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

TL;DR

This paper introduces aLENS, a new computational framework for simulating large-scale cytoskeletal assemblies, capturing emergent behaviors like bundle formation and buckling with high efficiency and stability.

Contribution

The authors develop aLENS, a novel simulation method that models molecular motors with thermodynamic kinetics and enforces steric interactions without molecular potentials, enabling large-scale active matter simulations.

Findings

Simulated self-organizing cytoskeletal phenomena such as bundle formation.

Demonstrated the impact of motor type and thermal fluctuations on assembly dynamics.

Achieved efficient simulation of hundreds of thousands of filaments and motors.

Abstract

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.