Parallelism and efficiency in discrete-event simulation

Discrete-event models depict systems where a discrete state is repeatedly altered by instantaneous changes in time, the events of the model. Such models have gained popularity in fields such as Com ...

[1]  Stefan Engblom,et al.  Parallel in Time Simulation of Multiscale Stochastic Chemical Kinetics , 2008, Multiscale Model. Simul..

[2]  Michael A. Gibson,et al.  Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels , 2000 .

[3]  Gabriel A. Wainer,et al.  Synchronization methods in parallel and distributed discrete-event simulation , 2013, Simul. Model. Pract. Theory.

[4]  Asad Malik,et al.  Optimistic Synchronization of Parallel Simulations in Cloud Computing Environments , 2009, 2009 IEEE International Conference on Cloud Computing.

[5]  Paul F. Reynolds,et al.  Elastic time , 1998, TOMC.

[6]  Paulette Clancy,et al.  Accurate implementation of leaping in space: the spatial partitioned-leaping algorithm. , 2010, The Journal of chemical physics.

[7]  Giancarlo Mauri,et al.  cuTauLeaping: A GPU-Powered Tau-Leaping Stochastic Simulator for Massive Parallel Analyses of Biological Systems , 2014, PloS one.

[8]  Randal E. Bryant,et al.  SIMULATION OF PACKET COMMUNICATION ARCHITECTURE COMPUTER SYSTEMS , 1977 .

[9]  Michael Mascagni,et al.  SPRNG: A Scalable Library for Pseudorandom Number Generation , 1999, PP.

[10]  Adelinde M. Uhrmacher,et al.  Exploring the performance of spatial stochastic simulation algorithms , 2011, J. Comput. Phys..

[11]  R Metzler,et al.  The future is noisy: the role of spatial fluctuations in genetic switching. , 2001, Physical review letters.

[12]  D. Gillespie.  Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .

[13]  W. O. Kermack,et al.  A contribution to the mathematical theory of epidemics , 1927 .

[14]  Stefan Engblom,et al.  On the Stability of Stochastic Jump Kinetics , 2012, 1202.3892.

[15]  Jaap A. Kaandorp,et al.  Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli , 2006, Bioinform..

[16]  Petr Plechác,et al.  Hierarchical fractional-step approximations and parallel kinetic Monte Carlo algorithms , 2011, J. Comput. Phys..

[17]  Bing Wang,et al.  Abstract Next Subvolume Method: A logical process-based approach for spatial stochastic simulation of chemical reactions , 2011, Comput. Biol. Chem..

[18]  K. Mani Chandy,et al.  Asynchronous distributed simulation via a sequence of parallel computations , 1981, CACM.

[19]  Concetto Spampinato,et al.  Parallel stochastic systems biology in the cloud , 2013, Briefings Bioinform..

[20]  P. Donnelly.  MARKOV PROCESSES Characterization and Convergence (Wiley Series in Probability and Mathematical Statistics) , 1987 .

[21]  Jason Liu.  Parallel Discrete-Event Simulation , 2010 .

[22]  Alois Ferscha.  Probabilistic adaptive direct optimism control in Time Warp , 1995, PADS.

[23]  J. Elf,et al.  Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases. , 2004, Systems biology.

[24]  N. Kampen,et al.  Stochastic processes in physics and chemistry , 1981 .

[25]  Richard M. Fujimoto,et al.  Parallel and Distribution Simulation Systems , 1999 .

[26]  Samir Ranjan Das.  Adaptive protocols for parallel discrete event simulation , 1996, Winter Simulation Conference.

[27]  C. W. Gardiner,et al.  Handbook of stochastic methods - for physics, chemistry and the natural sciences, Second Edition , 1986, Springer series in synergetics.

[28]  Christos G. Cassandras,et al.  Systems and Models , 2021, Introduction to Discrete Event Systems.

[29]  Andreas Hellander,et al.  Simulation of Stochastic Reaction-Diffusion Processes on Unstructured Meshes , 2008, SIAM J. Sci. Comput..

[30]  John G. Cleary,et al.  Scheduling critical channels in conservative parallel discrete event simulation , 1999, Proceedings Thirteenth Workshop on Parallel and Distributed Simulation. PADS 99. (Cat. No.PR00155).