Polyelectrolyte Translocation Through a Nanopore Studied by Molecular Dynamics Simulations
Pai-Yi Hsiao1*
1Department of Engineering and System Science, National Tsing Hua University, Hsinchu, Taiwan
* presenting author:Pai-Yi Hsiao, email:pyhsiao@ess.nthu.edu.tw
In the past decades, there are increasing demands on understanding the physics of charged polymers threading through small pores of nanometer size. The techniques can be developed to detect genetic codes of DNA or RNA molecules, and have become the new-generation genome-sequencing method. In this study, we perform molecular dynamics simulations to investigate translocation behavior of charged polymers driven by an electric field inside the pore. We show that the mean translocation time <τ> scales with the chain length N and the strength of electric field E as <τ>~Nα E where the exponents α and δ depend on E. The study of the radius of gyration and the shape descriptors of chain shows that translocation is a far-from-equilibrium process when the driving force is strong. The condensed ions can be stripped of the chain when the chain passes the pore and the total charge of condensed ions decreases. Due to fast translocation, the monomers are crowded near the wall and form a pancake-like density profile with a hump cloud over it. We study tension propagation on the chain and the chain section straightened by the tension force is determined by the ratio of the direct to the contour distances of the monomer to the pore. With the study of the waiting time function, the threading process is divided into the tension-propagation stage and the tail-retraction stage. The drift-diffusion properties are investigated. Owing to the non-equilibrium nature, translocation is not a simple diffusion process, but exhibits several intermediate behaviors, such as ballistic motion, normal diffusion and super diffusion, before ending with the last, negative-diffusion behavior. (This material is supported by Ministry of Science and Technology, under contract No. MOST 103-2112-M-007-014-MY3.)

Keywords: polymer translocation, polyelectrolyte, molecular dynamics simulations