Multiple timescales in a model for DNA denaturation dynamics

Details Multiple timescales in a model for DNA denaturation dynamics Multiple timescales in a model for DNA denaturation dynamics

2008-03-28

arxiv.org/abs/0803.4122v2

J. Phys. A: Math. Theor. 42 (2009) 082003

Physics

Condensed Matter

Statistical Mechanics

9 pages, 5 figures

Scientific paper

10.1088/1751-8113/42/8/082003

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 $\tau_1\sim L^{2.15}$ 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 $\tau_2\sim L^3$. This scenario is different from the picture in which the helical constraints are neglected.

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