Multiscale modeling of a rectifying bipolar nanopore: explicit-water versus implicit-water simulations

Ható, Zoltán and Valiskó, Mónika and Kristóf, Tamás and Gillespie, Dirk and Boda, Dezső (2017) Multiscale modeling of a rectifying bipolar nanopore: explicit-water versus implicit-water simulations. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 19 (27). pp. 17816-17826. ISSN 1463-9076

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Abstract

In a multiscale modeling approach, we present computer simulation results for a rectifying bipolar nanopore on two modeling levels. In an all-atom model, we use explicit water to simulate ion transport directly with the molecular dynamics technique. In a reduced model, we use implicit water and apply the Local Equilibrium Monte Carlo method together with the Nernst-Planck transport equation. This hybrid method makes the fast calculation of ion transport possible at the price of lost details. We show that the implicit-water model is an appropriate representation of the explicitwater model when we look at the system at the device (i.e., input vs. output) level. The two models produce qualitatively similar behavior of the electrical current for different voltages and model parameters. Looking at details of concentration and potential profiles, we find profound differences between the two models. These differences, however, do not influence the basic behavior of the model as a device because they do not influence the z-dependence of the concentration profiles which are the main determinants of current. These results then address an old paradox: how do reduced models, whose assumptions should break down in a nanoscale device, predict experimental data? Our simulations show that reduced models can still capture the overall device physics correctly, even though they get some important aspects of the molecular-scale physics quite wrong; reduced models work because they include the physics that is necessary from the point of view of device function. Therefore, reduced models can suffice for general device understanding and device design, but more detailed models might be needed for molecular level understanding.

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