On the ion-mediated interaction between protein and DNA

The mechanism allowing a protein to search of a target sequence on DNA is currently described as an intermittent process composed of 3D diffusion in bulk and 1D diffusion along the DNA molecule. Due to the relevant charge of protein and DNA, electrostatic interaction should play a crucial role during this search. In this paper, we explicitly derive the mean field theory allowing for a description of the protein-DNA electrostatics in solution. This approach leads to a unified model of the search process, where 1D and 3D diffusion appear as a natural consequence of the diffusion on an extended interaction energy profile.Comment: Proceedings of the 29th ICMP Conference, Tianjin, China (2013

Stabilization of ratchet dynamics by weak periodic signals

We study the influence of weak periodic signals on the transport properties of underdamped ratchets. We find that the constant current intervals related to the ratchet, can be significantly enlarged by a weak subharmonic signal which is in phase with the internal driver. This stabilization phenomenon is found to exist both in absence and in presence of noise. The dependence of this effect on the phase of the applied signal is also investigated.Comment: tex + 4 figures.ps in a .tar archive / submitted to PR

Vector Nonlinear Klein-Gordon Lattices: General Derivation of Small Amplitude Envelope Soliton Solutions

Group velocity and group velocity dispersion for a wave packet in vectorial discrete Klein-Gordon models are obtained by an expansion, based on perturbation theory, of the linear system giving the dispersion relation and the normal modes. We show how to map this expansion on the Multiple Scale Expansion in the real space and how to find Non Linear Schr\"odinger small amplitude solutions when a nonlinear one site potential balances the group velocity dispersion effect

Vector Nonlinear Klein-Gordon Lattices: General Derivation of Small Amplitude Envelope Soliton Solutions

Group velocity and group velocity dispersion for a wave packet in vectorial discrete Klein-Gordon models are obtained by an expansion, based on perturbation theory, of the linear system giving the dispersion relation and the normal modes. We show how to map this expansion on the Multiple Scale Expansion in the real space and how to find Non Linear Schr\"odinger small amplitude solutions when a nonlinear one site potential balances the group velocity dispersion effect

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