Numerical evidence for relevance of disorder in a Poland-Scheraga DNA denaturation model with self-avoidance: scaling behavior of average quantities |
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Authors: | B Coluzzi E Yeramian |
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Institution: | (1) 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 |
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Abstract: | 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). |
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Keywords: | 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 |
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