Helical polymer in cylindrical confining geometries

TL;DR

This study uses simulations to analyze the behavior of fluctuating helical polymers confined in cylindrical geometries, focusing on free energy, escape, and intersection phenomena depending on geometric parameters.

Contribution

It introduces a simulation algorithm to study equilibrium configurations of helical polymers in cylindrical confinement, providing new insights into their free energy and escape behavior.

Findings

Calculated the free energy of confinement for helical polymers.

Measured escape and intersection points as functions of pitch.

Provided scaling explanations for different pitch regimes.

Abstract

Using an algorithm for simulating equilibrium configurations, we study a fluctuating helical polymer either (i) contained in a cylindrical pore or (ii) wound around a cylindrical rod. We work in the regime where both the contour length and the persistence length of the helical polymer are much larger than the diameter of the cylinder. In case (i) we calculate the free energy of confinement and interpret it in terms of a worm-like chain in a pore with an effective diameter that depends on the parameters of the helix. In case (ii) we consider the possibility that one end of the helical polymer escapes from the rod and wanders away. The average numbers of turns at which the helix escapes or intersects the rod are measured in the simulations, as a function of the pitch $p_0$. The behavior for large and small $p_0$ is explained with simple scaling arguments.