Cell & Molecular Biophysics

Assignment 3

Fall 2015

1. A simple model of a polymer has a 1-D freely jointed chain where N links of length l can form
a 1-D random walk path. Suppose that n of the links point left and m links point right. The endto-end length of the polymer is L = (n-m) l and N = n + m.
a) Working by analogy with the entropy for particles in a box, and writing n and m in terms of N,
l and L as in the 1-D random walk derivation, show (using Stirlings approximation) that the
entropy, S, of a general configuration for the chain in terms of N, l and L is given by:
S

N
L
L
L
L

kB 1 ln 1 1 ln 1 2 ln 2
2 Nl Nl Nl Nl

b) If the polymer is completely stretched out so L = Nl, what is the entropy? What is the entropy
if L = 0?
c) Show that the entropy is a maximum when L = 0 (i.e. when m = n).
d) Suppose now, that the end-to-end length is much less than the total contour length the polymer
would have if all of its N links were stretched out into a line (i.e. if L/Nl << 1). Write down an
approximate form for the entropy for this case.
(Hint: recall that ln 1 x x 1 x 2 and ln 1 x x 1 x 2 if x << 1.
2

e) Using the form from part c) (you will use c) for the rest of this problem), the free energy of the
polymer chain is given by F = E TS. In the ideal freely jointed polymer chain, the links in the
chain do not interact with one another, so the internal energy E is the same for all configurations,
and E is a constant, independent of the end-to-end length, L. Write down the expression for the
free energy of the 1-D random walk polymer.
f) We can take a derivative of the free energy with respect to the end-to-end length, L to find a
quantity with units of force (i.e. f = dF/dL ). Evaluate this derivative and show that it has the
units of force (recall that the one Joule [kg m2/s2] = one Newton meter [kg m/s2 x m].
g) You should now we have a relation between force and polymer end-to-end length that looks
like Hookes law, f = kspringL. Pattern match to Hookes Law and find an expression for the
spring constant for this polymer spring. Such polymer is an example of an entropic spring
that resists stretching, gets stiffer as temperature increases and for which stiffness decreases as
the number of links, N, increases.
2. If one injects a spot of dye and allows it to undergo 2-D diffusion. The concentration, c, as a
function of time and distance from the initial location of the spot is given by:
r2
co
c r, t
exp
4 Dt 4 Dt
a) Verify that this expression satisfies the diffusion equation.
b) Verify using Gaussian integrals that <r2> = 4Dt as one would expect for 2-D diffusion
c) Show that the concentration seen by an observer at fixed distance r from the initial release
point peaks at a certain time and find that time in terms of r and D.
d) Find the concentration at distance r at this peak time and show that it is proportional to 1/r2
and find the proportionality constant.
3. Jean Perrin attempted to verify Einsteins predictions about Brownian motion around 1908.
Perrin took colloidal particles of gutta-percha (natural rubber) with radius 0.37 m and
suspended them in water at 20C. He watched the projection of their motion into the xy plane, so
a two-dimensional random walk should describe their motions. Following a suggestion of his
colleague P. Langevin, he observed the location of a particle, waited 30 s, then observed again

Cell & Molecular Biophysics

Assignment 3

Fall 2015

and plotted the net displacement in that time interval. He collected 500 data points in this way
and calculated <r2>1/2 for the displacement to be 7.84 m.
a) Use this information to obtain an estimate for the Boltzmann constant, kB.
b) Use this kB estimate to find an estimate of Avogadros Number.
4. [Required for Grad students/Optional for Undergrads] Brownian motion and gravitational
sedimentation can be combined naturally by considering that a particles position higher up in
the suspension has energy Egrav = mgz, where m is the difference between the mass of the
particles and the mass of the water they displace, g is the acceleration of gravity and z is the
height above the bottom of the tube. One can then write a Boltzmann factor to find equilibrium
particle concentration as a function of height.
a) N particles are initially mixed into volume V, to achieve concentration co = N/V. The density
of the particles is p. They are suspended in a fluid which has a density f. If the container is a
flat-bottomed cylindrical tube of height h = 0.1 m write the equation for the equilibrium
concentration profile as a function of height z. Note that the earth's gravity acts in the z-direction,
with acceleration g = 9.8 m/sec2. Hint: Use a Boltzmann factor for the relative probability wrt the
probability at the bottom of the container. Find the proportionality constant (it is not just co) from
the fact that integrating c ( z ) dV over the volume should give the total number of particles, N.

b) Plot the relative concentration c(z)/c0 as a function of height for z = 0 to h (= 0.1 m) for
mg/kBT = 2 m-1 and mg/kBT = 2 x 106 m-1.
c) One of the other experiments that Jean Perrin did to calculate Avogadros number involved
looking at the equilibrium concentration of emulsions of rubber particles suspended in water (see
the website http://web.lemoyne.edu/~giunta/perrin.html for more information). Perrin found the
relative concentration of granules of the vegetable latex gamboge (density = 1.2067 g/cm3;
radius = 0.213 m) by counting 13,000 granules in total. This was done at room temperature
(20C). If we define the relative concentration at h = 5 m from the bottom of the viewing
chamber to be 1.00, and then we get the following data for relative concentration as a function of
increasing height above the bottom of the chamber:
Height
(m)
5
35
65
95

Relative Density
[c/c(0)]
1.000
0.470
0.226
0.121

(the suspending medium is water). From this data, and the relation found in part a [which should
have been of the form c z / c(0) exp(mg[ z z 0 ] k BT ) ] find another estimate for
Boltzmanns constant kB and hence Avogadros number (the answer is, again, a little high).