Physics 347 Solution Set 5 due: Nov.

22 page 1
21. This problem is a small generalization of Example 4 in Lect. 23.2.
Consider a lattice polymer (cubic lattice) with immediate reversal forbidden, as in example 4, but now
assume that there is an energy penalty Δ to bend the polymer to the 90o configurations.
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(a) Show that the probability that the (n+1)st link continues in the direction of the nth link is r " .
1+ 4e# $%
# 1+ r &
(b) Show that the mean-square end-to-end length is R 2 = Na 2 % ( + O(1) . Feel free to assume that the
$1 " r '
polymer is long enough so that r N << 1. !
$ 1+ r ' a + / kBT
(c) Show that at low temperatures the Kuhn length l K " a& ) * e , i.e., it increases
! % 1 # r ( T *0 2
exponentially. !
22. Radius of gyration of a freely jointed polymer.
Consider a freely-jointed homopolymer
r of!step-length ar and rcontour rlengthr Na in three dimensions. The
r r r
N+1 monomers are at positions Rn , n = 0,1,...,N , with R1 = R0 + a1, R2 = R0 + a1 + a2 ,...
r r Nr 1 N r
(a) Show that the center of mass (C of M) is at RCofM = R0 + " ak # " kak .
k=1 (N +1) k=1
! R is defined by R !2 = 1
N r r 2
(b) The radius of gyration G G
(N +1) n=0 (
# Rn " RCofM ) , i.e., RG2 is the average over
all polymer configurations of the mean-square
! distance between a monomer and the C of M. RG like the rms
en-to-end length R 2 is a measure of the size of a random-coil polymer.
! N ( N + 2) a 2
Show for the model described above that RG2 = .
6( N +1)
! Na 2 1 2
Note: For large N, this means that RG2 " = R , where R 2 is the mean end-to-end length, as
N large 6 6
calculated in class. This relation!between the radius of gyration and the end-to-end length turns out to be
general for all ideal Gaussian polymers (but I am not asking you to prove that here).
!
23. Entropic Elasticity in!one dimension. (see Lect. 25.2)
Consider a 1D polymer model with N steps of length a. Whether each step n is to the right (+) or to the left
N N
(-) is controlled by variables {" n = ±1}n=1, so that the overall displacement X = a # " n . The end of this
n=1
polymer is attached to an agency (perhaps, a very long spring) which exerts a constant force to the right of
magnitude |f|. The energy E stored in this external “spring” is
E = E ({" n }) = # f !X = fX = (force) $ (distance) , where f is the force exerted by the polymer and points to
!
the left (negative). Note that positive energy is stored when the polmeric length X decreases.
(a) Calculate the Helmholtz free energy F of the whole system, including the external agency.
! Hint: Z = $ e" #En = $ e" #fX ({% }) .
n {% }
(b) In this formulation, the polymeric displacement X is not fixed but becomes a statistical variable. Show
# 2 #2
generally that X = " ln Z and ( X " X ) = 2
ln Z .
! # ( $ f ) # ( )
$f
(c) Using the results of (a) and (b), calculate X as a function of the applied force f and invert to find f as a
function of X .
! !
!
 k T # X &
Hint: The result is f = " B tanh"1% (. page 2
a $ Na '
k T
(d) By expanding your result in (c), show that f = " B X for small <X>, i.e., at low force, and
X2
k T !# X &
f = B ln%1 " #
( , as X "Na , i.e., at large force.
2a $ Na '
(e) Use your result in (b) to calculate!the variance " X of X and show that it goes as N , i.e., that the
fluctuations of X become negligible at large N.
!
! The next two problems deal with the folding of a simple HP model of a lattice heteropolymer. Assume
that the lattice is a two-dimensional square !
! lattice !
and that the only interactions present are (i) a
! interaction of energy " > 0 for every WH nearest-neighbor contact, (ii) an attractive
repulsive
interaction of energy "# for every WP nearest-neighbor contact, and (iii) an attractive interaction of
energy "# (# > 0) for every HH nearest-neighbor contact.

24. Consider the hexamer! “protein” with the (ordered) sequence HPHPPH.
(a) Show that!this protein has a ground (“native”) state which is unique in shape (up to rotations, reflections,
! translations).
(b) Find the partition function and calculate as a function of temperature T the probability Pnative that the
protein will be found in its native state. What are the low- and high-temperature limits?
Hints:
The total number of self-avoiding hexamer configurations is 4x71=4x(81-10). Can you show this?
You will find that only five distinct energies occur. What are they? Label them E 0 < E1 < ... < E 4 and write
your answer in terms of these energies.
25. Consider now other hexamers with different H,P sequences.
(a) There are only four “compact shapes,” counting distinct orderings !along the backbone (123456) but not
rotations, translations, and reflections. What are they?
(b) Show that a noncompact shape can never be a UNIQUE ground state for any H,P sequence.
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(c) Consider the set of all possible H,P hexamer sequences (there are 2 = 64 of them). Show that 57 of
these do not “code” for a unique ground state, 6 of them code for two of the compact shapes (Which ones?
These are “highly designable.”), 1 of them codes for a second compact shape (which one?), and the third
compact shape is not a unique “native” (ground) state for any sequence.
Comment: These results illustrate two general ideas in a very simple context:
A. Only special “amino-acid” sequences lead to uniquely folded, native shapes.
B. Certain “native” shapes can be “designed for” by choosing the “right” “amino-acid” sequence, while
others cannot. More extensive calculations suggest that it is common for some shapes to be easily
“designable” (i.e., that there may be many sequences leading to the same or similar shapes), while other
shapes are not.