In this thesis, miniaturized wavelength interrogators based on planar lightwave circuits (PLCs) are investigated and developed for the optical fiber sensing applications in the aircraft structural health monitoring (SHM) and optofluidic analysis. Two interrogation systems based on an arrayed waveguide grating (AWG) and an Echelle diffractive grating (EDG) are developed and used to convert the optical sensing signals into strain, temperature, vibration, damage, and humidity information for the aircraft SHM. A fiber Bragg grating (FBG) sensing system using developed interrogators is then demonstrated in a field test for aircraft SHM applications. For optofluidic analysis, a PLCs based optofluidic device consisting of two on-chip lens sets is built to enhance the optical manipulation capability of particles. Then, a solution to a multi-functional Lab-on-a-Chip platform for optofluidic analysis is proposed, which integrates the developed particle maneuvering device, grating-structured sensors, and miniaturized interrogators.

Optofluidic flow-through biosensor devices have been in development for fast bio-target detection. Utilizing the fabrication processes developed by the microelectronics industry, these biosensors can be fabricated into lab-on-a-chip devices with a degree of platform portability. This biosensor technology can be used to detect a variety of targets, and is particularly useful for the detection single molecules and nucleic acid strands. Microfabrication also offers the possibility of production at scale, and this will offer a fast detection method for a range of applications with promising economic viability. The development of this technology has advanced to now warrant a descriptive model that will aid in the design of future iterations. The biosensor consists of multiple integrated waveguides and a microfluidic channel. This platform therefore incorporates multiple fields of study: fluorescence, optical waveguiding, microfluidics, and signal counting. This dissertation presents a model theory that integrates all these factors and predicts a biosensor design's sensitivity. The model is validated by comparing simulated tests with physical tests done with fabricated devices. Additionally, the model is used to investigate and comment on designs that have not yet been allocated time and resources to fabricate. Tangentially, an improvement to the fabrication process is investigated and implemented.

“Lab on a Chip” technologies have revolutionized the field of bio-chemical analytics. The crucial role of optical techniques in this revolution resulted in the emergence of a field by itself, which is popularly termed as “optofluidics”. The miniaturization and integration of the optical parts in the majority of optofluidic devices however still remains a technical challenge. The works described in this thesis focuses on developing integration methods to combine various optical techniques with microfluidics in an alignment-free geometry, which could lead to the development of portable analytical devices, suitable for field applications. The integration approach was applied to implement an alignment-free optofluidic chip for optical chromatography; a passive optical fractionation technique fractionation for cells or colloids. This system was realized by embedding large mode area photonic crystal fiber into a microfluidic chip to achieve on-chip laser beam delivery. Another study on passive sorting envisages an optofluidic device for passive sorting of cells using an optical potential energy landscape, generated using an acousto-optic deflector based optical trapping system. On the analytical side, an optofluidic chip with fiber based microfluidic Raman spectroscopy was realized for bio-chemical analysis. A completely alignment-free optofluidic device was realized for rapid bio-chemical analysis in the first generation by embedding a novel split Raman probe into a microfluidic chip. The second generation development of this approach enabled further miniaturization into true microfluidic dimensions through a technique, termed Waveguide Confined Raman Spectroscopy (WCRS). The abilities of WCRS for online process monitoring in a microreactor and for probing microdroplets were explored. Further enhanced detection sensitivity of WCRS with the implementation of wavelength modulation based fluorescent suppression technique was demonstrated. WCRS based microfluidic devices can be an optofluidic analogue to fiber Raman probes when it comes to bio-chemical analysis. This allows faster chemical analysis with reduced required sample volume, without any special sample preparation stage which was demonstrated by analyzing and classifying various brands of Scotch whiskies using this device. The results from this study also show that, along with Raman spectroscopic information, WCRS picks up the fluorescence information as well, which might enhance the classification efficiency. A novel microfabrication method for fabricating polymer microlensed fibers is also discussed. The microlensed fiber, fabricated with this technique, was combined with a microfluidic gene delivery system to achieve an integrated system for optical transfection with localized gene delivery.

