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We review theory and simulation of rare event dynamics, diffusion and phase equilibrium in nanopores, focusing on benzene in Na-X and Na-Y zeolites because of persistent experimental discrepancies. We discuss transition state theory and its application to zeolite-guest systems, suggesting that calculations on flexible lattices and at finite guest loadings are important areas for future research. We consider many-body adsorption and diffusion in zeolites, focusing on the coupling between rare event dynamics and strong guest-guest interactions. We explore the possibility that benzene can undergo phase transitions from low to high sorbate density in Na-X, and find that this type of phase transition might explain intriguing loading dependencies of water and ammonia diffusion in terms of a subcritical droplet picture of adsorption in zeolites. We discuss various formulations of non-equilibrium diffusion through finite …