Can we model DNA at the mesoscale ? Comment on: Fluctuations in the DNA double helix: A critical review

Comment on "Fluctuations in the DNA double helix: A critical review" by Frank-Kamenetskii and Prakas

Discreteness effects on soliton dynamics: a simple experiment

We present a simple laboratory experiment to illustrate some aspects of the soliton theory in discrete lattices with a system that models the dynamics of dislocations in a crystal or the properties of adsorbed atomic layers. The apparatus not only shows the role of the Peierls-Nabarro potential but also illustrates the hierarchy of depinning transitions and the importance of the collective motion in mass transport.Comment: 9 pages, 4 Figures, to Appear in American Journal of Physic

Dynamical phase diagram of the dc-driven underdamped Frenkel-Kontorova chain

Multistep dynamical phase transition from the locked to the running state of atoms in response to a dc external force is studied by MD simulations of the generalized Frenkel-Kontorova model in the underdamped limit. We show that the hierarchy of transition recently reported [Braun et al, Phys. Rev. Lett. 78, 1295 (1997)] strongly depends on the value of the friction constant. A simple phenomenological explanation for the friction dependence of the various critical forces separating intermediate regimes is given.Comment: 12 Revtex Pages, 4 EPS figure

Dynamical transitions in correlated driven diffusion in a periodic potential

The diffusion of a two-dimensional array of particles driven by a constant force in the presence of a periodic external potential exhibits a hierarchy of dynamical phase transitions when the driving force is varied. This behavior can be explained by a simple phenomenological approach which reduces the system of strongly interacting particles to weakly interacting quasi-particles (kinks). The richness of the strongly coupled system is however not lost because, contrary to a single-Brownian particle, the array shows an hysteretic behavior even at non-zero temperature. The present investigation can be viewed as a first step toward understanding nanotribology.Comment: 4 pages, 3 pictures, revtex to appear in Phys Rev. Let

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)].Comment: 22 Revtex pages, 9 figures to appear in Phys. Rev.

Order of the phase transition in models of DNA thermal denaturation

We examine the behavior of a model which describes the melting of double-stranded DNA chains. The model, with displacement-dependent stiffness constants and a Morse on-site potential, is analyzed numerically; depending on the stiffness parameter, it is shown to have either (i) a second-order transition with "nu_perpendicular" = - beta = 1, "nu_parallel" = gamma/2 = 2 (characteristic of short range attractive part of the Morse potential) or (ii) a first-order transition with finite melting entropy, discontinuous fraction of bound pairs, divergent correlation lengths, and critical exponents "nu_perpendicular" = - beta = 1/2, "nu_parallel" = gamma/2 = 1.Comment: 4 pages of Latex, including 4 Postscript figures. To be published in Phys. Rev. Let