In recent years, the study of stimulated emission from and by biological systems has gained wide spread attention as a promising technology platform for novel biointegrated laser. However, the photonic properties and the associated physics of many biological laser systems are not yet fully understood and many promising resonator architectures and laser classes have not yet transitioned into the biological world. In this thesis, we investigate the fundamental photonic properties of lasers based on single biological cells and explore the potential of distributed feedback (DFB) gratings as novel biointegrated laser resonators. We show how the easy and flexible fabrication of DFB resonators helps to realize optofluidic and solid-state biological lasers. Lasing characteristics, such as tunable and single mode emission, are investigated and different applications are explored. Fourier-space emission studies on different biological lasers give insight in to the photonic dispersion relation of the system and the fundamental creation of lasing modes and their confinement in living systems. The first purely water based optofluidic DFB laser is demonstrated and novel sensing applications are suggested. This device shows low threshold lasing due to an optimized mode shape, which is achieved by a low refractive index substrate and the use of a mixed-order grating. Next, by integrating a high refractive index interlayer on a DFB resonator, a laser device incorporating the novel solid-state biological gain material green fluorescent protein (GFP) is realized. Lastly, we show how the thickness of organic polymer lasers can be reduced to its fundamental limit (< 500 nm) and the resulting membrane like laser devices can be applied to and operated on various body parts to potentially complement biometric identification.

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.

Exploiter le degré de liberté angulaire de la lumière pour contrôler les forces optiques ouvre une nouvelle voie pour la manipulation optique de systèmes matériels. Dans ce contexte, notre travail porte sur l’interaction lumière-matière en présence de chiralité, qu’elle soit matérielle ou ondulatoire. Expérimentalement, nous avons utilisé des gouttes de cristaux liquides cholestériques interagissant avec un ou plusieurs champs lumineux polarisés circulairement et nous avons apporté une description quantitative de nos observations. Notre principal résultat correspond à la démonstration que la pression de radiation optique peut être contrôlée par l’hélicité du photon. Ce phénomène est ensuite utilisé, d’une part pour faire une démonstration de principe du tri de la chiralité matérielle via une approche optofluidique et d’autre part pour réaliser un piège optique tridimensionnel sensible à la chiralité de l’objet piégé. / Exploiting the angular momentum degree of freedom of light to control the mechanical effects that result from light-matter exchanges of linear momentum is an intriguing challenge that may open new routes towards enhanced optical manipulation of material systems. In this context, our work addresses the interplay between the chirality of matter and the chirality of optical fields. Experimentally, this is done by using cholesteric liquid crystal droplets interacting with circularly polarized light and we provide with theoretical developments to quantitatively support our observations. Our main result is the demonstration of optical radiation force controlled by the photon helicity. This phenomenon is then used to demonstrate the optofluidic sorting of material chirality and the helicity-dependent three-dimensional optical trapping of chiral liquid crystal microspheres.

Significant technological advances of the last years have been possible by developments in Optofluidics, which is a field that deals with the integration of optics and microfluidics into single devices. The work described in this thesis is based on five scientific publications related to the use of fiber optic technology to build integrated optofluidic devices. The first three publications are within the field of life-science and point towards in-vivo and point-of-care applications, whereas the last two publications cover the study and the use of plasmonic nanoparticles for electrical modulation of light. Aiming at developing useful tools for in-vivo biological applications, the first publication consists of designing and testing a functional optical fiber for real-time monitoring and selective collection of fluorescent microparticles. This probe relies on a microstructured optical fiber with a hole along its cladding, which is used to selectively aspirate individual particles of interest once their fluorescence signal is detected. On the same line of research, the second publication contemplates the fabrication of a fiber probe that traps single microparticles and allows for remote detection of their optical properties. This probe is also based on a microstructured fiber that enables particle trapping by fluidic forces. The third publication addresses the development of an all-fiber miniaturized flow cytometer for point-of-care applications. This system can analyze, with excellent accuracy and sensitivity, up to 2500 cells per second by measuring their fluorescence and scattering signal. A novel microfluidic technique, called Elasto-inertial microfluidics, is employed for aligning the cells into a single-stream to optimize detection and throughput. The fourth publication involves the experimental and theoretical study of the electrical-induced alignment of plasmonic gold nanorods in suspension and its applicability to control light transmission. This study is done by using an all-fiber optofluidic device, based on a liquid-core fiber, which facilitates the interaction of light, electric fields, and liquid suspensions. Results show that nanorods can be aligned in microseconds, providing a much better performance than liquid-crystal devices. Finally, the fifth publication consists of an upgrade of the previous device by integrating four electrodes in the cladding of the liquid-core fiber. This improvement enables nanosecond response time and the possibility of digitally switching nanorods between two orthogonal aligned states, overcoming the limitation of slow thermal relaxation. The work presented here shows that optofluidics based on optical fibers is a robust and convenient platform, as well as a promising direction for the developing of novel instruments in fields such as life-science, non-linear optics, plasmonic, and sensing. / <p>QC 20171018</p>

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.

