Title :
A Bounded-Optimistic, Parallel Beta-Binders Simulator
Author :
Leye, Stefan ; Uhrmacher, Adelinde M. ; Priami, Corrado
Author_Institution :
Dept. of Comput. Sci., Univ. of Rostock, Rostock
Abstract :
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.
Keywords :
biology computing; cellular biophysics; molecular biophysics; parallel algorithms; pi calculus; synchronisation; tree data structures; bounded-optimistic parallel Beta-binders simulator; cell biology modeling; molecular modeling; parallel synchronization scheme; pi-calculus; state handling; time-bounded window approach; tree structures; Application software; Biological cells; Biological system modeling; Computational modeling; Computer science; Computer simulation; Discrete event simulation; Dynamic scheduling; Time of arrival estimation; Tree data structures; discrete event simulation; parallel and distributed simulation; process algebra;
Conference_Titel :
Distributed Simulation and Real-Time Applications, 2008. DS-RT 2008. 12th IEEE/ACM International Symposium on
Conference_Location :
Vancouver, BC
Print_ISBN :
978-0-7695-3425-1
DOI :
10.1109/DS-RT.2008.32