Article

Parallel and Distributed Spatial Simulation of Chemical Reactions

Authors:

Matthias Jeschke,

Richard Fujimoto,

Adelinde M. UhrmacherAuthors Info & Claims

PADS '08: Proceedings of the 22nd Workshop on Principles of Advanced and Distributed Simulation

Pages 51 - 59

https://doi.org/10.1109/PADS.2008.20

Published: 03 June 2008 Publication History

Abstract

The application of parallel and distributed simulation techniques is often limited by the amount of parallelism available in the model. This holds true for large-scale cell-biological simulations, a field that has emerged as data and knowledge concerning these systems increases and biologists call for tools to guide wet-lab experimentation. A promising approach to exploit parallelism in this domain is the integration of spatial aspects, which are often crucial to a model's validity. We describe an optimistic, parallel and distributed variant of the Next-Subvolume Method (NSM), a method that augments the well-known Gillespie Stochastic Simulation Algorithm (SSA) with spatial features. We discuss requirements imposed by this application on a parallel discrete event simulation engine to achieve efficient execution. First results of combining NSM and the grid-inspired simulation system Aurora are shown.

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Cited By

Patoary MTropper CMcDougal RLin ZLytton W(2019)Parallel Stochastic Discrete Event Simulation of Calcium Dynamics in NeuronIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2017.275693016:3(1007-1019)Online publication date: 1-May-2019
https://dl.acm.org/doi/10.1109/TCBB.2017.2756930
Lin ZTropper CMcDougal RIshlam Patoary MLytton WYao YHines M(2016)Multithreaded Stochastic PDES for Reactions and Diffusions in NeuronsACM Transactions on Modeling and Computer Simulation10.1145/298737327:2(1-27)Online publication date: 7-Nov-2016
https://dl.acm.org/doi/10.1145/2987373
Lin ZTropper CIshlam Patoary MMcDougal RLytton WHines MTaylor SMustafee NSon Y(2015)NTW-MTProceedings of the 3rd ACM SIGSIM Conference on Principles of Advanced Discrete Simulation10.1145/2769458.2769459(157-167)Online publication date: 10-Jun-2015
https://dl.acm.org/doi/10.1145/2769458.2769459
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Index Terms

Parallel and Distributed Spatial Simulation of Chemical Reactions
1. Applied computing
  1. Physical sciences and engineering
    1. Chemistry
2. Computing methodologies
  1. Modeling and simulation
    1. Simulation types and techniques
      1. Distributed simulation
      2. Massively parallel and high-performance simulations

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cover image ACM Conferences

PADS '08: Proceedings of the 22nd Workshop on Principles of Advanced and Distributed Simulation

June 2008

196 pages

ISBN:9780769531595

Sponsors

SIGSIM: ACM Special Interest Group on Simulation and Modeling

Publisher

IEEE Computer Society

United States

Publication History

Published: 03 June 2008

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PADS08

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SIGSIM

PADS08: PADS '08 - Principles of Advanced and Distributed Simulation

June 3 - 6, 2008

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PADS '08 Paper Acceptance Rate 21 of 52 submissions, 40%;

Overall Acceptance Rate 398 of 779 submissions, 51%

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Cited By

Patoary MTropper CMcDougal RLin ZLytton W(2019)Parallel Stochastic Discrete Event Simulation of Calcium Dynamics in NeuronIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2017.275693016:3(1007-1019)Online publication date: 1-May-2019
https://dl.acm.org/doi/10.1109/TCBB.2017.2756930
Lin ZTropper CMcDougal RIshlam Patoary MLytton WYao YHines M(2016)Multithreaded Stochastic PDES for Reactions and Diffusions in NeuronsACM Transactions on Modeling and Computer Simulation10.1145/298737327:2(1-27)Online publication date: 7-Nov-2016
https://dl.acm.org/doi/10.1145/2987373
Lin ZTropper CIshlam Patoary MMcDougal RLytton WHines MTaylor SMustafee NSon Y(2015)NTW-MTProceedings of the 3rd ACM SIGSIM Conference on Principles of Advanced Discrete Simulation10.1145/2769458.2769459(157-167)Online publication date: 10-Jun-2015
https://dl.acm.org/doi/10.1145/2769458.2769459
Kuwahara HGao XFages F(2011)An efficient parallel stochastic simulation method for analysis of nonviral gene delivery systemsProceedings of the 9th International Conference on Computational Methods in Systems Biology10.1145/2037509.2037522(83-93)Online publication date: 21-Sep-2011
https://dl.acm.org/doi/10.1145/2037509.2037522
Falk MOtt MErtl TKlann MKoeppl HFages F(2011)Parallelized agent-based simulation on CPU and graphics hardware for spatial and stochastic models in biologyProceedings of the 9th International Conference on Computational Methods in Systems Biology10.1145/2037509.2037521(73-82)Online publication date: 21-Sep-2011
https://dl.acm.org/doi/10.1145/2037509.2037521
Zunino R(2011)Trading Computation Time for Synchronization Time in Spatial Distributed SimulationProceedings of the 2011 IEEE Workshop on Principles of Advanced and Distributed Simulation10.1109/PADS.2011.5936766(1-8)Online publication date: 14-Jun-2011
https://dl.acm.org/doi/10.1109/PADS.2011.5936766
Uhrmacher ASchulz HSchumann HSchwabe LTimmermann DStea GMairesse JMendes J(2009)Regenerative systemsProceedings of the Fourth International ICST Conference on Performance Evaluation Methodologies and Tools10.4108/ICST.VALUETOOLS2009.7907(1-10)Online publication date: 20-Oct-2009
https://dl.acm.org/doi/10.4108/ICST.VALUETOOLS2009.7907
Jeschke MUhrmacher AJefferson TFowler JIngalls R(2008)Multi-resolution spatial simulation for molecular crowdingProceedings of the 40th Conference on Winter Simulation10.5555/1516744.1516986(1384-1392)Online publication date: 7-Dec-2008
https://dl.acm.org/doi/10.5555/1516744.1516986
Jeschke MEwald RPark AFujimoto RUhrmacher A(2008)A parallel and distributed discrete event approach for spatial cell-biological simulationsACM SIGMETRICS Performance Evaluation Review10.1145/1364644.136465235:4(22-31)Online publication date: 1-Mar-2008
https://dl.acm.org/doi/10.1145/1364644.1364652

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