Article ID Journal Published Year Pages File Type
423816 Electronic Notes in Theoretical Computer Science 2008 16 Pages PDF
Abstract

Spatial dynamics receive increasing attention in Systems Biology and require suitable modeling and simulation approaches. So far, modeling formalisms have focused on population-based approaches or place and move individuals relative to each other in space. SpacePi extends the π calculus by time and space. π processes are embedded into a vector space and move individually. Only processes that are sufficiently close can communicate. The operational semantics of SpacePi defines the interplay between movement, communication, and time-triggered events. A model describing the phototaxis of the Euglena micro-organism is presented as a practical example. The formalism's use and generality is discussed with respect to the modeling of molecular biological processes like diffusion, active transportation in cell signaling, and spatial structures.

Related Topics
Physical Sciences and Engineering Computer Science Computational Theory and Mathematics