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/).
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 -