Modeling dynamic molecular compartments: the bigraphical approach

Modeling dynamic molecular compartments: the bigraphical approach

Jean Krivine (Harvard Medical School, Boston US)

Joint work with Robin Milner (Cambridge University, UK), Angelo Troina (Turin University, Italy) and Troels Damgaard (ITU Copenhagen, Denmark).

Bigraphical Reactive Systems (BRSs) form a family of dynamical systems whose terms are generated by a formal syntax that relies on recent work initiated by Robin Milner. In the spirit of Ambient Calculi, BRSs address the problem of representing both connection and location of agents in a very general way. In this talk we will not focus on how Bigraphs are formed, although we will go briefly through this issue, but on how these terms can be specialized to address some problems in formal languages for biology, namely the question of dynamic compartments and membrane fission. First, we will show how to obtain a uniform stochastic interpretation of behavior in bigraphs that can be specialized to the entire range of BRSs. Second, we will show that BRSs provide a convenient "rule based" modeling environment that may extend the work on Kappa, by Danos et al, and BNGL, by Faeder and Hlavacek, through the representation of a simple membrane budding system.