Fluctuations of a long, semiflexible polymer in a narrow channel

Abstract

We consider an inextensible, semiflexible polymer or worm-like chain, with persistence length $P$ and contour length $L$, fluctuating in a cylindrical channel of diameter $D$. In the regime $D\ll P\ll L$, corresponding to a long, tightly confined polymer, the average length of the channel $ $ occupied by the polymer and the mean square deviation from the average vary as $ =[1-\alpha_\circ(D/P)^{2/3}]L$ and $<\Delta R_\parallel^{\thinspace 2}\thinspace>=\beta_\circ(D^2/P)L$, respectively, where $\alpha_\circ$ and $\beta_\circ$ are dimensionless amplitudes. In earlier work we determined $\alpha_\circ$ and the analogous amplitude $\alpha_\Box$ for a channel with a rectangular cross section from simulations of very long chains. In this paper we estimate $\beta_\circ$ and $\beta_\Box$ from the simulations. The estimates are compared with exact analytical results for a semiflexible polymer confined in the transverse direction by a parabolic potential instead of a channel and with a recent experiment. For the parabolic confining potential we also obtain a simple analytic result for the distribution of $R_\parallel$ or radial distribution function, which is asymptotically exact for large $L$ and has the skewed shape seen experimentally.