L’effet thermocapillaire (ou Marangoni) est la résultante mécanique d’un gradient de tensioninterfaciale induit par la présence d’un gradient de température sur une interface fluide. Il semanifeste par (i) la migration d’un objet fini (goutte, bulle) immergé, et (ii) une déflexion del’interface. Sa nature interfaciale le rend particulièrement pertinent à petite échelle, notammenten microfluidique diphasique. Ce travail de thèse montre comment un effet thermocapillaireinduit localement par chauffage laser peut être utilisé pour produire des composants optofluidiquesélémentaires (vanne, aiguillage, échantillonneur), et en présente une étude quantitative.La déstabilisation d’un jet microfluidique forcée par laser, conduisant à sa rupture, est égalementprésentée et caractérisée. Cette « boîte à outils » optique fournit ainsi une approche sans contact,pour produire et manipuler des gouttes en microfluidique digitale sans nécessité d’une microfabricationdédiée. Par ailleurs, afin de caractériser sur des temps longs les gouttes produites,et ainsi considérer des populations statistiquement significatives, un dispositif optoélectroniquesimple pour mesurer les gouttes et leur vitesse en temps réel a également été développé. / The thermocapillary (or Marangoni) effect is the mechanical result of an interfacial tension gradientinduced by a temperature gradient on a fluid interface. This effect manifests itself byinducing (i) the migration of an immersed finite-size object (droplet, bubble), and (ii) a deflexionof the interface. Due to its interfacial nature, the Marangoni effect is particularly relevantat small length scales, especially in the context of two-phase microfluidics. This thesis aims atapplying the thermocapillary effect locally induced by laser heating, in order to create some basicoptofluidic actuators (valve, switch, sampler). A quantitative study of these actuators is presented.The laser-forced destabilization of a co-flowing microfluidic jet, leading to its breakup,is also investigated. This “optical toolbox” represents a non-contacting, and microfabricationfreeapproach for the production and handling of droplets in digital microfluidics. Moreover, tocharacterize these droplet over long times, thus considering statistically significant populations,a simple optoelectronic device has been developed for measuring the size and velocity of thedroplets in real time.

Optofluidics is a new branch within photonics which attempts to unify concepts from optics and microfluidics. Unification of photonics and microfluidics enable us to carry out analysis of fluids through highly sensitive optical sensing device. These optical sensing devices are contained within a microchip, wherein light is made to pass through analyte (fluids of few nanoliters). The interaction between light and fluid gives rise to highly sensitive diagnostic systems. In this work the fabrication and performance characterization of a fluorescent green OLED for optofluidic applications is presented. The effect of thickness variation of hole injection (CuPc) and hole blocking (BCP) layers on the performance of fluorescent green organic light emitting diodes (OLEDs) have been studied. Even though these two organic layers have opposite functions, yet there is a particular combination of their thicknesses when they function in conjunction and luminous efficiency and power efficiency are maximized. The optimum thickness of CuPc layer, used as hole injection layer and BCP used as hole blocking layer were found to be 18 nm and 10 nm respectively. It is with this delicate adjustment of thicknesses, charge balancing was achieved and luminous efficiency and power efficiency were optimized. Such OLEDs with higher luminance can be monolithically integrated with other optical and fluidic components on a common substrate and can function as monolithically integrated internal source of light in optofluidic sensors. In this work the analysis of a fully integrated optofluidic lab-on-a-chip sensor for refractive index and absorbance based sensing using fluorescent green organic light emitting diode (OLED) as a light source is also presented. This device consists of collinear input and output waveguides which are separated by a microfluidic channel. When light is passed through the analyte contained in the fluidic gap an optical power loss due to absorption of light takes place. Apart from absorption a mode-mismatch between collinear input and output waveguide also occurs. The degree of mode-mismatch, quantum of optical power loss due to absorption of light by the fluid forms the basis of our analysis. Detection of minutest change in refractive index and changes in concentration of species contained in the analyte is indicative of sensitivity. Various parameters which influence the sensitivity of the sensor are mode spot size, refractive index of the fluid, molar concentration of the species contained in the analyte, width of the fluidic gap, waveguide geometry. By correlating various parameters, an optimal fluidic gap distance corresponding to a particular mode spot size to achieve the best sensitivity for refractive index based sensing and absorbance based sensing have been determined.