A generalized Langevin formalism of complete DNA melting transition

被引：13
作者：
Das, T. [1 ]
Chakraborty, S. [2 ]
机构：
[1] Indian Inst Technol, Dept Biotechnol & Biochem Engn, Kharagpur 721302, W Bengal, India
[2] Indian Inst Technol, Dept Mech Engn, Kharagpur 721302, W Bengal, India
来源：
EPL | 2008年 / 83卷 / 04期
关键词：
D O I：
10.1209/0295-5075/83/48003
中图分类号：
O4 [物理学];
学科分类号：
0702 ;
摘要：
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. Copyright (C) EPLA, 2008.
引用
收藏
页数：6
相关论文
共 18 条
  • [1] RANDOM-FORCE-DOMINATED REACTION-KINETICS - REACTANTS MOVING UNDER RANDOM FORCES
    ARAUJO, M
    HAVLIN, S
    LARRALDE, H
    STANLEY, HE
    [J]. PHYSICAL REVIEW LETTERS, 1992, 68 (12) : 1791 - 1794
  • [2] Bubble nucleation and cooperativity in DNA melting
    Ares, S
    Voulgarakis, NK
    Rasmussen, KO
    Bishop, AR
    [J]. PHYSICAL REVIEW LETTERS, 2005, 94 (03)
  • [3] Helicase mediated active DNA unwinding in a stochastic field
    Das, Tamal
    Chakraborty, Suman
    [J]. APPLIED PHYSICS LETTERS, 2006, 89 (15)
  • [4] ENTROPY-DRIVEN TRANSITION IN A ONE-DIMENSIONAL SYSTEM
    DAUXOIS, T
    PEYRARD, M
    [J]. PHYSICAL REVIEW E, 1995, 51 (05): : 4027 - 4040
  • [5] ENTROPY-DRIVEN DNA DENATURATION
    DAUXOIS, T
    PEYRARD, M
    BISHOP, AR
    [J]. PHYSICAL REVIEW E, 1993, 47 (01): : R44 - R47
  • [6] Langevin dynamics simulations of early stage shish-kebab crystallization of polymers in extensional flow
    Dukovski, I
    Muthukumar, M
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2003, 118 (14) : 6648 - 6655
  • [7] Statistical mechanics of base stacking and pairing in DNA melting
    Ivanov, V
    Zeng, Y
    Zocchi, G
    [J]. PHYSICAL REVIEW E, 2004, 70 (05): : 6
  • [8] Dynamical model based on finite stacking enthalpies for homogeneous and inhomogeneous DNA thermal denaturation
    Joyeux, M
    Buyukdagli, S
    [J]. PHYSICAL REVIEW E, 2005, 72 (05):
  • [9] Sequence-specific thermal fluctuations identify start sites for DNA transcription
    Kalosakas, G
    Rasmussen, KO
    Bishop, AR
    Choi, CH
    Usheva, A
    [J]. EUROPHYSICS LETTERS, 2004, 68 (01): : 127 - 133
  • [10] Intermediate phase in DNA melting
    Neher, RA
    Gerland, U
    [J]. PHYSICAL REVIEW E, 2006, 73 (03)
12