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Bubbles, clusters and denaturation in genomic DNA : modeling, parametrization, efficient computation

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2011

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https://doi.org/10.1142/S1402925111001611
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http://arxiv.org/abs/1102.0259

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Journal of Nonlinear Mathematical Physics. Taylor & Francis. 2011, 18(Suppl. 2), pp. 429-447. ISSN 1402-9251. eISSN 1776-0852. Available under: doi: 10.1142/S1402925111001611

Zusammenfassung

The paper uses mesoscopic, nonlinear lattice dynamics based (Peyrard–Bishop–Dauxois, PBD) modeling to describe thermal properties of DNA below and near the denaturation temperature. Computationally efficient notation is introduced for the relevant statistical mechanics. Computed melting profiles of long and short heterogeneous sequences are presented, using a recently introduced reparametrization of the PBD model, and critically discussed. The statistics of extended open bubbles and bound clusters is formulated and results are presented for selected examples.

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530 Physik

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DNA melting, denaturation bubbles, Peyrard–Bishop–Dauxois (PBD) model

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ISO 690THEODORAKOPOULOS, Nikos, 2011. Bubbles, clusters and denaturation in genomic DNA : modeling, parametrization, efficient computation. In: Journal of Nonlinear Mathematical Physics. Taylor & Francis. 2011, 18(Suppl. 2), pp. 429-447. ISSN 1402-9251. eISSN 1776-0852. Available under: doi: 10.1142/S1402925111001611
BibTex
@article{Theodorakopoulos2011Bubbl-51085,
  year={2011},
  doi={10.1142/S1402925111001611},
  title={Bubbles, clusters and denaturation in genomic DNA : modeling, parametrization, efficient computation},
  number={Suppl. 2},
  volume={18},
  issn={1402-9251},
  journal={Journal of Nonlinear Mathematical Physics},
  pages={429--447},
  author={Theodorakopoulos, Nikos}
}
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