Doctor of Philosophy (PhD) / Photonic crystals are optical structures that contain a periodic modulation of their refractive index, allowing them to control light in recent years of an unprecedented capacity. Photonic crystals may take on a variety of configurations, in particular the photonic crystal cavity, which may “hold” light in small volumes comparable to the light’s wavelength. This capability to spatially confine light opens up countless possibilities to explore for research in telecommunications, quantum electrodynamics experiments and high-resolution sensor applications. However, the vast functionality potentially made available by photonic crystal cavities is limited due to the difficulty in redefining photonic crystal components once they are formed in their (typically) solid material. The work presented in this thesis investigates several approaches to overcome this issue by reconfiguring photonic crystal cavities.

Doctor of Philosophy (PhD) / Photonic crystals are optical structures that contain a periodic modulation of their refractive index, allowing them to control light in recent years of an unprecedented capacity. Photonic crystals may take on a variety of configurations, in particular the photonic crystal cavity, which may “hold” light in small volumes comparable to the light’s wavelength. This capability to spatially confine light opens up countless possibilities to explore for research in telecommunications, quantum electrodynamics experiments and high-resolution sensor applications. However, the vast functionality potentially made available by photonic crystal cavities is limited due to the difficulty in redefining photonic crystal components once they are formed in their (typically) solid material. The work presented in this thesis investigates several approaches to overcome this issue by reconfiguring photonic crystal cavities.

High quality (Q) factor whispering gallery modes (WGMs) can induce nonlinear effects in liquid droplets through mechanisms such as radiation pressure, light scattering, thermocapillarity, Kerr nonlinearity, and thermal effect. However, such nonlinear effects have yet to be thoroughly investigated and compared in the literature. In this study, we first investigate a micron-sized liquid spherical resonator and present an approximated solution for the resonator interface deformation due to the radiation pressure. We then derive an analytical approach that can exactly calculate the droplet deformation induced by the radiation pressure. The accuracy of the analytical solution is confirmed through numerical analyses based on the boundary element method. We show that the nonlinear optofluidic effect induced by the radiation pressure is stronger than the Kerr effect and the thermal effect under a large variety of realistic conditions. Using liquids with ultra-low and experimentally attainable interfacial tension, we further confirm the prediction that it may only take a few photons to produce measurable WGM resonance shift through radiation pressure induced droplet deformation. Similar to the radiation pressure, the scattering force in the droplet can induce a rotational fluid motion which also leads to the interface deformation. The interface deformation can also be produced by the thermocapillarity as a result of the WGM energy absorption and temperature increase. In this study, we provide a numerical scheme to calculate the fluid motion and quantify the nonlinearity induced by the optical scattering force and thermocapillarity. The magnitude of the optofluidic nonlinearities induced by the radiation pressure, thermocapillary effect, light scattering and Kerr effect are compared. We show that the radiation pressure due to the WGM produces the strongest nonlinear optofluidic effect. / Ph. D.

This thesis presents optofluidic nanostructures for analyte transport, concentration and sensing. This work was part of a larger collaborative project between the BC Cancer Agency and the departments of Chemistry, Electrical and Mechanical Engineering at the University of Victoria. In this work, arrays of nanoholes are used as optofluidic platforms for sensing, combining the characteristics of these nanostructures for both fluidic transport and plasmonic (optical) sensing. Two different modes are considered: flow-over mode, where the sample solution containing the analyte flows on top of the nanohole arrays, and a novel flow-through mode, where the nanoholes are used as nanochannels, enabling solution transport and analyte sieving. Flow-through nanohole array operation and sensing is first demonstrated, offering a six-fold improvement in sensor response compared to established flow-over sensing formats. Through a subsequent theoretical scaling analysis and computational analyses, the benefits of the flow-through nanohole sensing format are further quantified. A first analysis is dedicated to study the enhancement offered by the flow-through operation mode using a mass transport approach. A second analysis offers an ample study of benefits and limitations of the flow-through nanostructure operation using the combination of mass transport and binding kinetic parameters for different analytes with characteristics of clinical relevance. The mass transport analysis indicates much higher analyte collection efficiency (~ 99%) offered by the flow-through mode, compared to the flow-over platform (~ 2%). The analysis including both mass transport and binding kinetics demonstrate up to 20-fold improvement in response time for typical biomarkers. This thesis also presents the use of the flow-through optofluidic platform as an active analyte concentrator. In combination with a pressure bias, an electric field is used to concentrate electrically charged analyte for subsequent sensing. Fluorescein enrichment of 180-fold in 60 s was achieved, and 100-fold enrichment and simultaneous surface plasmon resonance (SPR) sensing of a protein (bovine serum albumin, BSA) was demonstrated. These experiments represent the first active utilization of a nanohole metallic layer as an electrode, and the first demonstration of a photonic nanostructure achieving both concentration and sensing of analytes. Towards the integration of optofluidic nanostructures into microfluidic environments for portable lab-on-chip diagnostic systems, this dissertation also includes the development of two nanohole array based sensing systems with simple flow-over operation. The first system consisted of a hand-held device with a dual-wavelength light source to increase the spectral diversity. The second system consisted of nanohole arrays integrated with a microfluidic concentration gradient generator for the detection and quantification of ovarian cancer antibody and antigen. Additionally, this dissertation includes a novel technique to actuate liquids in microchannels through ground-directed electric discharges. Experiments demonstrate average fluid velocities on the order of 5cm/s and applicability of the technique in serpentine channels, for on-demand fluid routing, to initiate a mixing process, and through an on-chip integrated microelectrode. / Graduate

