PHYS 6327 HW 11

Due May 1 at 9am

1. The native state of some proteins contain an alpha helix, a three dimensional structure
determined by specific angles formed along the backbone. An unfolded protein will
lose its native structure and become disordered, becoming a random coil at high
temperature. A simple model[1] for the formation and denaturation of an alpha helix
is to assume each amino acid is in one of two states: a helical or coil state. A helical
state is assumed to have an internal partition function of qh and a coil an internal
partition function qc ; assuming the helical state is energetically favorable we expect
qh > qc . It is also assumed there is an interfacial energy ∆ > 0 for sites in the
helical state that neighbor a coil state, with no interfacial energy for neighboring
helix-helix or coil-coil states. Show that this model for helix formation in proteins is
equivalent to a one dimensional Ising model, and determine the equilibrium energy
of the protein at temperature T .
2. Consider an Ising Ladder, two one-dimensional Ising systems (tracks) that are con-
nected to one another as shown in the figure. The interaction strengths between
nearest neighbors are indicated, with Ji > 0. The spin states are si = ±1 and
ti = ±1 for the upper and lower sites, respectively. The sites have magnetic moment
µ = 1, and are both in a magnetic field B.

(a) Write down the Hamiltonian for this system.

(b) Determine an effective Hamiltonian on the mean field, where deviations from
the mean hsi i = σ and hti i = τ are assumed uncorrelated.
(c) Determine the self-consistent equations for the mean magnetizations. Show if
B = 0 that the critical temperature for spontaneous magnetization is predicted
to be kB Tc = 2J + |K|. Be sure to account for both K > 0 and K < 0 in this
calculation. Confirm that σ ∼ τ ∼ (Tc − T )1/2 in this limit.
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(d) Use the fact that tanh(x + y) ∼ tanh(x) + sech

(x) y/x in the limit as x → ∞
to show that σ = τ ∼ 1 − 2e −2βB 2J+K
1− B for B  0 and K > 0.
(e) Determine the mean magnetization for B → ∞ and K = −B in the mean field
approximation. Explain the physics of this situation.
(f) Argue why the exact solution for the Ising lattice will not permit spontaneous

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 magnetization for any values of the parameters J and K (despite the predictions
of the mean field approach). Note that you may do so by using a 4 × 4 transfer
matrix[2] and showing it’s true explicitly, but a physical argument that covers
all ranges of the parameters is fine (and less tedious).

References

[1] K Dill. Molecular Driving Forces Garland Science, 2010.

[2] G Xing-Ru and Y Zhan-Ru, Commun. Theor. Phys. Beijing 48 553 (2007)

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The Helix Coil model is a two state model with a nearest neighbor interaction through
the interfacial energy, and we naturally expect this will be equivalent to an Ising model.
If there was no interaction
P energy

n at all (so each site was distinct), the total partition
function would be QN = n N n g (h)g N −n (c) = [q(h) + q(c)]N . For a four-site system, we

would have the partition function

 
−2β∆ −2β∆ −2β∆
Q4 (h, h) = q(h) q(h)q(h) + q(h)q(c)e + q(c)q(h)e + q(c)q(c)e q(h)
 
−β∆ −β∆ −3β∆ −β∆
Q4 (h, c) = q(h) q(h)q(h)e + q(h)q(c)e + q(c)q(h)e + q(c)q(c)e q(c)
 
Q4 (c, h) = q(c) q(h)q(h)e−β∆ + q(h)q(c)e−β∆ + q(c)q(h)e−3β∆ + q(c)q(c)e−β∆ q(h)
 
−2β∆ −2β∆ −2β∆
Q4 (c, c) = q(c) q(h)q(h)e + q(h)q(c)e + q(c)q(h)e + q(c)q(c) q(c)

where the statistical weight of each site is the product of the state partition functions, and
the terms e−β∆ count the number of interfaces. We can write this as
Q(x, y) = v(x) · Tv(y) (1)
ν1 (x)e−βE(x,h)
 
v(x) = (2)
ν2 (x)e−βE(x,c)
α11 e−βE(h,h) α12 e−βE(h,c)
 
