Model For DNA Denaturation Research Articles

Numerical study of DNA denaturation with self-avoidance: pseudo-critical temperatures and finite size behaviour

We perform an extensive numerical study of the disordered Poland–Scheraga (PS) model for DNA denaturation in which self-avoidance is completely taken into account. To complement to our previous work, we focus here on the finite size scaling in terms of pseudo-critical temperatures. Notably, we find that the mean value and the fluctuations of the pseudo-Tc scale with the same exponent, the correlation length exponent (for which we provide the refined evaluation ). This result (coherent with the typical picture that describes random ferromagnets when disorder is relevant) is at variance with the numerical results reported in the literature for the PS model with self-avoidance, leading to an alternative scenario with a pseudo-first-order transition. We moreover introduce a crossover chain length N *, which we evaluate, appropriate for characterizing the approach to the asymptotic regime in this model. Essentially, below N *, the behaviour of the model in our study could also agree with such an alternative scenario. Based on an approximate prediction of the dependence of N * on the parameters of the model, we show that following the choice of such parameters it would not be possible to reach the asymptotic regime in practice. In such a context it becomes then possible to reconcile the apparently contradictory numerical studies.

On the disordered SAW model for DNA denaturation

We investigate numerically the transition properties for models of DNA denaturation, which can be relevant for certain classes of disordered systems. The investigation follows two, complementary, numerical approaches: on-lattice Monte Carlo like simulations or off-lattice statistical mechanics calculations, which can extend very significantly the affordable lengths for the sequences. The on-lattice model consists of two interacting self-avoiding walks with the same origin on a three-dimensional cubic lattice. We introduce two different contact energies, for the adenine–thymine coupling and the guanine–cytosine one, respectively, distributed according to a bimodal law. Whereas the transition is recognized to be of first order in the pure (homopolymer) case, the behaviour of quantities averaged over disorder suggests that the random system undergoes a second-order transition.

Topological origin of the phase transition in a model of DNA denaturation.

The hypothesis that phase transitions originate from some topological change of the critical level hypersurface of the potential energy receives direct evident support by our study of the Bishop-Peyrard model of DNA thermal denaturation.

Copper(II)-DNA denaturation. II. The model of DNA denaturation.

AbstractIn a continuing study of the denaturation of DNA as brought abought about by Cu(II) ions, results are presented for the dependence of Tm and τ (the terminal relaxation time) on ionic strength, pH, reactant concentrations, and temperature. Maximum stability of the double helix, as reflected by the longest relaxation times and highest Tm values, was observed between pH 5.3 and 6.2. Outside this range both Tm and τ decreased sharply. A second, faster relaxation time was deduced from the kinetic cureves. The apparent activation energies of the rapid and slow (“terminal”) relaxations were found to be 12 and 55 kcal/mole, respectively. Several lines of evidence led to the conclusions that (1) the rate‐determining step in DNA denaturation, when occurring in the transition region, is determined by chemical events and (2) the interactions which are disrupted kinetically in the rate‐determining step are those which account for the major portion of the thermal (Tm) stability of helical DNA.