Diffusion-limited encounter rate in a three-dimensional lattice of connected compartments studied by Brownian-dynamics simulations

We considered the rate at which a diffusing particle encounters a target in a three- dimensional lattice of compartments with semipermeable walls. This work expands a previous theory [Li et al., Phys. Rev. Lett. 113, 028303 (2014)] for the encounter rate in the dilute limit of targets to the general case of any density of targets. We also used Brownian dynamics simulations to evaluate the approximations in the analytical theory. We find that the largest errors in the analytical theory are on the order of 10%. This work therefore demonstrates an analytical theory capable of describing the encounter rates in compartmentalized environments for any level of confinement and any target density.