), turn off the hotplate and let
the glass cool down slowly. If the glass is moved too quickly from hot to cold it will crack. Even touching it
with the tweezers can sometimes be enough of a temperature shock to cause cracking. A small crack
usually wont cause problems with the effectiveness of the cell, but best to avoid. The plastic tweezers can
also melt so wait for the plate to cool.

DYEING THE TIO 2 ELECTRODE AND ASSEMBLING THE DSSC

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 1. Place 5 ml of the blackberry juice in a ziplock bag. When you use the ruthenium-based compound, you will
add 5 ml of the compound in solution (0.3 mMol in ethanol which works out to (and check this) 1 mg/5
ml) to a ziplock bag.

2. Take the TiO2 coated piece of glass and place it into the blackberry juice in the bag for 1-5 minutes. Be
sure that the glass is completely covered. The white TiO2 paste should turn completely purple so there is
no white left. The darker the better!

3. While you wait, take your other piece of FTO glass and find the conductive side as in step 1. Set the
conductive side face up and use the pencil to coat the entire surface with graphite (pencil lead).

4. It can be hard to see but as long as you colored there should be graphite on the surface. Set it aside but
keep the conductive side face up.

5. Using the tweezers grab the dyed TiO2 piece of glass out of the blackberry juice (try to avoid scratching
the film with the tweezers as it will chip off).

6. Holding the glass over the opening of a cup or beaker, rinse off the excess blackberry pieces and juice with
a squirt bottle of water. Catch the drippings in the cup or beaker. (You can also rinse over the bag being
held open by your partner to minimize supplies needed).

7. Set the rinsed glass onto a paper towel and very gently dab it with the towel to dry it off. DO NOT WIPE
the glass as the TiO2 coating will come off.

8. Take the two pieces of glass and assemble them into a sandwich with the two conductive and coated sides
facing in. Think of a PB&J sandwich: the coated sides face in.

9. Then, slide the graphite glass out so that its edge aligns with the beginning of the purple TiO 2 coating on
the other piece. Then using binder clips, clip together the two sides of the glass that are not offset.

10. Lastly, add the iodide/triiodide (I -/I3-) electrolyte solution using a pipette to the seam of the glass. A very
small amount should be sufficient. The purple area of the glass should turn darker as it is filled with the
electrolyte. If there are any spots that dont get coated, try removing a binder clip and then clipping it back
on to move the liquid around. If that doesnt fix it, add a little more electrolyte to the seam.

TESTING THE SOLAR CELLS

1. The DSSC is ready to generate electricity. All it needs is some light and a way to measure its output. Think
of the DSSC as a battery. It has the capacity to generate electricity but you cant see it until it is used to
power a device or tested with a multimeter, which is what you will do.
2. To test your solar cell, clip one end of an alligator clip to one of the overhanging pieces of glass. Clip the
other end of the alligator clip to one of the metal multimeter probes. Use the second alligator clip and clip
it to the other piece of overhanging glass and the other multimeter probe.

28 | P a g e
 3. Switch the multimeter setting to DCV (Direct Current Voltage) to measure the voltage of the DSSC. The
2000m setting is usually sufficient to measure the output in millivolts. An average reading in full sunlight is
around 350 mV.

4. If the reading is negative, this just means the meter is measuring electricity flowing in the opposite
direction. Simply switch which electrode the alligator clips are attached to and the reading will become
positive.

5. Flipping the DSSC over so the dye is closer to the light can sometime increase voltage dramatically.

6. Then switch the multimeter setting to DCA (Direct Current Amperage) to measure the current. The setting
of 2000u is usually sufficient to measure the current output. A typical reading in full sunlight is about 700
A.

7. Finally, the voltage and current readings can be multiplied together to obtain the overall power of the cell.
Power is defined as follows: P = current*voltage = I*V. Be sure to convert the voltage from mV to V and uA
to A before multiplying.

