Even though most of the properties of optical fields, such as wavelength, polarization, wavefront curvature or angular spectrum, have been commonly manipulated in a variety of remote sensing procedures, controlling the degree of coherence of light did not find wide applications until recently. Since the emergence of optical coherence tomography, a growing number of scattering techniques have relied on temporal coherence gating which provides efficient target selectivity in a way achieved only by bulky short pulse measurements. The spatial counterpart of temporal coherence, however, has barely been exploited in sensing applications. This dissertation examines, in different scattering regimes, a variety of inverse scattering problems based on variable spatial coherence gating. Within the framework of the radiative transfer theory, this dissertation demonstrates that the short range correlation properties of a medium under test can be recovered by varying the size of the coherence volume of an illuminating beam. Nonetheless, the radiative transfer formalism does not account for long range correlations and current methods for retrieving the correlation function of the complex susceptibility require cumbersome cross-spectral density measurements. Instead, a variable coherence tomographic procedure is proposed where spatial coherence gating is used to probe the structural properties of single scattering media over an extended volume and with a very simple detection system. Enhanced backscattering is a coherent phenomenon that survives strong multiple scattering. The variable coherence tomography approach is extended in this context to diffusive media and it is demonstrated that specific photon trajectories can be selected in order to achieve depth-resolved sensing. Probing the scattering properties of shallow and deeper layers is of considerable interest in biological applications such as diagnosis of skin related diseases. The spatial coherence properties of an illuminating field can be manipulated over dimensions much larger than the wavelength thus providing a large effective sensing area. This is a practical advantage over many near-field microscopic techniques, which offer a spatial resolution beyond the classical diffraction limit but, at the expense of scanning a probe over a large area of a sample which is time consuming, and, sometimes, practically impossible. Taking advantage of the large field of view accessible when using the spatial coherence gating, this dissertation introduces the principle of variable coherence scattering microscopy. In this approach, a subwavelength resolution is achieved from simple far-zone intensity measurements by shaping the degree of spatial coherence of an evanescent field. Furthermore, tomographic techniques based on spatial coherence gating are especially attractive because they rely on simple detection schemes which, in principle, do not require any optical elements such as lenses. To demonstrate this capability, a correlated lensless imaging method is proposed and implemented, where both amplitude and phase information of an object are obtained by varying the degree of spatial coherence of the incident beam. Finally, it should be noted that the idea of using the spatial coherence properties of fields in a tomographic procedure is applicable to any type of electromagnetic radiation. Operating on principles of statistical optics, these sensing procedures can become alternatives for various target detection schemes, cutting-edge microscopies or x-ray imaging methods.

Healthcare-associated infections present an escalating worldwide issue, further intensified by the emergence of antimicrobial resistance and the spread of pathogens on surfaces. Current infection prevention methods have shown limited effectiveness, leading to several health issues, an overuse of antibiotics, and a continuous threat of surface recontamination. In response, extensive research has focused on bioinspired omniphobic smart coatings that effectively reduce the contact area available for pathogen attachment, achieved through an increase in surface roughness and apparent surface energy. This thesis introduces a new class of an omniphobic spray-coating, featuring hierarchical structured polydimethylsiloxane (PDMS) microparticles coated with gold nanoparticles, encompassing primary microscale (~0.23 𝜇m) and secondary nanoscale (~5 nm) buckyball and labyrinth wrinkles. This substrate-independent coating efficiently repels a wide range of liquids, including pathogens, even under harsh conditions like high temperatures, ultraviolet (UV) exposure, and abrasions. Repellency tests comparing coated and uncoated gloves revealed that uncoated gloves spread contamination to 50 secondary surfaces, while coated gloves transferred fewer bacteria and viruses to just three and two surfaces, respectively. The investigation extended to the coating's biocidal capabilities, incorporating gold nanoparticles functionalized with