2016 MIE Graduate Student Conference April 16, 2016 SIMULATION OF VARIOUS SHAPES OF NANOPORE BASED NANOSENSORS FOR THE TRANSLOCATION OF NANOPARTICLES

Driving single nanoparticles like DNA and proteins by the electrophoretic force through a nanopore in the presence of an electric field produces an ionic current, which passes from the nanopore. The current blockage due to the nanoparticle translocation makes an observable change in the ionic current, which is useful for the study of bio molecules. Many efforts are made to perceive the electro kinetic behavior of the nanoparticles (DNA in perticular) translocation. The finite element (FE) model simulates the fluid flow, electric potential and ionic concentrations for the entire geometry and vicinity of the particle and nanopore in the steady state when the particle reaches to any position. The structure of nanopores simulated in FE are divided into three groups from the materials view: Silicon [1-3], glass [4-6] and polymeric [7] based nanopores. Several FE models were used to simulate the nanoparticle translocation through these different nanopores. Using the silicon, glass or PDMS nanopores has three major problems: The first problem is that changing the size of the nanopore for the silicon or glass structures requires a lot of efforts (or try and error) which requires changing the lithography or the fabrication process. Secondly, the fabrication of silicon or glass nanopores is more expensive comparing to the polymeric nanopore structures. Finally for the PDMS nanopores the hydrophobicity of the PDMS makes it difficult to fill the ionic solution through the entire channel and the nanopore. Experiment The goal for this experiment was to find the current drop values from the translocation of Lambda DNA molecules from nanopore-nanochannel structure. The baseline and the current drop values of the experiment were used to validate the simulation results. In this section, we described the geometry of the nanochannel as well as the nanopores and the translocation experiment results. We milled the structure of two nanopores and a nanochannel into a blank silicon by using the Focused Ion Beam (FIB). Figure 1 showed the Scanning Electron Microscope (SEM) image of the top (a, b) and down (c, d) nanopores. The width of the nanopores in the top views (a, c) are shown by 2b and the heights of the nanopores in the 52o tilted views (b, d) are shown by a' which is “sin(52)” times of the actual nanopore size. The length of the nanochannel was 120μm and the distance of the top and bottom nanopores from the inlet and the outlet of the nanochannel were either 30μm. The structure shown in Figure 1 from the silicon master was copied into polyurethane-acrylate (PUA) on a Polycarbonate (PC) substrate by UV imprint lithography. Then we imprinted the PUA stamp thermally into a Polydimethylsiloxane (PDMS) substrate. The final imprinted structure of the nanopore-nanochannel on the PDMS substrate was covered by a PC cover sheet and used for the DNA translocation experiment. Figure 1. Scanning Electron Microscope (SEM) images of the nanochannel-nanonanopore silicon master mold Simulation The FE model of the nanopore-nanochannel structure was built in COMSOL 5.0 Multiphysics software (www.comsol.com) [90]. For simplicity, an axisymmetric model was used for the nanopore-nanochannel simulation. The cross section area of the fabricated nanochannel and nanonanopores in the experiment were similar to half ellipses. Thus, circular areas with the same area as the half ellipse cross section areas of the nanochannel and two nanopores were used in the modelling. Table 1 showed the calculated corresponding radius of the circular area for the nanochannel and top and down nanopores in the modelling. As mentioned, the distance between the two nanopores is 60μm and the both top and down nanopores have 30μm distance from the inlet and outlet respectively. Table 1. Dimensions of the nanochannel-nanonanopore structure and their equivalent circular model Experiment Simulation