Figure 1:

Calculation of nanopore ionic current using the steric exclusion model (SEM). (a) All-atom representation of a solid-state nanopore harboring a protein in its constriction. Silicon and oxygen atoms are represented by gray and red spheres, respectively. Atoms of the proteins are colored according to the atom type: white, red, blue, and cyan indicate hydrogen, oxygen, nitrogen, and carbon atoms, respectively. The electrolyte solution is shown as a semitransparent surface. To reveal the presence of the nanopore, a cut-away view of the membrane is shown. (b) SEM representation of the nanopore system shown in panel a. The image shows a heatmap slice through the 3D map of local conductivity that, along with the boundary conditions, defines the system for ionic current calculations. Blue and red colors indicate regions of the system where local ion conductivity equals the bulk ion conductivity or zero, respectively. A yellow wireframe shows an isosurface of local conductivity value equal 50% of the bulk conductivity. (c) Close up view of the region near the protein. For clarity, the wireframe isosurface near the nanopore walls is not shown.