Depuis que l’optofluidique a été introduite au début des années 2000, beaucoup de dispositifs combinant à la fois l’optique et la microfluidique ont été développés. Ces travaux ont proposé de nombreuses voies originales pour l’analyse biologique et le diagnostique médical. Parmi ceux-ci, citons par exemple, les guides d’ondes liquide-liquide (également appelés guides d’ondes L2), les lentilles liquides adaptatives, les lasers multicolores à microgouttes, ou encore les microscopes optofluidiques sans lentilles.Ces systèmes offrent de nombreux avantages liés à la microfluidique comme leurs flexibilités et leurs accordabilités. Néanmoins, la plupart de ces systèmes reposent sur l’utilisation d’une source de pompage optique externe devant être couplée aux puces microfluidiques avec le plus grand soin.Le but de ces travaux de thèse est d’augmenter l’autonomie et la portabilité des systèmes optofluidiques en intégrant directement la source lumineuse sur les puces. Nous proposons donc ici d’exploiter la voie électrochimiluminescente comme méthode de pompage électrique. L’annihilation du luminophore 9,10-Diphenylanthracene permet ainsi d’obtenir une faible longueur d’onde d’émission dans le domaine du visible.Ainsi nous montrons dans ces travaux la mise en œuvre d’une nouvelle technologie de fabrication pour réaliser un circuit optofluidique d’une source lumineuse intégrée. La fabrication de cette puce a permis d’obtenir des résultats d’électrochimiluminescence sur puce montrant ainsi la compatibilité de cette approche. Les expériences effectuées pendant ces travaux ouvrent ainsi la voie au pompage électrique sur dispositifs optofluidiques. / Since optofluidics was introduced in the early 2000s, a lot of devices combining microfluidic and optic have been developed such as L2 waveguides, adaptive liquid lenses, microdroplet multicolour dye laser, or lensless optofluidics microscopes.These systems offer many advantages allowed by microfluidic like flexibility and accordability. However most of them generally need an external optical source carefully coupled to the microfluidic device.The purpose of this PhD thesis is to improve autonomy and portability of microfluidics systems integrating light source on the chip. Hence, we suggest here to use the electrochemiluminescence way to reach electrical pumping. 9,10-Diphenylanthracene annihilation allowed us to obtain a low wavelength in the visible domain.Therefore, we show here the implementation of a new fabrication technology to make an integrated on chip optical source. The chip fabrication allowed us to obtain on chip electrochemiluminescence results showing the compatibility of this approach. The experiments realised during these works open the way to electrical pumping way on optofluidic chips.

L'indice de réfraction est l'un des paramètres physiques les plus importants qui régissent les comportements à la lumière de cellules et d'autres micro-organismes. Son importance réside dans le fait qu'il peut être utilisé pour déterminer ou mettre en corrélation avec d'autres paramètres biophysiques importants de la cellule tels que la masse sèche, la masse humide, l'élasticité et est utilisé pour étudier les activités dynamiques cellulaires. L'objectif principal de cette recherche est d'étudier et de mesurer les indices de réfraction de bactérie et de cellules unitaires ainsi que leur réponse à des stimulations micro-environnementales.Notre étude expérimentale comprend deux approches. La première consiste en une plate-forme microfluidique intégrée de réfractomètrie par immersion pour mesurer les paramètres biophysiques (taille, forme et indice de réfraction) de trois espèces de bactéries, à savoir Escherichia coli, Shigella flexneri et Vibrio cholerae. Ces paramètres peuvent fournir des signatures biophysiques des bactéries ciblées. L'importance de ce travail de recherche réside dans l'établissement d'un système rapide, sans label fluorescent et à bas coût pour la détection d'une quantité infime de bactéries nocives dans l'eau potable.L'autre approche consiste à obtenir la distribution de l'indice de réfraction au sein d'une seule cellule avec l'accent mis sur l'étude des gouttelettes lipidiques intracellulaires ainsi que leur réponse à une stimulation micro-environnementale. A cet effet, nous avons recouru à un système de diffraction tomographique optique intégré avec imagerie par fluorescence. Ce type d'étude sur l'indice de réfraction de gouttelettes lipidiques cellulaires initie une nouvelle approche pour une meilleure compréhension des gouttelettes lipidiques et leurs rôles essentiels dans le métabolisme cellulaire / Refractive index is one of the most important physical parameters in governing the light-reaction behaviors of cells and other microorganisms. Its significance lies in the fact that it can be used to determine or correlate with other important biophysical parameters such as dry mass, wet mass, elasticity and used to study dynamic cell activities. The main objective of this research is to study and measure refractive indices of single bacterium and cell as well as cell’s response to microenvironment stimulations.The experimental study includes two approaches. One approach is the development of an integrated microfluidic immersion refractometer platform to measure the biophysical parameters (the size, shape and refractive index) of three bacteria species, namely Echerichia coli, Shigella flexneri and Vibrio cholera. These parameters could provide biophysical signatures of the targeted bacteria. The significance of this research work lies in establishing a rapid, label-free and low-cost system for detection of minute amount of harmful waterborne bacteria in drinking water.The other experimental approach is to obtain the refractive index distribution of a single cell with the focus on studying the intracellular lipid droplets and their response towards microenvironmental stimulation using an optical diffraction tomographic system integrated with fluorescence imaging. The investigation of the refractive index of cellular lipid droplets initiates a novel approach for deeper understanding of the lipid droplets and their critical roles in metabolism