Dans cette thèse, des systèmes nano-opto-mécaniques (NOMS) sont explorés et deux composants nano-opto-mécaniques sont conçus, simulés, fabriqués et analysés. Premièrement, un générateur de moment angulaire composé d'un résonateur en anneau, un guide d'onde et un ensemble de nano-plots est conçu, analysé théoriquement et simulé. L'analyse théorique et les résultats numériques montrent qu'une série de champs tournants optiques (ROFs) sont générés lorsque différentes longueurs d'onde de résonance sont couplées dans le générateur. Par la suite, la force optique, le potentiel optique et le couple optique du ROF généré sont analysés théoriquement, simulés numériquement et discutés. Les distributions de forces optiques sont affectées par le ROF en fonction des ordres angulaires et des différents nano objets considérés. Les couples optiques sont analysés et discutés pour des objets différents, àsavoir les nano-particules sphériques, des nano-fils et un nano-rotor. Enfin, un système accordable de transparence induite par résonateurs couplés (Coupled-Resonator-Induced Transparency –CRIT), qui est entraîné par la force optique exercée entre le résonateur en anneau et le substrat, est conçu, analysé théoriquement, simulé,fabriqué et mesuré expérimentalement. Le système CRIT accordable est constitué d'un guide d'onde et de deux résonateurs en anneau couplés, dans lequel un anneau est fixe et l’autre libre de se mouvoir. Différentes puissances d'entrée produisent différentes forces optiques sur l'anneau libéré, qui produisent différentes déformations et changements de l'accumulation du champ optique, et ainsi différents décalages du spectre de transmission optique et une variation du retard de groupe / In this PhD thesis, the nano-opto-mechanical system (NOMS) is explored and two nano-opto-mechanical devices are designed, analyzed, simulated and fabricated. Firstly, an angular momentum generator consisting of a ring resonator, a wave guide and a group of nano-rods is designed, theoretically analyzed and simulated. The theoretic alanalysis and numerical results show that a series of rotating optical field (ROF) are generated when different resonant wave lengths are coupled into the generator. Subsequently, the optical force, the optical potential and the optical torque of the generated ROF are theoretically analyzed, numerically simulated and discussed. The optical force distributions are affected by the ROF with different angular orders and different objects. The optical torques are analyzed and discussed for different objects, i.e. spherical nano-particle, nano-wire and nano-rotor. Finally, a tunable coupled-resonator-induced transparency (CRIT) system, which is driven by the optical force between the ring resonator and the substrate, is designed, theoretically analyzed, simulated, fabricated and experimented. The tunable CRIT system consists of a bus wave guide and two coupled ring resonators, in which one is the released ring and the other is the fixed ring. Different input powers produce different optical forces on the released ring, which produce different final deformations, change the optical field buildup, shift the transmission spectrum and vary the group delay

Femtosecond laser direct writing (FLDW) is a versatile process that uses focused femtosecond pulses to modify the physical structure of a material, which can result in a shift of optical properties such as the linear and nonlinear refractive index. If the photon energy of the femtosecond pulses lies below the material bandgap, nonlinear absorption rather than linear absorption becomes the dominant mechanism of energy transfer to the material. In this manner, a focused femtosecond pulse train can be used to fabricate functional features such as optical waveguides, diffractive optical elements, or micro-fluidic elements within the volume of a transparent medium. In this dissertation, the utility of femtosecond laser processing as a fabrication technique of optical and micro-fluidic elements in chalcogenide glasses is explored. The photo-induced modifications of optical and chemical parameters of new germanium-based Chalcogenide glasses in both bulk and thin-film form are characterized for the first time and the impact of material composition and laser fabrication parameters are discussed. The glasses are found to display an increase in volume, a decrease of the linear optical refractive index, and an increase of the nonlinear refractive index when exposed to femtosecond laser pulses. A model based on avalanche ionization and multi-photon ionization is used to describe the highly nonlinear absorption of laser light in the material and correlate the photo-induced modifications to the electron density generated during irradiation. The magnitude of the induced photomodification is shown to be dependent on laser parameters such as laser dose and repetition rate. The fabrication of microfluidic elements through both direct ablation and the preferential etching of photo-modified regions is also explored. Finally, the integration of both optical elements and fluidic elements fabricated by FLDW into a single substrate is discussed. iv TABLE OF CONT

