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Stefan Leye, Corrado Priami, and Adelinde M Uhrmacher (2008)

A bounded-optimistic, parallel Beta-binders Simulator

In: Proceedings of the 12th IEEE International Symposium on Distributed Simulation and Real-Time Applications, ed. by David Roberts, Abdulmotaleb El Saddik and Alois Ferscha, pp. 139-148, IEEE Computer Society, IEEE Press.

Compartments play an important role in molecular and cell biology modeling, which motivated the development of BETA-BINDERS, a formalism that forms 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 BETA-BINDERS 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.

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