Whole-cell modeling is a grand challenge for computational biology in the 21st century. We have been working to develop a particle-based cell simulator where particles represent proteins or other biomolecules. Particles diffuse via Brownian motion within a cellular geometry bounded by triangulated surfaces that represent cellular or organelle membranes. Reactions between nearby particles are carried out via Monte Carlo rules to model an input set of chemical rate equations.
Our open-source simulator is called ChemCell. It will soon have its own WWW site where it can be downloaded. Documentation, pictures, movies, etc will also be available on the WWW site.
ChemCell is similar in spirit to other particle-based biological cell simulators such as MCell, Smoldyn, and MesoRD.
Collaborators on ChemCell:
This paper discusses results from network analyses performed with ChemCell.
Sensitivity Analysis of a Computational Model of the IKK-NF-kB-A20 Signal Transduction Network, J. Joo, S. J. Plimpton, S. Martin, L. Swiler, J. L. Faulon, Annals of the New York Acadamey of Sciences, Volume on Reverse Engineering Biological Networks, 1115, 221-239 (2007). (abstract)
This paper gives a brief overview of ChemCell and computational challenges for cell modeling:
Microbial cell modeling via reacting diffusing particles, S. J. Plimpton and A. Slepoy, Journal of Physics: Conference Series 16, 305-309 (2005). (abstract) (pdf)
This paper is about our Genomics:GTL (Genomes-to-Life) project funded by DOE's OBER and OASCR offices, that provided funding and motivation for the development of ChemCell. The author list is our entire project team!
Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling, G. S. Heffelfinger, ..., S. J. Plimpton, ..., OMICS - A Journal of Integrative Biology, 6, 305-330 (2002). (abstract)