In this dissertation fluorescence-based sensors for dissolved gases were developed for remote health monitoring applications including urine analysis. Detection of dissolved gases demonstrate diagnostic potential in body fluids, and indicate the metabolism of microorganisms driven by contaminated water. The emphasis of this research was on optimizing the sensitivity of fluorescence-based fluid sensing systems by configuring key design parameters towards cost reduction. A review of urine analysis indicated several methods for imaging, particle analysis, and detection of dissolved analytes. The review encourages readers to consider integrating sensing systems to provide additional context to results. An optical Dissolved Oxygen (DO) sensor was reproduced using phosphorescent organometallic dyes. The sensitivity of the DO sensor was experimentally optimized by employing Total Internal Reflection (TIR) of excitation light within the multilayered device by controlling the incident angle and sensitive film thickness. Novel 3D ray tracing-based computer models were developed based on the experimental results to explain the sensitivity enhancement mechanism of TIR. The path of light within the device and fluorescence generation sites were visualized and relative sensitivity was predicted. The model was validated by comparison with experimental results and expanded to predict the relative sensitivity of devices using different coupling strategies. This new optical model enables researchers to select an optimal coupling and detection scheme given their unique sensor design and application. A fluorescence based optofluidic sensor for Ammonia was redesigned based on experiment and simulation results. An optofluidic chip reader was produced to measure fluorescence sensors using low cost consumer electronics. The sensitivity of the ammonia sensor module has not been demonstrated; however, identified design challenges will be overcome in future efforts. As a result of this research, the cost of optofluidic sensing systems may be reduced towards enabling widely deployed remote monitoring networks for health and water quality. / Thesis / Doctor of Philosophy (PhD) / Dissolved gases have been detected in fluid samples as indicators of health and microbial activity by measuring changes in the intensity of fluorescence emitted from gas sensitive fluorescent dyes. These sensors can often be miniaturized and integrated to measure several parameters from a single platform. Several sensing platforms may be integrated into a continuous monitoring network. However, the cost of complete remote sensing networks prohibits the widespread deployment of these devices. The aim of this research was to improve the sensitivity of fluorescence-based sensors, reducing dependence on expensive detectors and light sources. The sensitivity of a fluorescence based dissolved oxygen sensor was optimized using Total Internal Reflection. A computer model was developed to identify important design parameters and their contributions to sensor performance. The model was validated by comparison with experimental measurements. Finally, an optical ammonia sensor is under development based on the dissolved oxygen experiments and model results.

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.

