Solid biomechanics mock exam

Problem 1
Before starting we recall the basic assumptions for an ideal Gaussian chain (GC) in 2D:

1. The chain is made of N elements each of length b. |~

ri | = b. N >> 1.

2. Each element is freely jointed to the neighboring elements meaning that there is no bias (< r~i > =
0) and no correlation (< r~i · r~j > = 0).

3. Rotation at any joints between two elements has no energy cost, Urotation = 0.

4. Chain elements are rigid and have no bending stiffness, Ubend = 0.

5. Using the first law of thermodynamics ∆U = Q − W and combining 3) and 4) we find that
W = Q − ∆U = Q = T ∆S meaning that GC behaviour is purely entropically driven.
~ 2 | << L2c
6. The end-to-end distance is much smaller than the contour length Lc : |R
N N N
7. The average end-to-end distance < R~2 > = r i )2 > = < r~i2 + < r~i2 > =
P P P P
< (~ r~i · r~j > =
i=1 i=1 i6=j i=1
N b2

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(a) A 2D ideal GC can be treated as two independent 1D systems where R ~ = R~x + R~y (projection
~ ~ ~ 2
onto x and y axis). We thus have < R2 > = < Rx2 > + < Ry2 > = N b .
Since R~x and R~y are independent, we have
1
< R~x2 > = < R~y2 > = N b2
2

We can describe the probability of arriving at a specific position for a GC in 1D given N elements
(eg : x-direction) by a Gaussian distribution function (mean µx and variance σx2 ):

s
1 −(Rx − µx )2
p(R~x , N ) = · exp( )
2πσx2 2σx2

where σx2 = < R~x2 > = 12 N b2 and µx = < R~x > = 0

r
1 Rx2
p(R~x , N ) = · exp(− ) in 1D
πN b2 N b2

Since x and y axes are independent, we can write the 2D probability as

~ N ) = p(R~x , N ) · p(R~y , N )
p(R,
1 Rx2 + Ry2
= · exp(− )
πN b2 N b2
1 ~ 2
|R|
= · exp(− ) in 2D
πN b2 N b2

~ = T in lecture notes.
Note : |R|
Here we consider an ideal GC in 2D. From the 5) above we demonstrated that W = T ∆S.
Using the second law of thermodynamics and the probability calculted above, we can derive the
force-extension relationship

W = < F~ > dR
~ = T ∆S.
~
= T Kb ln Ω(R)

~ = number of configurations of end-to-end separation R

ln Ω(R) ~
~
= p(R, N ) · Ωtot

W = < F~ > dR
~ = T ∆S.
~
= T Kb ln Ω(R)
~ N ) · Ωtot )
= T Kb ln(p(R,
h i
~ N ) + ln Ωtot
= Kb T ln p(R,
h 1 ~ 2
|R| i
= Kb T ln + (− ) + ln Ωtot
πN b2 N b2
Kb T ~ 2
= · |R| + constant
N b2

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 Finally we obtain

∂W 2Kb T ~
FGC = = · |R|
~
∂|R| N b2

(b) Similarly, we can derive the relationship in 3D (see class notes)

∂W 3Kb T ~
FGC = = · |R|
~
∂|R| N b2

~ less force is needed to extend a chain in 2D vs 3D. We can

Therefore, for a same extension |R|,
justify it using entropy :

∆S = T Kb ln Ω(R)~
Kb T ~ 2
= · |R| in 2D
N b2
3Kb T ~ 2
= · |R| in 3D
2N b2

~ we have ∆S3D = 3 ∆S2D meaning that there is a larger entropy

Thus we find that for a fixed |R|, 2
change in 3D because there are more possible configurations.

(c) The GC model is valid

~ since it predicts a linear force-extension relationship which does not hold as
(1) at small |R|
~
|R| → Lc for real DNA.
(2) at N >>1 because of the assumption that p(R, ~ N ) is a Gaussian distribution.

(d) We know that

κ EI
lp = =
Kb T Kb T
p
~ >=
Using b ≡ 2lp , we have < |R| < R~2 > = N b2 = N b · b = Lc · 2Lp .
Thus if the temperature T increases, the persistence length lp decreases resulting in < |R| ~ >
decreasing as well. Physically, as T increases, the chain elements experience greater thermal
fluctuations which allows them to more frequently sample their high entropy configurations due
to a decreased persistence length. It results that the average end-to-end distance decreases as T
increases.
The protein titin displays a saw-tooth force extension behavior. Each peak shows a globular
domain unfolding (see Figure 1).
~ ∼
The energy required to unfold 1 domain Eunf old = F · ∆|R| = 200 pN · 25nm = 5000 pN · nm
Let’s consider that the length of each chain element of a titin protein in a folded state is b1 .
When the globular domain unfolds, the length increases to b2 > b1 . In order to know whether
the thermal energy at 50◦ C is sufficient to unfold globular domains :
~ will not decrease monotonically when increasing the temperature. Lc will increase
If yes, then |R|
energy time a globular domain unfolds.

