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

Area of Science:

• Biophysics
• Cell Biology
• Computational Science

Background:

• The cytoskeleton, composed of filaments, motors, and crosslinkers, exemplifies active matter and forms cellular organelles.
• Simulating cytoskeletal assemblies is crucial for understanding cellular processes and material properties.

Purpose of the Study:

• Introduce aLENS (a Living Ensemble Simulator), a new computational framework to overcome limitations in current simulation methods.
• Enable efficient and stable simulation of large-scale cytoskeletal systems.

Main Methods:

• Model molecular motors with crosslinking kinetics on a thermodynamic energy landscape.
• Integrate system dynamics while enforcing hard-body repulsion between filaments without molecular potentials.
• Utilize parallel computing for simulating tens to hundreds of thousands of filaments and motors.

Main Results:

• Successfully simulated large-scale cytoskeletal assemblies, including tens to hundreds of thousands of filaments and motors.
• Recapitulated emergent phenomena like bundle formation and buckling in cytoskeletal networks.
• Demonstrated the framework's ability to avoid molecular potentials for steric constraints.

Conclusions:

• aLENS provides a powerful new tool for simulating complex cytoskeletal active matter.
• The framework can elucidate the roles of motor type, thermal fluctuations, stress, and confinement in cytoskeletal dynamics.
• Facilitates deeper understanding of how cytoskeletal active matter evolves and dictates cellular functions.