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Mathias John

last modified 2010-09-23 13:50

Title of PhD thesis:
Reaction Constraints in the π-Calculus for the Spatial and Stochastic Modeling of Cell-Biological Processes


Adelinde M. Uhrmacher, University of Rostock, Rostock, Germany

Joachim Niehren, INRIA Lille Nord Europe, Lille, France

Corrado Priami, Microsoft Research, Trento, Italy


For cell-biological processes it is their player’s complex interaction, impacted by stochastic effects and spatial aspects, which draws the overall picture. Computational modeling allows to overcome the limits of experimental observation in the wet-lab, by moving to the abstract world of the computer. The limits of the abstract world again depend on the expressiveness of the modeling language used to formally describe the system under study. In this thesis, a π-calculus with reaction constraints is proposed for the stochastic and spatial modeling of cell-biological processes. A major goal is to provide sufficient expressive power to model dynamic cell structures, like fusing compartments. In this context, reaction constraints are augmented with two language constructs: priority and global variables, yielding two different modeling languages, including non-deterministic and stochastic semantics. By several modeling examples, e.g. of Euglena’s phototaxis, and extensive expressiveness studies, e.g. encodings of the spatial modeling languages BioAmbients and π@, including proves for their correctness, the usefulness of reaction constraints, priority, and global variables for the modeling of cell-biological processes is shown. Thereby, besides dynamic cell structures, different modeling styles, e.g. individual-based vs. population-based, and different abstraction levels, e.g. reaction kinetics like Mass action or Michaelis-Menten kinetics, are considered.

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