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

Abstract

In a multiscale modeling approach, we present computer simulation results for a rectifying bipolar nanopore at 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 explicit-water 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 the 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.

Application of a bipolar nanopore as a sensor: rectification as an additional device function

“…Because the shapes of the I−U curves are similar for every case, we can characterize the ON and OFF states by two chosen voltages, ±200 mV as in our previous studies [44,45,1,48]. Therefore, we define our device functions as the ON-…”

“…If the concentration of a given ionic species is very small in a given region of the pore along the z-axis, then this region behaves as a large-resistance element of the regions imagined as resistors connected in series. This large-resistance region, called depletion zone, tend to determine the resistance of the whole device especially in the case of bipolar nanopores whose device function is determined by the appearance of depletion zones controlled by the sign of the voltage and the polarity of the surface charge distribution [44].…”

“…In other studies, where reference was available, we fitted the D pore i value to experimental [42,46] or molecular dynamics [44,48] data.…”

“…We apply the Nernst-Planck (NP) transport equation and couple it to LEMC resulting in a hybrid method, called NP+LEMC. This method was successfully applied for various problems in the last couple of years such as particle transport through model membranes [39,40], ion channels [41,42,43], and nanopores [44,45,8,46,47,1,48].…”

“…Reduced models work because they include those degrees of freedom that are relevant for device function. This question has been analyzed in detail in our papers for bipolar nanopores [43,44,48].…”