Optofluidics, born of the desire to create a system containing microfluidic environments with integrated optical elements, has seen dramatic increases in popularity over the last 10 years. In particular, the application of this technology towards chip based molecular sensors has undergone significant development. The most sensitive of these biosensors interface liquid- and solid-core antiresonant reflecting optical waveguides (ARROWs). These sensor chips are created using conventional silicon microfabrication. As such, ARROW technology has previously been unable to utilize state-of-the-art microfluidic developments because the technology used—soft polydimethyl siloxane (PDMS) micromolded chips—is unamenable to the silicon microfabrication workflows implemented in the creation of ARROW detection chips. The original goal of this thesis was to employ hybrid integration, or the connection of independently designed and fabricated optofluidic and microfluidic chips, to create enhanced biosensors with the capability of processing and detecting biological samples on a single hybrid system. After successful demonstration of this paradigm, this work expanded into a new direction—direct integration of sensing and detection technologies on a new platform with dynamic, multi-dimensional photonic re-configurability.

This thesis reports a number of firsts, including:

• 1,000 fold optical transmission enhancement of ARROW optofluidic detection chips through thermal annealing

• Detection of single nucleic acids on a silicon-based ARROW chip

• Hybrid optofluidic integration of ARROW detection chips and passive PDMS microfluidic chips

• Hybrid optofluidic integration of ARROW detection chips and actively controllable PDMS microfluidic chips with integrated microvalves

• On-chip concentration and detection of clinical Ebola nucleic acids

• Multimode interference (MMI) waveguide based wavelength division multiplexing for detection of single influenza virions

• All PDMS platform created from monolithically integrated solid- and liquid-core waveguides with single particle detection efficiency and directly integrated microvalves6, featuring:

o Tunable/tailorable PDMS MMI waveguides

o Lightvalves (optical switch/fluidic microvalve) with the ability to dynamically control light and fluid flow simultaneously

o Lightvalve trap architecture with the ability to physically trap, detect, and analyze single biomolecules.

Effects of thermal annealing on liquid- and solid-core antiresonant reflective optical waveguides (ARROW) are herein investigated. Transmission changes of 10 to 1000 fold increases are observed post annealing at either 300 or 700 °C. Furthermore, upon 700 °C annealing, the detectable photoluminescence of tantalum oxide cladding layers is reduced to half that of its original value. The suggestible cause for change in transmission is increased modal confinement within the ridge waveguides. Although annealing cracks form at all temperatures, their effect on transmission seems intermittent. A final culmination of the transmission changes is observed in a protein detection experiment where a 6.3 fold signal increase is observed after annealing.