Protein interactions are the basis of synaptic function, and studying these interactions on a molecular level is crucial for understanding basic brain function, as well as mechanisms underlying neurological disorders. In this thesis, kinetic and mechanistic characterization of synaptic protein interactions was performed by using surface plasmon resonance biosensor technology. Fragment library screening against the reverse transcriptase of HIV was included, as it served as an outlook for future drug discovery against ligand-gated ion channels. The protein-protein interaction studies of postsynaptic Ca2+ -binding proteins revealed caldendrin as a novel binding partner of AKAP79. Caldendrin and calmodulin bind and compete at similar binding sites but their interactions display different mechanisms and kinetics. In contrast to calmodulin, caldendrin binds to AKAP79 both in the presence and absence of Ca2+ suggesting distinct in vivo functional properties of caldendrin and calmodulin. Homo-oligomeric β3 GABAA receptors, although not yet identified in vivo, are candidates for a histamine-gated ion channel in the brain. To aid the identification of the receptor, 51 histaminergic ligands were screened and a unique pharmacology was determined. A further requirement for identifying β3 receptors in the brain, is the availability of specific high-affinity ligands. The developed biosensor assay displayed sufficient sensitivity and throughput for screening for such ligands, as well as for being employed for fragment-based drug discovery. AMPA receptors are excitatory ligand-gated ion channels, involved in synaptic plasticity, and modulated by auxiliary proteins. Previous results have indicated that Noelin1, a secreted glycoprotein, interacts with the AMPA receptor. By using biochemical methods, it was shown that Noelin1 interacts directly with the receptor. The kinetics of the interaction were estimated by biosensor analysis, thereby confirming the interaction and suggesting low nanomolar affinity. The results provide a basis for functional characterization of a novel AMPA receptor protein interaction. The results demonstrate how secrets of synaptic protein interactions and function were revealed by using a molecular based approach. Improving the understanding of such interactions is valuable for basic neuroscience. At the same time, the technical advancements that were achieved to study interactions of ligand-gated ion channels by surface plasmon resonance technology, provide an important tool for discovery of novel therapeutics against these important drug targets.

Optical microcavities exhibit high resonance quality, so that, they are of key interest for the design of low-threshold lasers or for achieving strong coupling regime. But, such systems support modes whose the volume remain diffraction limited.In this manuscript, we are interested in their plasmonic counterparts because they support confined modes at the sub-wavelength scale. First, we study an in-plane plasmonic cavity which is the transposition of 1D optical cavity to surface wave. We characterize the cavity by measuring the fluorescence lifetime of dye molecules deposited inside.Then, we are interested in 3-dimension mode confinement achieved by spherical metal nanoparticles. We discuss on the definition of the mode volume used in cavity quantum electrodynamic and based on the calculation of energy confinement around the particle. We also simulate the fluorescence enhancement of rare-earth ions embedded inside core-shell plasmonic particles. Finally, we disturb the photodynamic emission of a single-photon source by puttingthe extremity of a plasmonic tip nearby the emitter

A novel process for the fabrication of Long Range Surface Plasmon Polariton (LRSPP) waveguide based biosensors is presented herein. The structure of the biosensor is comprised of Au stripe waveguide devices embedded in thick CYTOP claddings with a SiO2 solvent diffusion barrier and etch-stop layer. The SiO2 layer is introduced to improve the end quality of Au waveguide structures, which previously deformed during the deposit of the upper cladding process and to limit the over-etching of CYTOP to create micro-fluidic channels. The E-beam evaporation method is adapted to deposit a thin SiO2 on the bottom cladding of CYTOP. A new micro-fluidic design pattern is introduced. Micro-fluidic channels were created on selective Au waveguides through O2 plasma etching. The presented data and figures are refractive index measurements of different materials, thickness measurements, microscope images, and AFM images. Optical power cutback measurements were performed on fully CYTOP-cladded symmetric LRSPP waveguides. The end-fire coupling method was used to excite LRSPP modes with cleaved polarization maintaining (PM) fibre. The measured mode power attenuation (MPA) was 6.7 dB/mm after using index-matched liquid at input and output fibre-waveguide interfaces. The results were compared with the theoretical calculations and simulations. Poor coupling efficiency and scattering due to the SiO2 are suspected for off-target measurements.