T = (3)
α21 e−βE(c,h) α22 e−βE(c,c)
where E(x, y) = (1 − δxy )∆, where there is zero interfacial energy if x = y and a fixed
interfacial energy ∆ if x 6= y, and where αij and νi (x) are coefficients that depend on the
partition functions q(h) and q(c). The coefficients must be determined somehow, and we
can see immediately that
α11 = q(h) α22 = q(c) (4)
which arises from the fact that if only the helix or coil states existed (so q(c) = 0 or
q(h) = 0, respectively), we would expect that QN ∼ TN ∼ q N (h). We can determine the
remaining coefficients by multiplying
v(h) · Tv(h) = ν12 (h)q(h) + ν22 (h)q(c)e−2β∆ + 2ν1 (h)ν2 (h)α12 e−2β (5)
v(c) · Tv(c) = ν12 (c)q(h)e−2β∆ + ν22 (c)q(c) + 2ν1 (c)ν2 (c)α12 e −2β
(6)
The first two terms of each correspond to the cases hhhh and hcch in the first equation,
or chhc and cccc in the second equation. These terms must match the partition function
we computed, from which we immediately see
ν1 (h) = q 3/2 (h) ν2 (h) = q(h)q −1/2 (c) (7)
−1/2 3/2
ν1 (c) = q(c)q (h) ν2 (c) = q (c) (8)

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which leads to
v(h) · Tv(h) = q 4 (h) + q 2 (h)q 2 (c)e−2β∆ + 2q 5/2 (h)q −1/2 (c)α12 e−2β (9)
2 2 −2β∆ 4 5/2 −1/2 −2β
v(c) · Tv(c) = q (h)q (c)e + q (c) + 2q (c)q (h)α12 e (10)
p
From this, we find α12 = q(h)q(c) gives the correct contribution to the partition function.
We immediately see this looks like the transfer matrix that exactly represents the Ising
model but with different symbols needing rearrangement:
e−βJ
 βJ+βµB 
e
Tising = (11)
e−βJ eβJ−βµB
g(h)g(c)e−β∆
 p 
g(h)
THC = (12)
g(h)g(c)e−β∆
p
g(c)
 q 
q(h) β∆/2 −β∆/2
q(c) e e
q(h)q(c)e−β∆/2 
p
= q
g(c) β∆/2
 (13)
e −β∆/2 e
g(h)
−βJ
 βJ+βµB 
e e
= q(c)eβµB−βJ (14)
e−βJ eβJ−βµB
where we’ve defined J = ∆/2 and µB = kB T log[q(h)/q(c)]/2. Note that this means the
magnetic field is effectively a free energy difference between the helix and coil states, driving
the system into the lower free energy state. Under the assumption that the helix state is
energetically favorable, we expect Fh = −kB T log(q(h)) < Fc , so that kB T log(q(h)/q(c)) =
−Fh + Fc = µB > 0. The transfer matrix is the same as the ising transfer matrix, up to a
multiplicative constant. The endpoint vector term is
 βJ   −βJ 
βµB/2 e −βµB/2 e
vising (1) = e −βJ vising (−1) = e (15)
e eβJ
 βJ+βµB/2 −1/2
q 3/2 (h)
  
5βµB/2−βJ e q (c)
vHC (h) = = q(c)e (16)
q(h)q 1/2 (c)eβ∆ e−βJ+βµB/2 q 1/2 (c)
 −βJ−βµB/2 −1/2
q(c)q 1/2 (h)eβ∆
  
−βJ e q (h)
vHC (c) = = q(c)e (17)
q 3/2 (c) eβJ−βµB/2 q 1/2 (c)
in our notation. Thus, we have a correspondence
THC = q(c)eβµB−βJ Tising (18)
but there is no direct correspondence between the ising model’s endpoint term and that of
the helix coil model. This produces an inextensive contribution to the partition function,
with
QN (s1 , sN ) = eN βµB−N βJ v(s1 ) · TN −3 v(sN ) (19)
QN = [q(h)q(c)]N/2 e−N β∆/2 λN
+ × g(β) (20)

