After more in-depth study of CompuCell3D and other papers/projects, I'm thinking that the best way to represent the biological model is using voxels/cellular automata. It certainly makes some of the rendering easier, if efficiency isn't an issue. It might make some of the computation harder, though. And of course, I've not played much at all with voxels...
According to a paper entitled "Volume Graphics", voxelization refers to taking geometric objects and converting them to a voxel representation. Going in the opposite direction is referred to as volume rendering.
A number of data structures have been developed to represent volume data, including octrees and BSP trees.
Voxels (spatial occupancy enumeration) are just one form of solid modeling; others include cellular decomposition, constructive solid geometry, etc.
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