GENERATING THE IV CURVE

Terrestrial solar irradiation typically has an intensity of ~90-100 mW/cm 2. Indoor lighting sources can be calibrated
to this intensity by changing the distance of the cell from the light source to match the current values obtained
when exposed to outdoor irradiation.[4]

1. If the halogen lamp is off, make sure you turn it on and allow it to warm up for 10 minutes.

2. Use the light meter to determine the distance from the lamp that is consistant with 100 mW/cm 2. Make
sure you record this distance and all measurements in this lab.

3. Make sure you set up the circuit with the breadboard like figure 4.

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Figure 4: (a) Picture of the solar cell device assembly. Light enters through the TiO 2-dye/ITO anode side. (b)
Schematic for measuring the performance of the device.

4. Under illumination, set the resistance at the maximum value and record the voltage. Decrease the
resistance and record the voltage once again. Repeat this procedure until the voltage reads nearly zero.
The current can be recorded for each corresponding point by using Ohms law

V
i (1)
R

where the current (i) equals the voltage (V) divided by the resistance (R).

5. Ultimately, youll plot up the data.

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Figure 5: Sample i-V curve of a typical PV cell showing the measured parameters used for characterizing the
performance of a device.

A typical i-V curve is shown in Figure 5. From here we can use this data to determine the power conversion
efficiency () of the cell. The power (P) can be determined by developing a spreadsheet or table using the following
relationship,

P(Watt)=i(Amps)xV(volt) (2)

Once the table is developed, Pm or maximum power is the maximum of the data set. This is the knee of the graph
in Figure 5. The corresponding current and voltage to the maximum power value are often assigned the
nomenclature of im and Vm, respectively. Moreover, on the curve in Figure 5, the current value of zero potential is
known as the short circuit current, or iSC, while the potential of the cell at zero current is known as the open circuit
potential (VOC). These parameters are used to determine the fill factor (f or FF) of the cell, which is a lumped
parameter, and is a theoretical measure (ratio) of how much power that can be extracted from the photocell.
Further, these measurements also provide insight into recombination of electron-hole pairs at the electrode-
electrolyte interface as well as ohmic losses due to poor cell construction. The f can be calculated by the
expression:

imVm
ff (3)
iSCVOC

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 The power conversion efficiency is a quantitative measurement of the effectiveness with which a solar cell
converts solar energy to electrical energy. Silicon solar cells, often found atop of buildings and in solar harvesting
fields, typically operate with an value of 20-25%[5] while DSSC have an value of ~11%.[6] So far, the best-
recorded value for a solar cell in a laboratory setting is 42.3% using InGaP/GaAs/InGaAs under concentrated solar
light (over 400x the terrestrial solar irradiation).[5] The efficiency value is determined by the following relationship,

iSCVOC ff
% 100 (4)
PI

where PI is the incident light power which the cell is exposed to, often expressed in units of light intensity
(mW/cm2). It should be noted that the nomenclature used in the literature may differ slightly from source to

source, but still conveys the same information. If the incident light power is not readily known/determined, the f
can be used as a metric for cell performance.

These equations give rise to a method to qualitatively as well as quantitatively measure the performance of a solar
cell. These metrics are often used in academic research as well in industry to determine solar cell performance.

CLEANING UP
1. Bags of blackberry juice can go in the trash and any rinsing of juice in a cup can go down the
sink. The ruthenium solution should be collected in a waste bottle. Paper towels go in the trash.
You can choose to toss plastic pipettes or rinse and reuse them for future classes.
2. Save the FTO glass and simply wipe clean with water and a towel. Graphite is easily removed by
a rubber eraser.
3. All other parts are reusable and should be packed away for future use.

THINGS TO CONSIDER AND DISCUSS IN YOUR PAPER

The paper should focus on the development of the DSSCs in the context of solar cells more broadly. What kinds of
cells make sense under what conditions? What are the most important parameters for the major applications?
What are the challenges of the DSSCs? Look at the literature and see what kinds of solutions there are for tackling
the major challenges and include this in your discussion.

