The content in the dissertation is divided into two main categories: (1) micro-particle characterization techniques based on elastic light scattering, and (2) ultra-compact on-chip plasmonic light concentration and its applications. For category (1), I developed two techniques, one is in vitro and the other is in the scenario of flow cytometry. I investigated theoretically and experimentally the spectra of scattered light from spherical dielectric particles at certain fixed angles, and demonstrate the linearity between the peak positions in the Fourier domain and the diameter of the particle. Based on this discovery, I demonstrate an efficient and accurate technique for in-vitro micro-particle sizing. Moreover, I theoretically analyzed the far-field elastic scattering signals from micro-particles passing through a flow cytometer with tightly focused incident beams, and established an algorithm to extract size information from the detected signals with higher accuracy than that in conventional flow cytometry systems. For category (2), I proposed an on-chip plasmonic nanofocusing technique whose unit device is a plasmonic triangle-shaped nanotaper mounted upon a dielectric optical waveguide. This structure provides highly efficient and robust light concentration into the tip of the nanotaper. Near-field measurements were performed to thoroughly investigate a fabricated sample and prove the concept. I also proposed theoretically a novel concept named phase-induced local-field configuration with logic behaviors, whose actuators are composite devices built on units of single on-chip plasmonic light concentrators mentioned above.

Dans un contexte mondial de prolifération de pathogènes résistants aux antibiotiques, il y a un réel besoin de nouvelles techniques de diagnostic microbiologique rapides et fiables. Ce travail de thèse vise à apporter une meilleure compréhension de la technique d’identification microbienne par diffusion élastique (ELS pour Elastic Light Scattering). Cette méthode phénotypique utilise la diffraction d’un faisceau de lumière cohérente sur une colonie microbienne directement sur son milieu de culture. L’image de diffraction alors obtenue est considérée comme la signature phénotypique du microorganisme étudié. Cette image est ensuite transformée au moyen de descripteurs mathématiques afin de la comparer à une base de données pré-calculée au moyen d’algorithmes d’apprentissage automatiques. Dans un premier temps, l’architecture optique de l’instrument a été modifiée afin de le rendre compatible avec les milieux de culture opaque très répandus en diagnostic clinique. Deux approches ont ensuite été proposées afin de modéliser l’interaction lumière/colonie microbienne. Une première approche d’optique géométrique par lancer de rayons nous a permis d’apprécier les besoins en termes d’ouverture numérique pour l’acquisition des images de diffraction selon le profil morphologique des colonies. La seconde approche basée sur la théorie scalaire de la diffraction a permis de mettre en évidence l’importance de la répartition de la biomasse à l’intérieur de colonies. En effet, les macrostructures résultantes de l’empilement des cellules microbiennes jouent un rôle majeur dans la formation des images de diffraction. Dans un second temps, une procédure systématique d’amélioration des performances de classification a été proposée. Elle combine une description plus fidèle des images de diffraction via la projection sur une base de Fourier-Bessel, une optimisation par recherche de grille sur les paramètres de l’algorithme d’apprentissage automatique supervisé et enfin l’application d’une méthode de réduction de dimensionnalité. Grâce à cela nous pouvons par exemple proposer un test Gram+/Gram-/Levures avec un taux de discrimination de plus de 98% sur une base de 15 espèces. Enfin, l’utilisation de l’illumination cohérente a également été étendue à la lecture d’antibiogrammes par analyse dynamique de speckle. / The current health situation across the world is of great concern. There is an urgent need for novel and innovative diagnostic methods that would speed up accurate treatments decisions and be of significant utility for public health in the fight against antibiotic resistance.This Ph. D. work aims to better understand the Elastic Light Scattering (ELS) method for microbial identification. This phenotypic technique is based on the elastic scattering of a coherent light beam by a microorganism colony growing on its culture plate. The resulting scattering pattern can be considered as the phenotypic signature of the microorganism. Then this image is translated using mathematical descriptors so that it can be compared to a database previously obtained using learning algorithms.Part of this work was dedicated to the improvement of the optical design so that the instrument can handle opaque culture media widely used in clinical diagnosis. Then two approaches were proposed to model the interaction between light and bacterial colonies. A first geometrical approach could help us, using ray tracing algorithms, to estimate the numerical aperture needed for the acquisition depending on the colonies morphologies. The second approach, based on scalar diffraction theory, highlighted the importance of the biomass distribution inside the colonies. Macro-structures resulting from cells arrangement play a great role in the scattering patterns formation indeed. In addition, the features extraction step from images using a Bessel-Fourier basis significantly improved the description accuracy. A systematic approach comprising the optimization of the learning algorithm and a dimensionality reduction technique was proposed. Great improvements of classification rates were achieved. Among them: a Gram+/Gram-/Yeasts discrimination at 98.1% was obtained over 15 species. Finally the use of coherent lighting for the reading of antibiotics susceptibility test by means of dynamic speckle analysis was introduced and showed promising results.

