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Stochastic simulation algorithms for Interacting Particle Systems
Interacting Particle Systems (IPSs) are used to model spatio-temporal stochastic systems in many disparate areas of science. We design an algorithmic framework that reduces IPS simulation to simulation of well-mixed Chemical Reaction Networks (CRNs). This framework minimizes the number of associated...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7924777/ https://www.ncbi.nlm.nih.gov/pubmed/33651796 http://dx.doi.org/10.1371/journal.pone.0247046 |
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author | Stutz, Timothy C. Landeros, Alfonso Xu, Jason Sinsheimer, Janet S. Sehl, Mary Lange, Kenneth |
author_facet | Stutz, Timothy C. Landeros, Alfonso Xu, Jason Sinsheimer, Janet S. Sehl, Mary Lange, Kenneth |
author_sort | Stutz, Timothy C. |
collection | PubMed |
description | Interacting Particle Systems (IPSs) are used to model spatio-temporal stochastic systems in many disparate areas of science. We design an algorithmic framework that reduces IPS simulation to simulation of well-mixed Chemical Reaction Networks (CRNs). This framework minimizes the number of associated reaction channels and decouples the computational cost of the simulations from the size of the lattice. Decoupling allows our software to make use of a wide class of techniques typically reserved for well-mixed CRNs. We implement the direct stochastic simulation algorithm in the open source programming language Julia. We also apply our algorithms to several complex spatial stochastic phenomena. including a rock-paper-scissors game, cancer growth in response to immunotherapy, and lipid oxidation dynamics. Our approach aids in standardizing mathematical models and in generating hypotheses based on concrete mechanistic behavior across a wide range of observed spatial phenomena. |
format | Online Article Text |
id | pubmed-7924777 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-79247772021-03-10 Stochastic simulation algorithms for Interacting Particle Systems Stutz, Timothy C. Landeros, Alfonso Xu, Jason Sinsheimer, Janet S. Sehl, Mary Lange, Kenneth PLoS One Research Article Interacting Particle Systems (IPSs) are used to model spatio-temporal stochastic systems in many disparate areas of science. We design an algorithmic framework that reduces IPS simulation to simulation of well-mixed Chemical Reaction Networks (CRNs). This framework minimizes the number of associated reaction channels and decouples the computational cost of the simulations from the size of the lattice. Decoupling allows our software to make use of a wide class of techniques typically reserved for well-mixed CRNs. We implement the direct stochastic simulation algorithm in the open source programming language Julia. We also apply our algorithms to several complex spatial stochastic phenomena. including a rock-paper-scissors game, cancer growth in response to immunotherapy, and lipid oxidation dynamics. Our approach aids in standardizing mathematical models and in generating hypotheses based on concrete mechanistic behavior across a wide range of observed spatial phenomena. Public Library of Science 2021-03-02 /pmc/articles/PMC7924777/ /pubmed/33651796 http://dx.doi.org/10.1371/journal.pone.0247046 Text en © 2021 Stutz et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Stutz, Timothy C. Landeros, Alfonso Xu, Jason Sinsheimer, Janet S. Sehl, Mary Lange, Kenneth Stochastic simulation algorithms for Interacting Particle Systems |
title | Stochastic simulation algorithms for Interacting Particle Systems |
title_full | Stochastic simulation algorithms for Interacting Particle Systems |
title_fullStr | Stochastic simulation algorithms for Interacting Particle Systems |
title_full_unstemmed | Stochastic simulation algorithms for Interacting Particle Systems |
title_short | Stochastic simulation algorithms for Interacting Particle Systems |
title_sort | stochastic simulation algorithms for interacting particle systems |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7924777/ https://www.ncbi.nlm.nih.gov/pubmed/33651796 http://dx.doi.org/10.1371/journal.pone.0247046 |
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