mercapto-silane to create a "Repel and Kill" coating. This process initiates chemisorption through thiol-gold bonding, allowing for the formation of diverse surface structures, including three-dimensional self-assembly, multilayers, and island structures. These modifications significantly enhance the roughness and hydrophobicity of the gold nanoparticles, amplifying their biocidal effectiveness. The wrinkled structure of PDMS contribute to repellency, while the functionalized gold nanoparticles play a crucial role in the antimicrobial property. This enhancement was evident in the antibacterial tests, which exhibited an immediate 99.90% reduction in bacterial adhesion for both MRSA and Pseudomonas aeruginosa (P. aeruginosa), followed by an additional 99.70% and 99.90% reduction in bacterial growth after 8 hours for MRSA and P. aeruginosa, respectively. Moreover, the coating's antiviral properties were confirmed, demonstrating a 98% reduction in the transfer of the bacterial virus Phi6. Recognizing the role of hospital fabrics as potential reservoirs for infection transmission, primarily due to their ability to sustain bacterial growth for extended periods, especially in the presence of bodily fluids, we took further steps to modify the wrinkled PDMS microparticles. This involved the incorporation of silver nanoparticles, capped with a positively charged ligand known as branched polyethyleneimine (bPEI). Additionally, we integrated a colorimetric sensor, giving rise to the "Repel, Kill, and Detect" smart coating. The transition of color from blue to green-yellow provided a tangible indicator of contamination detection based on the acidic mileu of the biofilms. To evaluate its realworld effectiveness, we conducted simulations of infection transmission in hospital environments, resulting in a remarkable reduction in pathogen adhesion from urine and feces by 99.88% and 99.79%, respectively, compared to uncoated fabrics. To further enhance the validation of our results, we employed a powerful deep learning network architecture, that determined whether the surfaces are contaminated or safe. In the face of evolving health challenges, this coating emerges as a resilient and adaptable solution, promising to enhance overall safety and alleviate the burden of infectious diseases. / Thesis / Doctor of Engineering (DEng) / The prolonged survival of pathogens on surfaces, significantly highlighted by the COVID-19 global pandemic, has intensified the urgency of addressing contamination on high-touch surfaces. Engineered surface coatings with repellent properties have emerged as a long-lasting and health-conscious solution for infection prevention and control. In this thesis, we introduce a new class of multifunctional engineered coatings featuring hierarchical structures adorned with biocidal nanoparticles and an integrated colorimetric sensor. We comprehensively investigate these coatings' multifunctional capabilities to repel, exterminate, and detect contaminants. Through specific characterization tests involving a wide range of pathogens, including viruses, bacteria, and fungi, within complex biological fluids like urine and feces, this research culminates in the development of surface coatings equipped with both antimicrobial and pathogen-sensing capabilities. In addition to advancing our understanding of surface hierarchy and chemical modifications for repellency and biocidal activity, this thesis yields insights into the dynamics of biofouling and pathogen transfer, with the overarching goal of reducing pathogen transmission via surfaces.

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Noble metal nanoparticles supporting localized surface plasmon resonances (LSPR) have been extensively investigated for label free detection of various biological and chemical interactions. When compared to other optical sensing techniques, LSPR sensors offer label-free detection of biomolecular interactions in localized sensing volume solutions. However, these sensors also suffer from a major disadvantage – LSPR sensors remain highly susceptible to interference because they respond to both solution refractive index change and non-specific binding as well as specific binding of the target analyte. These interactions can severely compromise the measurement of the target analyte in a complex unknown media and hence limit the applicability and impact of the sensor. In spite of the extensive amount of work done in this field, there has been a clear absence of efforts to make LSPR sensors immune to interfering effects. The work presented in this document investigates, both experimentally and numerically, dual- and tri-mode LSPR sensors that utilize the multiple surface plasmon modes of gold nanostructures to distinguish target analyte from interfering bulk and non-specific binding effects. Finally, a series of biosensing experiments are performed to examine various regeneration assays for LSPR sensors built on indium tin oxide coated glass substrate.

