This thesis presents a computational study of water and ion dynamics in modified hydrophobic silicon nitride (Si3N4) nanopores, aimed at enhancing protein sequenc- ing technologies. By employing molecular dynamics (MD) simulations, the research investigates the wetting-dewetting behavior within nanopores as an indirect measure of amino acid residue hydrophobicity, focusing on how post-translational modifications (PTMs) of lysine, particularly the acetylation of lysine residues, influence nanopore hydrophobicity and ionic conductance. The study reveals that nanopore radius and hydrophobicity significantly affect water and ion permeation, with smaller nanopores oscillating between open and closed states, while larger ones remain open.  Using umbrella sampling and the Weighted Histogram Analysis Method (WHAM), the potential of mean force (PMF) for potassium (K+), chloride (Cl−), and water within the nanopores was determined, showing distinct PMF profiles based on lysine and acetyl- lysine presence. The modulation of ionic currents as a tool for protein sequencing was explored, demonstrating that different amino acid residues affect ionic currents by par- tially blocking the pore and altering local permeability, thereby enabling differentiation based on size, shape, charge, and hydrophobicity.  The findings suggest that silicon nitride pore hydrophobicity can be tailored for nanopore sequencing, correlating changes in ionic currents with amino acid residue translocation. This research enhances the understanding of interactions within nanopore environments, potentially leading to more precise nanopore-based sequencing methods.

This dissertation outlines the research and development of ground-breaking nanometer sized openings (nanopores) integrated with an on-chip optofluidic platform. This platform represents a significant advancement for single nanoparticle sensing. In this work specifically, the integrated optofluidic platform has been used to electrically and optically filter and detect single nanoparticles using ionic current blockade and fluorescence experiments. The correlation of electrical and optical signal has provided the highest sensitivity single nanoparticle measurements ever taken with integrated optofluidic platforms. The particular optofluidic platform used for this work is an antiresonant reflecting optical waveguide (ARROW). ARROW hollow and solid core waveguides are interference based waveguides that are designed to guide light in low index media such as liquids and gases. Because of this unique guiding property, ARROW hollow cores can be used to sense and analyze low concentrations of single particles. Additionally, because ARROW platforms are based upon standard silicon processing techniques and materials, they are miniature sized (~1 cm2), inexpensive, highly parallelizable, provide a high degree of design flexibility, and can be integrated with many different optical and electrical components and sources. Finally, because of the miniature, integrated nature of the ARROW platform, it has the potential to be incorporated into hand held devices that could provide quick, inexpensive, user-friendly diagnostics. The ARROW platform has been through many revisions in the past several years in an attempt to improve performance and functionality. Specifically, advanced fabrication techniques that have been used to decrease the production time, increase the yield, and improve the optical quality of ARROW platforms are discussed in the first part of this work. These advancements were all developed in order to facilitate the production of high quality integrated nanopores and ARROW platforms. The second part of this work then focuses on the actual integration of micrometer sized openings (micropores) and nanopores in the hollow waveguide section of ARROW platforms for filtering, detecting, and analyzing single nanoparticles. The successes and attempts at achieving these results are the basis of this dissertation of work.