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where g(β) accounts for the differing terms at the endpoints, and does not scale with
N.
The energy of the HC model will be

∂ log(Q) N N ∂λ+
U =− = (Uh + Uc ) + ∆ − N + O(N 0 ) (21)
∂β 2 2 ∂β
For the energy contribution of the ising model, we can just use the periodic boundary
condition expression, with
 q 
βJ 2 −4βJ
λ+ = e cosh(βµB) + sinh (βµB) + e (22)
    s    
βJ 1 q(h) 1 q(h) −4βJ
= e cosh log + sinh log +e (23)
2 q(c) 2 q(c)

This is difficult to evaluate further, since q(h) and q(c) depend on β. Leaving it in this
form is sufficient, and various limits are possible (e.g. J = 0 or q(h) ≈ q(c)), but none are
particularly enlightening.
FYI: You can certainly have done this using other approaches in your own notation. This
is the method we used in class to generate the ising transfer matrices, so is pretty straight-
forward for this problem.
2(a)
The Hamiltonian is
X X X X 
H = −J si sj − J ti tj − K si ti − µB si + ti (24)
hiji hiji i i

2(b)
There are two ways to do this, either is fine. The first is the standard Bragg Williams, we
replace nearest neighbors by σ or τ respectively. We have

Jqσ X Jqτ X X X 
H≈− si − ti − K si ti − µB si + ti (25)
2 2
i i i i

where q = 2 since each track is a 1D lattice. The advantage is is this super trivial to
evaluate: replace a single symbol. The disadvantage
Pis that this
P still has a couplingPbetween
the two fields. This can be improved by writing i si ti = i (si ti + si ti )/2 ≈ i (si τ +
ti σ)/2.

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Alternatively, we can drop correlations in the fluctuations by writing
X X
H = −J (δsi + σ)(δsj + σ) − J (δti + τ )(δtj + τ ) (26)
hiji hiji
X X
−K (δsi + σ)(δti + τ ) − µB (si + ti )
i i
N Jqσ 2 X N Jqτ 2 X
≈ − Jqσ si + − Jqτ ti (27)
2 2
i i
N Jqστ Kq X X
+ − (si τ + ti σ) − µB (si + ti ) (28)
2 2
i i

The advantage of this approach is that the coupling between the fields is completely re-
moved. The disadvantage is that fiddling with the constants is more tedious.
2(c)
There are two ways to do this, and you’ll probably have chosen one in part (b). The
standard Bragg Williams approach is to flip the state of spin si from down to up and see
what the mean change in energy is. We find

−∆E = 2qJσ + 2Kτ + 2µB (29)

Assuming the number of up or down spins for the first track is boltzmann distributed, we’d
have
N−s
  
1−σ −β∆
= = e = exp 2β qJσ + Kτ + µB (30)
N+s 1+σ

which, remembering that tanh−1 (x) = 12 log[(1 − x)/(1 + x)], yields

  
σ = tanh β 2Jσ + Kτ + µB (31)

Symmetry immediately implies that

  
τ = tanh β 2Jτ + Kσ + µB (32)

The advantage of this approach is that you don’t need to evaluate a sum. The disadvantage
is you have to remember a funny property of the inverse hyperbolic tangent, and also must
compute a change in energy that is not obvious from your Hamiltonian.
An equivalent calculation uses the Hamiltonian from 2(b), summing over the decoupled
fields. It is useful to also decouple the fields (meaning we define Bs = Bt arbitrarily, with

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no change to the Hamiltonian), We find
X  N X  N
−N βJ(σ 2 +τ 2 )
X
−βH (2Jσ+Kτ +µBs )βsi (2Jτ +Kσ+µBt )βti
QN = e =e e e
si =±1,ti =±1 si =±1 ti =±1
N −N βJ(σ 2 +τ 2 ) N
= 4 e cosh [(2Jσ + Kτ + µBs )β] cosh[(2Jτ + Kσ + µBt )β] (33)

