Literature DB >> 14754236

Thermal denaturation of a helicoidal DNA model.

Maria Barbi1, Stefano Lepri, Michel Peyrard, Nikos Theodorakopoulos.   

Abstract

We study the static and dynamical properties of DNA in the vicinity of its melting transition, i.e., the separation of the two strands upon heating. The investigation is based on a simple mechanical model which includes the helicoidal geometry of the molecule and allows an exact numerical evaluation of its thermodynamical properties. Dynamical simulations of long-enough molecular segments allow the study of the structure factors and of the properties of the denaturated regions. Simulations of finite chains display the hallmarks of a first order transition for sufficiently long-ranged stacking forces although a study of the model's "universality class" strongly suggests the presence of an "underlying" continuous transition.

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Year:  2003        PMID: 14754236     DOI: 10.1103/PhysRevE.68.061909

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN: 1539-3755


  11 in total

1.  Stationary solutions for a modified Peyrard-Bishop DNA model with up to third-neighbor interactions.

Authors:  Z Rapti
Journal:  Eur Phys J E Soft Matter       Date:  2010-06-17       Impact factor: 1.890

2.  Thermal fluctuation spectroscopy of DNA thermal denaturation.

Authors:  K S Nagapriya; A K Raychaudhuri
Journal:  Biophys J       Date:  2010-10-20       Impact factor: 4.033

3.  Model for DNA hairpin denaturation.

Authors:  S Cuesta-López; M Peyrard; D J Graham
Journal:  Eur Phys J E Soft Matter       Date:  2005-03       Impact factor: 1.890

4.  Statistical theory of force-induced unzipping of DNA.

Authors:  N Singh; Y Singh
Journal:  Eur Phys J E Soft Matter       Date:  2005-03-18       Impact factor: 1.890

5.  How topological constraints facilitate growth and stability of bubbles in DNA.

Authors:  Jae-Hyung Jeon; Wokyung Sung
Journal:  Biophys J       Date:  2008-07-11       Impact factor: 4.033

6.  The pathway of oligomeric DNA melting investigated by molecular dynamics simulations.

Authors:  Ka-Yiu Wong; B Montgomery Pettitt
Journal:  Biophys J       Date:  2008-10-24       Impact factor: 4.033

7.  An effective mesoscopic model of double-stranded DNA.

Authors:  Jae-Hyung Jeon; Wokyung Sung
Journal:  J Biol Phys       Date:  2013-12-05       Impact factor: 1.365

Review 8.  Ideas and methods of nonlinear mathematics and theoretical physics in DNA science: the McLaughlin-Scott equation and its application to study the DNA open state dynamics.

Authors:  Ludmila V Yakushevich; Larisa A Krasnobaeva
Journal:  Biophys Rev       Date:  2021-05-13

9.  Effect of genome sequence on the force-induced unzipping of a DNA molecule.

Authors:  N Singh; Y Singh
Journal:  Eur Phys J E Soft Matter       Date:  2006-02-28       Impact factor: 1.624

10.  Hysteresis in pressure-driven DNA denaturation.

Authors:  Enrique Hernández-Lemus; Luz Adriana Nicasio-Collazo; Ramón Castañeda-Priego
Journal:  PLoS One       Date:  2012-04-09       Impact factor: 3.240

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