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<<P<<L the free energy of confinement DeltaF and the length of the channel R parallel occupied by the polymer are given by Odijk's relations DeltaF/R parallel=A(o)kB(TP)-1/3 D(-2/3) and R parallel =L[1-alpha(o)(D/P)2/3], where A(o) and alpha(o) are dimensionless amplitudes. Using a simulation algorithm inspired by the pruned enriched Rosenbluth method, which yields results for very long polymers, we determine A(o) and alpha(o) 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.