A calculus of mobile processes, I
Information and Computation
A calculus of mobile processes, II
Information and Computation
Communicating and mobile systems: the &pgr;-calculus
Communicating and mobile systems: the &pgr;-calculus
Information Processing Letters
On the expressive power of polyadic synchronisation in π-calculus
Nordic Journal of Computing
BioAmbients: an abstraction for biological compartments
Theoretical Computer Science - Special issue: Computational systems biology
A time-dependent extension of gillespie algorithm for biochemical stochastic π-calculus
Proceedings of the 2006 ACM symposium on Applied computing
A core calculus for a comparative analysis of bio-inspired calculi
ESOP'07 Proceedings of the 16th European conference on Programming
Tau leaping stochastic simulation method in p systems
WMC'06 Proceedings of the 7th international conference on Membrane Computing
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
A graphical representation for biological processes in the stochastic pi-calculus
Transactions on Computational Systems Biology VII
Efficient Stochastic Simulation of Biological Systems with Multiple Variable Volumes
Electronic Notes in Theoretical Computer Science (ENTCS)
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
A Translation of Beta-binders in a Prioritized Pi-calculus
Electronic Notes in Theoretical Computer Science (ENTCS)
Multi-resolution spatial simulation for molecular crowding
Proceedings of the 40th Conference on Winter Simulation
Stochastic biological modelling in the presence of multiple compartments
Theoretical Computer Science
π@: a π-based process calculus for the implementation of compartmentalised bio-inspired calculi
SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
The attributed pi-calculus with priorities
Transactions on Computational Systems Biology XII
Measurable stochastics for Brane Calculus
Theoretical Computer Science
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The Gillespie stochastic simulation algorithm represents one of the main physical abstractions exploited for the simulation of biological systems modeled by means of concurrent calculi. While the faithful modelling of bio-systems often requires multi-compartment semantics, the original Gillespie algorithm considers only one fixed-size volume. In this paper we introduce an extended formalisation of the above algorithm which preserves the original model but allows the stochastic simulation in presence of multiple compartments with dynamical structure and variable sizes. The presented algorithm can be then used as basis for simulating systems expressed in an extended version of the stochastic π-Calculus, the Sπ@ language, obtained by means of polyadic synchronisation. Despite of its conservativeness, Sπ@ is showed to allow flexible modelling of multiple compartments with dynamical structure and to provide increased biological faithfulness.