Effect of charge distribution on the translocation of an inhomogeneously charged polymer through a nanopore (original) (raw)

Controlling polymer translocation and ion transport via charge correlations

Langmuir : the ACS journal of surfaces and colloids, 2014

We develop a correlation-corrected transport theory in order to predict ionic and polymer transport properties of membrane nanopores under physical conditions where mean-field electrostatics breaks down. The experimentally observed low KCl conductivity of open α-hemolysin pores is quantitatively explained by the presence of surface polarization effects. Upon the penetration of a DNA molecule into the pore, these polarization forces combined with the electroneutrality of DNA sets a lower boundary for the ionic current, explaining the weak salt dependence of blocked pore conductivities at dilute ion concentrations. The addition of multivalent counterions to the solution results in the reversal of the polymer charge and the direction of the electroosmotic flow. With trivalent spermidine or quadrivalent spermine molecules, the charge inversion is strong enough to stop the translocation of the polymer and to reverse its motion. This mechanism can be used efficiently in translocation expe...

Polymer translocation through a nanopore: a geometry dependence study

2003

The translocation of a single stranded nucleic acid polymer through a nanopore, by an external electric field applied across the pore, may be well described by a 1-D drift-diffusion model. Translocation times and velocities are calculated for a homopolymer driven through a nanopore, where the polymerpore interaction dominates the polymer dynamics. In this model a purely electrostatic polymer-pore interaction is introduced, based on atomic charges on the polymer and pore. Simulation results show that the peak repulsion force occurs on the polymer during entry into the pore. In addition, the peak polymer-pore interaction is shown to decrease with polymer length for strands less than 20 nucleotides in length. The modeling results offers an explanation for the enhanced drift velocities experimentally observed for such short polymers. The dependence of the polymer translocation time on the pore geometry is investigated. For increasing pore radius the translocation velocity approaches the free space drift velocity for the surrounding ionic solution.

Dynamics of Polymer Translocation through Nanopores: Theory Meets Experiment

Physical review …, 2006

The dynamics of translocation of polymer molecules through nanopores is investigated via molecular dynamics. We find that an off-lattice minimalist model of the system is sufficient to reproduce quantitatively all the experimentally observed trends and scaling behavior. Specifically, simulations show (i) two translocation regimes depending on the ratio of pore and polymer length, (ii) two different regimes for the probability of translocation depending on applied voltage, (iii) an exponential dependence of translocation velocity upon applied voltage, and (iv) an exponential decrease of the translocation time with temperature. We also propose a simple theoretical explanation of each of the observed trends within a free energy landscape framework.

Communication: Charge, diffusion, and mobility of proteins through nanopores

The Journal of chemical physics, 2014

Implementation of Einstein's law connecting charge, diffusion coefficient, and mobility to interpret experimental data on proteins from single molecule electrophoresis through nanopores faces serious difficulties. The protein charge and diffusion coefficient, inferred with the Einstein law, can be orders of magnitude smaller than their bare values depending on the electrolyte concentration, pore diameter, chemical nature of the pore wall, and the externally applied voltage. The main contributors to the discrepancies are the coupled dynamics of the protein and its counterion cloud, confinement effects inside the pore, and the protein-pore-surface interaction. We have addressed these ingredients by harking on classical theories of electrophoresis of macroions and hydrodynamics inside pores, and deriving new results for pore-protein interactions. Putting together various components, we present approximate analytical formulas for the effective charge, diffusion coefficient, and mobi...

