Stochastic approach to DNA breathing dynamics
(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:
https://lup.lub.lu.se/record/2857a4e3-ce92-4e53-bde6-9639f2c084bd
- author
- Banik, S. K ; Ambjörnsson, T LU and Metzler, R
- publishing date
- 2005-09-01
- 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
- 2022-03-31 17:21:51
@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}}, doi = {{10.1209/epl/i2005-10144-9}}, volume = {{71}}, year = {{2005}}, }