ACM Transactions on Programming Languages and Systems (TOPLAS)
Parallel discrete-event simulation of FCFS stochastic queueing networks
PPEALS '88 Proceedings of the ACM/SIGPLAN conference on Parallel programming: experience with applications, languages and systems
Parallel discrete event simulation
Communications of the ACM - Special issue on simulation
Analysis of parallel replicated simulations under a completion time constraint
ACM Transactions on Modeling and Computer Simulation (TOMACS)
Analysis if initial transient deletion for parallel steady-state simulations
SIAM Journal on Scientific and Statistical Computing
A generalized carrier-null method for conservative parallel simulation
PADS '94 Proceedings of the eighth workshop on Parallel and distributed simulation
Parallel independent replicated simulation on a network of workstations
PADS '94 Proceedings of the eighth workshop on Parallel and distributed simulation
Parallel replicated simulation of Markov chains: implementation and variance reduction
WSC '93 Proceedings of the 25th conference on Winter simulation
Automating parallel simulation using parallel time streams
ACM Transactions on Modeling and Computer Simulation (TOMACS)
Pre-sampling as an approach for exploiting temporal uncertainty
PADS '00 Proceedings of the fourteenth workshop on Parallel and distributed simulation
Some Deadlock Properties of Computer Systems
ACM Computing Surveys (CSUR)
ACM Transactions on Modeling and Computer Simulation (TOMACS)
Concurrent Replication of Parallel and Distributed Simulations
Proceedings of the 19th Workshop on Principles of Advanced and Distributed Simulation
Parallel Implementation of Stochastic Simulation for Large-scale Cellular Processes
HPCASIA '05 Proceedings of the Eighth International Conference on High-Performance Computing in Asia-Pacific Region
Distributed Simulation: A Case Study in Design and Verification of Distributed Programs
IEEE Transactions on Software Engineering
Parallel and Distributed Spatial Simulation of Chemical Reactions
Proceedings of the 22nd Workshop on Principles of Advanced and Distributed Simulation
Computational Biology and Chemistry
Proceedings of the 9th International Conference on Computational Methods in Systems Biology
An efficient parallel stochastic simulation method for analysis of nonviral gene delivery systems
Proceedings of the 9th International Conference on Computational Methods in Systems Biology
Stability analysis of biological network topologies during stochastic simulation
Proceedings of the 4th International ICST Conference on Simulation Tools and Techniques
Smoldyn on Graphics Processing Units: Massively Parallel Brownian Dynamics Simulations
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
The Relevance of Topology in Parallel Simulation of Biological Networks
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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The parallel simulation of biochemical reactions is a very interesting problem: biochemical systems are inherently parallel, yet the majority of the algorithms to simulate them, including the well-known and widespread Gillespie SSA, are strictly sequential. Here we investigate, in a general way, how to characterize the simulation of biochemical systems in terms of Discrete Event Simulation. We dissect their inherent parallelism in order both to exploit the work done in this area and to speed-up their simulation. We study the peculiar characteristics of discrete biological simulations in order to select the parallelization technique which provides the greater benefits, as well as to touch its limits. We then focus on reaction-diffusion systems: we design and implement an efficient parallel algorithm for simulating such systems that include both reactions between entities and movements throughout the space.