Marc Joyeux and Ana-Maria Florescu 2009 J. Phys.: Condens. Matter 21 034101 doi:10.1088/0953-8984/21/3/034101
Marc Joyeux and Ana-Maria Florescu
Show affiliationsWe recently proposed a dynamical mesoscopic model for DNA, which is based, like the statistical ones, on site-dependent finite stacking and pairing enthalpies. In the present paper, we first describe how the parameters of this model are varied to get predictions in better agreement with experimental results that were not addressed up to now, like mechanical unzipping, the evolution of the critical temperature with sequence length and temperature resolution. We show that the model with the new parameters provides results that are in quantitative agreement with those obtained from statistical models. Investigation of the critical properties of the dynamical model suggests that DNA denaturation looks like a first-order phase transition in a broad temperature interval, but that there necessarily exists, very close to the critical temperature, a crossover to another regime. The exact nature of the melting dynamics in this second regime still has to be elucidated. We finally point out that the descriptions of the physics of the melting transition inferred from statistical and dynamical models are not completely identical and discuss the relevance of our model from the biological point of view.
87.15.La Mechanical properties
87.15.H- Dynamics of biomolecules
87.15.Cc Folding: thermodynamics, statistical mechanics, models, and pathways
Issue 3 (21 January 2009)
Received 2 April 2008, in final form 9 June 2008
Published 17 December 2008
Marc Joyeux and Ana-Maria Florescu 2009 J. Phys.: Condens. Matter 21 034101
Marc Joyeux 1996 J. Phys. A: Math. Gen. 29 5963
L Blanchet and G Schafer 1993 Class. Quantum Grav. 10 2699
Jürgen Ehlers 1997 Class. Quantum Grav. 14 A119
Steven S. Vogt et al. 2002 ApJ 568 352
C Tieg et al 2010 J. Phys.: Conf. Ser. 211 012024
V Sannibale et al 2008 J. Phys.: Conf. Ser. 122 012010
K Agatsuma et al 2008 J. Phys.: Conf. Ser. 122 012013
Yang Xu et al 2008 Nanotechnology 19 435102
C C Escott et al 2007 Nanotechnology 18 235401