3-D simulation of nanopore structure for DNA sequencing

In this paper, we propose a method for simulating nanopore structure by using conventional 3-D simulation tool to mimic the I-V behavior of the nanopore structure. In the simulation, we use lightly doped silicon for ionic solution where some parameters like electron af?nity and dielectric constant are ?tted to consider the ionic solution. By using this method, we can simulate the I-V behavior of nanopore structure depending on the location and the size of the sphere shaped silicon oxide which is considered to be an indicator of a DNA base. In addition, we simulate an Ionic Field Effect Transistor (IFET) which has basically the nanopore structure, and show that the simulated curves follow suf?ciently the I-V behavior of the measurement data. Therefore, we think it is reasonable to apply parameter modeling mentioned above to simulate nanopore structure. The key idea is to modify electron af?nity of silicon which is used to mimic the KCl solution to avoid band bending and depletion inside the nanopore. We could ef?ciently utilize conventional 3-D simulation tool to simulate the I-V behavior of nanopore structures.