Numerical study of the disordered Poland–Scheraga model of DNA denaturation

DOI10.1088/1742-5468/2005/06/P06004MaRDI QIDQ4968857zbMATH OpenOpenAlexFDO

Authors Thomas Garel, Cécile Monthus

Publication date 9 July 2019

Published in Journal of Statistical Mechanics: Theory and Experiment (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/cond-mat/0504094

zbMATH Keywords

disordered systems (theory)copolymers

Mathematics Subject Classification ID

Monte Carlo methods (65C05) Biochemistry, molecular biology (92C40) Genetics and epigenetics (92D10) Statistical mechanics of polymers (82D60) Molecular structure (graph-theoretic methods, methods of differential topology, etc.) (92E10)

Abstract: We numerically study the binary disordered Poland-Scheraga model of DNA denaturation, in the regime where the pure model displays a first order transition (loop exponent $c=2.15>2$). We use a Fixman-Freire scheme for the entropy of loops and consider chain length up to $N=4cdot10^5$, with averages over $10^4$ samples. We present in parallel the results of various observables for two boundary conditions, namely bound-bound (bb) and bound-unbound (bu), because they present very different finite-size behaviors, both in the pure case and in the disordered case. Our main conclusion is that the transition remains first order in the disordered case: in the (bu) case, the disorder averaged energy and contact densities present crossings for different values of $N$ without rescaling. In addition, we obtain that these disorder averaged observables do not satisfy finite size scaling, as a consequence of strong sample to sample fluctuations of the pseudo-critical temperature. For a given sample, we propose a procedure to identify its pseudo-critical temperature, and show that this sample then obeys first order transition finite size scaling behavior. Finally, we obtain that the disorder averaged critical loop distribution is still governed by $P(l)sim1/l^c$ in the regime $lllN$, as in the pure case.

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Cites work

• Poland-Scheraga models and the DNA denaturation transition
• Renormalization of polymer networks and stars

Cited in

(10)

• Numerical study of DNA denaturation with self-avoidance: pseudo-critical temperatures and finite size behaviour
• Two-dimensional random walk and critical behavior of double-strand DNA
• Strong disorder renewal approach to DNA denaturation and wetting: typical and large deviation properties of the free energy
• Generalized Poland-Scheraga denaturation model and two-dimensional renewal processes
• Poland-Scheraga models and the DNA denaturation transition
• The free energy in the Derrida-Retaux recursive model
• Scaling limit of the disordered generalized Poland-Scheraga model for DNA denaturation
• Influence of disorder on DNA denaturation: the disordered generalized Poland-Scheraga model
• Disorder and denaturation transition in the generalized Poland-Scheraga model
• DNA melting structures in the generalized Poland-Scheraga model

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