The self consistent equations are determined by N µσ = ∂ log(Q)/∂Bs (and similarly for
τ ), yielding

σ = tanh[β(2Jσ + Kτ + µB)] τ = tanh(β(2Jτ + Kσ + µB)] (34)

an identical solution in comparison to the earlier approach. The advantage of this approach
is we just sum the Hamiltonian, without having to do some other independent calculation.
The disadvantage is we must split the field in order to determine the magnetization in each
track.
At B = 0, a solution to the self consistent equation is certainly σ = sgn(K)τ , with the sign
determined by the sign of K; with this substitution we have two identical self-consistent
equations since tanh(−x) = − tanh(x). Then we can write

σ = tanh(2βJσ + β|K|σ) (35)

and similarly for τ . This is identical to the self consistent equation for the 1D ising
model with the substitution of qJ → 2J + |K|, confirming the desired result. Because the
functional form has not changed, we still have tanh(x) ∼ x − x3 /3 for x = Tc σ/T , leading
the desired scaling of σ ∼ (Tc − T )1/2 .
2(d)
For strong fields, we might guess that σ ≈ τ (as the answer suggests), and write

sech2 (βµB)
 
σ ≈ tanh β(2J + K)σ + βµB ≈ tanh(βµB) + β(2J + K)σ (36)
βµB
tanh(x)
σ ≈ (37)
1 − sech2 (x) xc

where x = βµB and c = β(2J + K). In order to recover the asymptotic limit, we can
write tanh(x) ≈ 1 − 2e−x and sech(x) ≈ 2e−2x (neglecting terms smaller than e−2x ) and
find
    
−2x −2x c −2βµB 2J + K
σ ≈ 1 − 2e 1 + 2e ≈ 1 − 2e 1− (38)
x µB

2(e)

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If K = −B = 0, there’s nothing particularly interesting about the solution: we have two
disconnected 1D ising lattices in the absence of a magnetic field. However, if K = −B 6= 0
and µ = 1, there is a nontrivial behavior: we have
   
σ = tanh β[2Jσ − τ B + B] τ = tanh β[2Jτ − σB + B] (39)

In the limit of B → ∞, an interesting solution emerges. We would certainly imagine

that in a strong magnetic field one of our tracks would be aligned with the external field.
Suppose then that σ ≈ 1 (meaning it’s perfectly aligned with the field). Then we would
find that

τ ≈ tanh(2βJτ ) (40)

which is 1D self consistent equation in the absence of a field in the other track. That
is: we expect to find one track perfectly aligned with the field, and the other completely
decoupled from the field. This is due to the choice of the strength K = −B: the energy
decrease due to alignment with an external field is exactly counterbalanced by an energy
increase due to alignment with an antiferromagnetic interaction with the other lattice. Of
course, there is nothing special about σ over τ , so the other track may be aligned as well.
K = −B thus is predicted to correspond to one 1D ising model in a field, and one 1D ising
model in the absence of a field.
2(f)
If K = 0, we expect to find two independent 1D ising models, neither of which will exhibit
spontaneous magnetization (as we showed in class for the exact calculation). If K → ∞,
we expect to find two perfectly correlated 1D ising models (with si ≡ ti ), which is the
same thing as a 1D ising model. Thus, no spontaneous magnetization. If K → −∞,
we expect to find two perfectly anticorrelated 1D Ising models (with si ≡ −ti ), which
again is the same thing as a 1D ising model, so no magnetization in this limit either. In
every extreme value of K we would not find spontaneous magnetization exactly. Varying
J cannot cause spontaneous magnetization, as it is the interaction parameter in 1D. If we
were to postulate spontaneous magnetization at some finite value of K, we would therefore
be able to lose that magnetization by increasing the absolute magnitude of the coupling
between the two tracks. That is physically nonsensical: if both tracks are spontaneously
magnetized at some finite |K|, they would remain spontaneously magnetized at |K 0 | > |K|
(since the coupling between them would be increasing). Thus, at no K can spontaneous
magnetization occur.