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.

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.

Controlling ion transport through nanopores: modeling transistor behavior.

We present a modeling study of a nanopore-based transistor computed by a mean-field continuum theory (Poisson-Nernst-Planck, PNP) and a hybrid method including particle simulation (Local Equilibrium Monte Carlo, LEMC) that is able to take ionic correlations into account including the finite size of ions. The model is composed of three regions along the pore axis with the left and right regions determining the ionic species that is the main charge carrier, and the central region tuning the concentration of that species and, thus, the current flowing through the nanopore. We consider a model of small dimensions with the pore radius comparable to the Debye-screening length (Rpore/λD≈ 1), which, together with large surface charges provides a mechanism for creating depletion zones and, thus, controlling ionic current through the device. We report the scaling behavior of the device as a function of the Rpore/λD parameter. Qualitative agreement between PNP and LEMC results indicates that mean-field electrostatic effects predominantly determine device behavior.

Multiscale modeling of a rectifying bipolar nanopore: Comparing Poisson-Nernst-Planck to Monte Carlo.

In the framework of a multiscale modeling approach, we present a systematic study of a bipolar rectifying nanopore using a continuum and a particle simulation method. The common ground in the two methods is the application of the Nernst-Planck (NP) equation to compute ion transport in the framework of the implicit-water electrolytemodel. The difference is that the Poisson-Boltzmann theory is used in the Poisson-Nernst-Planck (PNP) approach, while the Local Equilibrium Monte Carlo (LEMC) method is used in the particle simulation approach (NP+LEMC) to relate the concentration profile to the electrochemical potential profile. Since we consider a bipolar pore which is short and narrow, we perform simulations using two-dimensional PNP. In addition, results of a non-linear version of PNP that takes crowding of ions into account are shown. We observe that the mean field approximation applied in PNP is appropriate to reproduce the basic behavior of the bipolar nanopore (e.g., rectification) for varying parameters of the system (voltage, surface charge,electrolyte concentration, and pore radius). We present current data that characterize the nanopore's behavior as a device, as well as concentration, electrical potential, and electrochemical potential profiles.