This research demonstrates technology for detection of pathogens and environmental monitoring using a handheld optofluidic immunosensor and CFD simulation. The current methods such as ELISA and PCR require few hours for identification which means it is unavailable for early-monitoring. The use of a near-real-time, handheld biosensor device in a real animal/human environment is the key to monitoring the spread of dangerous pathogens. A 3-D computational fluid dynamics (CFD) simulation is needed to track the pathogens within an environment.This dissertation has four papers that demonstrate technologies for the detection and monitoring of pathogens and the miniaturization of these detection systems for in field applications with a handheld immunosensor and CFD simulation.In the first paper, an environmental prediction model was developed for optimal ventilation in a mushroom house by using sensible heat balance and 3-D CFD method. It is shown that the models can be used for farmers to predict the environmental conditions over different locations in a mushroom house.In the second paper, a field lab-on-a-chip system was constructed to detect mouse immunoglobulin G and Escherichia coli by using light scattering detection of particle immunoagglutination. Antibody-conjugated particles were able to be stored in a 4°C refrigerator for at least 4 weeks and to be lyophilized as a powder form for the storage in room temperature.In the third paper, rapid monitoring of the spreads of porcine reproductive and respiratory syndrome virus (PRRSV) was attempted using samples collected from nasal swabs of pigs and air samplers within an experimental swine building. An optofluidic device containing liquid-core waveguides was used to detect. It is shown that the developed optofluidic device and 3-D CFD model can serve as a good model for monitoring the spread of airborne viruses within animal and human environments.In the fourth paper, a handheld optofluidic immunosensor was developed for rapid detection of H1N1/2009 virus inside a 1:10 scale mock classroom. Both miniature spectrometer and cell phone camera were used as detector. A 3-D computational fluid dynamics (CFD) model was developed to track the transport/distribution of H1N1/2009 viruses, and corresponded very well with immunosensor readings.

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.

The three-dimensional (3-D) writing capability of a high repetition rate (1 MHz) fiber-amplified femtosecond laser with a wavelength of 522 nm was harnessed together with wet-chemical etching for laser-patterning of 3-D optofluidic microsystems in fused silica glass, by the method of Femtosecond Laser Irradiation followed by Chemical Etching (FLICE). Selective chemical etching of laser irradiated glass with dilute hydrofluoric acid (HF) enabled micro-fabrication of high aspect-ratio embedded micro-channels and fine-period 3-D glass meshes in a 3-D inverted woodpile (IWP) arrangement that permitted high density lab-on-a-chip (LOC) integration of flow channels, reservoirs, glass chromatography columns, and optical circuit devices. Optical waveguides, reservoirs, micro-channels, and IWP structures were first laser patterned and followed by selective wet etching controlled by the polarization orientation of the writing laser. With the laser polarization perpendicular to the scanning direction, the volume nanogratings were aligned perpendicular to glass surfaces to facilitate HF etching and thus created designer shaped micro-channels with the smoothest sidewall surfaces measured at present and terminated with open reservoirs. An array of vertical access holes spaced periodically apart facilitated etching of continuous and highly uniform buried channels of unrestricted length in the glass to interconnect flow channels and reservoirs. Alternatively, laser polarization parallel to the scan direction provided low-loss optical waveguides with nanograting walls resisting the acid etching, providing a convenient one-step laser scanning process of optofluidic microsystems prior to wet etching. For the first time, dual-channel capillary electrophoresis was demonstrated by simultaneous fluorescent detection of separating dyes in a 3-D microsystem having over- and under-passing crossed channels in fused silica. In addition, an on-chip particle counting device based on capillary force to drive analytes through an embedded micro-channel into a calibrated reservoir for particle counting was designed and demonstrated. Further, a new type of glass mesh structure is presented where a 3-D IWP micro-channel array with diamond-like symmetry was integrated inside a micro-channel for capillary electrophoretic chromatography. The FLICE technique thus enables rapid prototyping of fully integrated 3-D optofluidic systems in bulk fused silica glasses for numerous applications, and these provide the groundwork and open new 3-D design approaches for advanced microsystems in the future.

