Helical polymer in cylindrical confining geometries

Details Helical polymer in cylindrical confining geometries Helical polymer in cylindrical confining geometries

2004-07-05

arxiv.org/abs/cond-mat/0407097v1

Phys. Rev. E 70, 051804 (2004)

Physics

Condensed Matter

Soft Condensed Matter

5 figures

Scientific paper

10.1103/PhysRevE.70.051804

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.

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