Microbial cell modeling via reacting diffusive particles

We describe a particle-based simulator called ChemCell that we are developing with the goal of modeling the protein chemistry of biological cells for phenomena where spatial effects are important. Membranes and organelle structure are represented by triangulated surfaces. Diffusing particles represent proteins, complexes, or other biomolecules of interest. Particles interact with their neighbors in accord with Monte Carlo rules to perform biochemical reactions which can represent protein complex formation and dissociation, ligand binding, etc. In this brief paper we give the motivation for such a model, describe a few of the code's features, and highlight interesting computational issues that arise in particle-based cell modeling.