Golden aspect ratio for ion transport simulation in nanopores

TL;DR

This paper introduces a universal 'golden aspect ratio' for simulation cells in ion transport studies, which minimizes finite size effects in molecular dynamics simulations of nanopores, enabling more accurate and scalable analysis.

Contribution

It proposes and validates a scaling theory predicting a specific aspect ratio that eliminates finite size effects in ion transport simulations, applicable across different conditions.

Findings

Existence of a universal golden aspect ratio in simulations.

Validation through continuum and all-atom simulations.

Applicability across linear and moderate concentration regimes.

Abstract

Access resistance indicates how well current carriers from a bulk medium can converge to a pore or opening, and is an important concept in nanofluidic devices and in cell physiology. In simplified scenarios, when the bulk dimensions are infinite in all directions, it depends only on the resistivity and pore radius. These conditions are not valid in all-atom molecular dynamics (MD) simulations of transport, due to the computational cost of large simulation cells, and can even break down in micro- and nano-scale systems due to strong confinement. Here, we examine a scaling theory for the access resistance that predicts a special simulation cell aspect ratio -- the golden aspect ratio -- where finite size effects are eliminated. Using both continuum and all-atom simulations, we demonstrate that this golden aspect ratio exists and that it takes on a universal value in linear response and moderate concentrations. Outside of linear response, it gains an apparent dependence on characteristics of the transport scenario (concentration, voltages, etc.) for small simulation cells, but this dependence vanishes at larger length scales. These results will enable the use of all-atom molecular dynamics simulations to study contextual properties of access resistance -- its dependence on protein and molecular-scale fluctuations, the presence of charges, and other functional groups -- and yield the opportunity to quantitatively compare computed and measured resistances.