Bubbles, clusters and denaturation in genomic DNA : modeling, parametrization, efficient computation
Bubbles, clusters and denaturation in genomic DNA : modeling, parametrization, efficient computation
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2011
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Journal of Nonlinear Mathematical Physics ; 18 (2011), Suppl. 2. - S. 429-447. - Taylor & Francis. - ISSN 1402-9251. - eISSN 1776-0852
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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THEODORAKOPOULOS, Nikos, 2011. Bubbles, clusters and denaturation in genomic DNA : modeling, parametrization, efficient computation. In: Journal of Nonlinear Mathematical Physics. Taylor & Francis. 18(Suppl. 2), pp. 429-447. ISSN 1402-9251. eISSN 1776-0852. Available under: doi: 10.1142/S1402925111001611BibTex
@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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