Brownian dynamics simulations of the ionic current traces for a neutral nanoparticle translocating through a nanopore

Abstract

In this work, the ionic current blockades due to the translocation of a neutral spherical nanoparticle through a nanopore in a solid state membrane are computed. We use a Brownian dynamics approach, in conjunction with a full three-dimensional self-consistent solution of the Poisson-Nernst-Planck and Navier-Stockes system of equations to describe realistic ionic current response arising due to the random motion of a nanoparticle through a nanopore. We find that in addition to the usual geometric blockade, the variations of the current along the axis of the pore are largely caused by a concentration polarization induced by the presence of the translocating nanoparticle in the nanopore while the current changes in the radial (perpendicular to the axis) direction occur because of the local build up of the ionic charge between the particle and the nanopore surface. By performing statistical analysis of the current traces, we also observe that, in general, smaller current blockade values correspond to faster translocation times, while increased dwell times result in a larger current decrease.

Kulturimmobilien – Erfolgsfaktor Projektmanagement

“…Initial work on predicting the permeation of ions and water through biological transmembrane channels was focused towards ion channels [297,298,299]. As was the case with MD, to date, virtually all the continuum modeling studies of BNPs have been performed with αHL as the subject of interest [300,301,302,290,249,292,303], though its use in the SSNP field is significantly more prevalent [304,293,294,210,295,194,305,306,307]. However, despite the widespread use of continuum transport models, their ability to quantitatively predict ionic currents-in their unmodified form-is typically poor [308,183].…”

“…Such corrections can be based on theory, experiment, or extracted from other simulations (e.g., MD). Conversely, the field distributions (electric field and electro-osmotic flow) can also be used as input for Brownian dynamics (BD) simulations as to stochastically map the capture dynamics of individual particles [249,305]. Given that chapter 5 of this dissertation is devoted to building an improved PNP-NS framework for the predictive modeling of biological nanopores, a more detailed discussion of this topic can be found there.…”

Multi-resolution simulation of DNA transport through large synthetic nanostructures

“…As introduced above, CG simulations have already provided invaluable information about nanopore systems that would have been difficult to obtain otherwise. 17–21 Specific examples include CG MD simulation of DNA translocation through both the biological nanopore alpha-hemolysin 22 and solid-state nanopores, 23 Brownian dynamics simulations of polymer and nanoparticle translocation through passive and gated solid-state nanopores, 24–26 and protein translocation through a nanopore containing a receptor protein. 27 However, the removal of explicit ions means that ion currents can no longer be calculated directly.…”

“…27 However, the removal of explicit ions means that ion currents can no longer be calculated directly. Several methods have already been developed to back-calculate the ionic current from a CG MD trajectory, 22,25,27,28 which is typically done at the level of the Poisson–Nernst–Planck formalism, 29,30 explicit-ion Brownian dynamics simulations 31,32 and continuum calculations. 33,34…”

The Influence of Electric Field Intensity and Particle Length on the Electrokinetic Transport of Cylindrical Particles Passing through Nanopore

“…On the basis of successfully preparing nanopores, other researchers further investigated the movement of DNA using nanopores made of SiO 2 [ 17 ], alumina film [ 18 ], graphene nanopore [ 19 ], molybdenum disulfide [ 20 ], and glass capillary [ 21 , 22 ]. To complement experimental investigations demanding complex preparation processes of solid nanopores and expensive detection equipment, a large number of researchers have applied the continuum model [ 23 , 24 , 25 , 26 , 27 ], molecular dynamics [ 28 , 29 , 30 ], atomic level Brownian dynamics [ 31 ], Brownian kinematics [ 32 ] to carry out numerical simulation on particle motion and ion current change in nanopores.…”