A generalized Langevin formalism of complete DNA melting transition

¹  Department of Biotechnology and Biochemical Engineering, Indian Institute of Technology - Kharagpur-721302, India
²  Department of Mechanical Engineering, Indian Institute of Technology - Kharagpur-721302, India

Corresponding author: suman@mech.iitkgp.ernet.in

Received: 20 December 2007
Accepted: 2 July 2008

Abstract

Melting transition of double-stranded oligonucleotide sequences, in contact with a Langevin fluctuation-dissipation thermal bath, is investigated. A general framework for studying stochastic phase transitions in single dimension is developed for realistic regimes of temperatures, by postulating base pair separation-dependent damping characteristics in the Langevin formalism. Close agreements are obtained between the simulation predictions and the experimental results for heterogeneous DNA sequences having a wide range of sequence lengths, without incurring any sequence-specific tuning of the conventional Peyrard-Bishop-Dauxois model. Certain universal characteristics of the free energy parameters of melting transition are also discovered, with a power law form of temperature dependence.