REFERENCES

1. Anunson, P.N., et al., Involving students in a collaborative project to help discover inexpensive, stable
materials for solar photoelectrolysis. Journal of Chemical Education, 2013. 90(10): p. 1333-1340.

2. Cost, A.L., High-Efficiency Solar Cell Based on Dye-Sensitized Colloidal TiO2 Film, Brian OReagan and
Michael Gretzel. Nature, 1991. 353: p. 737-746.

32 | P a g e
3. Smalley, R.E., Future global energy prosperity: the terawatt challenge. Mrs Bulletin, 2005. 30(6): p. 412-
417.

4. Smestad, G.P. and M. Gratzel, Demonstrating Electron Transfer and Nanotechnology: A Natural Dye
Sensitized Nanocrystalline Energy Converter. J Chem Educ, 1998. 75: p. 752-756.

5. Green, M.A., et al., Solar cell efficiency tables (version 37). Prog Photo: Res App, 2011. 19: p. 84-92.

6. O'Regan, B. and M. Gratzel, A low-cost, high-efficiency solar cell based on dye-sensitized colloidal TiO2
films. Nature, 1991. 353: p. 737-740.

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THE JOYS OF PAPER WRITING OR MAKING YOUR NAME IN THE FIELD

Adapted from a Guide to grad. School by Erin Lavik

First rule of paper writing: it didnt happen if it wasnt published.

Second rule of paper writing: See first rule.

OUTLINE FOR A SCIENTIFIC PAPER

ABSTRACT

Ironically, while the abstract is at the beginning of the paper, it is the last thing you will write. The abstract hits on
all the major points of the paper: the introduction, key experimental steps, the results, the discussion, and the
conclusion. It does so in a way that should both summarize the findings and get someone excited enough to
actually hunt down the paper. You want people to know what you did and why it matters in the abstract.

INTRODUCTION

The purpose of the introduction is to give the reader the context for the results you will present. You need to
answer the following:

Why does this work matter?

What is the application? How big is the need? What is currently being used? What are the limits on
current technologies?

What has been done?

This is where one cites the relevant work in the field that applies to this experiment. Chances are that
others have done something before you. What are strengths and what are the limitations that your
system/approach/technology aims to address?

What have you done that is new?

This is that now infamous statement where you sum the whole thing up and say what in the paper matters
(the last line of the intro in most casessometimes it is actually the entire last paragraph.)

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Along with this, many people also cite the work of competitors who may review the manuscript. Once one submits
a manuscript to a journal, the editor will send it to reviewers who are familiar with the area (hence your
competitors are likely to be involved). Scientists sometimes request certain reviewers and request others not be
used, but the review process is anonymous, and the editor can consider or ignore ones request.

EXPERIMENTAL

Typically, you want the reader to be able to identify the techniques quickly so you break them down by subheading.
The purpose of the experimental section is to give the relevant details a scientist familiar with the techniques
would need to replicate your work. Things like the ratios of antibodies, where they were from (NF, 1:200, Sigma)
are important. When you are done with the materials and methods (the experimental section), ask yourself if
someone could replicate the work based on the information present.

MATERIALS
Here one can spell out any unique materials used in the work. Antibodies are usually found in the
immunocytochem. Section, but they could be here instead. Make sure when you list anything with an abbreviation
or acronym that you spell it out the first time. DCM means different things to different audiences.

RESULTS

The results explain what you found from doing the experiments. Typically, researchers put their figures together
and then use that to guide the writing of the results.

I make sure that every experiment in the experimental has a matching component in the results.

Examples of figures:

Fig 1: SEM images of scaffolds or schematics of design

Fig 2: Examples of mech. Testing curves.

Fig 3: Quantification of mech results

Fig. 4: Histology

The figures go at the end of the paper after the references and figure captions unless the journal states that they
should be in the text (ACS journals often ask for this, and more and more journals follow this protocol.) For the
purposes of the lab, please put the figures in with the text.

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DISCUSSION

This is where you say what it all means. What did you find? How does it relate to the big picture you described in
the intro?