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La mise au point de capteurs optiques moyen infrarouge (MIR) pour la surveillance des polluants organiques dans l'environnement aquatique est actuellement un défi de grande importance. Les capteurs MIR basés sur la spectroscopie à ondes évanescentes sont des outils d'analyse prometteurs pour la détection et la quantification simultanées d'une variété de polluants tels que les composés hydrocarbonés. Les verres de chalcogénure sont particulièrement bien adaptés aux applications de détection en raison de leur large domaine de transparence (jusqu'à 10-16 µm en fonction de leur composition). Ainsi, des films minces de chalcogénure pour le développement de plates-formes optiques intégrées ont été synthétisés. Leur fonctionnalisation par des polymères afin d'augmenter la sensibilité des capteurs a également été réalisée. Parmi les compositions de verre (GeSe2)100-x(Sb2Se3)x, deux cibles en verre séléniure ont été choisies pour leurs propriétés optiques et physiques. Grâce à la spectroscopie de réflexion totale atténuée, des mesures ont été effectuées dans l'eau pour détecter les hydrocarbures aromatiques (benzène, toluène et les trois isomères du xylène) dans des concentrations comprises entre 250 ppb et 40 ppm. Des mesures de détection ont également été effectuées à l'aide d'eau de mer et d'eau souterraine. Pour augmenter leur sensibilité, l'utilisation de nanoparticules métalliques est l'une des solutions prometteuses basées sur l'absorption infrarouge améliorée en surface (SEIRA). Ainsi, des structures hybrides combinant nanoparticules d'or déposées sur des verres de chalcogénure ont été fabriquées et caractérisées. / The development of middle-infrared (MIR) sensors for organic pollutants monitoring in the aquatic environment is currently a challenge of great importance. The mid-infrared sensor based on evanescent wave spectroscopy is a promising analytical tool for simultaneous detection and quantification of a variety of pollutants such as hydrocarbon compounds. Chalcogenide glasses are particularly well adapted for sensing applications due to their wide domain of transparence (up to 10-16 µm depending on their composition). The aims of this study are to synthetize chalcogenide thin films for developing mid-infrared optical integrated platforms and perform their functionalization with polymers in order to increase the sensor sensitivity. Among (GeSe2)100-x(Sb2Se3)x glass compositions, two selenide glass targets were chosen for their optical and physical properties. Thanks to attenuated total reflection spectroscopy, measurements were performed in water to detect aromatic hydrocarbons (benzene, toluene and the three xylene isomers) in the concentrations range of 25 ppb to 10 ppm. Detection measurements have also been fulfilled using seawater and ground-water. To increase their sensitivity, the use of metallic nanoparticles is one of the promising solutions based on Surface Enhanced Infrared Absorption (SEIRA). Thus, hybrid structures combining gold nanoparticles/chalcogenide glass and waveguides were fabricated and characterized.

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A nutrição nitrogenada, apesar de intensamente estudada, continua sendo um desafio aos produtores, especialmente em função da variabilidade encontrada no desenvolvimento da cultura nas áreas de produção comercial, muitas vezes em curtas distâncias. Recentemente esta variabilidade vem sendo associada ao uso de sensores opticos que detectam a refletância do dossel da cultura como forma de estimar a nutrição nitrogenada das plantas, podendo estes serem associados à aplicação em taxa variável em tempo real do fertilizante nitrogenado. Em cana-de-açúcar esses estudos ainda são escassos, e sendo uma cultura voltada para a produção de biomassa para geração de energia, tais sensores podem contribuir para otimizar o saldo positivo em produção de energia e baixar as emissão de carbono no sistema. Este trabalho apresenta o processo e mostra os resultados obtidos utilizando um sensor de nitrogênio e biomassa (N-SensorTM ALS, Yara International ASA) com o objetivo de indicar exigência na aplicação de nitrogênio em plantações comerciais de cana-de-açúcar. Oito talhões em produção comercial da cultura, localizados na região de Ribeirão Preto, SP, variando de 16 a 21 ha cada, foram monitorados. As condições de solo variaram de arenosos a argilosos, se dando a colheita de quatro deles em maio (período seco e frio) e os demais quatro em outubro de 2009 (estação úmida e quente), incluindo três soqueiras (primeira, segunda e terceira) em cada estação e quatro variedades, duas por estação. Cada talhão foi escaneado com o sensor três vezes durante seu desenvolvimento (0,2, 0,4 e 0,6 m de altura de colmo/palmito). Os dados georreferenciados de cada medição foram interpolados gerando mapas contendo cinco classes e em cada classe foram alocados dois pontos amostrais, dez por área, onde foram avaliados número e altura de perfilhos, teor de clorofila com medidor portátil e colhidas amostras para biomassa e extração de nitrogênio, as quais foram comparadas com os valores apresentados pelo sensor nos mesmos locais. Os resultados demonstram não haver relação significativa entre o medidor de clorofila e os parâmetros avaliados, porem alta correlação entre os valores do sensor e da biomassa de cana e sua absorção de nitrogênio, dando suporte à utilização desses dados em forma de um algoritmo para gerenciar a aplicação em taxa variável e tempo real de nitrogênio baseada nas leituras do sensor em áreas cultivadas com cana-de-açúcar. / Nitrogen nutrition of sugarcane, although extensively studied, remains a challenge for producers, especially due variability found in commercial production areas, often in short distances. Recently, this variability has been associated with the use of optical sensors that can detect crop canopy reflectance as a way to estimate the nitrogen nutrition of plants, these measurements can be associated with variable rate application on-the-go of nitrogen fertilizer based on sensor readings. On sugarcane those studies are yet scarce and as a biofuel crop the energy input matters, looking for a high positive energy balance production and low carbon emission on the whole production system. This study presents the procedure and shows the results obtained using a nitrogen and biomass sensor (N-SensorTM ALS, Yara International ASA) aiming to indicate nitrogen application demands on commercial sugar cane fields. Eight commercial fields from one Sugar Mill in the state of São Paulo, Brazil, vary from 16 to 21 hectares each, were monitored. Conditions ranging from sandy to heavy soils and the previous harvesting occurred in May (dry and cold season) and October 2009 (wet and warm season), including first, second, and third ratoon stages over four varieties, two per season. Each field was scanned with the sensor three times in the season (0.2, 0.4, and 0.6 m of stem height). The georeferenced data from each measurement was interpolated generating maps containing five classes, in each class two sample points were allocated, ten per area were the stem height and number, chlorophyll content (Ntester) were evaluated followed by tissue sampling for biomass and nitrogen uptake which were compared with the sensor readings for the same locations. The results show no significant relationship between the chlorophyll meter and the parameters evaluated, but high correlation between the sensor values and sugarcane biomass and their nitrogen uptake, supporting the use of these data as an algorithm to manage onthe- go variable rate application of nitrogen based on sensor readings over sugar cane cultivated areas.

