Numerical evidence for relevance of disorder in a Poland-Scheraga DNA denaturation model with self-avoidance: scaling behavior of average quantities
CERES-ERTI (Plateforme Environnement) École Normale Supérieure, 24 rue Lhomond, 75005 Paris, France
2 Unité de Bio-Informatique Structurale, CNRS URA 2185, Institut Pasteur, 25-28 rue du Docteur Roux, 75015 Paris, France
Corresponding author: a firstname.lastname@example.org
Published online: 24 May 2007
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 cp = 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 , as observed in the on-lattice simulations, and the apparent asymptotic behavior indicative of disorder relevance, with an (average) correlation length exponent νr ≥2/d (=2).
PACS: 64.60.Fr – Equilibrium properties near critical points, critical exponents / 82.39.Pj – Nucleic acids, DNA and RNA bases / 02.60.Cb – Numerical simulation; solution of equations
© EDP Sciences, Società Italiana di Fisica, Springer-Verlag, 2007