Bubbles, clusters and denaturation in genomic DNA: modeling, parametrization, efficient computation
Statistical Mechanics
2015-03-18 v1 Soft Condensed Matter
Biological Physics
Biomolecules
Abstract
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.
Cite
@article{arxiv.1102.0259,
title = {Bubbles, clusters and denaturation in genomic DNA: modeling, parametrization, efficient computation},
author = {Nikos Theodorakopoulos},
journal= {arXiv preprint arXiv:1102.0259},
year = {2015}
}
Comments
to appear in a special issue of the Journal of Nonlinear Mathematical Physics (ed. G. Gaeta)