A mesoscopic framework, derived from first principles via a rigorous coarse-graining of an underlying master equation, has proven to be a powerful tool in bridging the disparate scales between atomistic simulations and practical applications involving diffusion of interacting species through microporous films. This mesoscopic framework is validated here via gradient continuous time Monte Carlo (G-CTMC) simulations for realistic boundary conditions in the limit of thin, single crystal membranes. It is shown that intermolecular forces have a non-Arrhenius effect on the permeation flux, and a stationary concentration pattern develops for strong repulsive interactions. It is found that diffusion through complex multiple site lattices, such as those encountered in diffusion of benzene in Na-Y zeolite films, exhibits strongly nonlinear behavior even in the absence of interactions between molecular species. Finally, the mesoscopic framework is applied to diffusion/reaction systems, where excellent agreement between G-CTMC and mesoscopic solutions is demonstrated for the first time. (C) 2003 Elsevier Science Ltd. All rights reserved.