Simulation of a model nanopore sensor: Ion competition underlies device behavior

Abstract

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.

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

“…The bulk value is experimental (D bulk K + = 1.849 × 10 −9 m 2 s −1 and D bulk Cl − = D bulk X = 2.032 × 10 −9 m 2 s −1 ), while D pore i just scales the current without influencing the I/I 0 ratio. Following our previous studies [45,8,46,47] here we set the relation D…”

“…1). Each ring contains 4 binding sites [8]. The binding potential between a site and an analyte ion is the square-well (SW) potential:…”

“…The SW potential acts only on the X ions in the simulations. An analysis on the effect of the ε SW and d SW parameters has been given in our previous work [8].…”

“…This case was already studied in our first paper on the subject [8] considering a symmetric sensor. The device function is the current in the presence of the X ions (I) in relation to the current in the absence of the X ions (I 0 ).…”

“…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].…”