Some Aspects of Non-equilibrium Polymer Translocation Dynamics

Abstract

Polymer translocation is an important biological process which has become an active field of research in recent past due to its potential application in DNA sequencing, drug design, virus injection, etc. This work was aimed to study and understand the different aspects of the non-equilibrium phenomena observed in driven polymer translocation using computer simulations. We have broadly looked into two aspects of polymer translocation based on the application of the force on the polymer, namely the pore driven translocation and the end pulled translocation. First section looks into the effect of charge modulation of polymer surface and nanopore for the pore driven translocation to mimic experimental conditions like pH change and protein engineering. Different translocation times obtained from Langevin dynamics simulation and free-energy calculations shows the importance of different stages of the translocation. The next section looks into the end-pulled translocation for single and folded polymer movement through ananopore. This kind of situations are found in atomic force microscopy and optical/magnetic tweezers experiments. The calculations were able to quantitatively estimate the tension propagation by waiting time and velocity calculations of the monomers on the chain. Lastly, we considered a model particle in a viscous heat bath which is dragged with a harmonic potential and its total entropy production is calculated, which has implications in non-equilibrium thermodynamic principles in single molecule experiments.