Journal of Nonlinear Mathematical Physics

Volume 18, Issue Supplement 2, December 2011, Pages 429 - 447

Bubbles, Clusters and Denaturation in Genomic DNA: Modeling, Parametrization, Efficient Computation

Authors
Nikos Theodorakopoulos
Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, Vasileos Constantinou 48, 116 35 Athens, Greece
Fachbereich Physik, Universität Konstanz, 78457 Konstanz, Germany,ntheodor@eie.gr,Nikos.Theodorakopoulos@uni-konstanz.de
Received 31 October 2010, Accepted 2 February 2011, Available Online 7 January 2021.
DOI
10.1142/S1402925111001611How to use a DOI?
Keywords
DNA melting; denaturation bubbles; Peyrard–Bishop–Dauxois (PBD) model
Abstract

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.

Copyright
© 2011 The Authors. Published by Atlantis Press and Taylor & Francis
Open Access
This is an open access article distributed under the CC BY-NC 4.0 license (http://creativecommons.org/licenses/by-nc/4.0/).

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Journal
Journal of Nonlinear Mathematical Physics
Volume-Issue
18 - Supplement 2
Pages
429 - 447
Publication Date
2021/01/07
ISSN (Online)
1776-0852
ISSN (Print)
1402-9251
DOI
10.1142/S1402925111001611How to use a DOI?
Copyright
© 2011 The Authors. Published by Atlantis Press and Taylor & Francis
Open Access
This is an open access article distributed under the CC BY-NC 4.0 license (http://creativecommons.org/licenses/by-nc/4.0/).

Cite this article

TY  - JOUR
AU  - Nikos Theodorakopoulos
PY  - 2021
DA  - 2021/01/07
TI  - Bubbles, Clusters and Denaturation in Genomic DNA: Modeling, Parametrization, Efficient Computation
JO  - Journal of Nonlinear Mathematical Physics
SP  - 429
EP  - 447
VL  - 18
IS  - Supplement 2
SN  - 1776-0852
UR  - https://doi.org/10.1142/S1402925111001611
DO  - 10.1142/S1402925111001611
ID  - Theodorakopoulos2021
ER  -