Multiple timescales in a model for DNA denaturation dynamics

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 ${\tau }_1\sim L^{2.15}$ 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.

9 pages, 5 figures

References in corpus (1)

• Bubble coalescence in breathing DNA: Two vicious walkers in opposite potentials

Cited by in corpus (1)

• Path Integral Method for DNA Denaturation