Fluctuations of a long, semiflexible polymer in a narrow channel

Burkhardt, T.W.; Gompper, G.; Yang, Y.

doi:10.1103/PhysRevE.82.041801

Journal Article

PreJuSER-11458

Fluctuations of a long, semiflexible polymer in a narrow channel

Burkhardt, T. W.FZJ* ; Yang, Y.FZJ* ; Gompper, G.FZJ*

2010
APS College Park, Md.

Physical review / E 82(4), 041801 (2010) [10.1103/PhysRevE.82.041801]

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Please use a persistent id in citations: http://hdl.handle.net/2128/9310 doi:10.1103/PhysRevE.82.041801

Abstract: We consider an inextensible, semiflexible polymer or wormlike chain, with persistence length P and contour length L, fluctuating in a cylindrical channel of diameter D. In the regime D << P << L, corresponding to a long, tightly confined polymer, the average length of the channel < R-parallel to > occupied by the polymer and the mean-square deviation from the average vary as < R-parallel to > = [1-alpha(o)(D/P)(2/3)]L and <Delta R-parallel to(2)> = beta(o)(D-2/P)L, respectively, where alpha(o) and beta(o) are dimensionless amplitudes. In earlier work we determined alpha(o) and the analogous amplitude alpha(square) for a channel with a rectangular cross section from simulations of very long chains. In this paper, we estimate beta(o) and beta(square) 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 to or radial distribution function, which is asymptotically exact for large L and has the skewed shape seen experimentally.

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Note: T. W. B. thanks Theo Odijk for correspondence, Thomas Pfohl for sending the experimental data considered in Sec. IV, Dieter Forster for a helpful discussion, and Robert Intemann for help with MATHEMATICA. Y.Y. acknowledges financial support from the International Helmholtz Research School "BioSoft."

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