A Bounded-Optimistic, Parallel Beta-Binders Simulator

Compartments play an important role in molecular and cell biology modeling, which motivated the development of BETA-BINDERS, a formalism which is an extension of the pi-CALCULUS. To execute BETA-BINDERS models, sophisticated simulators are required to ensure a sound and efficient execution. Parallel and distributed simulation represents one means to achieve the later. However, stochastically scheduled events hamper the definition of look aheads for a conservative parallel synchronization scheme, while an optimistic parallel simulation implies expensive rollback operations due to the dynamic structures of BETABINDERS models. Therefore, a time-bounded window approach is suggested, which allows the different logical processes to proceed optimistically up to a barrier. Rollbacks are thus temporally constrained. In addition, the dynamic structure of BETA-BINDERS models requires a special state handling. BETA-BINDERS models and states are represented as tree structures to facilitate state updates and rollbacks by the simulation engine.