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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...

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Detalles Bibliográficos
Autores principales: Yan, Wen, Ansari, Saad, Lamson, Adam, Glaser, Matthew A, Blackwell, Robert, Betterton, Meredith D, Shelley, Michael
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2022
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.
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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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