A Spatial Extension to the Pi-Calculus

Mathias John (1) , Roland Ewald (1) , Adelinde Uhrmacher (1)

1 Computer Science and Electrical Engineering

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 pi-calculus by time and space. pi 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.

Domaines: Modélisation et simulation; Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]

Mathias John, Roland Ewald, Adelinde Uhrmacher. A Spatial Extension to the Pi-Calculus. From Biology To Concurrency and back, Sep 2007, Lissabon, Portugal. ⟨10.1016/j.entcs.2007.12.010⟩. ⟨hal-00656206⟩