Many students avoid the discussion or are brief to the point of mute. Ill admit, that when I am publishing in a new
area, I am very cautious with making huge claims and pondering wildly on the results, but in the end, the
discussion is the meat of things. A discussion that boils down to Yep, this stuff is really important stinks.

So, how to do you get beyond the because my PI said I needed to publish so I wrote this up? Its not easy, but
hopefully, the following will help.

Ask yourself the following:

What if I never discovered what I know in this work? What would I be doing differently? Do my findings fit with
what other people have seen in the field? How so, and how not? Where the findings fit, it is easy to say that it isnt
important. But, why did you study it to begin? It may be exciting that it is expected, but that doesnt mean it isnt
important.

Its always a bit tougher when things are unexpected because you now have to make a case to people in the field
that your findings are real and important. Remember all those essays you wrote in high school where you had a
thesis and had to use supporting evidence to aruge your case? Welcome to your discussion.

Whats your thesis? (What you found/assert based on what you found) Whats your supporting evidence? First, you
have your data. Heres where you really show that it supports your thesis. Second, you have the broader findings in
the field. You need to include the data that supports your findings and address the data (good data) that
contradicts themwhy are the results different?

REFERENCES

These are the endnotes. Editors dont like footnotes. They have too many formatting issues. If you have access to
the program, Endnote, it will revolutionize your creating bibliographies and references. ACS Chemworx is also
pretty fantastic and free. Zotaro is extremely popular and free.

FIGURE CAPTIONS

The captions come next. When a paper is published, the captions are placed below the figures and above the tables
once they are set into the publication.

Many people ask what should be said in figure captions. In my experience, a large number of readers will look at
the figures and, potentially, just glace at the textmy clinician colleagues often do this. Make sure your captions
give enough context for someone to know what youve found without reading all of the results.

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Example of figure caption with little context: GFAP expression (green) scale bar= 200 microns

Example of caption with context: GFAP expression (green) in the cortext of postnatal day 1 rats is consistent with B
cell migration along the rostral migratory stream. Scale bar- 200 microns

I like figures where the labels are on the image so I dont have to read the figure caption and fgure out what the 12
panels show. If a column involves images of GFAP expression, label that column GFAP. If all the images in a row are
for postnatal day 1 label the row in the figure.

When in doubt, make it easier on your reader.

FIGURES

This is the meat. Everything that really matters, the data, should be here. It is your job to put together the figures
so they tell a story. Make sure there is logic to them.

Label them. Make them as easy to understand as possible. Organize and guide the reader through them so they see
the story you are telling. If your story is about comparing GFAP expression, make sure the images are aligned next
to each other to highlight that comparison.

SINCE THE STORY IS THE KEY, HOW DO YOU FIGURE OUT WHAT IS THE STORY

There are options. People have different ways of figuring out their story.

Figures. Many people like to figure out the figures and feel that helps them figure out the story. This can work well
if you know the gist of what youre trying to convey.

Give a talk to your research group. It forces you to craft a story. It can help refine it.

Talk one on one with your PI/colleague. Have them play devils advocate. Youll see what holds water and what
doesnt.

Do you have a paper?

Things work. Things dont. Theres lots of grey area, and honestly, you need to graduate. So, what do you do?

Make a chart. What do you know. What do you not know (This is often the harder part.) Get the devils advocate
involved. Take every piece of data. Note under each column what you know from this and what you dont. When
you go through everything youve got, look at what you know. What is the most cohesive story based on this? What
in the you dont know column do you need to know to complete the story? How can you figure it out? How
critical is it?
37 | P a g e
Remember, this doesnt happen in a vacuum. Few papers are single author papers. Use the other authors, your
colleagues, your team. Help each other.

APPENDICIES

Many papers have supplemental information. This includes raw data, data that is relevant to but not critical to the
story, and supporting information. Code, raw data, and the like should be in a section following the paper called the
appendix or supplementary information. Key findings or pictures of instruments that are critical to explain their
function should go in the body of the paper.

