arXiv subjects

Michel Peyrard

Publications and source records attributed to Michel Peyrard.

40 records · Page 3Linked to original sources

arXiv1999

Helicoidal model for DNA opening

We present a new dynamical model of DNA. This model has two degrees of freedom per base-pair: one radial variable related to the opening of the hydrogen bonds and an angular one related to the twisting of each base-pair responsible for the helicoidal structure of the molecule. The small amplitude dynamics of the model is studied analytically : we derive small amplitude envelope solutions made of a breather in the radial variables combined with a kink in the angular variables, showing the role of the topological constraints associated to the helicoidal geometry. We check the stability of the solutions by numerical integration of the motion equations.

chao-dyn↗

arXiv1998

Effective Breather Trapping Mechanism for DNA Transcription

Collective coordinate and direct numerical integration methods are applied to the analysis of a one-dimensional DNA model. A modification of the coupling constant in an extended region is found to be less selective towards the breather it can trap than an isolated impurity. Therefore it provides a possible physical mechanism for the effect of an enzyme on DNA transcription.

cond-mat↗

arXiv1996

Solitonic-exchange mechanism of surface~diffusion

We study surface diffusion in the framework of a generalized Frenkel-Kontorova model with a nonconvex transverse degree of freedom. The model describes a lattice of atoms with a given concentration interacting by Morse-type forces, the lattice being subjected to a two-dimensional substrate potential which is periodic in one direction and nonconvex (Morse) in the transverse direction. The results are used to describe the complicated exchange-mediated diffusion mechanism recently observed in MD simulations [J.E. Black and Zeng-Ju Tian, Phys. Rev. Lett. {\bf 71}, 2445-2448(1993)].

patt-sol↗

arXiv1996

Mobility and diffusivity in a generalized Frenkel-Kontorova model

Molecular dynamics simulations are used to investigate the atomic mobility and diffusivity of a generalized Frenkel-Kontorova model which takes into account anharmonic (exponential) interaction of atoms subjected to a three-dimensional substrate potential periodic in two dimensions and nonconvex (Morse) in the third dimension. The numerical results are explained by a phenomenological theory which treats a system of strongly interacting atoms as a system of weakly interacting quasiparticles (kinks). Model parameters are chosen close to those for {\bf K}-{\bf W}(112) adsorption system.

patt-sol↗