Polarity-Programmed Topological Gating of Knotting in Spatially Patterned Active Polymers

Abstract

Spatially patterned tangential activity provides a route to program polymer topology through both geometry and propulsion direction. We use Langevin-dynamics simulations of a flexible, self-avoiding linear polymer to determine how active-domain placement and independently assigned propulsion polarities control nonequilibrium knotting. Reversing the polarities of two terminal active blocks switches the steady state from a nearly always-knotted regime to effective knot suppression, changing the knotting probability by more than three orders of magnitude despite identical active-block positions and activity magnitude. Across symmetric terminal two-block architectures, we further identify an approximate zero-one-two free-end-alignment rule: zero, one, and two free-end-aligned active blocks correspond, respectively, to suppressed, intermediate, and high-knotting states. A two-state kinetic decomposition shows that the conditional knot-formation rate changes only by about threefold under polarity reversal, whereas the mean knot lifetime changes by several orders of magnitude, demonstrating that knot survival and passive-region storage dominate the polarity-controlled switch. Block placement provides an additional geometrical gate: moving an active domain from the chain interior to a terminal region strongly enhances both knot formation and survival. Knot-center residence, knotted-arc distributions, and episode-resolved kymographs reveal formation near free-end-aligned active blocks, directed contour migration, tightening, and long-lived retention in passive regions. Together, these results support a source-conveyor-reservoir-sink mechanism in which signed polarity and spatial activity patterning control whether knots are generated, transported, stored, or rapidly lost, providing a route to programmable topological states in nonequilibrium active polymers.