SO YOU WANT TO PUBLISH IN SCIENCE? (HONESTLY, THIS IS MOSTLY TRUE FOR ANY
PUBLICATION)

1. Tell a good, compelling story

2. Have a money shotthe image that tells the story. Along these lines, it should be noted that a good
illustration has played a role in a number of papers getting published in high impact journals
a. Money shot: beautiful, compelling image. Directly relevant to story. Rarely is this a graph
although it can be a key image that represents what is quantified (eg rat walks versus doesnt as
opposed to graph quantifying it)
b. Illustrations. It must not only tell the story, it must be incredibly cool. There are reasons that in
the age of illustrator, graphic designers still have jobs.
3. Write the cover letter of a lifetime.
a. Many students think that the letter is the perfunctory, heres my paper part of the process.
WRONG.
b. The letter is what makes an editor back an article. You need a friendly editor. A friendly editor is
not just a friend today, they are a friend for life. Give them a reason to care, and give them
ammunition to defend your article.
i. What is super cool about your work? Tell them. Tell them how it is special
ii. Create the simple figure including the money shot that summarizes everything thats
fabulous about your article
iii. Why would the audience of the journal (the very broad audience of a high impact one)
care about this? Tell them explicitly.

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HOW TO GIVE A PRESENTATION

A presentation is a story. You need to draw in your audience, tell them why to care (motivation) tell them how your
work fits, and leave them on a good note.

THE MOTIVATION

Why is this important?

What do you hope to achieve?
Do not give an outline
Tell a story that addresses why, what, how, and when
The motivation is the why
(along those lines, what is the purpose of your talk. Meeting, job, proposal, $)

TEXT STINKS

Always go with an image over text. People can read or they can listen. They cant do both

THE WHAT

Youve told them why to care. So, what are you actually doing that matters?

HOW: THE METHODS

Keep it simple and only tell the critical pieces that they need to follow your work

WHEN: FOR PROPOSALS

In proposals for theses or funding, you need to map out when things will happen. For talks at conferences,
this is not included

A timeline
A flow chart
A gantt chart

DONT READ FROM THE SLIDES AND OTHER IMPORTANT ADVICE

Most struggle with text smaller than 18 point

If you add text and talk, the audience can read or listen, not both
Lots of text is overwhelming
Stick with pictures as much as possible

39 | P a g e
 Face the audience.
Remember that you know this better than anyone. Take a deep breath, and tell them your story. Theyre
there because they are interested.
Project!
A slide a minute
Take your time. You WILL rush.
Enthusiasm can overcome a great deal of problems
You are the master of your destiny-- you tell the story YOU want to tell
What to do with that stupid pointer
Dont blind people
Point. Dont circle.
When in doubt, avoid it

THE LAST WORD

What do you want the audience to remember?

You tell the story
1-2 key points

QUESTIONS?

What do you do when you dont know the answer?

Admit it
Often, the issue is the question isnt clear. Restate what you think the question is and answer that
Most people ask simple questions. Dont assume theres something really complicated going on
If the questioner keeps going, suggest you talk off line or after the session

MAKING A POSTER FOR A CONFERENCE

An example of a decent poster:

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Whats good: clear graphics, limited text, something one could read quickly if needed. Lots of white (faster and
cheaper to print than colored background posters.)

What could be betterthe drug delivery part is clearly just plopped in. One doesnt need a lot more text, but it
would be good to have a bit more context.

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SATISTICS AND ANALYSIS OF DATA

This is brazenly summarized from Stanton Glantzs Primer of Biostatistics, which is one of the most accessible and
brilliant books one can read. There are several references to In STAT. In my lab, we use either Prism or InSTAT to
analyze data. R is freely available but does lack a particularly accessible interface.

After lots of careful work and analysis, you have lots of data. Now comes the time where you need to see what it all
means. Statistics is the math of describing and analyzing information.

