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

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

2006-10-26

arxiv.org/abs/cond-mat/0610752v1

Europhys Lett 77, 48001 (2007)

Physics

Condensed Matter

Statistical Mechanics

7 pages, 4 figures

Scientific paper

10.1209/0295-5075/77/48001

We investigate the coalescence of two DNA-bubbles initially located at weak segments and separated by a more stable barrier region in a designed construct of double-stranded DNA. The characteristic time for bubble coalescence and the corresponding distribution are derived, as well as the distribution of coalescence positions along the barrier. Below the melting temperature, we find a Kramers-type barrier crossing behaviour, while at high temperatures, the bubble corners perform drift-diffusion towards coalescence. The results are obtained by mapping the bubble dynamics on the problem of two vicious walkers in opposite potentials.

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