Statistical Mechanics of thermal denaturation of DNA oligomers

Double stranded DNA chain is known to have nontrivial elasticity. We study the effect of this elasticity on the denaturation profile of DNA oligomer by constraining one base pair at one end of the oligomer to remain in unstretched (or intact) state. The effect of this constraint on the denaturation profile of the oligomer has been calculated using the Peyrard-Bishop Hamiltonian. The denaturation profile is found to be very different from the free (i.e. without the constraint) oligomer. We have also examined how this constraint affects the denaturation profile of the oligomer having a segment of defect sites located at different parts of the chain.Comment: Appeared in Proceeding of Conference on "Liquid Crystals and other Soft materials", held at RRI, Bangalore Indi

The Structure and Freezing of fluids interacting via the Gay-Berne (n-6) potentials

We have calculated the pair correlation functions of a fluid interacting via the Gay-Berne(n-6) pair potentials using the \PY integral equation theory and have shown how these correlations depend on the value of n which measures the sharpness of the repulsive core of the pair potential. These results have been used in the density-functional theory to locate the freezing transitions of these fluids. We have used two different versions of the theory known as the second-order and the modified weighted density-functional theory and examined the freezing of these fluids for $8 \leq n \leq 30$ and in the reduced temperature range lying between 0.65 and 1.25 into the nematic and the smectic A phases. For none of these cases smectic A phase was found to be stabilized though in some range of temperature for a given $n$ it appeared as a metastable state. We have examined the variation of freezing parameters for the isotropic-nematic transition with temperature and $n$. We have also compared our results with simulation results wherever they are available. While we find that the density-functional theory is good to study the freezing transitions in such fluids the structural parameters found from the \PY theory need to be improved particularly at high temperatures and lower values of $n$.Comment: 21 Pages (in RevTex4), 6 GIF and 4 Postscript format Fig