The health and viability of cells and tissues in the human body depend on the functional integrity of proteins. A small number of long-lived proteins, including the crystallins in the lens of the eye, evade protein turnover, a typical cellular mechanism for repair and regeneration, and remain extant throughout life. The cumulative effect of post-translational modifications on the structure, function, and conformation of these long-lived proteins records the history of molecular aging in an individual. Along with absence of protein turnover, the optical accessibility, transparency, and age-related spatial order make the lens an ideal target for in vivo assessment of molecular aging. Accordingly, this doctoral thesis investigated the hypothesis that age-related perturbations that alter the protein environment in the human lens can be detected and monitored as a quantitative biomarker of molecular aging detectable by quasi-elastic light scattering (QLS). To test this hypothesis, QLS was applied in vitro and in vivo to study time-dependent changes in lens proteins. Water-soluble human lens protein extract was used in vitro as a model system that mimics the lens fiber cell cytoplasm. The effects of long-term incubation (nearly one year, proxy for aging), oxidative stress, ionizing radiation, metal-protein and pathogenic protein-protein interactions were investigated by QLS as a function of time. In vitro results were validated by protein gel electrophoresis and transmission electron microscopy. In vivo, age-dependent changes in lens proteins were assessed in healthy subjects across a broad age-range (5–61 years of age). Pathogenic protein aggregation in the lens was examined in vivo using Down syndrome (DS) subjects, a common chromosomal disease associated with an age-related Alzheimer’s disease (AD)-linked lens phenotype. Results obtained from the in vitro studies noted, for the first time, QLS detection of long-term supramolecular changes in a complex lens protein model system. Our FDA-approved QLS device was successful in assessing age-dependent lens protein changes in a clinical study at Boston Children’s Hospital (BCH). In two landmark studies conducted at BCH, we detected statistically significant AD-related lens protein changes in DS subjects aged 10–20 years, when compared with age-matched controls. These studies are the first clinical application of QLS in DS, and demonstrate protein changes in DS earlier than any previously reported studies. Due to the discrepancy in chronological and biological age and the lack of an objective index for the latter, we propose the application of QLS in the human lens as a quantitative biomarker of molecular aging.

<p>  </p> <p>An optical technique that discriminates microbial organisms using an elastic light scatter (ELS) pattern, known as BActeria Rapid Detection using Optical Technology (BARDOT), has shown excellence in pathogen screening which effectively saves time and cost during the identification. Owing to the successful implementation of the light-scattering technique in microbiology, a series of studies on the light scatter pattern have been conducted to improve the technology. As an extended study of the multispectral application in BARDOT, a hyperspectral elastic light-scatter phenotyping instrument (HESPI) was developed to increase the ability to discriminate and detect foodborne pathogens. The newly designed instrument integrated a supercontinuum (SC) laser into the traditional BARDOT system to provide a broad spectrum of the light source. An acousto-optic tunable filter (AOTF) was utilized to select the wavelength of interest, allowing multiple spectral patterns in a single measurement. Owing to the filtering mechanism of AOTF, the wavelength of the laser was shifted rapidly so the overall acquisition time of 80 hyperspectral patterns was less than30 seconds. A pair of optical lenses were used to compensate for the beam spot movement caused by the wavelength-dependent separation angle at the exit of AOTF. To capture the transmitted scattering patterns, a complementary metal-oxide-semiconductor (CMOS) sensor was placed under the bacteria sample plate.</p> <p>For a comprehensive understanding of the ELS patterns, at first, the diverse nature of bacterial colony morphology was explored. Using the optical scatter model based on the scalar diffraction theory, the forward light-scatter patterns were simulated with respect to various colony shapes. The numerical predictions were then compared to the scattering patterns that were experimentally obtained from the colonies with various elevation profiles. The experimental verification proved a strong correlation between the colony morphology and the ELS pattern, as an excellent agreement between the simulation and the experiment observed. Second, the wavelength-dependent characteristics of the ELS patterns were investigated. Based on the theoretical and experimental interrogation, the wavelength of the incident laser beam affected the shape of ELS patterns by the overall size, the number of diffraction rings, and the gap distance between the rings. </p> <p>The performance of HESPI was validated by differentiating green leafy microflora using the hyperspectral ELS patterns. A group of bacteria that were poorly classified with the traditional single-wavelength method was selected to prove the improvement of the classification by the hyperspectral application. HESPI was utilized to measure the hyperspectral ELS patterns of their colonies, and for the classification, the descriptive features were extracted from the patterns at 70 selected wavelengths within the 473 – 709 nm region. A classification model was constructed for every wavelength, and the classification accuracy of the individual model ranged from 88.7% to 93.2%. The classification result also showed that colonies of varied species produced distinctive scatter features at a particular spectral band. When employing the entire wavelengths for the classification, the more number of wavelengths consequently led to an increase in the number of scatter-pattern features. This could cause the classifier's overfitting and negatively affect the classification. Therefore, the presented work incorporated various feature reduction and selection procedures to enhance the robustness and ultimately lessen the complexity of data collection. A classification model with feature reduction improved the overall classification rate to 95.9% after selecting meaningful predictors.</p>

