Stochastic simulation algorithms for Interacting Particle Systems.
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2021
2021
Historique:
received:
27
08
2020
accepted:
29
01
2021
entrez:
2
3
2021
pubmed:
3
3
2021
medline:
26
8
2021
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 33651796
doi: 10.1371/journal.pone.0247046
pii: PONE-D-20-26892
pmc: PMC7924777
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0247046Subventions
Organisme : NCATS NIH HHS
ID : KL2 TR000122
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM053275
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG006139
Pays : United States
Organisme : NHGRI NIH HHS
ID : T32 HG002536
Pays : United States
Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
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