Role of Non-Equilibrium Conformations on Driven Polymer Translocation

Abstract

One of the major theoretical methods in understanding polymer translocation through a nanopore is the Fokker-Planck formalism based on the assumption of quasi-equilibrium of polymer conformations. The criterion for applicability of the quasi-equilibrium approximation for polymer translocation is that the average translocation time per Kuhn segment, $⟨\tau ⟩/N_K$ is longer than the relaxation time ${\tau }_0$ of the polymer. Towards an understanding of conditions that would satisfy this criterion, we have performed coarse-grained three dimensional Langevin dynamics and multi-particle collision dynamics simulations. We have studied the role of initial conformations of a polyelectrolyte chain (which were artificially generated with a flow field) on the kinetics of its translocation across a nanopore under the action of an externally applied transmembrane voltage $V$ (in the absence of the initial flow field). Stretched (out-of-equilibrium) polyelectrolyte chain conformations are deliberately and systematically generated and used as initial conformations in translocation simulations. Independent simulations are performed to study the relaxation behavior of these stretched chains and a comparison is made between the relaxation timescale and the mean translocation time ($⟨\tau ⟩$). For such artificially stretched initial states, $⟨\tau ⟩/N_K<{\tau }_0$, demonstrating the inapplicability of the quasi-equilibrium approximation. Nevertheless, we observe a scaling of $⟨\tau ⟩\sim 1/V$ over the entire range of chain stretching studied, in agreement with the predictions of the Fokker-Planck model. On the other hand, for realistic situations where initial artificially imposed flow field is absent, a comparison of experimental data reported in the literature with the theory

arXiv commentAccepted for publication in The Journal of Chemical Physics

References in corpus (20)

• Polymer Translocation througha Pore in a Membrane
• Nonequilibrium dynamics of polymer translocation and straightening
• Dynamics of short polymer chains in solution
• Polymer translocation through a nanopore - a showcase of anomalous diffusion
• Unifying model of driven polymer translocation
• Driven polymer translocation through a nanopore: a manifestation of anomalous diffusion
• When translocation dynamics becomes anomalous
• Influence of non-universal effects on dynamical scaling in driven polymer translocation
• Iso-Flux Tension Propagation Theory of Driven Polymer Translocation: The Role of Initial Configurations
• Scaling theory of driven polymer translocation
• Process Time Distribution of Driven Polymer Transport
• Electrophoretic Capture of a DNA Chain into a Nanopore
• Polymer Translocation Dynamics in the Quasi-Static Limit
• Chain deformation helps translocation
• Propagation of Tension along a Polymer Chain
• Driven translocation of a polymer: fluctuations at work
• Stochastic sensing of polynucleotides using patterned nanopores
• Using a Péclet Number for the Translocation of Polymer through a Nanopore to Tune Coarse-Grained Simulations to Experimental Conditions
• Electrophoresis of a DNA Coil Near a Nanopore
• Evaluating the Applicability of the Fokker-Planck Equation in Polymer Translocation: A Brownian Dynamics Study

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• An efficient Kinetic Monte Carlo to study analyte capture by a nanopore: Transients, boundary conditions and time-dependent fields
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• Controlling Solvent Quality by Time: Self-Avoiding Sprints in Nonequilibrium Polymerization