Capture and translocation of a stiff oligomer by a nanopore*

Both the translational diffusion coefficient D and the electrophoretic mobility μ of an oligomer that is pulled towards a nanopore by an electric field depend on its orientation. Since a charged rod-like molecule tends to orient in the presence of an electric field gradient, D and μ will change as the molecule approaches the nanopore, and this will impact the capture radius (a somewhat ill-defined measure of the efficiency of the nanopore to attract analytes in its vicinity). We present a study of this problem using theoretical arguments and Langevin Dynamics simulations. In particular, we define an alignment radius which we compare to the capture radius, and we examine different physical limits. The hydrodynamic interactions with the wall are also investigated by coupling the Langevin MD oligomer to a Lattice-Boltzmann fluid.