A Spatial Extension to the π Calculus

  • Authors:

  • Mathias John;Roland Ewald;Adelinde M. Uhrmacher

  • Affiliations:

  • Department of Computer Science, University of Rostock, D-18051 Rostock, Germany;Department of Computer Science, University of Rostock, D-18051 Rostock, Germany;Department of Computer Science, University of Rostock, D-18051 Rostock, Germany

  • Venue:
  • Electronic Notes in Theoretical Computer Science (ENTCS)
  • Year:
  • 2008

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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 @p calculus by time and space. @p 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.