In this paper, we report the progress made in our project recently funded by the US Department of Energy (DOE) toward developing a computational capability, which includes a two-phase, three-dimensional PEM (polymer electrolyte membrane) fuel cell model and its coupling with DAKOTA (a design and optimization toolkit developed and being enhanced by Sandia National Laboratories). We first present a brief literature survey in which the prominent/notable PEM fuel cell models developed by various researchers or groups are reviewed. Next, we describe the two-phase, three-dimensional PEM fuel cell model being developed, tested, and later validated by experimental data. Results from case studies are presented to illustrate the utility of our comprehensive, integrated cell model. The coupling between the PEM fuel cell model and DAKOTA is briefly discussed. Our efforts in this DOE-funded project are focused on developing a validated computational capability that can be employed for PEM fuel cell design and optimization.