Out of Equilibrium Characteristics of a Forced Translocating Chain through a Nanopore

Abstract

Polymer translocation through a nano-pore in a thin membrane is studied using a coarse-grained bead-spring model and Langevin dynamics simulation with a particular emphasis to explore out of equilibrium characteristics of the translocating chain. We analyze the out of equilibrium chain conformations both at the $cis$ and the $trans$ side separately either as a function of the time during the translocation process or as as function of the monomer index $m$ inside the pore. A detailed picture of translocation emerges by monitoring the center of mass of the translocating chain, longitudinal and transverse components of the gyration radii and the end to end vector. We observe that polymer configurations at the $cis$ side are distinctly different from those at the $trans$ side. During the translocation, and immediately afterwards, the chain is clearly out of equilibrium, as different parts of the chain are characterized by a series of effective Flory exponents. We further notice that immediately after the translocation the last set of beads that have just translocated take a relatively compact structure compared to the first set of beads that translocated earlier, and the chain immediately after translocation is described by an effective Flory exponent $0.45\pm 0.01$. The analysis of these results is further strengthened by looking at the conformations of chain segments of equal length as they cross from the $cis$ to the $trans$ side, We discuss implications of these results to the theoretical estimates and numerical simulation studies of the translocation exponent reported by various groups.

35 pages, 16 figures. Submitted to Phys. Rev. E

References in corpus (16)

• Nonequilibrium dynamics of polymer translocation and straightening
• Influence of polymer-pore interactions on translocation
• Sequence dependence of DNA translocation through a nanopore
• Langevin Dynamics Simulations of Polymer Translocation through Nanopores
• Polymer translocation through a nanopore - a showcase of anomalous diffusion
• Driven polymer translocation through nanopores: slow versus fast dynamics
• Driven polymer translocation through a nanopore: a manifestation of anomalous diffusion
• Anomalous Dynamics of Unbiased Polymer Translocation through a Narrow Pore
• Comment on ``Passage Times for Unbiased Polymer Translocation through a Narrow Pore''
• Dynamical Scaling Exponents for Polymer Translocation through a Nanopore
• Pore-blockade Times for Field-Driven Polymer Translocation
• Dynamics of forced biopolymer translocation
• Heteropolymer translocation through nanopores
• Polymer Translocation out of Planar Confinements
• Critical evaluation of the computational methods used in the forced polymer translocation
• Scaling in rupture of polymer chains

Cited by in corpus (24)

• Unifying model of driven polymer translocation
• Influence of non-universal effects on dynamical scaling in driven polymer translocation
• Forced translocation of a polymer: dynamical scaling vs. MD-simulation
• 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
• Polymer translocation into a fluidic channel through a nanopore
• Polymer Translocation Dynamics in the Quasi-Static Limit
• Theory of polymer translocation through a flickering nanopore under an alternating driving force
• The chain sucker: translocation dynamics of a polymer chain into a long narrow channel driven by longitudinal flow
• Non-monotonous polymer translocation time across corrugated channels: comparison between Fick-Jacobs approximation and numerical simulations
• Directed translocation of a flexible polymer through a cone-shaped channel
• Driven polymer translocation through a cylindrical nanochannel: Interplay between the channel length and the chain length
• Driven translocation of a polymer: role of pore friction and crowding
• Cis-Trans Dynamical Asymmetry in Driven Polymer Translocation
• Dynamics of polymer translocation into a circular nanocontainer through a nanopore
• Polymer translocation into laterally unbounded confined environments
• Anomalous zipping dynamics and forced polymer translocation
• Evaluating the Applicability of the Fokker-Planck Equation in Polymer Translocation: A Brownian Dynamics Study
• Non-Markovian dynamics of reaction coordinate in polymer folding
• Tug-of-War in a Double-Nanopore System
• Driven polymer translocation in good and bad solvent: effects of hydrodynamics and tension propagation
• Driven translocation of a semiflexible polymer through a conical channel in the presence of attractive surface interactions
• Non-equilibrium effects in chaperone-assisted translocation of a stiff polymer