Distributed discrete-event simulation
ACM Computing Surveys (CSUR)
A calculus of mobile processes, I
Information and Computation
Communicating and mobile systems: the &pgr;-calculus
Communicating and mobile systems: the &pgr;-calculus
Parallel and Distribution Simulation Systems
Parallel and Distribution Simulation Systems
BioAmbients: an abstraction for biological compartments
Theoretical Computer Science - Special issue: Computational systems biology
Developing An Hierarchical Simulator for Beta-binders
Proceedings of the 20th Workshop on Principles of Advanced and Distributed Simulation
ANSS '07 Proceedings of the 40th Annual Simulation Symposium
A Spatial Extension to the π Calculus
Electronic Notes in Theoretical Computer Science (ENTCS)
The event queue problem and PDevs
SpringSim '07 Proceedings of the 2007 spring simulation multiconference - Volume 2
A Grid-Inspired Mechanism for Coarse-Grained Experiment Execution
DS-RT '08 Proceedings of the 2008 12th IEEE/ACM International Symposium on Distributed Simulation and Real-Time Applications
Beta binders for biological interactions
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
Regenerative systems: challenges and opportunities for modeling, simulation, and visualization
Proceedings of the Fourth International ICST Conference on Performance Evaluation Methodologies and Tools
A flexible architecture for performance experiments with the pi-Calculus and its extensions
Proceedings of the 3rd International ICST Conference on Simulation Tools and Techniques
Trading Computation Time for Synchronization Time in Spatial Distributed Simulation
PADS '11 Proceedings of the 2011 IEEE Workshop on Principles of Advanced and Distributed Simulation
A model reduction approach for improving discrete event simulation performance
Proceedings of the 6th International ICST Conference on Simulation Tools and Techniques
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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.