Numerical simulation on polymer translocation into crowded environment with nanoparticles

Abstract

The effects of crowded environment with nano particles are studied for polymer translocation through a small pore. The translocation time τ is simulated by Fokker-Planck equation at different free energy landscapes F and diffusion coefficients of polymer D. The free energy is calculated using the Rosenbluth-Rosenbluth method, and the diffusion coefficient is followed the relation $D \sim \frac {1}{N} e^{-\triangle F}$ . We find that the free energy is dependent on polymer-nanoparticle interaction, size of the nanoparticle, and position of the nanoparticle. The attractive nanoparticles at the trans side can provide a driving force to polymer by lowering the free energy, but the exclusive effect of nanoparticle can raise the free energy of polymer. There exists an optimum interaction that τ is roughly independent on the size and position of nanoparticles. It is found that these effects are related to the conformational change of polymer chain in crowded environment.