Single-molecule detection and characterization with nanopores is a powerful technique that does not require labeling. Multinanopore systems, especially double nanopores, have attracted wide attention and have been applied in many fields. However, theoretical studies of electrokinetic ion transport in nanopores mainly focus on single nanopores. In this paper, for the first time, a theoretical study of pH-regulated double-barreled nanopores is conducted using three-dimensional Poisson–Nernst–Planck equations and Navier–Stokes equations. Four ionic species and the surface chemistry on the walls of the nanopores are included. The results demonstrate that the properties of the bulk salt solution significantly affect nanopore conductivity and ion transport phenomena in nanopores. There are two ion-enriched zones and two ion-depleted zones in double-barreled nanopores. Due to the symmetry of the double-barreled nanopore structure and surface charge density, there is no ionic rectification effect in double-barreled nanopores. The ion selectivity is similar to that of conventional single pH-regulated nanopores.

Nanopore single-molecule technology, especially DNA/RNA sequencing based on nanopores, requires a high spatial resolution. In this paper, we theoretically studied the spatial resolution of the cross-disjoint mortise-confined solid-state nanopore (CDM-nanopore) structure that is formed by two perpendicular and disjoint nanochannels and a middle nanopore. When the thickness of the middle layer (nanopore) is 0 nm (i.e., the zero-depth interfacial nanopore), 0.6 nm, and 1 nm, the geometric resolution (δ z ) is 0.24, 0.32, and 0.39 nm, respectively. The ultrahigh spatial resolution of the CDM nanopore with an ultrathin middle layer is comparable with that of the conventional ultrashort nanopore (e.g., two-dimensional material nanopore). We also demonstrate that for cylindrical segments with a diameter difference of 0.2 nm, the current difference (δ I ) will reach the maximum when the middle layer is about half of the length of one segment. In addition to the high resolution of CDM nanopores with an ultrathin middle layer, its outstanding mechanical stability and low noise characteristics provide the possibility of extending the application of the CDM nanopore to DNA/RNA sequencing.