A generalized Langevin formalism of complete DNA melting transitionT. Das1 and S. Chakraborty2
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
received 20 December 2007; accepted in final form 2 July 2008; published August 2008
published online 19 August 2008
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.
87.14.gk - DNA.
05.10.Gg - Stochastic analysis methods (Fokker-Planck, Langevin, etc.).
87.15.A- - Theory, modeling, and computer simulation.
© EPLA 2008