The proton transfer mechanism is the fundamental principle of how the proton exchange membrane fuel cell (PEMFC) works. This paper develops a molecular dynamics technique to simulate the transfer mechanism of the hydrogen protons inside a Nafion 117 membrane. The realistic polymer structure of the Nafion is extremely huge and very complex, it is simplified to be a repeated structure with part of the major carbon-fluoride backbone and a side chain with radicals of SO3 in this paper. Water molecules were assigned to distribute between side chains randomly. The simulation package of DLPOLY was employed as the platform. Simulation results show that the water molecules will cluster together due to the polarization characteristics, and the clusters are attracted by the side chain of the membrane electrolyte. Hydrogen protons are then transferred from one side chain to another through the water clusters. The migration process of the hydrogen protons within the membrane is a function of the water uptakes and many other factors. They are investigated to further improve the ionic conduction of the fuel cell membrane.

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