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.

7 pages, 4 figures

References in corpus (1)

• Sequence sensitivity of breathing dynamics in heteropolymer DNA

Cited by in corpus (6)

• Dynamics of DNA-breathing: Weak noise analysis, finite time singularity, and mapping onto the quantum Coulomb problem
• Simplified Langevin approach to the Peyrard-Bishop-Dauxois model of DNA
• Diffusion of two particles with a finite interaction potential in one dimension
• Multiple timescales in a model for DNA denaturation dynamics
• Finding the optimum activation energy in DNA breathing dynamics: A Simulated Annealing approach
• Bubble merging in breathing DNA as a vicious walker problem in opposite potentials