In Part 1 of this series we developed a new model for nanoporous materials and inorganic membranes, with a pore space that consists of interconnected pores of irregular shapes, sizes, and connectivity. To test the validity of the model, we utilized it to model adsorption in three distinct silicon-carbide (SiC) membranes, and demonstrated that, using at most one adjustable parameter, the simulated isotherms and the experimental data are in very good agreement. In this paper we use the model of the SiC membrane developed in Part 1, and non-equilibrium molecular dynamics simulations, in order to study transport and separation in the membrane of two binary gaseous mixtures, namely, H-2/CO2 and H-2/CH4, and test the accuracy of the results by comparing them with the experimental data. The model is demonstrated to provide reasonably accurate predictions for various properties of interest, and in particular for the separation factors of the mixtures, without utilizing any new adjustable parameter. The effect of the temperature, the membrane's porosity, and the pressure drop applied externally to the membrane is described, and possible approaches for improving the model further are discussed. (C) 2009 Elsevier B.V. All rights reserved.