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

Valiskó, Mónika and Matejczyk, Bartlomiej and Ható, Zoltán and Kristóf, Tamás and Mádai, Eszter and Fertig, Dávid and Gillespie, Dirk and Boda, Dezső (2019) 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. JOURNAL OF CHEMICAL PHYSICS, 155 (14). p. 144703. ISSN 0021-9606

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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, 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 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.

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