Abstract
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.
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