Sample Cellontro Applications

These simulations of a biological cell include enzymes that continuously transform substrate chemicals into products, and lipid bilayers and transport proteins that move chemicals between compartments. The various related models include the Glycolytic Pathway, and Mitochondria with the TCA Cycle. This and other Cellontro models are scalable. You can specify any quantity of cells, mitochondria or other entities.

For more information on this model, see:

Webb, K., and White, T. (2005). UML as a cell and biochemistry modeling language. BioSystems, 80, 283-302.

Webb, K., and White, T. (2004). Cell Modeling using Agent-based Formalisms. AAMAS 2004, New York.

This simulation extends the basic cell. Many instances of a cell are embedded within multiple subsystems of a mammalian organism, which in turn is embedded within an ecosystem. This demonstrates a deeply nested hierarchical structure, the ability to reuse structures, and the ability to create new structures at runtime (e.g. synapses). A large number of biochemical reactions occur in parallel within the many individual compartments. The example simulation includes over 20,000 entities.

This is a variation of the Cell Model in which the cell bilayer contains lipids. These lipids are created within the Cytosol. Because they are hydrophobic, the water in the cytosol tends to push them towards the cell bilayer, which gradually incorporates them. The activity of the cell bilayer is causally dependent on the quantity of lipids it contains.

For more information, see:

Webb, K., and White, T. (2004). Combining Analysis and Synthesis in a Model of a Biological Cell. SAC '04, March 14-17, 2004, Nicosia, Cyprus.

This is a simple cell simulation that can produce VRML files for 3D visualization. You will be able to view the cells, nuclei, mitochondria, other organelles, enzymes and small molecules specified in your models. A third-party VRML viewer is required.