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A generalized Langevin formalism of complete DNA melting transition

T. Das1 and S. Chakraborty2

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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.


PACS

87.14.gk DNA

87.15.A- Theory, modeling, and computer simulation

05.10.Gg Stochastic analysis methods (Fokker-Planck, Langevin, etc.)

Subjects

Computational physics

Biological physics

Statistical physics and nonlinear systems

Dates

Issue 4 (August 2008)

Received 20 December 2007, accepted for publication 2 July 2008

Published 19 August 2008



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