Study of the directed motion of polymers in a cone-shaped nano-structure as a method of polymer separation

Abstract

Flowing through a nano-channel is used as a method for separating particles [1] and combined fluids [2]. Here, an asymmetric nano-channel is presented and optimized for the separation of polymers. To this end, motion of a charged polymer inside the asymmetric nano-channel under an alternative electric field is studied using molecular dynamics simulations. The asymmetric nano-channel is composed of consecutive nano-cones, which acts as a Brownian ratchet under an alternative electric field. The motion of the polymer is smoother in the funneling direction of the cones, while it is slower in the reverse direction as a result of the entropic traps. It is observed that the velocity of the directed motion inside the asymmetric cone-shaped nano-channel depends on the polymer length, as is needed for the separation of the polymers. Dependence of the polymer velocity on the cone angle and the field frequency is studied to find the optimum parameters for rectification and the resulting separation. The simulation results show that the velocities of the directed motion decreases with the cone angle and the field frequency for all studied polymers. However, difference between the velocities of the polymers of different lengths increases with the cone angle and the field frequency. Difference between the velocities is required for a successful separation. On the other hand, higher velocities are needed for a fast separation. So, middle values for the cone angle and the field frequency are suggested for a good separation, according to our simulation results.