Subconductance states in a semimicroscopic model for a tetrameric pore.

A physical model for a structured tetrameric pore is studied. The pore is modeled as a device composed of four subunits, each one exhibiting two possible states (open and closed). The pore is located within a membrane that separates two reservoirs with ionic solutions.

Erratum: Fixed-density boundary conditions in overdamped Langevin simulations of diffusion in channels [Phys. Rev. E 98, 013302 (2018)].

This corrects the article DOI: 10.1103/PhysRevE.98.

Fixed-density boundary conditions in overdamped Langevin simulations of diffusion in channels.

We consider the numerical integration of Langevin equations for particles in a channel, in the presence of boundary conditions fixing the concentration values at the ends. This kind of boundary condition appears, for instance, when considering the diffusion of ions in molecular channels, between the different concentrations at both sides of the cellular membrane. For this application the overdamped limit of Brownian motion (leading to a first order Langevin equation) is most convenient, but in previous works some difficulties associated with this limit were found for the implementation of the boundary conditions.

Single-molecule diffusion in a periodic potential at a solid-liquid interface.

We used single-molecule tracking experiments to observe the motion of small hydrophobic fluorescent molecules at the interface between water and a solid surface that exhibited periodic chemical patterns. The dynamics were characterized by non-ergodic, continuous time random walk statistics. The step-size distributions displayed enhanced probability of steps to periodic distances, consistent with theoretical predictions for diffusion in an atomic/molecular scale periodic potential.

Speeding chemical reactions by focusing.

We present numerical results for a chemical reaction of colloidal particles which are transported by a laminar fluid and are focused by periodic obstacles in such a way that the two components are well mixed and consequently the chemical reaction is speeded up. The roles of the various system parameters (diffusion coefficients, reaction rate, and obstacles sizes) are studied. We show that focusing speeds up the reaction from the diffusion limited rate ∼t(-1/2) to very close to the perfect mixing rate, ∼t(-1).

Sharp-interface projection of a fluctuating phase-field model.

We present a derivation of the sharp-interface limit of a generic fluctuating phase-field model for solidification. As a main result, we obtain a sharp-interface projection which presents noise terms in both the diffusion equation and in the moving boundary conditions. The presented procedure does not rely on the fluctuation-dissipation theorem, and can therefore be applied to account for both internal and external fluctuations in either variational or nonvariational phase-field formulations.

Numerical study of the shape and integral parameters of a dendrite.

We present a numerical study of sidebranching of a solidifying dendrite by means of a phase-field model. Special attention is paid to the regions far from the tip of the dendrite, where linear theories are no longer valid. Two regions have been distinguished outside the linear region: a first one in which sidebranching is in a competition process and a second one further down where branches behave as independent of each other.

Blue sky catastrophe in double-diffusive convection.

A global bifurcation of the blue sky catastrophe type has been found in a small Prandtl number binary mixture contained in a laterally heated cavity. The system has been studied numerically applying the tools of bifurcation theory. The catastrophe corresponds to the destruction of an orbit which, for a large range of Rayleigh numbers, is the only stable solution.

Kinematic reduction of reaction-diffusion fronts with multiplicative noise: derivation of stochastic sharp-interface equations.

We study the dynamics of generic reaction-diffusion fronts, including pulses and chemical waves, in the presence of multiplicative noise. We discuss the connection between the reaction-diffusion Langevin-like field equations and the kinematic (eikonal) description in terms of a stochastic moving-boundary or sharp-interface approximation. We find that the effective noise is additive and we relate its strength to the noise parameters in the original field equations, to first order in noise strength, but including a partial resummation to all orders which captures the singular dependence on the microscopic cutoff associated with the spatial correlation of the noise.

Phase-field model for Hele-Shaw flows with arbitrary viscosity contrast. II. Numerical study.

We implement a phase-field simulation of the dynamics of two fluids with arbitrary viscosity contrast in a rectangular Hele-Shaw cell. We demonstrate the use of this technique in different situations including the linear regime, the stationary Saffman-Taylor fingers, and the multifinger competition dynamics, for different viscosity contrasts. The method is quantitatively tested against analytical predictions and other numerical results.

Phase-field model for Hele-Shaw flows with arbitrary viscosity contrast. I. Theoretical approach.

We present a phase-field model for the dynamics of the interface between two inmiscible fluids with arbitrary viscosity contrast in a rectangular Hele-Shaw cell. With asymptotic matching techniques we check the model to yield the right Hele-Shaw equations in the sharp-interface limit, and compute the corrections to these equations to first order in the interface thickness. We also compute the effect of such corrections on the linear dispersion relation of the planar interface.

Modeling of spatiotemporal patterns in bacterial colonies.

A diffusion-reaction model for the growth of bacterial colonies is presented. The often observed cooperative behavior developed by bacteria which increases their motility in adverse growth conditions is here introduced as a nonlinear diffusion term. The presence of this mechanism depends on a response which can present hysteresis.

Sidebranching induced by external noise in solutal dendritic growth.

We have studied sidebranching induced by fluctuations in dendritic growth. The amplitude of sidebranching induced by internal (equilibrium) concentration fluctuations in the case of solidification with solutal diffusion is computed. This amplitude turns out to be significantly smaller than values reported in previous experiments.

Brownian motion of spiral waves driven by spatiotemporal structured noise.

Spiral chemical waves subjected to a spatiotemporal random excitability are experimentally and numerically investigated in relation to the light-sensitive Belousov-Zhabotinsky reaction. Brownian motion is identified and characterized by an effective diffusion coefficient which shows a rather complex dependence on the time and length scales of the noise relative to those of the spiral. A kinematically based model is proposed whose results are in good qualitative agreement with experiments and numerics.