As the microelectronics industry pushes microfabrication processes further, the lab-on-a-chip field has continued to piggy-back off the industry's fabrication capabilities with the goal of producing total chemical and biological systems on small chip-size platforms. One important function of such systems is the ability to perform single molecule detection. There are currently many methods being researched for performing single molecule detection, both macro and micro in scale. This dissertation focuses on an optofluidic, lab-on-a-chip platform called the ARROW biosensor, which possesses several advantages over macro-scale single molecule detection platforms. These advantages include an amplification-free detection scheme, cheap parallel fabrication techniques, rapid single molecule detection results, and extremely low volume sample probing, which leads to ultra-sensitive detection. The ARROW biosensor was conceived in the early 2000s; however, since then it has undergone many design changes to improve and add new functionality to the lab-on-a-chip; however, water absorption in the plasma enhanced chemical vapor deposited silicon dioxide has been a problem that has plagued the biosensor platform for some time. Moisture uptake in the oxide layer of the ARROWs leads to loss of waveguiding confinement and drastically decreases the overall sensitivity of the ARROW biosensors. New ARROW designs were investigated to alleviate the negative water absorption effects in the ARROWs. The new waveguide designs were tested for resiliency to water absorption and the buried ARROW (bARROW) design was determined to be the most successful at preventing negative water absorption effects from occurring in the PECVD oxide waveguides. The bARROWs were integrated into the full biosensor platforms and used to demonstrate high sensitivity single molecule detection without any signs of water absorption affecting the bARROWs' waveguiding capabilities. The bARROW biosensors are not only water resistant, they also proved to be the most sensitive biosensors yet fabricated with average signal-to-noise ratios around 80% higher than any previously fabricated ARROW biosensors.

The focus of this work is the integration of alkali vapor atomic vapor cells into common silicon wafer microfabrication processes. Such integrated platforms enable the study of quantum coherence effects such as electromagnetically induced transparency, which can in turn be used to demonstrate slow light. Slow and stopped light devices have applications in the optical communications and quantum computing fields. This project uses hollow core anti-resonant reflecting optical waveguides (ARROWs) to build such slow light devices. An explanation of light-matter interactions and the physics of slow light is first provided, as well as a detailed overview of the fabrication process. Following the discovery of a vapor transport issue, a custom capillary-based testing platform is developed to quantify the effect of confinement, temperature, and wall coatings on rubidium transport. A mathematical model is derived from the experimental results and predicts long transport times. A new design methodology is presented that addresses the transport problem by increasing the number of rubidium entry points. This design also improves chip durability and decreases environmental susceptibility through the use of a single copper reservoir and buried channel waveguides (BCWs). New chips are successfully fabricated, loaded, and monitored for rubidium spectra. Absorption is observed in several chips and absorption peaks depths in excess of 10% are reported. The chip lifetime remains comparable to previous designs. This new design can be expanded to a multi-core platform suitable for slow and stopped light experimentation.

The rapid development of optofluidics, the combination of microfluidics and integrated optics, since its formal conception in the early 2000's has aided in the advance of single-molecule analysis. The optofluidic platform discussed in this dissertation is called the liquid core anti-resonant reflecting optical waveguide (LC-ARROW). This platform uses ARROW waveguides to orthogonally intersect a liquid core waveguide with solid core rib waveguides for the excitation of specifically labeled molecules and collection of fluorescence signal. Since conception, the LC-ARROW platform has demonstrated its effectiveness as a lab-on-a-chip fluorescence biosensor. However, until the addition of optical multiplexing excitation waveguides, the platform lacked a critical functionality for use in rapid disease diagnostics, namely the ability to simultaneously detect different types of molecules and particles. In disease diagnostics, the ability to multiplex, detect and identify multiple biomarkers simultaneously is paramount for a sensor to be used as a rapid diagnostic system. This work brings optofluidic multiplexing to the sensor through the implementation of three specific designs: (1) the Y-splitter was the first multi-spot excitation design implemented on the platform, although it did not have the ability to multiplex it served as a critical stepping stone and showed that multi-spot excitation could improve the signal-to-noise ratio of the platform by ~50,000 times; (2) a multimode interference (MMI) waveguide which took the multi-spot idea and then demonstrated spectral multiplexing capable of correctly identifying multiple diverse biomarkers simultaneously; and, (3) a Triple-Core design which incorporates excitation and collection along multiple liquid cores, enabling spatial multiplexing which increases the number of individual molecules to be identified concurrently with the MMI waveguide excitation. In addition to describing the development of optical multiplexing, this dissertation includes an investigation of another LC-ARROW based design that enables 2D bioparticle trapping, the Anti-Brownian Electrokinetic (ABEL) trap. This design demonstrates two-dimensional compensation of a particle's Brownian motion in solution. The capability to maintain a molecule suspended in solution over time enables the ability to gain a deeper understanding of cellular function and therapies based on molecular functions.

This thesis presents rubidium packaging methods for integration using anti-resonant reflecting optical waveguides (ARROWs) on a planar chip. The atomic vapor ARROW confines light through rubidium vapor, increases the light-vapor interaction length, decreases the size of the atomic cell to chip scales, and opens up possibilities for waveguide systems on chips for additional optoelectronic devices. Rubidium vapor packaging for long-life times are essential for realizing feasibly useful devices. Considerations of outgassing, leaking and chemical compatibilities of materials in rubidium vapor cells lead to an all-metal design. The effect of these characteristics on the rubidium D2 line spectra is considered.

Nanopore technology has introduced new techniques for single particle detection and analysis. A nanopore consists of a small opening in a membrane on the nanometer scale. Nanopores are found in nature and are utilized for transporting molecules through biological membranes. Researchers have been able to mimic naturally forming biological nanopores and utilize them for a variety of sensing applications. Nanopores, fabricated either organically or inorganically, can be used for detecting biomarkers such as proteins, nucleic acids, and metabolites that translocate the membrane by way of the nanopore. Constant ionic current flow is measured through the nanopore by way of a sensitive ammeter. In the presence of a biomarker, the ionic current flow will be impeded, causing the electrical signal to drop. This drop uniquely corresponds to the type of particle passing through the nanopore. In this work, the thin membrane on which the nanopore resides is created through a newly developed meniscus shaped sacrificial technique. The sacrificial polymer material starts as a liquid and is confined to the microfluidic channel through the capillary effect, giving it the meniscus profile. It is used as a structural support on which a thin silicon dioxide layer is grown. The layer of oxide takes on the same natural meniscus shape as the sacrificial material. The polymer is subsequently etched, resulting in a hollow core liquid channel with a suspended meniscus membrane. This process allows a thin membrane to be fabricated on top of a microfluidic channel that ranges from 50-200 nm in thickness. The meniscus membrane is crucial to the success of nanopore formation. The nanoscale membrane allows for smaller, more precise nanopores to be created. Reduced nanopore dimensions are advantageous for the detection of smaller biomarkers. The platform described in this dissertation integrates solid-state naturally forming meniscus membranes with solid-core and optofluidic waveguides for nanopore detection applications. The waveguides allow for a particle trap to be introduced to the system. The ability to trap particles directly under the nanopore is critical to the speed of which the nanopore can operate. This dissertation focuses on the fabrication, characterization, and testing of an optofluidic platform that features a nanopore for rapid single molecule detection and analysis.