Computer simulation of biological systems is computationally intensive, to say the least. Fortunately, living cells are not just random collections of billions of molecules: they are extremely well-organized (although stochastic) systems. If we can model their organization, we should be able to simulate them abstractly and effectively. A large part of the organization of (eukaryotic) cells depends on hierarchies of nested membranes, their properties, the proteins bound to membrane surfaces, and the way membranes interact dynamically with each other. I discuss some preliminary efforts in modeling dynamic membrane systems. The long-term goal is to represent the structure and function of biological systems via formal languages, for description, simulation, analysis and (eventually) compilation.
