  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.
