Special Biophysics Seminar

Polymer translocation driven by asymmetry:
effects due to differing viscosities or obstacle arrangements on either side of the nanopore

Hendrick de Haan

University of Ottawa

For both its biological relevance and nanotechnology applications, the translocation of a polymer through a nanopore has been the subject of intense study. On the theory side, there have been many simulation studies examining aspects of both biased and unbiased translocation. While the bias in the latter case most commonly arises from application of an external field, in this talk I will present results from two studies in which we examine translocation as driven by asymmetry in the system. To begin, we consider a system in which the viscosity of the fluid varies across the membrane. We find that, starting with the polymer half-way, translocation will increasingly occur preferentially to one side as the viscosity difference increases. Somewhat surprisingly, the direction of this preferential direction depends upon the simulation approach. For the second example, we consider translocation when “obstacles” are placed on both sides of the pore. When the concentration of obstacles is different across the pore, translocation preferentially occurs to the less dense side as expected. More interestingly, we also find that even for an equal number of obstacles on either side of the pore, varying arrangement of the obstacles can yield a preferential direction. For both the viscosity gradient and obstacle cases, simulation results estimating the magnitude of the effective driving force within the pore are presented.