Confined actin ring assembly through bundle coarsening prior to kinetic arrest

Controlled assembly of large cytoskeletal architectures in living or synthetic cells requires overcoming thermodynamic and kinetic barriers. Prototypical examples include the assembly of fission yeast cytokinetic rings, red blood cell marginal bands, and equatorial actin rings by passive cross-linkers when confined within a sphere. Recent in vitro experiments have demonstrated that actin rings form when the confining geometry is sufficiently small while complex bundled networks form for larger geometries. Exploring the determinants and pathways for forming cytoskeletal rings requires new computational methods that can systematically vary molecular interactions and concentrations over micron length and minute timescales. We used the high-performance, open-source software aLENS where a constraint method enforces hard-core repulsion between rigid spherocylinders and crosslinking forces in a unified implicit solver. We simulate polymerization to correspond with a depleting monomer pool and varying distributions of nucleating actin seeds. Under typical in vitro polymerization conditions, we find that single elongating filaments merge into growing bundles, reaching an overlap threshold, which significantly slows down their diffusive dynamics. However, the topology of these bundle networks continues to evolve through filament merging, zippering, and cross-linker condensation, resulting in thicker bundles. Confinement aids network coarsening and loop formation with a ring or open bundle being the stable end state of this dynamical system if reached prior to kinetic arrest. We explored the effects of viscosity, nucleation rate, and type of passive cross-linkers. Our study informs the structure and mechanics of both confined and bulk networks of semiflexible filaments.