Agent-based simulation study of confined active nematic filaments*

To model self-organized dynamics in a confined active nematic, we perform agent-based simulations of flexible filaments driven by inter-filament shear propulsion. Each filament is represented as an elastic bead-spring chain. Inter-filament forces mimic the action produced by ATP-powered kinesin motor clusters and produce extensile stresses like those observed in experiment (see, e.g. Opathalge et al, PNAS 2018). Depletion forces between nearby filaments are introduced to drive bundle formation. As a novel way to introduce hydrodynamic forces, we model interaction with a background fluid represented as a coarse-grained liquid sublayer. Active filaments are thermostatted only via interaction with the fluid sublayer, which is subject to a momentum-conserving thermostat. Adjustable model parameters include: inter-filament active driving force, driving force against the confining wall, filament bead-spring stretch and bend elastic parameters, fluid interaction intensity, temperature and dissipation parameters of the thermostat, filament and fluid sublayer densities, and depletion forces. We consider confinement in both disk-shaped and more complex confinement geometries, and examine resulting topological defect trajectories and flow patterns. The confining boundary is represented by an assembly of immobile particles with short-range, repulsive interactions, allowing us to model confining geometries of arbitrary shape. We compare results to relevant experiments.