Interplay of frequency-synchronization with noise: current resonances, giant diffusion and diffusion-crests

We elucidate how the presence of noise may significantly interact with the synchronization mechanism of systems exhibiting frequency-locking. The response of these systems exhibits a rich variety of behaviors, such as resonances and anti-resonances which can be controlled by the intensity of noise. The transition between different locked regimes provokes the development of a multiple enhancement of the effective diffusion. This diffusion behavior is accompanied by a crest-like peak-splitting cascade when the distribution of the lockings is self-similar, as it occurs in periodic systems that are able to exhibit a Devil's staircase sequence of frequency-lockings.Comment: 7 pages, 6 figures, epl.cls. Accepted for publication in Europhysics Letter

Viral self-assembly as a thermodynamic process

The protein shells, or capsids, of all sphere-like viruses adopt icosahedral symmetry. In the present paper we propose a statistical thermodynamic model for viral self-assembly. We find that icosahedral symmetry is not expected for viral capsids constructed from structurally identical protein subunits and that this symmetry requires (at least) two internal "switching" configurations of the protein. Our results indicate that icosahedral symmetry is not a generic consequence of free energy minimization but requires optimization of internal structural parameters of the capsid proteins.Comment: pdf file, 13 pages, three figure

Entropic stochastic resonance: the constructive role of the unevenness

We demonstrate the existence of stochastic resonance (SR) in confined systems arising from entropy variations associated to the presence of irregular boundaries. When the motion of a Brownian particle is constrained to a region with uneven boundaries, the presence of a periodic input may give rise to a peak in the spectral amplification factor and therefore to the appearance of the SR phenomenon. We have proved that the amplification factor depends on the shape of the region through which the particle moves and that by adjusting its characteristic geometric parameters one may optimize the response of the system. The situation in which the appearance of such entropic stochastic resonance (ESR) occurs is common for small-scale systems in which confinement and noise play an prominent role. The novel mechanism found could thus constitute an important tool for the characterization of these systems and can put to use for controlling their basic properties.Comment: 8 pages, 8 figure

Biased diffusion in confined media: Test of the Fick-Jacobs approximation and validity criteria

We study biased, diffusive transport of Brownian particles through narrow, spatially periodic structures in which the motion is constrained in lateral directions. The problem is analyzed under the perspective of the Fick-Jacobs equation which accounts for the effect of the lateral confinement by introducing an entropic barrier in a one dimensional diffusion. The validity of this approximation, being based on the assumption of an instantaneous equilibration of the particle distribution in the cross-section of the structure, is analyzed by comparing the different time scales that characterize the problem. A validity criterion is established in terms of the shape of the structure and of the applied force. It is analytically corroborated and verified by numerical simulations that the critical value of the force up to which this description holds true scales as the square of the periodicity of the structure. The criterion can be visualized by means of a diagram representing the regions where the Fick-Jacobs description becomes inaccurate in terms of the scaled force versus the periodicity of the structure.Comment: 20 pages, 7 figure

Kinetic Equations for Diffusion in the Presence of Entropic Barriers

We use the mesoscopic nonequilibrium thermodynamics theory to derive the general kinetic equation of a system in the presence of potential barriers. The result is applied to the description of the evolution of systems whose dynamics is influenced by entropic barriers. We analyze in detail the case of diffusion in a domain of irregular geometry in which the presence of the boundaries induces an entropy barrier when approaching the exact dynamics by a coarsening of the description. The corresponding kinetic equation, named Fick-Jacobs equation, is obtained, and its validity is generalized through the formulation of a scaling law for the diffusion coefficient which depends on the shape of the boundaries. The method we propose can be useful to analyze the dynamics of systems at the nanoscale where the presence of entropy barriers is a common feature.Comment: 16 pages, 5 figures. Accepted for publication in Phys. Rev.