Self-assembly and dynamics of active filaments in weak confinement

Geometric confinement is ubiquitous in biological and synthetic active matter systems and plays a crucial role in regulating their organization and dynamics. Most studies on confined active polymers (APs) have concentrated on the condition of strong confinement, where the chain dimensions are far larger than the confining domain-a condition that corresponds to DNA within the cell nucleus or the viral capsid. Here, we investigate by Langevin dynamics simulations the self-assembly and collective behavior of polar AP chains under weak confinement where the confining domain exceeds the polymer's intrinsic size. By systematically comparing circular and polygonal confinements, we demonstrate that boundary geometry strongly influences both single-chain conformations and multi-chain collective states. For isolated chains, confinement markedly enhances the formation of spiral conformations with spiral nucleation occurring predominantly near the boundary and especially at sharper corners. In contrast, confinement suppresses spiral formation for systems containing multiple interacting chains. The system instead exhibits a diverse set of collective morphologies, including an aggregate state and two distinct vortex states characterized by single-layer (s-vortex) and double-layer (d-vortex) rotating boundary bands. Our results reveal that weak confinement regulates active-polymer self-organization through a competition between collision-induced bending and boundary-induced crowding. These findings provide new insights into the behavior of active polymers in confined environments and offer potential strategies for designing functional active materials through geometric confinement.