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 (9)

• Why is the DNA Denaturation Transition First Order?
• Dynamical scaling of the DNA unzipping transition
• Thermal denaturation of an helicoidal DNA model
• Bubble dynamics in DNA
• Crossover behavior for long reptating polymers
• Inter-strand distance distribution of DNA near melting
• Effects of mechanical strain on thermal denaturation of DNA
• Bubble coalescence in breathing DNA: Two vicious walkers in opposite potentials
• Structure factor and dynamics of the helix-coil transition

Cited by in corpus (8)

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• Twist/Writhe Partitioning in a Coarse-Grained DNA Minicircle Model
• Path Integral Method for DNA Denaturation
• Unwinding dynamics of double-stranded polymers
• Equilibrium winding angle of a polymer around a bar
• A lattice polymer study of DNA renaturation dynamics
• Rotational dynamics of entangled polymers
• Hotter isn't faster for a melting RNA hairpin