PHYS 329 Winter 2020

Assignment 1

Due date: Wednesday, Feb 5th, 9:30 AM. Please upload a scanned copy of your assignment on
mycourses AND hand the physical copy in class for easier grading.

There are 3 independent problems. You are welcome to discuss these problems with your peers,
however the solution you hand should reflect your own work/understanding.

1. Density fluctuations
A cell, volume V , contains N statistically independent identical molecules, assumed to be
uniformly spread. Let us consider a subvolume v = rV of the cell (e.g. corresponding to an
organelle).
(a) What is the probability p for one given molecule to be in the organelle of volume v ?
(b) The probability p(Nv ) to have Nv of those molecules within the volume v is given by
the binomial law p(Nv ) = Nv !(NN−N
!
v )!
pNv (1 − p)N −Nv (you do not have to show this).
i. Check first that this is consistent with what we did in class for p = 1/2.
ii. Then, using Stirling formula, check that this probability is maximum for Nv = pN ,
which is the result we claimed in class without demonstrating it.
iii. In class, we saw that when r = 1/2, the state with highest multiplicity is Nv = N/2.
What is the state with highest multiplicity here ?
(c) In eucaryotes, the cell nucleus occupies roughly 20 % of the cell volume. With minimal
calculations, estimate the relative fluctuations ∆Nv /Nv that we expect for
i. transcribed RNA molecules corresponding to one gene (N = 10) ?
ii. some house-keeping protein (N = 10000) ?
iii. water molecules N = 1023 ?
2. Max Entropy model for casino game
Consider the following casino game: I toss two coins. If I get two heads the casino gives
me 1 $, if I get a head an a tail, nothing happens (I get 0), and if I get two tails, I have
to pay 1 $ to the casino. I play this game for 100 times in a row. So my potential “gain”
ranges anywhere between −100 $ and 100 $. N players (with N big) play this game, and
after careful examination, it turns out that the average “gain” (after 100 trials) is −20 $. We
call pHH , pHT and pT T the respective probabilities of obtaining two heads, one head/one tail
and two tails
(a) compute those probabilities and the expected average gain if the coins are identical, fair,
balanced, and independent.
(b) write a maximum entropy model using probabilties pHH , pHT and pT T . Show that the
result is given by a Boltzman-like distribution. In particular, show that pHH /pHT =
pHT /pT T , and use this with normalization to compute the numerical values of the max-
imum likelihood probabilities (this can be done analytically but I am OK if you write a
small code -please provide a copy then- and give numerical results).
(c) A maximum entropy model does not assume anything on the coins. They could be
different, coupled in a weird way, or the casino could cheat .... Now imagine I KNOW
that the two coins are identical and independent. Then we actually do not need a
maximum likelihood model. Show rather that we have pHH = x2 , pHT = 2x(1 − x),
and pT T = (1 − x)2 , where x is the probability to obtain one head with one coin. Write
then the average gain as a function of x, and compute the value of x as a function of
the average gain. Compare with the previous questions and comment on the similarities
and differences.

1
 F
Large distance
d to other end of
DNA molecule

Unbroken links
(energy 0, no internal states)

broken links
(energy � ,g internal states)

Figure 1: DNA zipper

3. DNA zipper
We model a DNA molecule as a zipper with N links. Links are spaced at equal intervals d
along the DNA strand. Each link is modelled as a two state system. A closed link has energy
0, while a broken link has energy  > 0. We further assume there are g internal degrees of
freedom for each broken link (meaning that each broken link can exist in g configurations).

(a) We first assume that all links are independent. Compute the probability for one link to
be broken. Show that the partition function of the entire DNA zipper is

Z = (1 + e−β(−µ) )N

where µ is a function of g. Compute the average energy of the DNA zipper by differ-
entiating the partition function, and check that this is consistent with what you would
obtain by directly computing the average energy of one link based on its probabilities
to be closed/broken.
(b) We require now that the zipper can only unzip from the left end, and that
the link number s can only open if all links to the left (1, 2, 3, ..., s − 1) are
already open. See Figure 1. We first consider the case g = 1, i.e. each link can be
either closed, either broken (1 state for each configuration). No force is applied.
i. Show that the partition function is, in the limit N → ∞
1
Z= 
1 − e− kT

You might need to use the famous mathematical identity ( ∞ n 1

P
n=0 x = 1−x ) that we
we use many times in this class.
ii. Compute the probability of link n to be broken. On a graph, plot this probability
as function of n. How does this situation compare to question (a) ?
iii. Compute < s >, the average number of open links. You might need this other
P s = x
mathematical identity s sx (1−x)2
(I would advise you to rederive it as an
exercise). What happens to the DNA molecule in the limit T → 0 and T → ∞ ?