Immobilization of photosynthetic cultures has been used to generate biofuels and high value compounds through direct conversion of CO2 and water using sunlight. Compared with suspended cultures, immobilized bacteria can achieve much higher densities resulting in greater areal productivity. Limitations exist however, on the density that can be reached without compromising access to light and other nutrients. In this thesis an optofluidic approach to overcoming the challenge of light delivery to high density cultures of cyanobacteria is described and proof of concept experiments presented. This approach uses optical waveguides to deliver light to cells through bacterial interaction with the evanescent field and is tailored to meet each cell's need for light and nutrients. Experiments presented here demonstrate biofilm proliferation in the presence of evanescent fields. Illumination of surfaces by surface plasmon enhanced evanescent fields is also shown to be an effective and potentially useful technique to grow biofilms within optofluidic architectures.

Title from PDF of title page (University of Missouri--Columbia, viewed on March 10, 2010). The entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file. Thesis advisor: Dr. Xudong Fan. Includes bibliographical references.

This dissertation develops biosensors for rapid detection of pathogens for environmental monitoring and food safety applications and utilizes the multidisciplinary and multi-application characteristics of biosensors to develop a lesson plan that can be implemented in secondary education classrooms. The detection methods evolve from particle immunoagglutination assay, PDMS optofluidic lab-on-a-chip, and spectrum analysis to smartphone and image analysis without any reagent; the potential application in secondary education also underlines the extended value of biosensors. In the first paper presented here, an optofluidic lab-on-a-chip system and subsequent sampling procedure were developed for detecting bacteria from soil samples utilizing Mie scattering detection of particle immunoagglutination assay. This system and protocol detected the presence of Escherichia coli K12 from soil particles in near real-time (10 min) with a detection limit down to 1 CFU mL⁻¹ and has the potential to be implemented in the field. We also compared the interaction between E. coli and soil particles to the two-step protein-surface interaction. In the second paper, a smartphone-utilized biosensor consisting of a near-infrared (NIR) LED (wavelength of 880 nm) and a digital camera of a smartphone was developed for detecting microbial spoilage on ground beef, without using any reagents. The method was further improved by programming a smartphone application that allows the user to position the smartphone at an optimum distance and a range of angles utilizing its internal gyro sensor to measure a series of scatter intensities against the detection angle. This handheld device can be used as a preliminary screening tool to monitor microbial contamination on meat products. In the third paper, we designed a lesson plan for secondary education classrooms using biosensors as a core and branching out to different applications and fields of study with the goal of heightening students' interest and motivation toward attaining degrees and careers in STEM fields. Results revealed that the lesson was more effective in affecting younger students than older students, and more effective in teaching about the applications of biosensors than about the techniques of biosensor development.

This dissertation develops biosensors for rapid detection of pathogens for environmental monitoring and food safety applications and utilizes the multidisciplinary and multi-application characteristics of biosensors to develop a lesson plan that can be implemented in secondary education classrooms. The detection methods evolve from particle immunoagglutination assay, PDMS optofluidic lab-on-a-chip, and spectrum analysis to smartphone and image analysis without any reagent; the potential application in secondary education also underlines the extended value of biosensors. In the first paper presented here, an optofluidic lab-on-a-chip system and subsequent sampling procedure were developed for detecting bacteria from soil samples utilizing Mie scattering detection of particle immunoagglutination assay. This system and protocol detected the presence of Escherichia coli K12 from soil particles in near real-time (10 min) with a detection limit down to 1 CFU mL⁻¹ and has the potential to be implemented in the field. We also compared the interaction between E. coli and soil particles to the two-step protein-surface interaction. In the second paper, a smartphone-utilized biosensor consisting of a near-infrared (NIR) LED (wavelength of 880 nm) and a digital camera of a smartphone was developed for detecting microbial spoilage on ground beef, without using any reagents. The method was further improved by programming a smartphone application that allows the user to position the smartphone at an optimum distance and a range of angles utilizing its internal gyro sensor to measure a series of scatter intensities against the detection angle. This handheld device can be used as a preliminary screening tool to monitor microbial contamination on meat products. In the third paper, we designed a lesson plan for secondary education classrooms using biosensors as a core and branching out to different applications and fields of study with the goal of heightening students' interest and motivation toward attaining degrees and careers in STEM fields. Results revealed that the lesson was more effective in affecting younger students than older students, and more effective in teaching about the applications of biosensors than about the techniques of biosensor development.