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A global method for fast simulations of molecular dynamics in multiscale agent-based models of biological tissues

Agent-based models (ABMs) are a natural platform for capturing the multiple time and spatial scales in biological processes. However, these models are computationally expensive, especially when including molecular-level effects. The traditional approach to simulating this type of multiscale ABM is t...

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Detalles Bibliográficos
Autores principales: Bergman, Daniel, Sweis, Randy F., Pearson, Alexander T., Nazari, Fereshteh, Jackson, Trachette L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9142654/
https://www.ncbi.nlm.nih.gov/pubmed/35637730
http://dx.doi.org/10.1016/j.isci.2022.104387
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author Bergman, Daniel
Sweis, Randy F.
Pearson, Alexander T.
Nazari, Fereshteh
Jackson, Trachette L.
author_facet Bergman, Daniel
Sweis, Randy F.
Pearson, Alexander T.
Nazari, Fereshteh
Jackson, Trachette L.
author_sort Bergman, Daniel
collection PubMed
description Agent-based models (ABMs) are a natural platform for capturing the multiple time and spatial scales in biological processes. However, these models are computationally expensive, especially when including molecular-level effects. The traditional approach to simulating this type of multiscale ABM is to solve a system of ordinary differential equations for the molecular events per cell. This significantly adds to the computational cost of simulations as the number of agents grows, which contributes to many ABMs being limited to around [Formula: see text] cells. We propose an approach that requires the same computational time independent of the number of agents. This speeds up the entire simulation by orders of magnitude, allowing for more thorough explorations of ABMs with even larger numbers of agents. We use two systems to show that the new method strongly agrees with the traditionally used approach. This computational strategy can be applied to a wide range of biological investigations.
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spelling pubmed-91426542022-05-29 A global method for fast simulations of molecular dynamics in multiscale agent-based models of biological tissues Bergman, Daniel Sweis, Randy F. Pearson, Alexander T. Nazari, Fereshteh Jackson, Trachette L. iScience Article Agent-based models (ABMs) are a natural platform for capturing the multiple time and spatial scales in biological processes. However, these models are computationally expensive, especially when including molecular-level effects. The traditional approach to simulating this type of multiscale ABM is to solve a system of ordinary differential equations for the molecular events per cell. This significantly adds to the computational cost of simulations as the number of agents grows, which contributes to many ABMs being limited to around [Formula: see text] cells. We propose an approach that requires the same computational time independent of the number of agents. This speeds up the entire simulation by orders of magnitude, allowing for more thorough explorations of ABMs with even larger numbers of agents. We use two systems to show that the new method strongly agrees with the traditionally used approach. This computational strategy can be applied to a wide range of biological investigations. Elsevier 2022-05-13 /pmc/articles/PMC9142654/ /pubmed/35637730 http://dx.doi.org/10.1016/j.isci.2022.104387 Text en © 2022 The Author(s) https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Article
Bergman, Daniel
Sweis, Randy F.
Pearson, Alexander T.
Nazari, Fereshteh
Jackson, Trachette L.
A global method for fast simulations of molecular dynamics in multiscale agent-based models of biological tissues
title A global method for fast simulations of molecular dynamics in multiscale agent-based models of biological tissues
title_full A global method for fast simulations of molecular dynamics in multiscale agent-based models of biological tissues
title_fullStr A global method for fast simulations of molecular dynamics in multiscale agent-based models of biological tissues
title_full_unstemmed A global method for fast simulations of molecular dynamics in multiscale agent-based models of biological tissues
title_short A global method for fast simulations of molecular dynamics in multiscale agent-based models of biological tissues
title_sort global method for fast simulations of molecular dynamics in multiscale agent-based models of biological tissues
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9142654/
https://www.ncbi.nlm.nih.gov/pubmed/35637730
http://dx.doi.org/10.1016/j.isci.2022.104387
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