SUMMARIZE THE DATA

For the purposes of this brief introduction, lets assume your data is numeric. And lets assume that you have two
or more groups. The most common way to summarize the data is to use the mean and the standard deviation. The
is only suitable if the data is normal or parametric (meaning that it exhibits a guassian distribution). The
Kolmogorov-Smirnov goodness of fit test can be used to check how guassian a set of data is. IT is only really useful
if you have a reasonably large population of data on which to test.

Below is a summary from the InStat help guide about the KS test:

TESTING FOR NORMALITY

InStat tests for deviations from Gaussian distribution. Since the Gaussian distribution is also called the Normal
distribution, the test is called a normality test. InStat tests for normality using the Kolmogorov-Smirnov test. The KS
statistic (which some other programs call D) quantifies the discrepancy between the distribution of your data and
an ideal Gaussian distribution - a larger value denotes a larger discrepancy. It is not informative by itself, but is used
to compute a P value.

InStat uses the method of Kolmogorov and Smirnov to calculate KS. However, the method originally published by
those investigators cannot be used to calculate the P value because their method assumes that you know the mean
and SD of the overall population (perhaps from prior work). When analyzing data, you rarely know the overall
population mean and SD. You only know the mean and SD of your sample. To compute the P value, therefore,
InStat uses the Dallal and Wilkinson approximation to Lilliefors' method (Am. Statistician, 40:294-296, 1986). Since
that method is only accurate with small P values, InStat simply reports "P>0.10" for large P values.

The P value from the normality test answers this question: If you randomly sample from a Gaussian population,
what is the probability of obtaining a sample that deviates as much from a Gaussian distribution (or more so) as
this sample does. More precisely, the P value answers this question: If the population was really Gaussian, what is
the chance that a randomly selected sample of this size would have a KS distance as large, or larger, as observed?

By looking at the distribution of a small sample of data, it is hard to tell if the values came from a Gaussian

42 | P a g e
 distribution or not. Running a formal test does not make it easier. The tests simply have little power to discriminate
between Gaussian and nongaussian populations with small sample sizes. How small? If you have fewer than five
values, InStat doesn't even attempt to test for normality. But the test doesn't really have much power to detect
deviations from Gaussian distribution unless you have several dozen values.

Lets assume the data is Gaussian for now.

X sumofthevaluesofthepop.
Mean:
N Numberinpop.

(X ) 2 sum(valofpopmember pop.mean) 2
Standard Deviation:
N numberinpop

LOOKING FOR DIFFERENCES BETWEEN GROUPS (ANOVA)

An analysis of variance (ANOVA) is used to look for differences between groups. It is your next step after describing
the populations in the groups. There are a few assumptions which must be true for the ANOVA to be able to
accurately recognize whether or not there are differences.

All the samples are independent

All the samples are randomly selected from their populations
All have normal (Gaussian) distributions
All of the variances (standard deviations) are equal, meaning that they have the same distributions
What we want to see is whether or not the differences between the groups are greater than the differences within
the groups. If the differences between the groups are much larger than the differences within the groups, it is very
likely that the differences between the groups are not the result of the expected spread in the population, but are,
in fact, the result of some external force (such as a treatment or using different polymers to make the scaffold).

We can use our standard deviations to define the variation. (Variance=SD 2 by definition)

The average variance within the groups is:

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 1 2 2
Avg var iance swithin
2

n
s1 s2 ... sn2
where n is the number of groups

The average variance between groups is:

2
sbetween nsX2

Where n is the number in the group, and sX2 is the standard deviation of the means of the groups. (If one takes the
means of the groups, one can determine the mean of the means as well as the standard deviation.)

One can then take the ratio of these two, which well call F.

2
var iancefromsamplemeans sbetween
F 2
var iancefromaveragingsample var iances swithin

If all the data is from the same population, then F should be 1. (This would be the case if the treatment has no
effect) If F is very large, it means that the variance between the groups is much larger than that within the groups,
and there is a great probability that there are differences between the groups.

One now needs to determine what a big F is. That depends on the size of the groups and the number of groups
being studied.