Translocation dynamics with attractive nanopore-polymer interactions

Physical Review E, 2008

Using Langevin dynamics simulations, we investigate the influence of polymer-pore interactions on the dynamics of biopolymer translocation through nanopores. We find that an attractive interaction can significantly change the translocation dynamics. This can be understood by examining the three components of the total translocation time τ ≈ τ1 + τ2 + τ3 corresponding to the initial filling of the pore, transfer of polymer from the cis side to the trans side, and emptying of the pore, respectively. We find that the dynamics for the last process of emptying of the pore changes from non-activated to activated in nature as the strength of the attractive interaction increases, and τ3 becomes the dominant contribution to the total translocation time for strong attraction. This leads to a new dependence of τ as a function of driving force and chain length. Our results are in good agreement with recent experimental findings, and provide a possible explanation for the different scaling behavior observed in solid state nanopores vs. that for the natural α-hemolysin channel.

Polymer translocation through a nanopore: A two-dimensional Monte Carlo study

The Journal of Chemical Physics, 2006

We investigate the problem of polymer translocation through a nanopore in the absence of an external driving force. To this end, we use the two-dimensional fluctuating bond model with single-segment Monte Carlo moves. To overcome the entropic barrier without artificial restrictions, we consider a polymer which is initially placed in the middle of the pore and study the escape time tau required for the polymer to completely exit the pore on either end. We find numerically that tau scales with the chain length N as tau approximately N(1+2nu), where nu is the Flory exponent. This is the same scaling as predicted for the translocation time of a polymer which passes through the nanopore in one direction only. We examine the interplay between the pore length L and the radius of gyration R(g). For L&amp;amp;amp;lt;R(g), we numerically verify that asymptotically tau approximately N(1+2nu). For L&amp;amp;amp;gt;R(g), we find tau approximately N. In addition, we numerically find the scaling function describing crossover between short and long pores. We also show that tau has a minimum as a function of L for longer chains when the radius of gyration along the pore direction R( parallel) approximately L. Finally, we demonstrate that the stiffness of the polymer does not change the scaling behavior of translocation dynamics for single-segment dynamics.

Polymer translocation through a nanopore under an applied external field

The Journal of Chemical Physics, 2006

We investigate the dynamics of polymer translocation through a nanopore under an externally applied field using the 2D fluctuating bond model with single-segment Monte Carlo moves. We concentrate on the influence of the field strength E, length of the chain N, and length of the pore L on forced translocation. As our main result, we find a crossover scaling for the translocation time τ with the chain length from 2

Polymer translocation through α-hemolysin pore with tunable polymer-pore electrostatic interaction

The Journal of Chemical Physics, 2010

We have measured the ionic current blockages produced by single molecules of sodium poly(styrene sulfonate) passing through an α-hemolysin protein pore under an electric field. Most of the blockage events were composed of one or two blockage levels of ionic current. By analyzing the statistics of different event types for different polymer lengths, applied voltages, and pH conditions, we have identified the molecular mechanism behind the two-level blockages. Our analysis of the data shows that not all blockages are successful translocation events and the propensity of successful translocation can be tuned by pH gradients across the protein pore. We interpret our results as the change in protein-polymer interaction via protonation of charged amino acid residues of α-hemolysin pore. In addition, we have constructed a stochastic theory for polymer translocation through α-hemolysin pore with tunable polymer-pore interactions. The theoretical calculations capture many features observed i...

Dynamics of polymer translocation through a nanopore induced by different sizes of crowding agents

The Journal of Chemical Physics, 2013

Effects of interaction between nanopore and polymer on translocation time

arXiv: Computational Physics, 2017

Here using LAMMPS molecular dynamics (MD) software, we simulate polymer translocation in 2 dimensions. We do the simulations for weak and moderate forces and for different pore diameters. Our results show that in both non-equilibrium and equilibrium initial conditions, translocation time will always increase by increasing binding energy and or increasing pore diameter. Moreover, scaling exponent of time versus force is -0.9531 in accordance to our predecessors. The comparison between equilibrium and non-equilibrium initial condition shows that the translocation time is very sensitive to the initial condition. Translocation time of the relaxed polymers for interaction energy of 8k_B T is smaller from the non-equilibrium case even in the small energy of 1k_B T.

Effect of charge distribution on the translocation of an inhomogeneously charged polymer through a nanopore (original) (raw)

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