Numerical Modelling of Nanopores

Abstract

Nanopores are used for resistive pulse sensing of single analytes and as nanopipette probes for electrochemical scanned probe microscopy. The current-voltage responses of nanopores display a rich range of behaviors, which arise due to interactions between the electric fields (applied potential and surface charges), ion concentrations, and fluid flows.1 To understand these behaviors and interpret experimental results, numerical simulation of the coupled physics are typically performed.2 Yet despite simulations of conical nanopores being commonplace, they remain challenging. As the electric double layer requires resolution of concentrations and electric fields at sub-nm length scales, while concentration enhancements and depletions occur 10s of μm inside the pore simulations must resolve differences over length scales that vary by ~5 orders of magnitude. While various strategies have been employed to make these simulations more manageable including simulating a small portion of the pore, ignoring surface charge beyond a certain distance [others]. However, no consensus exists as to best practices or the impact of these simplifications.In this work we assess the impact of commonly made simplifications and describe best practices for efficient modelling of conical nanopores to ensure accurate results are readily obtained. Suggestions include effective choices of mesh, initial conditions, and the handling of semi-infinite boundaries.(1) Lan, W.-J.; Holden, D. A.; White, H. S. Pressure-Dependent Ion Current Rectification in Conical-Shaped Glass Nanopores. J. Am. Chem. Soc. 2011, 133 (34), 13300–13303. https://doi.org/10.1021/ja205773a.(2) White, H. S.; Bund, A. Ion Current Rectification at Nanopores in Glass Membranes. Langmuir 2008, 24 (5), 2212–2218. https://doi.org/10.1021/la702955k.