Distribution of randomly diffusing particles in inhomogeneous media

Stochastic self-assembly of reaction-diffusion patterns in synaptic membranes

Synaptic receptor and scaffold molecules self-assemble into membrane protein domains, which play an important role in signal transmission across chemical synapses. Experiment and theory have shown that the formation of receptor-scaffold domains of the characteristic size observed in nerve cells can be understood from the receptor and scaffold reaction and diffusion processes suggested by experiments. We employ here kinetic Monte Carlo (KMC) simulations to explore the self-assembly of synaptic receptor-scaffold domains in a stochastic lattice model of receptor and scaffold reaction-diffusion dynamics. For reaction and diffusion rates within the ranges of values suggested by experiments we find, in agreement with previous mean-field calculations, self-assembly of receptor-scaffold domains of a size similar to that observed in experiments. Comparisons between the results of our KMC simulations and mean-field solutions suggest that the intrinsic noise associated with receptor and scaffold reaction and diffusion processes accelerates the self-assembly of receptor-scaffold domains, and confers increased robustness to domain formation. In agreement with experimental observations, our KMC simulations yield a prevalence of scaffolds over receptors in receptor-scaffold domains. Our KMC simulations show that receptor and scaffold reaction-diffusion dynamics can inherently give rise to plasticity in the overall properties of receptor-scaffold domains, which may be utilized by nerve cells to regulate the receptor number at chemical synapses.

Interplay of adsorption and surface mobility in tracer diffusion in porous media

We model the diffusion of a tracer that interacts with the internal surface of a porous medium formed by a packing of solid spheres. The tracer executes a lattice random walk in which hops from surface to bulk sites and hops on the surface have small probabilities compared to hops from bulk sites; those probabilities are related to bulk and surface diffusion coefficients and to a desorption rate. A scaling approach distinguishes three regimes of steady state diffusion, which are confirmed by numerical simulations. If the product of desorption rate and sphere diameter is large, dominant bulk residence is observed and the diffusion coefficient is close to the bulk value. If that product is small and the surface mobility is low, the tracers are adsorbed most of the time but most hops are executed in the bulk. However, for high surface mobility, there is a nontrivial regime of dominant surface displacement, since the connectivity of solid walls allows the tracers to migrate to long distances while they are adsorbed. In this regime, we observe rounded tracer paths on the sphere walls, which are qualitatively similar to those of a recent experiment on polystyrene particle diffusion. The calculated average residence times are proportional to the bulk and surface densities of an equilibrium ensemble of noninteracting tracers, and the relation between those densities sets the adsorption isotherm. Simulations performed with initially uniform (nonequilibrium) distribution of tracers in the pores show other nontrivial results in cases of dominant surface residence: slow increase of the mean-square displacement at short times, since the tracer has not explored a homogeneous medium, and a remarkable slowdown between the first encounter with a solid wall and the first hop from that point. Relations between our results and other models of diffusion and adsorption in porous media are discussed.