SOLID STATE NANOPORE : SIMULATION, CHARACTERIZATION AND MOLECULAR SENSING

• Author / Creator

  Rengarajan, Uppiliappan

• Single molecule passing through a nanopore is a process that is important in science. Some molecules develop a surface charge when diffused into a salt solution, when these molecules pass through the nanopore, they reduce or increase the ionic current. The drop or rise in the current level is dependent on the size and shape of the molecule, and consequently differs for each molecule. Hybrid nanopores, a sensing device which integrates biological and synthetic nanopores is a powerful tool for nanopore-based sensing. A detailed characterization of the synthetic or solid state nanopores is required to integrate it with biological nanopores. In this thesis a detailed characterization of solid state nanopores is performed by comparing experimental and simulated conductance models. Solid state nanopores fabricated using Transmission Electron Microscope, ranging in size from 4 to 10 nm were measured for conductance, using Axopatch 200B. Cleanroom-based cleaning and mounting of the nanopore (and related accessories) was utilized to improve the yield of functional nanopores, prior to conductance measurements. The experimentally measured conductance was then matched with conductance obtained from finite element modeling (using COMSOL Multiphysics platform) of the electrokinetic processes occurring in a nanopore. Poisson-Nernst-Planck system coupled with Navier stokes equations was used for this purpose. The experimental and simulated conductance results of various solid state nanopores matched within an error range of 10 - 25 %. Upon validation of the COMSOL model, the model was used for analyzing various parametric effects on conductance. Conductance dependence on pore shape and size was analyzed in detail. The simulation technique can be used to predict the required size and shape of a solid state pore for desired conductance. Effect of pore size, shape, thickness and the membrane surface charge on nanopore conductance has been discussed. Nanopore sensing has been explored, by testing translocation of different molecules, namely, DNA, polysaccharides and proteins. Size and conformation prediction of DNA, polysaccharide molecules as they translocate through nanopores has been demonstrated. An attempt to create a hybrid nanopore, by inserting protein pore (OmpG) onto a solid state nanopore was conducted. Protein pore(s) insertion onto the solid state nanopore with and without guiding DNA molecule was observed. Subsequently, protein partial closing and opening has also been observed, hinting at the capability of nanopore sensors to act as powerful tools in selective sensing. In summary, this thesis demonstrates the ability of simulation technique to predict the conductance of a solid state nanopore under different chemical, physical and surface property conditions of the pore. These results could be further used to fine tune the fabrication of solid state nanopores to better understand and facilitate formation of hybrid nanopores elegantly.

• Subjects / Keywords

  • Nanofluidics
  • Hybrid systems
  • Nanopore conductance
  • Nano-sensing
  • Electrokinetics

• Graduation date

  Fall 2016

• Type of Item

  Thesis

• Degree

  Master of Science

• DOI

  https://doi.org/10.7939/R31Z42677

• License

  This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for non-commercial purposes. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.