TY - JOUR
T1 - Toward the cellular-scale simulation of motor-driven cytoskeletal assemblies
AU - Yan, Wen
AU - Ansari, Saad
AU - Lamson, Adam
AU - Glaser, Matthew A.
AU - Blackwell, Robert
AU - Betterton, Meredith D.
AU - Shelley, Michael
N1 - Funding Information:
MJS acknowledges support from NSF grants DMR-2004469 and CMMI-1762506. SA, ARL, MAG, and MB acknowledge support from NSF grants DMS-1821305, and NIH grant RGM124371A. This work utilized resources from the University of Colorado Boulder Research Computing Group, which is supported by the National Science Foundation (awards ACI-1532235 and ACI-1532236), the University of Colorado Boulder, and Colorado State University. We thank Prof. Dimitrios Vavylonis for discussions on implementing flexible filaments.
Funding Information:
National Science Foundation DMR-2004469 Michael Shelley National Science Foundation CMMI-1762506 Michael Shelley National Science Foundation DMS-1821305 Saad Ansari Matthew A Glaser Meredith D Betterton Foundation ACI-1532235 Saad Ansari Matthew A Glaser Meredith D Betterton National Science Foundation ACI-1532236 Saad Ansari Matthew A Glaser Meredith D Betterton National Science Foundation RGM124371A Saad Ansari Matthew A Glaser Meredith D Betterton.
Publisher Copyright:
© Yan et al.
PY - 2022/5
Y1 - 2022/5
N2 - 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.
AB - 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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U2 - 10.7554/eLife.74160
DO - 10.7554/eLife.74160
M3 - Article
C2 - 35617115
AN - SCOPUS:85130787640
SN - 2050-084X
VL - 11
JO - eLife
JF - eLife
M1 - e74160
ER -