Y.M. Nuwan D.Y. Bandara, Buddini Iroshika Karawdeniya, James T. Hagan, Jason R. Dwyer, MinJun Kim, JungSoo Lee, Cassandra Hammond, George Alexandrakis, Gaurav Goyal


Solid-state nanopore sensors have attracted considerable attraction as a tool for solution-based single-molecule studies and have been successfully utilized for characterization of biomolecules such as nucleic acids, proteins, glycans, viruses, etc. Among these, characterization of proteins has been more challenging due to their charge heterogeneity and the complex energy landscape associated with different protein conformations. Presented in this thesis is the fabrication of solid-state nanopores and their application for characterizing proteins and understanding their transport through nanopores. Fabrication of nanometer-sized pores in SixNy membranes was achieved using the conventional controlled dielectric breakdown method as well as a simple modified version of it that resulted in ultra-stable nanopores devoid of legacy issues associated with the conventional nanopores. The noise characteristics of the fabricated nanopores were studied as a function of solution pH, electrolyte type and concentration, applied voltage and pore diameter. SixNy-based solid-state nanopores were used for studying the voltage and pH-induced conformational changes of the human serum transferrin protein and for distinguishing between its two forms – apo (iron-free) and holo (iron-rich). Finally, the transport of protein through nanopores was studied, first in symmetric salt conditions and then in asymmetric salt conditions. Investigating protein transport phenomena in different electrolyte types and concentrations as well as different electrolyte concentration gradients provided valuable insights into the electrokinetic phenomena such as electrophoresis and electroosmosis that govern analyte capture and transport through solid-state nanopores.

Degree Date

Spring 5-14-2022

Document Type


Degree Name



Mechanical Engineering


MinJun Kim

Subject Area

Mechanical Engineering, Bioengineering and Biomedical Engineering, Biophysics

Number of Pages




Creative Commons License

Creative Commons Attribution-Noncommercial 4.0 License
This work is licensed under a Creative Commons Attribution-Noncommercial 4.0 License