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 Figure 1: Titin saw-tooth force extension behavior

~ will behave like DNA as temperature increases.

If no, then |R|
The thermal energy at 50◦ C is Kb T = (1.38 · 10−23 K
J
) · (323 K) = 4.5 pN · nm.
We can see that Eunf old >> Kb T at 50◦ C meaning that globular domains are unlikely to unfold
~ varies
at 50◦ C. Therefore the titin protein is expected to behave like DNA (meaning that |R|
only with lp ).

EI
(e) lp = Kb T

x2 dA ∝ a4 where a = effective radius of DNA fibers.

R
with I =
If we go from a dsDNA to a ssDNA, a decreases thus I decreases resulting in decreasing of lp
From a) we have

2Kb T ~ Kb T ~
FGC,2D = 2
· |R| = · |R|
Nb Lc Lp
1
⇒ FGC,2D ∝
lp

Thus the force increases when the persistence length decreases meaning that ssDNA requires
more force to extend to any given extension than dsDNA.

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Problem 2
From Darcy’s law, we define the hydraulic conductivity as

κρg
K=
µ
with κ being the hydraulic permeability, ρ the fluid density and µ the fluid viscosity.
(i) We have different test configurations. We can measure the following equilibrium constants :

(a) The longitudinal (confined-compressed) modulus H

(b) The elastic modulus E
(c) No single
(d) The longitudinal (confined-compressed) modulus H

(ii) Remember that the ”characteristic length” is the length over the fluid flows. For a poroelastic
material, we have a scaling

length2
τporo ∼
(mod) · (κ)
where mod is the relevant modulus from part (i). We thus have
L2 L2
(a) τ ∼ H·κ . The exact answer (not required) is π 2 ·K

R2
(b) τ ∼ E·κ

D2 (D/2)2
(c) τ ∼ (mod)·κ or (mod)·κ where mod is from your part (i)

L2
(d) τ ∼ H·K

(iii) The poroelastic relaxation time measuread in (a) and (d) are the same τporo (a) ≡ τporo (d). We
can argue in several different ways. Here it is demonstrated by superposition. Let’s consider a
displacement u (x,t), we obtain the following curves

We thus have have that the superposition of (A) and (B) gives of (d) but takes the same time
as (a).

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Problem 3
Let’s calculate the complex modulus of each cases. Remember that in series strains add whereas
stress are the same and in parallel strains are the same whereas stresses add. Furthermore, the use of
complex numbers allow to simplify a lot the differential equation. In fact, we have

d dσ
(t) = 0 eiωt ⇒ = iω0 eiωt = iω and σ(t) = σ0 eiωt ⇒ = iωσ0 eiωt = iωσ
dt dt
(i) Kelvin-Voigt model

d
σ = E + η
dt

In complex notation, we have

σ = E + η(iω)

The complex modulus G(iω) is

σ(t)
G(iω) = = E + iωη
(t)
p
The magnitude |G(iω)| is E 2 + ω2η2

(ii) Maxwell model

d 1 dσ σ
= +
dt E dt η

In complex notation, we have

iωσ σ
iω = +
E η

The complex modulus G(iω) is

iω 1 −1 ω 2 η 2 E + i(ωE 2 η)
 
σ(t)
G(iω) = = iω + =
(t) E η E 2 + ω2η2
s 2  2
ω2 η2 E ωE 2 η
The magnitude |G(iω)| is E 2 +ω 2 η 2
+ E 2 +ω 2 η 2

(iii) Standard Linear Solid (SLS) model

σ 
σ+α = E1  + β
dt dt

η E1
With α = E2 and β = η(1 + E2 )

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 In complex notation, we have

σ + αiωσ = E1  + βiω

The complex modulus G(iω) is

σ(t) E1 + βiω E1 − E1 αiω + βiω + αβω 2

G(iω) = = =
(t) 1 + αiω 1 + α2 ω 2
s 2  2
E1 +αβω 2 ω(β−E1 α)
The magnitude |G(iω)| is 1+α2 ω 2
+ 1+α2 ω 2

(iv) Poroelastic model

We solve this model qualitatively:

ω → 0, the material looks elastic (E)
ω → ∞, the water does not have time to move ⇒ looks incompressible (νef f ective ∼ 0.5)

Overall, we have the following plots

Part A : (iii) and (iv)

Part B : (i)