Esta tese descreve a demonstração experimental de dispositivos baseados em fibras de cristal fotônico (PCFs), que aproveitam a flexibilidade estrutural oferecida pela matriz de capilares que compõe a seção reta da fibra, de forma a preencher estes capilares com líquidos e materiais nanoestruturados. Para o caso de materiais nanoestruturados, uma vez preenchida a fibra, os materiais nela inseridos interagem eficientemente com a luz guiada. Essa arquitetura diferenciada em relação às fibras ópticas convencionais abre novas perspectivas no desenvolvimento de aplicações como óptica não-linear e sensoriamento. PCFs de núcleo líquido, por outro lado, impõe dificuldades para a implementação de dispositivos práticos, devido às altas taxas de evaporação dos líquidos inseridos. Por esta razão, foi desenvolvida uma nova técnica para vedar seletivamente ambas as faces externas do núcleo líquido de uma PCF, utilizando um polímero curável. Estes tampões poliméricos evitam a evaporação, causando um impacto mínimo no guiamento da luz, tornando o dispositivo usável por semanas. Esta nova técnica de vedação foi empregada em um experimento para a geração de supercontínuo em uma PCF com núcleo de água destilada, proporcionando uma estabilidade de pelo menos 1 hora. Combinando líquidos e materiais nanoestruturados, foi também foi desenvolvido um sensor de temperatura baseado no preenchimento do núcleo de uma PCF por uma amostra coloidal de nanopartículas semicondutoras de CdSe/ZnS, dispersas em óleo mineral. O espectro de luminescência destes pontos quânticos coloidais é fortemente dependente da temperatura e os resultados obtidos mostraram que a grande interação entre a luz e o colóide, aliada a geometria da fibra, proporcionando uma sensibilidade ~5,5 vezes maior que a apresentada por uma rede de Bragg escrita em uma fibra óptica padrão, com boa relação sinal-ruído. / This thesis describes the experimental demonstration of devices based on photonic crystal fibers (PCFs). PCFs are optical fibers whose core is surrounded by a regular matrix of holes, which runs longitudinally across its length. This singular configuration allows the insertion of liquids and nanostructured material into the fiber. Nanostructured materials embedded inside the fiber efficiently interact with the guided light, opening up possibilities of novel applications regarding the fields of non-linear optics, as well as optical sensing. On the other hand, liquid-core PCFs suffer from some disadvantages concerning practical device applications, on account of the high evaporation of the inserted liquids. In order to address this issue, we developed a novel technique to selectively seal the external faces of a liquid-core PCF, by using a polymer plug. These polymer plugs avoid evaporation while causing a minimum impact on the light guiding characteristics of the PCF. This novel sealing technique was employed in a supercontinuum generation experiment, by using a PCF whose core was water-filled. A temporal stability of at least one-hour on the resulting spectrum was achieved. Combining the above techniques, we also developed a temperature sensor based on the core-filling of a PCF by a colloidal ensemble of CdSe/ZnS semiconductor nanoparticles dispersed in mineral oil. Those colloidal quantum-dots display a luminescence spectrum which is strongly dependent on temperature and the experimental results indicated that the greater interaction between the guided light and the colloidal sample, provided by the fiber geometry, allowed a sensitivity which is approximately 5.5 times than possible with a conventional Bragg grating, while keeping a satisfactory signal-to-noise ratio.