The three-dimensional (3-D) writing capability of a high repetition rate (1 MHz) fiber-amplified femtosecond laser with a wavelength of 522 nm was harnessed together with wet-chemical etching for laser-patterning of 3-D optofluidic microsystems in fused silica glass, by the method of Femtosecond Laser Irradiation followed by Chemical Etching (FLICE). Selective chemical etching of laser irradiated glass with dilute hydrofluoric acid (HF) enabled micro-fabrication of high aspect-ratio embedded micro-channels and fine-period 3-D glass meshes in a 3-D inverted woodpile (IWP) arrangement that permitted high density lab-on-a-chip (LOC) integration of flow channels, reservoirs, glass chromatography columns, and optical circuit devices. Optical waveguides, reservoirs, micro-channels, and IWP structures were first laser patterned and followed by selective wet etching controlled by the polarization orientation of the writing laser. With the laser polarization perpendicular to the scanning direction, the volume nanogratings were aligned perpendicular to glass surfaces to facilitate HF etching and thus created designer shaped micro-channels with the smoothest sidewall surfaces measured at present and terminated with open reservoirs. An array of vertical access holes spaced periodically apart facilitated etching of continuous and highly uniform buried channels of unrestricted length in the glass to interconnect flow channels and reservoirs. Alternatively, laser polarization parallel to the scan direction provided low-loss optical waveguides with nanograting walls resisting the acid etching, providing a convenient one-step laser scanning process of optofluidic microsystems prior to wet etching. For the first time, dual-channel capillary electrophoresis was demonstrated by simultaneous fluorescent detection of separating dyes in a 3-D microsystem having over- and under-passing crossed channels in fused silica. In addition, an on-chip particle counting device based on capillary force to drive analytes through an embedded micro-channel into a calibrated reservoir for particle counting was designed and demonstrated. Further, a new type of glass mesh structure is presented where a 3-D IWP micro-channel array with diamond-like symmetry was integrated inside a micro-channel for capillary electrophoretic chromatography. The FLICE technique thus enables rapid prototyping of fully integrated 3-D optofluidic systems in bulk fused silica glasses for numerous applications, and these provide the groundwork and open new 3-D design approaches for advanced microsystems in the future.

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.

Nanopore sensors are emerging as a promising technology for single molecule analysis and polymer sequencing. Traditionally, measurements are taken by monitoring the ionic current through the nanopore, which gives information (e.g. size, shape, charge) about a molecule of interest while it is in the confined geometry of the nanopore. The dynamics of the molecule before the arrival to the nanopore, such as the capture dynamics, or molecular conformation prior to translocation, as well as clogging mechanisms and features of anomalous translocation events, are not assessed by the electrical measurements alone. To study the whole process of nanopore diffusion, capture and passage it is necessary to complement the electrical signal with another detection mode. Particularly, optical visualization of the molecules as they translocate through the nanopore has great potential. In this Thesis I present the design, construction, optimization and testing of a nanopore--‐based optofluidic instrument, which uses fluorescence microscopy to visualize individual fluorescently stained DNA molecules as they translocate a solid--‐state nanopore, while in parallel record the ionic current signal through the pore. The following challenges were overcome to achieve the integration of the optical and electrical systems: (i) the electrical detection system must account for the physical constrains of a wide field fluorescence microscope, and the optical system should in turn not affect the low--‐noise electrical detection of individual DNA molecules. The design of the instrument included a microfluidic device, so to position the nanopore within the working distance (<170--‐μm) of the microscope objective (Chapter 2). (ii) Electrical noise was optimized to a level that is indistinguishable from a standard (with no optics) nanopore system (Chapter 3). The custom instrument was used to demonstrate: 1) Electrical detection of DNA translocations with a laser light illuminating the nanopore; 2) Optical tracking of DNA capture and translocation dynamics; 3) Synchronization of the optical and electrical signals in preparation for simultaneous detection. In the process of noise optimization, a strong noise coupling between the illumination source and the ionic current was found, characterized and eliminated. Consequently, the noise performance of the custom instrument is the lowest of any other nanopore--‐based optofluidic systems described in the literature to date. This opens up the way to many new and exciting investigations of polymer translocation dynamics through nanoconfined geometries. Lastly, during the development of this custom instrument, a method to localize the fabrication of a nanopore by controlled dielectric breakdown on a membrane, with a focused laser beam, was discovered.