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A numerical model for proton exchange membrane (PEM) fuel cell is developed, which can simulate such basic transport phenomena as gas-liquid two-phase flow in a working fuel cell. Boundary conditions for both the conventional and the interdigitated modes of flow are presented on a three-dimensional basis. Numerical techniques for this model are discussed in detail. Validation shows good agreement between simulating results and experimental data. Furthermore, internal transport phenomena are discussed and compared for PEM fuel cells with conventional and interdigitated flows. It is found that the dead-ended structure of an interdigitated flow does increase the oxygen mass fraction and decrease the liquid water saturation in the gas diffusion layer as compared to the conventional mode of flow. However, the cathode humidification is important for an interdigitated flow to acquire better performance than a conventional flow fuel cell.