281 research outputs found
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
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