Using molecular dynamics simulations, the two-phase flow of water and methane through slit-shaped nanopores carved from muscovite is studied. The simulations are designed to investigate the effect of flow patterns on fluids transport and on pore structure. The results indicate that the Darcy's law, which describes a linear relation between flow rate and pressure drop, can be violated when the flow pattern is altered. This can happen when the driving force, that is, the pressure drop, increases above a pore-size dependent threshold. Because the system considered here contains two phases, when the fluid structure changes, the movement of methane with respect to that of water changes, leading to the violation of the Darcy's law. Our results illustrate the importance of the capillary force, due to the formation of water bridges across the model pores, not only on the fluid flow, but also on the pore structure, in particular its width. When the water bridges are broken, perhaps because of fast fluid flow, the capillary force vanishes leading to significant pore expansion. Because muscovite is a model for illite, a clay often found in shale rocks, these results advance our understanding regarding the mechanism of water and gas transport in tight shale gas formations. (c) 2015 American Institute of Chemical Engineers AIChE J, 61: 2993-2999, 2015