Free energy and extension of a semiflexible polymer in cylindrical confining geometries

Abstract

We consider a long, semiflexible polymer, with persistence length $P$ and contour length $L$, fluctuating in a narrow cylindrical channel of diameter $D$. In the regime $D\ll P\ll L$ the free energy of confinement $\Delta F$ and the length of the channel $R_\parallel$ occupied by the polymer are given by Odijk's relations $\Delta F/R_\parallel=A_\circ k_BTP^{-1/3}D^{-2/3}$ and $R_\parallel=L[1-\alpha_\circ(D/P)^{2/3}]$, where $A_\circ$ and $\alpha_\circ$ are dimensionless amplitudes. Using a simulation algorithm inspired by PERM (Pruned Enriched Rosenbluth Method), which yields results for very long polymers, we determine $A_\circ$ and $\alpha_\circ$ and the analogous amplitudes for a channel with a rectangular cross section. For a semiflexible polymer confined to the surface of a cylinder, the corresponding amplitudes are derived with an exact analytic approach. The results are relevant for interpreting experiments on biopolymers in microchannels or microfluidic devices.