Polymer Reptation in Disordered Media

The effect of ambient disorders and sequence heterogeneities on the reptation of a long polymer is studied with the aid of a disordered tube model. The dynamics of a random heteropolymer is found to be much slower than that of a homopolymer due to collective pinning effects. The asymptotic properties belong to the universality class of a directed path in (1+1)-dimensional random media.Comment: 4 pages, to appear in PRL; text, figures and related (p)reprints also available at http://matisse.ucsd.edu/~hwa/pub.htm

Dynamical Properties of a Growing Surface on a Random Substrate

The dynamics of the discrete Gaussian model for the surface of a crystal deposited on a disordered substrate is investigated by Monte Carlo simulations. The mobility of the growing surface was studied as a function of a small driving force $F$ and temperature $T$. A continuous transition is found from high-temperature phase characterized by linear response to a low-temperature phase with nonlinear, temperature dependent response. In the simulated regime of driving force the numerical results are in general agreement with recent dynamic renormalization group predictions.Comment: 10 pages, latex, 3 figures, to appear in Phys. Rev. E (RC

Effects of mechanical strain on thermal denaturation of DNA

As sections of a strand duplexed DNA denature when exposed to high temperature, the excess linking number is taken up by the undenatured portions of the molecule. The mechanical energy that arises because of the overwinding of the undenatured sections can, in principle, alter the nature of the thermal denaturation process. Assuming that the strains associated with this overwinding are not relieved, we find that a simple model of strain-altered melting leads to a suppression of the melting transition when the unaltered transition is continuous. When the melting transition is first order in the absence of strain associated with overwinding, the modification is to a third order phase transition.Comment: 4 pages, 5 figures, RevTe

Statistical mechanics of base stacking and pairing in DNA melting

We propose a statistical mechanics model for DNA melting in which base stacking and pairing are explicitly introduced as distinct degrees of freedom. Unlike previous approaches, this model describes thermal denaturation of DNA secondary structure in the whole experimentally accessible temperature range. Base pairing is described through a zipper model, base stacking through an Ising model. We present experimental data on the unstacking transition, obtained exploiting the observation that at moderately low pH this transition is moved down to experimentally accessible temperatures. These measurements confirm that the Ising model approach is indeed a good description of base stacking. On the other hand, comparison with the experiments points to the limitations of the simple zipper model description of base pairing.Comment: 13 pages with figure

New evidence for super-roughening in crystalline surfaces with disordered substrate

We study the behavior of the Binder cumulant related to long distance correlation functions of the discrete Gaussian model of disordered substrate crystalline surfaces. We exhibit numerical evidence that the non-Gaussian behavior in the low-$T$ region persists on large length scales, in agreement with the broken phase being super-rough.Comment: 10 pages and 4 figures, available at http://chimera.roma1.infn.it/index_papers_complex.html . We have extended the RG discussion and minor changes in the tex

Crystal surfaces with correlated disorder: Phase transitions between roughening and superroughening

A theory for surface transitions in the presence of a disordered pinning potential is presented. Arbitrary disorder correlations are treated in the framework of a dynamical functional renormalization group. The roughening transition, where surface roughness and mobility behave discontinuously, is shown to turn smoothly into the continuous superroughening transition, when the range of disorder correlations is decreased. Implications for random-field $XY$-models and vortex glasses are discussed.Comment: 13 pages with 2 figures, latex+revte

Roles of stiffness and excluded volume in DNA denaturation

The nature and the universal properties of DNA thermal denaturation are investigated by Monte Carlo simulations. For suitable lattice models we determine the exponent c describing the decay of the probability distribution of denaturated loops of length l, $P \sim l^{-c}$. If excluded volume effects are fully taken into account, c= 2.10(4) is consistent with a first order transition. The stiffness of the double stranded chain has the effect of sharpening the transition, if it is continuous, but not of changing its order and the value of the exponent c, which is also robust with respect to inclusion of specific base-pair sequence heterogeneities.Comment: RevTeX 4 Pages and 4 PostScript figures included. Final version as publishe

Force fluctuation in a driven elastic chain

We study the dynamics of an elastic chain driven on a disordered substrate and analyze numerically the statistics of force fluctuations at the depinning transition. The probability distribution function of the amplitude of the slip events for small velocities is a power law with an exponent $+AFw-tau$ depending on the driving velocity. This result is in qualitative agreement with experimental measurements performed on sliding elastic surfaces with macroscopic asperities. We explore the properties of the depinning transition as a function of the driving mode (i.e. constant force or constant velocity) and compute the force-velocity diagram using finite size scaling methods. The scaling exponents are in excellent agreement with the values expected in interface models and, contrary to previous studies, we found no difference in the exponents for periodic and disordered chains.Comment: 8 page

Effect of defects on thermal denaturation of DNA Oligomers

The effect of defects on the melting profile of short heterogeneous DNA chains are calculated using the Peyrard-Bishop Hamiltonian. The on-site potential on a defect site is represented by a potential which has only the short-range repulsion and the flat part without well of the Morse potential. The stacking energy between the two neigbouring pairs involving a defect site is also modified. The results are found to be in good agreement with the experiments.Comment: 11 pages including 5 postscript figure; To be appear in Phys. Rev.