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Toward the cellular-scale simulation of motor-driven cytoskeletal assemblies
The cytoskeleton – a collection of polymeric filaments, molecular motors, and crosslinkers – is a foundational example of active matter, and in the cell assembles into organelles that guide basic biological functions. Simulation of cytoskeletal assemblies is an important tool for modeling cellular p...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
eLife Sciences Publications, Ltd
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9135453/ https://www.ncbi.nlm.nih.gov/pubmed/35617115 http://dx.doi.org/10.7554/eLife.74160 |
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author | Yan, Wen Ansari, Saad Lamson, Adam Glaser, Matthew A Blackwell, Robert Betterton, Meredith D Shelley, Michael |
author_facet | Yan, Wen Ansari, Saad Lamson, Adam Glaser, Matthew A Blackwell, Robert Betterton, Meredith D Shelley, Michael |
author_sort | Yan, Wen |
collection | PubMed |
description | The cytoskeleton – a collection of polymeric filaments, molecular motors, and crosslinkers – is a foundational example of active matter, and in the cell assembles into organelles that guide basic biological functions. Simulation of cytoskeletal assemblies is an important tool for modeling cellular processes and understanding their surprising material properties. Here, we present aLENS (a Living Ensemble Simulator), a novel computational framework designed to surmount the limits of conventional simulation methods. We model molecular motors with crosslinking kinetics that adhere to a thermodynamic energy landscape, and integrate the system dynamics while efficiently and stably enforcing hard-body repulsion between filaments. Molecular potentials are entirely avoided in imposing steric constraints. Utilizing parallel computing, we simulate tens to hundreds of thousands of cytoskeletal filaments and crosslinking motors, recapitulating emergent phenomena such as bundle formation and buckling. This simulation framework can help elucidate how motor type, thermal fluctuations, internal stresses, and confinement determine the evolution of cytoskeletal active matter. |
format | Online Article Text |
id | pubmed-9135453 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | eLife Sciences Publications, Ltd |
record_format | MEDLINE/PubMed |
spelling | pubmed-91354532022-05-27 Toward the cellular-scale simulation of motor-driven cytoskeletal assemblies Yan, Wen Ansari, Saad Lamson, Adam Glaser, Matthew A Blackwell, Robert Betterton, Meredith D Shelley, Michael eLife Computational and Systems Biology The cytoskeleton – a collection of polymeric filaments, molecular motors, and crosslinkers – is a foundational example of active matter, and in the cell assembles into organelles that guide basic biological functions. Simulation of cytoskeletal assemblies is an important tool for modeling cellular processes and understanding their surprising material properties. Here, we present aLENS (a Living Ensemble Simulator), a novel computational framework designed to surmount the limits of conventional simulation methods. We model molecular motors with crosslinking kinetics that adhere to a thermodynamic energy landscape, and integrate the system dynamics while efficiently and stably enforcing hard-body repulsion between filaments. Molecular potentials are entirely avoided in imposing steric constraints. Utilizing parallel computing, we simulate tens to hundreds of thousands of cytoskeletal filaments and crosslinking motors, recapitulating emergent phenomena such as bundle formation and buckling. This simulation framework can help elucidate how motor type, thermal fluctuations, internal stresses, and confinement determine the evolution of cytoskeletal active matter. eLife Sciences Publications, Ltd 2022-05-26 /pmc/articles/PMC9135453/ /pubmed/35617115 http://dx.doi.org/10.7554/eLife.74160 Text en © 2022, Yan et al https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited. |
spellingShingle | Computational and Systems Biology Yan, Wen Ansari, Saad Lamson, Adam Glaser, Matthew A Blackwell, Robert Betterton, Meredith D Shelley, Michael Toward the cellular-scale simulation of motor-driven cytoskeletal assemblies |
title | Toward the cellular-scale simulation of motor-driven cytoskeletal assemblies |
title_full | Toward the cellular-scale simulation of motor-driven cytoskeletal assemblies |
title_fullStr | Toward the cellular-scale simulation of motor-driven cytoskeletal assemblies |
title_full_unstemmed | Toward the cellular-scale simulation of motor-driven cytoskeletal assemblies |
title_short | Toward the cellular-scale simulation of motor-driven cytoskeletal assemblies |
title_sort | toward the cellular-scale simulation of motor-driven cytoskeletal assemblies |
topic | Computational and Systems Biology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9135453/ https://www.ncbi.nlm.nih.gov/pubmed/35617115 http://dx.doi.org/10.7554/eLife.74160 |
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