dorsal/arxiv
View SchemaStochastic approach to DNA breathing dynamics
| Authors | Suman Kumar Banik, Tobias Ambjornsson, Ralf Metzler |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0506025 |
| URL | https://arxiv.org/abs/q-bio/0506025 |
| DOI | 10.1209/epl/i2005-10144-9 |
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.
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"abstract": "We propose a stochastic Gillespie scheme to describe the temporal\nfluctuations of local denaturation zones in double-stranded DNA as a single\nmolecule time series. It is demonstrated that the model recovers the\nequilibrium properties. We also study measurable dynamical quantities such as\nthe bubble size autocorrelation function. This efficient computational approach\nwill be useful to analyse in detail recent single molecule experiments on\nclamped homopolymer breathing domains, to probe the parameter values of the\nunderlying Poland-Scheraga model, as well as to design experimental conditions\nfor similar setups.",
"arxiv_id": "q-bio/0506025",
"authors": [
"Suman Kumar Banik",
"Tobias Ambjornsson",
"Ralf Metzler"
],
"categories": [
"q-bio.BM",
"cond-mat.soft"
],
"doi": "10.1209/epl/i2005-10144-9",
"title": "Stochastic approach to DNA breathing dynamics",
"url": "https://arxiv.org/abs/q-bio/0506025"
},
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"type": "Model",
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