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

Tomas Novotný; Jonas Nyvold Pedersen; Tobias Ambjörnsson; Mikael Sonne Hansen; Ralf Metzler

doi:10.1209/0295-5075/77/48001

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

Tomas Novotný, Jonas Nyvold Pedersen, Tobias Ambjörnsson, Mikael Sonne Hansen, Ralf Metzler

Research output: Contribution to journal › Journal article › Research › peer-review

Abstract

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.

Original language	English
Journal	EPL
Volume	77
Pages (from-to)	48001
ISSN	0295-5075
DOIs	https://doi.org/10.1209/0295-5075/77/48001
Publication status	Published - 2007

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title = "Bubble coalescence in breathing DNA: Two vicious walkers in opposite potentials",

abstract = "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.",

author = "Tomas Novotn{\'y} and Pedersen, {Jonas Nyvold} and Tobias Ambj{\"o}rnsson and Hansen, {Mikael Sonne} and Ralf Metzler",

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language = "English",

volume = "77",

pages = "48001",

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TY - JOUR

T1 - Bubble coalescence in breathing DNA

T2 - Two vicious walkers in opposite potentials

AU - Novotný, Tomas

AU - Pedersen, Jonas Nyvold

AU - Ambjörnsson, Tobias

AU - Hansen, Mikael Sonne

AU - Metzler, Ralf

PY - 2007

Y1 - 2007

N2 - 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.

AB - 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.

U2 - 10.1209/0295-5075/77/48001

DO - 10.1209/0295-5075/77/48001

M3 - Journal article

VL - 77

SP - 48001

JO - EPL

JF - EPL

SN - 0295-5075

ER -