Confinement and Activity-Driven Dynamics of Semiflexible Polymers in Motility Assays

TL;DR

This study models the complex behavior of semiflexible polymers driven by motor proteins in confined environments, revealing how activity, rigidity, and confinement influence transitions, conformations, and dynamics relevant to biological and synthetic systems.

Contribution

We develop a coarse-grained agent-based model to analyze how activity, filament rigidity, and confinement interact, uncovering a two-state transition and scaling relations supported by simulations.

Findings

Identified a transition from trapped to free states with an intermediate coexistence region.

Found that filament flexibility affects trapping, with more flexible filaments being more easily trapped.

Observed stable spiral conformations under moderate confinement and activity.

Abstract

We investigate the nonequilibrium dynamics of semiflexible polymers driven by motor proteins (MPs) in two-dimensional motility assays under harmonic confinement. Using a coarse-grained agent-based model that incorporates stochastic motor attachment, detachment, and force generation, we study how activity, filament rigidity, and confinement interact to control polymer behavior. We construct dynamical behavior maps as a function of P\'eclet number, motor processivity, and trap strength. We find a two-state transition from a trapped to a free polymer, with an intermediate coexistence region, and obtain a scaling relation for the critical P\'eclet number, which is supported by simulation data across a range of parameters. Polymer flexibility strongly influences confinement: flexible filaments are more easily trapped, while increasing rigidity destabilizes confinement. Processivity of MPs can also induce a change in the effective rigidity of the polymer and, therefore, influence confinement by the trap. Under moderate confinement and activity, we observe the emergence of stable spiral conformations. The center-of-mass dynamics is analyzed through the mean square displacement, showing diffusive, ballistic, and diffusive regimes that depend on the trap strength and activity. Additionally, time series analysis of the excess kurtosis shows the variation of the non-Gaussian fluctuations with trap strength and activity. Our results provide a minimal physical framework to understand the dynamic organization of active filaments under confinement, with relevance to in vitro motility assays, cytoskeletal filament manipulation by optical traps, and synthetic active polymer systems.