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N. Theodorakopoulos- Nonlinear physics (solitons, chaos, discrete breathers)

N. Theodorakopoulos- Nonlinear physics (solitons, chaos, discrete breathers)

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02/28/2012

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At any finite temperature, we will have to consider the competition of the two possible
structures: the one corresponding to the fixed point, and the corresponding to the DW with
the least energy. Strictly speaking, in the latter case we are considering the totality of all
possible values of L.

Free energy associated with a given minimum

For small displacements around any given local minimum {¯yn}, i.e.

yn = ¯yn +un

the total potential energy will be given, to quadratic order in the displacements, by

Φ(u)E(¯y) + 1
2

i,j

hijuiuj ,

where E(¯y) is the energy of the local minimum.

The associated configurational part of the partition function will be

Z(¯y) = e−βE(¯y)


−∞

N

m=1

dum

e−β

2

i,j

hijuiuj

= e−βE(¯y)

N
ν=1


βΛν

1/2

(14.35)

where the product runs over all eigenvalues of the Hessian. Note that the eigenvalues must be
strictly positive, not just nonnegative. The free energy associated with any given minimum
will then be

F(¯y) =T lnZ(¯y) = E(¯y) T
2

N
ν=1

ln


βΛν

(14.36)

Comparison of free energies

The spectra of (i) the fixed point and (ii) the stable DW with the minimal energy at some
finite L are shown in Fig. 14.2.2.

142

14 Unbinding the double helix

Now consider the difference in free energies between the DW with the minimal energy at
some finite L and the fixed point

∆F(L) = E∗(L) T
2

N
ν=1

ln

Λ0

ν
Λ∗ν

(14.37)

where the star in the superscript denotes the DW and the 0 the fixed point.

The second term represents the difference in entropies. Formation of the DW generates a
gain in entropy. The quantity

1
2

N
ν=1

ln

Λ0

ν
Λ∗ν

L

p∗σ(R)

is generally proportional to the number L/p∗ of unbound sites. The extra entropy comes
exclusively from the unbound part. It is due to the fact that the acoustic phonons which
live in the unbound region have lower frequencies than the optical phonons which live in the
bound state defined by fixed point.

Combining terms, the difference in free energy can be written as

∆F(L) = [2Tσ(R)] L
p∗

(14.38)

which becomes zero at

Tc(R) = 2

σ(R)

(14.39)

and negative at higher temperatures. Thus, if the temperature is raised beyond Tc(R) a DW
of any length can be formed spontaneously - since it generates a net gain in free energy.
Denaturation can occur spontaneously.

Alternatively, we may look at the derivative

p = dF(L)

dL = [2Tσ(R)] 1
p∗

(14.40)

which represents the unzipping force at a finite temperature T. Spontaneous thermal de-
naturation is, in this sense, equivalent to the vanishing of the unzipping force.

For not too large values of R, the proportionality constant is

σ(R) = ln

R/2 + 1 +R/2

.

(14.41)

In the continuum limit, R 1, this gives a Tc = 2(2/R)1/2

, which is exactly the critical

temperature found in Section 14.1.2.

In summary, what I have presented in this lecture is an alternative picture of the DNA
instability, based on the underlying, competing nonlinear equilibrium structures (domain
walls vs. fixed point). The results suggest that the domain wall, via the entropic gain it
generates, can overcome the energetic cost of its production. In other words, spontaneous
formation of a DW at the instability temperature is what really “drives” DNA denaturation.

143

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