The strong links between COMSOL and MATLAB offers a useful option for the self-automated geometrical optimization process in PEMFC, which overcomes the difficulties on geometry optimization in Computational Fuel Cell Dynamics based design. Geometry optimization of self-breathing PEMFC, including the channel-rib ratio at anode and the open ratio at the cathode side are investigated in order to improve the fuel cell performance. A sequential quadratic programming method is selected to deal with the constrained design problem, while the objective function is calculated by running the 3D simulation script of COMSOL in the MATLAB environment. Simulation results show that for the self-breathing PEMFC operating at 353K and 1 atm with a voltage of 0.7V, when the channel-rib ratio at anode side is fixed at 10%, the optimal open ratio of the self-breathing cathode is found to be 49.8%. While, when the open ratio at the cathode is set at 80%, the optimal channel-rib ratio is located at 34.7%. However, the differences in the current density are not significant when the channel-rib ratio at the anode is varied while maintaining the open ratio at 80% for the cathode side.

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