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

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

2011-02-01

arxiv.org/abs/1102.0259v1

Journal of Nonlinear Mathematical Physics (JNMP) vol. 18, Supplementary Issue 2(2011) pp. 429-447

Physics

Condensed Matter

Statistical Mechanics

to appear in a special issue of the Journal of Nonlinear Mathematical Physics (ed. G. Gaeta)

Scientific paper

10.1142/S1402925111001611

The paper uses mesoscopic, non-linear 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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