Simulating confined cytoskeletal structures with explicit motors and crosslinkers

Confined cytoskeletal filaments, motor proteins, and passive crosslinkers organize into networks whose structure and dynamics depend on the interplay of filament mechanical rigidity, kinetics of polymerization, and interaction with confining boundaries. Several experimental studies have reconstituted a variety of confined structures in vitro, such as asters and contractile rings, paving the way for synthetic cell applications. However, understanding the space of all possible confined cytoskeletal patterns requires the development of computational methods that allow systematic variation of molecular interactions, at varying concentrations, over micron scales. To overcome the limitations of prior methods, we used and modified the high-performance, open-source software aLENS. In aLENS, a constraint method enforces hard-core repulsion between rigid spherosylinders with crosslinking and motor forces incorporated in a unified implicit solver. We further implemented filament flexibility by connecting short spherocylinders by pairs of springs, under the same aLENS solver, tuned to reproduce the desired persistence length. Polymerization was simulated as the addition of segments at a rate that decreases according to a depleting uniform monomer pool. We use this method to show how confined actin filaments form structures such as contractile rings or bundled networks in the presence of myosin motors, passive crosslinkers, and surface-attached linkers or motors.