The degrees of freedom, based on the number of groups and size of the groups can be used to determine how big F
has to be for there to be a reasonable chance (eg a 95% chance) that the groups are different. Tables have been
created based on the degrees of freedom and the F values for particular P values. P is the chance that the groups
are actually the samea 0.05 value for P (commonly used in science) means that there is a 95% chance that the
samples are different. The P value may also be thought of as the probability of being wrong.

From F, for the denominator (within groups) is:

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 d m(n 1)

Where m is the number of groups and n is the number in each group.

for the numerator (between groups) is:

d m 1

Which is just the number of groups minus 1

Now, one can go to a table and determine (based on previous calculations) whether there are significant
differences between groups.

Luckily, many computer programs now will do the calculations based on the group means and standard deviations.

DETERMINING WHICH GROUPS ARE DIFFERENT

With an F value greater than the critical value for significance, it becomes time to figure out which of the groups
are significant as compared to the others. If there are only two groups, then the ANOVA tells one which is
significant compared to the others since there is only one other. The students t test is a special case of an ANOVA
applied to two groups.

The critical value for determining significance in the t test is (shockingly) t.

t F where F is the critical value from the ANOVA test, (the F test) above.

So, if there are two groups, A and B, then the t test comes down to

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 diffinsamplemeans X XB
t A
SEofdifferenceinsamplemeans sA2 sB2

nA nB

The standard error is related to the standard deviation as follows:

SD
SE
n

Remember that n is defined as the number in a group.

It is worth noting that the t test can be used with different size groups. This can be extremely helpful. Ideally,
though, one wants the groups to be the same size for the most accurate statistical analysis.

One can take the t value one gets, and along with the degrees of freedom in the two groups

nA nB 2

One can look up whether there is a significant difference between the groups.

So, this tells us which groups are different from which. If there are two groups, one need only to apply the students
t test to determine significance. If there are more than two groups, it would seem logical, then that one should just
perform an ANOVA for the whole thing and follow up with t tests on pairs of groups.

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 If ones does this, one will introduce a great degree of inaccuracy into the proceedings. Essentially, when choosing a
P value, you are choosing the probability that you are wrong. If you apply the t test once with a P=0.05, you are
saying that there is a 5% chance you are wrong. It you do two t tests, you are likely to be wrong 5% plus 5%
(approximately) because there is a 5% chance you are wrong in the first one, and a 5% chance you are wrong in the
second one. Thus, if you have three groups and apply t tests between each set, A, B, and C, you will have 3 t tests
and if you use a P=0.05 for each of them, the overall P will be closer to 0.3. Its not very comforting.

This, in fact, explains things seen in papers such as times where two treatments are statistically the same as a
control but different from each other. Misappropriate of statistics.

So, one needs to apply a correction to the t test.

CORRECTIONS TO THE T TEST FOR MULTIPLE COMPARISONS

Bonferroni came in and realized a correction needed to be made. He essentially said to divide the P that one wants
at the end (for example, P=0.05) with the number of times one will apply the t test so Ptest=Ptotal/times applied.

Bonferroni expressed the statement as:

T k

Where is the error rate we would like overall, k is the number of tests performed, and is the error rate in each
test.

This correction is extremely conservative meaning that even if there is a difference, one may not find it with this
test.

There are a few other tests typically used, in order from more to less conservative:

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Tukey Test

Student-Newman-Keuls (SNK) Test

The SNK test is derived from the Tukey test. For details on their expressions and derivations, please look at Glantzs
text.

MULTIPLE COMPARISONS AGAINST A SINGLE CONTROL

This arises when you are not comparing all groups with all other groupsjust different treatments against a
control. If you have 3 groups and a control, you would do 3 tests. The Bonferroni test could be used with k=3, or
one could use a less conservative test such as Dunnetts test.

NON-PARAMETRIC DATA

What if your groups dont exhibit Gaussian distributions? There are non parametric methods which are similar to
the parametric ones described above but are not based on describing the data with a mean and standard
deviation. Glantzs book goes into great descriptions of the basic tests, when they apply, and how to apply them.

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