Advanced

Stochastic approach to DNA breathing dynamics

Banik, S. K; Ambjörnsson, T LU and Metzler, R (2005) In Europhysics Letters 71(5). p.852-858
Abstract
We propose a stochastic Gillespie scheme to describe the temporal fluctuations of local denaturation zones in double-stranded DNA as a single-molecule time series. It is demonstrated that the model recovers the equilibrium properties. We also study measurable dynamical quantities such as the bubble size autocorrelation function. This efficient computational approach will be useful to analyse in detail recent single-molecule experiments on clamped homopolymer breathing domains, to probe the parameter values of the underlying Poland-Scheraga model, as well as to design experimental conditions for similar setups.
Please use this url to cite or link to this publication:
author
publishing date
type
Contribution to journal
publication status
published
subject
in
Europhysics Letters
volume
71
issue
5
pages
852 - 858
publisher
EDP Sciences
external identifiers
  • scopus:24344507289
ISSN
0295-5075
DOI
10.1209/epl/i2005-10144-9
language
English
LU publication?
no
id
2857a4e3-ce92-4e53-bde6-9639f2c084bd
alternative location
http://stacks.iop.org/0295-5075/71/i=5/a=852?key=crossref.37b5cfd9ddb7b32bc59d7bff539d9be2
date added to LUP
2019-05-03 11:44:34
date last changed
2019-08-28 04:51:14
@article{2857a4e3-ce92-4e53-bde6-9639f2c084bd,
  abstract     = {We propose a stochastic Gillespie scheme to describe the temporal fluctuations of local denaturation zones in double-stranded DNA as a single-molecule time series. It is demonstrated that the model recovers the equilibrium properties. We also study measurable dynamical quantities such as the bubble size autocorrelation function. This efficient computational approach will be useful to analyse in detail recent single-molecule experiments on clamped homopolymer breathing domains, to probe the parameter values of the underlying Poland-Scheraga model, as well as to design experimental conditions for similar setups.},
  author       = {Banik, S. K and Ambjörnsson, T and Metzler, R},
  issn         = {0295-5075},
  language     = {eng},
  month        = {09},
  number       = {5},
  pages        = {852--858},
  publisher    = {EDP Sciences},
  series       = {Europhysics Letters},
  title        = {Stochastic approach to DNA breathing dynamics},
  url          = {http://dx.doi.org/10.1209/epl/i2005-10144-9},
  volume       = {71},
  year         = {2005},
}