Multiscale analysis of the effect of surface charge pattern on a nanopore's rectification and selectivity properties: from all-atom model to Poisson-Nernst-Planck

Abstract

We report a multiscale modeling study for charged cylindrical nanopores using three modeling levels that include (1) an all-atom explicit-water model studied with molecular dynamics (MD), and reduced models with implicit water containing (2) hard-sphere ions studied with the Local Equilibrium Monte Carlo simulation method (computing ionic correlations accurately), and (3) point ions studied with Poisson-Nernst-Planck (PNP) theory (mean-field approximation). We show that reduced models are able to reproduce device functions (rectification and selectivity) for a wide variety of charge patterns; that is, reduced models are useful in understanding the mesoscale physics of the device (i.e., how the current is produced). We also analyze the relationship of the reduced implicit-water models with the explicit-water model and show that diffusion coefficients in the reduced models can be used as adjustable parameters with which the results of the explicit- and implicit-water models can be related. We find that the values of the diffusion coefficients are sensitive to the net charge of the pore, but are relatively transferable to different voltages and charge patterns with the same total charge.

References in corpus (11)

• Canonical sampling through velocity-rescaling
• Poisson Nernst-Planck Model of Ion Current Rectification through a Nanofluidic Diode
• An Efficient Algorithm for Classical Density Functional Theory in Three Dimensions: Ionic Solutions
• Multiple Scales in the Simulation of Ion Channels and Proteins
• Ions in Fluctuating Channels: Transistors Alive
• Multiscale modeling of a rectifying bipolar nanopore: Comparing Poisson-Nernst-Planck to Monte Carlo
• Controlling ion transport through nanopores: modeling transistor behavior
• Simulation study of a rectifying bipolar ion channel: Detailed model versus reduced model
• Simulation of a model nanopore sensor: ion competition underlies device behavior
• Asking Biological Questions of Physical Systems: the Device Approach to Emergent Properties
• Controlling ionic current through a nanopore by tuning pH: a Local Equilibrium Monte Carlo study

Cited by in corpus (3)

• Rectification of bipolar nanopores in multivalent electrolytes: effect of charge inversion and strong ionic correlations
• Application of a bipolar nanopore as a sensor: rectification as an additional device function
• Towards a unified mechanistic understanding of the electrical response of bipolar nanofluidic systems