Spatial profiles of potential, ion concentration and flux in short unipolar and bipolar nanopores

Abstract

During release of vesicular content the resistance of the fusion pore sometimes changes rapidly and repeatedly. However, it is not clear why the pore ‘flickers’. Engineered nanopores often rectify, but how different factors influence the rectification requires clarification. To better understand the ionic ‘causes’ of pore conductivity and its changes we simulated ion transport through a short nanopore using Poisson–Nernst–Planck equations, coupling it to the transport of water using Navier–Stokes equations. We extracted the potential, concentration, and ion flux profiles. In uniformly charged nanopores the voltage bias determines which counter-ion flux dominates, and it is carried by the counter-ions of the highest concentration. In unipolar nanopores this simple rule breaks down. The dominant counter-ion in the charged half is from the adjacent compartment, but the bias determines what counter-ion flux is dominant — the same ion (regular bias), or a different and smaller (reverse bias), and this difference determines the level of rectification. In bipolar nanopores the dominant counter-ions in each half are from the adjacent compartments, and the total ion concentration dips in the middle near the wall. With regular bias the total ion concentration peaks in the pore center; the ions that carry the current through the nanopore start as counter-ions and their fluxes are large. With reverse bias the total concentration dips near the wall and in the center, both dominant ion fluxes through the nanopore start as co-ions and are very small, whereas those starting as counter-ions do not go through.