The narrow escape problem for diffusion in cellular microdomains

Abstract

The study of the diffusive motion of ions or molecules in confined biological microdomains requires the derivation of the explicit dependence of quantities, such as the decay rate of the population or the forward chemical reaction rate constant on the geometry of the domain. Here, we obtain this explicit dependence for a model of a Brownian particle (ion, molecule, or protein) confined to a bounded domain (a compartment or a cell) by a reflecting boundary, except for a small window through which it can escape. We call the calculation of the mean escape time the narrow escape problem. This time diverges as the window shrinks, thus rendering the calculation a singular perturbation problem. Here, we present asymptotic formulas for the mean escape time in several cases, including regular domains in two and three dimensions and in some singular domains in two dimensions. The mean escape time comes up in many applications, because it represents the mean time it takes for a molecule to hit a target binding site. We present several applications in cellular biology: calcium decay in dendritic spines, a Markov model of multicomponent chemical reactions in microdomains, dynamics of receptor diffusion on the surface of neurons, and vesicle trafficking inside a cell.