T. Das and S. Chakraborty 2008 EPL 83 48003 doi:10.1209/0295-5075/83/48003
T. Das1 and S. Chakraborty2
Show affiliationsMelting 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.
87.15.A- Theory, modeling, and computer simulation
05.10.Gg Stochastic analysis methods (Fokker-Planck, Langevin, etc.)
Issue 4 (August 2008)
Received 20 December 2007, accepted for publication 2 July 2008
Published 19 August 2008
T. Das and S. Chakraborty 2008 EPL 83 48003
Vesselin Petkov 1999 Nonlinearity 12 1663
Gemma De las Cuevas et al J. Stat. Mech. (2009) P07001
Jianjun Yang et al 2010 J. Phys.: Condens. Matter 22 095503
Caterina-E Mora et al 2008 New J. Phys. 10 083027
Ben-Hwa Jang et al 2008 J. Micromech. Microeng. 18 055020
Slava Krylov et al 2008 J. Micromech. Microeng. 18 055026
S Bermejo et al 2008 J. Micromech. Microeng. 18 055004
H Veladi et al 2008 J. Micromech. Microeng. 18 055033
A. P. Sarma et al. 2005 The Astronomical Journal 130 2566