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Edouard Yeramian

Publications and source records attributed to Edouard Yeramian.

3 recordsLinked to original sources

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. In complement to our previous work, we focus here on the finite size scaling in terms of pseudo-critical temperatures. We find notably that the mean value and the fluctuations of the pseudo-$T_c$ scale with the same exponent, the correlation length exponent $ν_r$ (for which we provide the refined evaluation $ν_r=2.9 \pm 0.4$). This result (coherent with the typical picture that describes random ferromagnets, when disorder is relevant) is at variance with 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 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 could be not possible to reach the asymptotic regime in practice. In such context it becomes then possible to reconcile the apparently contradictory numerical studies.

cond-mat.soft

Numerical evidence for relevance of disorder in a Poland-Scheraga DNA denaturation model with self-avoidance: Scaling behavior of average quantities

We study numerically the effect of sequence heterogeneity on the thermodynamic properties of a Poland-Scheraga model for DNA denaturation taking into account self-avoidance, i.e. with exponent c_p=2.15 for the loop length probability distribution. In complement to previous on-lattice Monte Carlo like studies, we consider here off-lattice numerical calculations for large sequence lengths, relying on efficient algorithmic methods. We investigate finite size effects with the definition of an appropriate intrinsic length scale x, depending on the parameters of the model. Based on the occurrence of large enough rare regions, for a given sequence length N, this study provides a qualitative picture for the finite size behavior, suggesting that the effect of disorder could be sensed only with sequence lengths diverging exponentially with x. We further look in detail at average quantities for the particular case x=1.3, ensuring through this parameter choice the correspondence between the off-lattice and the on-lattice studies. Taken together, the various results can be cast in a coherent picture with a crossover between a nearly pure system like behavior for small sizes N < 1000, as observed in the on-lattice simulations, and the apparent asymptotic behavior indicative of disorder relevance, with an (average) correlation length exponent ν_r >= 2/d (=2).

cond-mat.dis-nn

Generalized Poland-Scheraga model for supercoiled DNA

The Poland-Scheraga (PS) model for the helix-coil transition of DNA considers the statistical mechanics of the thermally induced binding of two complementary strands of DNA. In this paper, we show how to modify the PS model when a torque is applied to the extremities of DNA: We propose a simple model for the energy of twisted DNA and compute the entropy of a loop, subject to angular constraints (supercoiling). The denaturation curves are shifted towards lower or higher temperatures depending on the sign of the torque, and the UV absorption peaks are softened. The properties of supercoiled DNA can be deduced through the use of a numerical Legendre transform. In the homogeneous case, we find that for weak supercoiling, the phenomenological quadratic law relating the torsional energy to the number of unpaired bases is recovered.

q-bio.BM