  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 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 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.