Le développement de techniques de suivi in situ de réactions de polymérisation en émulsion est un véritable enjeu, motivé par le désir d’établir des relations entre structure, propriétés physico-chimiques et propriétés d’usage du latex final. Par ailleurs, ces techniques fournissent des informations sur les phénomènes chimiques et physico-chimiques mis en jeu qui contribuent à une meilleure compréhension. Des études récentes montrent que la spectroscopie Raman peut être une technique adaptée à cette problématique, de par sa simplicité de mise en œuvre (transportabilité, adaptabilité de l’appareillage, etc.), la performance de la mesure (temps d’acquisition de l’ordre de la seconde) et la richesse des informations fournies (de l’échelle moléculaire à celle du matériau). L’objectif de notre travail a été de déterminer le potentiel de la spectroscopie Raman quant au contrôle de la polymérisation en macroémulsion du styrène tant au niveau du bon déroulement de la réaction (conversion…) qu’au niveau des propriétés du latex formé (stabilité…). Pour réaliser ce travail expérimental, un pilote de polymérisation a été installé pour la première fois au sein du laboratoire des Matériaux Optiques, Photonique et Systèmes (LMOPS). La particularité de notre système est qu’il a été conçu pour conserver le maximum de liberté pour la réalisation de l’étude spectroscopique (montages optiques). La première partie de notre projet a donc été de déterminer un protocole adapté à ce pilote, tant au niveau de la réalisation de la synthèse de latex de polystyrène stabilisé qu’au niveau de l’acquisition de données spectroscopiques. Par la suite, nous avons démontré que la spectroscopie Raman était une technique adaptée au suivi in situ de la cinétique de polymérisation du styrène en macroémulsion. Le suivi du taux de conversion du styrène en polystyrène a été réalisé selon deux méthodes qui reposent sur des principes différents : la première basée sur la variation de l’aire de bandes spécifiques est une approche classique de la quantification de cette grandeur alors que la deuxième, basée sur la modification de la position d’une bande commune au monomère et à son polymère est une méthode innovante. A partir de ces données expérimentales et grâce à une méthode de filtrage adaptée, la quantification de la vitesse de polymérisation a été proposée pour la première fois. Ces données expérimentales ont été comparées à la théorie mécanistique et cinétique de référence de ce procédé, ainsi qu’à de précédents résultats expérimentaux, obtenus par d’autres techniques. Alors que les résultats expérimentaux s’accordent, ils montrent tous une déviation par rapport à la théorie. Enfin, par l’étude approfondie de la variation de l’aire d’une bande de référence, commune au monomère et au polymère, nous avons démontré que la spectroscopie Raman était sensible au phénomène de diffusion élastique, diffusion du faisceau laser par les éléments dispersés dans le milieu réactionnel. Cela se traduit par une modification de l’intensité du signal collecté et permet donc de détecter une transition caractéristique du procédé de polymérisation étudié : la disparition des gouttelettes réservoir de monomère, qui apparaît vers 40% de conversion dans le cas du styrène / The development of in situ monitoring techniques of emulsion polymerization reactions is a real current challenge. First, it may help establish relations between the structure, the physicochemical properties and the performance properties of final latexes. Moreover, it brings a better understanding of chemical and physicochemical phenomenon that happened. Easy installation, performance of measures and abundance of information gathered (from molecular to material scales) make the Raman spectroscopy an adequate technique for this kind of issue, as shown in recent studies. The main goal of that work was to demonstrate the capacity of the Raman spectroscopy to control the polymerization of styrene via macroemulsion process, in terms of smooth reaction process (conversion, …) and final properties of the latex (stability, …). This work was carried in the laboratoire des Matériaux Optiques, Photonique et Systèmes (LMOPS) where a polymerization pilot was implemented for the first time. The latest has been designed in order to ensure a maximum freedom for spectroscopic measurements (optical setup). Because of this special design, the first part of this work was to adapt experimental conditions, in terms of polymer latex synthesis and spectroscopic data acquisition. Thereafter, we proved that Raman spectroscopy could be a suitable technique for real time in situ conversion monitoring in the case of the polymerization of styrene via macroemulsion process. The monomer conversion monitoring has been realized in two different methods: the first one is well-known and is based on monitoring changes in the normalized Raman signal of specific band and the second one is an innovative method that is based on the Ramanshift of a common band of styrene and polystyrene. On the basis of these experimental data and using a suitable smoothing method, the polymerization rate was quantified for the first time. The results were compared to the theory of this polymerization process and previous experimental results from other experimental techniques. Whereas experimental results show similarities, they all show a deviation from the theory. Finally, an in-depth study of the impact of the heterogeneity of the reaction media on the Raman signal has been made. We have demonstrated that this latest was sensitive to elastic scattering of light by dispersed particles. The influence of elastic scattering on the intensity of the collected Raman signal makes the Raman spectroscopy a suitable method to detect a specific transition of the polymerization process: the disappearance of monomer droplets around 40 % of conversion in case of styrene