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International Conference on Complex Systems (ICCS2006)

Cell Level Modeling Using CompuCell3D

Maciej Swat
Biocomplexity Institute / Indiana University

James Glazier
Biocomplexity Institute / Indiana University

     Full text: Not available
     Last modified: May 15, 2006

Abstract
Between the realms of molecular dynamics and continuum mechanics lies the little explored land of cell-level modeling. Morphogenesis, the process by which individual cells grow and change into patterned, functional structure, is primarily a cell-level process. Cells interact with physical and chemical signals. Some of these are local, such as adhesion, and some long-range such as chemotaxis and other responses to chemicals. We are developing a computational tool which uses these interactions to model morphogenesis at the cell-level. Our computational framework, called CompuCell3D is based on the large-Q Pott's model. We define an energy functional based on assigned average behaviour of cells, such as volume, relative adhesivity, response to chemical gradients, etc. As we minimize the global energy with the Metropolis algorithm, the system self-organizes through morphogenetic stages. In general, we strive to include as few physical interactions as possible to end up with the desired development. CompuCell3D uses xml to build a simulation and is probably the easiest to learn and use CPM modeling framework around. CompuCell3D package includes intuitive front-end and rich set of visualization tools. So far, successful models include: cell sorting, haptotactic condensation on a substrate, Dictyostelium development, primitive streak formation in chick embryos, somitogenesis, tumor growth, and more. In this talk we will introduce CompuCell3D concepts and present several models and their results.




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