Cargando…
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...
Autores principales: | , , , , |
---|---|
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 |
_version_ | 1784715620872355840 |
---|---|
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. |
format | Online Article Text |
id | pubmed-9142654 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT bergmandaniel aglobalmethodforfastsimulationsofmoleculardynamicsinmultiscaleagentbasedmodelsofbiologicaltissues AT sweisrandyf aglobalmethodforfastsimulationsofmoleculardynamicsinmultiscaleagentbasedmodelsofbiologicaltissues AT pearsonalexandert aglobalmethodforfastsimulationsofmoleculardynamicsinmultiscaleagentbasedmodelsofbiologicaltissues AT nazarifereshteh aglobalmethodforfastsimulationsofmoleculardynamicsinmultiscaleagentbasedmodelsofbiologicaltissues AT jacksontrachettel aglobalmethodforfastsimulationsofmoleculardynamicsinmultiscaleagentbasedmodelsofbiologicaltissues AT bergmandaniel globalmethodforfastsimulationsofmoleculardynamicsinmultiscaleagentbasedmodelsofbiologicaltissues AT sweisrandyf globalmethodforfastsimulationsofmoleculardynamicsinmultiscaleagentbasedmodelsofbiologicaltissues AT pearsonalexandert globalmethodforfastsimulationsofmoleculardynamicsinmultiscaleagentbasedmodelsofbiologicaltissues AT nazarifereshteh globalmethodforfastsimulationsofmoleculardynamicsinmultiscaleagentbasedmodelsofbiologicaltissues AT jacksontrachettel globalmethodforfastsimulationsofmoleculardynamicsinmultiscaleagentbasedmodelsofbiologicaltissues |