Multiple timescales in a model for DNA denaturation dynamics

DOI10.1088/1751-8113/42/8/082003MaRDI QIDQ3608942zbMATH OpenOpenAlexFDO

Authors Marco Baiesi, Roberto Livi

Publication date 6 March 2009

Published in Journal of Physics A: Mathematical and Theoretical (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/0803.4122

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40)

Abstract: The denaturation dynamics of a long double-stranded DNA is studied by means of a model of the Poland-Scheraga type. We note that the linking of the two strands is a locally conserved quantity, hence we introduce local updates that respect this symmetry. Linking dissipation via untwist is allowed only at the two ends of the double strand. The result is a slow denaturation characterized by two time scales that depend on the chain length $L$. In a regime up to a first characteristic time $a{u}_{1}sim{L}^{2.15}$ the chain embodies an increasing number of small bubbles. Then, in a second regime, bubbles coalesce and form entropic barriers that effectively trap residual double-stranded segments within the chain, slowing down the relaxation to fully molten configurations, which takes place at $a{u}_{2}sim{L}^3$. This scenario is different from the picture in which the helical constraints are neglected.

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