Multiple timescales in a model for DNA denaturation dynamics

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 slow denaturation characterized by two timescales that depend on the chain length L. In a regime up to a first characteristic time τ1 ∼ L2.15, 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 segmentswithin the chain, slowing down the relaxation to fully molten configurations, which takes place at τ2 ∼ L3. This scenario is different from the picture in which the helical constraints are neglected.