  We study a model nanopore sensor with which a very low concentration of
analyte molecules can be detected on the basis of the selective binding of the
analyte molecules to the binding sites on the pore wall. The bound analyte ions
partially replace the current-carrier cations in a thermodynamic competition.
This competition depends both on the properties of the nanopore and the
concentrations of the competing ions (through their chemical potentials). The
output signal given by the device is the current reduction caused by the
presence of the analyte ions. The concentration of the analyte ions can be
determined through calibration curves. We model the binding site with the
square-well potential and the electrolyte as charged hard spheres in an
implicit background solvent. We study the system with a hybrid method in which
we compute the ion flux with the Nernst-Planck (NP) equation coupled with the
Local Equilibrium Monte Carlo (LEMC) simulation technique. The resulting
NP+LEMC method is able to handle both strong ionic correlations inside the pore
(including finite size of ions) and bulk concentrations as low as micromolar.
We analyze the effect of bulk ion concentrations, pore parameters, binding site
parameters, electrolyte properties, and voltage on the behavior of the device.
