This research paper describes the design and prototyping of a simulation tool that provides a platform for studying how behavior of proteins in the cell membrane influences macro-level, emergent behaviors of cells. Whereas most current simulation tools model cells as homogeneous objects, this new tool is designed to modularly represent the cell's complex morphology and the varying distribution of proteins across the membrane. The simulation tool uses a physics engine to manage motion and collisions between objects. It also represents dynamic fluid environments, experimental surfaces, attachment bonds and interactions between the dynamically changing cell surface proteins. The prototype tool is described along with proposals for its use and further development.