Comparison of explicit and mean-field models of cytoskeletal filaments with crosslinking motors

Lamson, Adam; Moore, Jeffrey M.; Fang, Fang; Glaser, Matthew A.; Shelley, Michael; Betterton, Meredith D.

doi:10.1140/epje/s10189-021-00042-9

Cited by 8 publications

(13 citation statements)

References 81 publications

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“…Building on our previous work, CyLaKS implements Brownian dynamics to model physical movement of filaments and kinetic Monte Carlo to model state change (such as protein binding and unbinding) and chemical reactions (such as ATP hydrolysis) [71][72][73][74][75][76][77][78][79]. Each simulation time step includes first a kinetic Monte Carlo (kMC) substep, then a Brownian dynamics (BD) substep.…”

Section: Model and Simulationmentioning

confidence: 99%

“…In the future, extending the model to multiple protofilaments or actin filaments would be straightforward. We implement the Brownian dynamics algorithm of Tao et al [89], as in our previous work [71][72][73][74][75][76][77][78][79]. The microtubule center-of-mass position r evolves according to…”

Section: A Filamentsmentioning

confidence: 99%

“…CyLaKS is designed to facilitate modeling and simulation of cytoskeletal filaments (represented as long, thin rods with a lattice of binding sites for motors and other proteins), motor proteins, and other filament-binding proteins for problems in which spatiotemporal variation of motor or filament properties is significant. CyLaKS uses kinetic Monte Carlo-Brownian dynamics (kMC-BD) methods [71][72][73][74][75][76][77][78][79]. A primary goal in developing CyLaKS was to build on previous work modeling the mechanochemical cycle of individual motor proteins [80][81][82][83][84][85][86] by incorporating the motor ATP hydrolysis cycle in a simulation in which many motors can interact along filaments.…”

Section: Introductionmentioning

confidence: 99%

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CyLaKS: the Cytoskeleton Lattice-based Kinetic Simulator

Betterton

2021

Preprint

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Interaction of cytoskeletal filaments, motor proteins, and crosslinkers drives important cellular processes including cell division and cell movement. Cytoskeletal networks also undergo nonequilibrium self-organization in reconstituted systems. An emerging problem in cytoskeletal modeling and simulation is spatiotemporal alteration of the dynamics of filaments, motors, and associated proteins. This can occur due to motor crowding and obstacles along filaments, motor interactions and direction switching, and changes, defects, and heterogeneity in the filament lattice. How such spatiotemporally varying cytoskeletal filaments and motor interactions affect their collective properties is not fully understood. We developed the Cytoskeleton Lattice-based Kinetic Simulator (CyLaKS) for problems with significant spatiotemporal variation of motor or filament properties. The simulation builds on previous work modeling motor mechanochemistry into a simulation with many interacting motors and/or associated proteins. CyLaKS also includes detailed-balance in binding kinetics and movement and lattice heterogeneity. The simulation framework is flexible and extensible for future modeling work. Here we illustrate use of CyLaKS to study long-range motor interactions, filament heterogeneity, motion of a heterodimeric motor, and how changing crosslinker number affects filament separation.

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Section: Model and Simulationmentioning

confidence: 99%

Section: A Filamentsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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CyLaKS: the Cytoskeleton Lattice-based Kinetic Simulator

Betterton

2021

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“…Here, we describe aLENS , a framework of computational methods and software designed to more efficiently and accurately simulate large cytoskeletal systems ( Figure 1 ). Since motor proteins must bind, crosslink, and unbind from filaments to evolve such systems, aLENS simulates motors as traversing a (well-defined) free energy landscape Lamson et al, 2021 . This prevents artificial energy flux during crosslinking and maintains detailed balance in the passive limit.…”

Section: Introductionmentioning

confidence: 99%

Toward the cellular-scale simulation of motor-driven cytoskeletal assemblies

Yan

Ansari

Lamson

et al. 2022

eLife

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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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“…1). Since motor proteins must bind, crosslink, and unbind from filaments to evolve such systems, aLENS simulates motors as traversing a (well-defined) free energy landscape [24]. This prevents artificial energy fluxes during crosslinking processes and maintains detailed balance in the passive limit.…”

Section: Introductionmentioning

confidence: 99%

aLENS: towards the cellular-scale simulation of motor-driven cytoskeletal assemblies

Yan,

Ansari,

Lamson

et al. 2021

Preprint

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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 novel computational framework 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 different mixtures of tens to hundreds of thousands of cytoskeletal filaments and crosslinking motors, recapitulating self-emergent phenomena such as bundle formation and buckling, and elucidating how motor type, thermal fluctuations, internal stresses, and confinement determine the evolution of active matter aggregates.

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Comparison of explicit and mean-field models of cytoskeletal filaments with crosslinking motors

Cited by 8 publications

References 81 publications

CyLaKS: the Cytoskeleton Lattice-based Kinetic Simulator

CyLaKS: the Cytoskeleton Lattice-based Kinetic Simulator

Toward the cellular-scale simulation of motor-driven cytoskeletal assemblies

aLENS: towards the cellular-scale simulation of motor-driven cytoskeletal assemblies

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