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

Theodorakopoulos, Nikos

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

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Datum

2011

Publikationstyp

Zeitschriftenartikel

Publikationsstatus

Published

Erschienen 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

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.

Fachgebiet (DDC)

530 Physik

Schlagwörter

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

Zitieren

ISO 690

THEODORAKOPOULOS, 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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