Exploring the performance of spatial stochastic simulation algorithms

DOI10.1016/J.JCP.2010.12.030MaRDI QIDQ543671zbMATH OpenOpenAlexFDO

Authors Matthias Jeschke, Roland Ewald, Adelinde M. Uhrmacher

Publication date 17 June 2011

Published in Journal of Computational Physics (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.jcp.2010.12.030

zbMATH Keywords

performance evaluationstochastic simulationperformance analysisSSA\(\tau \)-leapingGillespie multi-particle methodnext sub-volume methodspatial \(\tau \)-leaping

Mathematics Subject Classification ID

Numerical solutions to stochastic differential and integral equations (65C30)

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Cites work

• scientific article; zbMATH DE number 6472612 (Why is no real title available?)
• Accuracy limitations and the measurement of errors in the stochastic simulation of chemically reacting systems
• An adaptive algorithm for simulation of stochastic reaction-diffusion processes
• Continuous system simulation
• Karl Pearson and the Chi-Squared Test
• Needed: An Empirical Science of Algorithms
• Temporal acceleration of spatially distributed kinetic Monte Carlo simulations

Cited in

(6)

• Semantics and efficient simulation algorithms of an expressive multilevel modeling language
• Lattice Monte Carlo simulation of Galilei variant anomalous diffusion
• Multithreaded stochastic PDES for reactions and diffusions in neurons
• Abstract next subvolume method: a logical process-based approach for spatial stochastic simulation of chemical reactions
• Scaling limits of spatial compartment models for chemical reaction networks
• Design of fractional-order variants of complex LMS and NLMS algorithms for adaptive channel equalization

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