Les réseaux de nanotrous sont des structures plasmoniques ayant un énorme potentiel en tant que transducteurs pour la conception de biocapteurs. De telles structures sont prometteuses pour l’élaboration de biocapteurs capable d’effectuer du criblage à haut débit. L’intérêt de travailler avec des réseaux de nanotrous est dû à la simplicité d’excitation des polaritons de plasmons de surface en transmission directe, à la sensibilité et à la facilité de fabrication de ces senseurs. L’architecture de tels réseaux métalliques permet la conception de nanostructures ayant de multiples propriétés plasmoniques. L’intensité, la signature spectrale et la sensibilité du signal plasmonique sont grandement affectées par l’aspect physique du réseau de nanotrous. L’optimisation du signal plasmonique nécessite ainsi un ajustement du diamètre des trous, de la périodicité et de la composition métallique du réseau. L'agencement de l'ensemble de ces paramètres permet d'identifier une structure optimale possédant une périodicité de 1000 nm, un diamètre des nanotrous de 600-650 nm et un film métallique ayant une épaisseur de 125 nm d'or. Ce type de transducteur a une sensibilité en solution de 500-600 nm/RIU pour des bandes plasmoniques situées entre 600-700 nm. L'intérêt de travailler avec cette structure est la possibilité d'exciter les plasmons de polaritons de surface (SPPs) selon deux modes d'excitation : en transmission exaltée (EOT) ou en réflexion totale interne par résonance des plasmons de surface (SPR). Une comparaison entre les propriétés plasmoniques des senseurs selon les modes d'excitation permet de déterminer expérimentalement que le couplage de la lumière avec les ondes de SPP de Bloch (BW-SPPs) en transmission directe résulte en un champ électromagnétique davantage propagatif que localisé. D'un point de vue analytique, la biodétection de l'IgG en SPR est 6 fois plus sensible par rapport au mode EOT pour une même structure. Une étude du signal plasmonique associé au BW-SPP pour un certain mode de diffraction démontre que la distance de pénétration de ces structures en EOT est d'environ 140 nm. La limite de détection de l'IgG humain pour un réseau de nanotrous de 1000 nm de périodicité est d'environ 50 nM en EOT. Ce mémoire démontre la viabilité des réseaux de nanotrous pour effectuer de la biodétection par criblage à haut débit lors de prochaines recherches. L'investigation de l'effet de l'angle d'excitation en transmission exaltée par rapport au signal plasmonique associé au mode (1,0) d'un réseau de nanotrous de 820 nm d'or démontre que la sensibilité en solution n'est pas proportionnelle à la sensibilité en surface du senseur. En fait, une optimisation de l'angle d'incidence pour le mode (1,0) de diffraction des BW-SPP permet d'amplifier la sensibilité en surface du senseur jusqu'à 3-fois pour un angle de 13,3°. Ce mémoire démontre ainsi la nécessité d'optimiser l'angle d'excitation et les propriétés physiques du senseur afin de développer un transducteur de grande sensibilité basé sur l'excitation en transmission de réseaux de nanotrous. / This research aims at developing a multiplexed biosensor for protein detection based on the nanohole array technology. Gold nanohole arrays exhibit distinct plasmonics properties depending on the excitation mode of the surface plasmon polaritons (SPPs). The interest of working with nanohole arrays is related to their high sensitivity, ease of fabrication and simple setup of excitation in transmission. The architecture of nanohole arrays leads to a nanostructure having multiple plasmonics properties. The intensity, the spectral signature and the sensitivity of the plasmonic signal were highly affected by the shape of the nanohole arrays. Varying the diameter of the holes, the periodicity and the metallic composition of the array were used to optimize the plasmonic signal. The optimal structure was found to have a periodicity of 1000 nm, a diameter of 600-650 nm and a metallic film with a thickness of 125 nm of gold. Such a transducer exhibits a bulk refractive index sensitivity of 500-600 nm/RIU for plasmonic bands absorbing around 600-700 nm. Surface plasmon resonance (SPR) in the Kretschmann configuration and enhanced optical transmission (EOT) mode were compared using large gold nanohole arrays (1000 nm periodicity, 600 nm diameter and 125 nm depth) in order to assess their relative analytical performance. Biodetection of IgG was found to be 6 times more sensitive with SPR in the Kretschmann configuration than in EOT mode for the same structure. The decay length of the electromagnetic field in EOT mode was determined experimentally to be around 140 nm with a layer-by-layer polyelectrolyte deposition. This results suggests that the plasmonic properties of EOT for nanohole arrays is much more associated to a Bloch wave SPPs mode rather than a localized SPR. Variation of the incident angle of excitation of the BW-SPPs in transmission leads to a higher surface sensitivity for the (1,0) diffraction mode for gold nanohole arrays of 820 nm periodicity. Optimization of the physical properties and the excitation angle of the nanohole arrays is essential in order to develop a transducer having a potential towards multiplexed biosensors.

An efficient numerical analysis method for wavelength-scale and sub-wavelength-scale photonic structures is developed. It is applied to metal-clad nano-lasers and photonic crystal-based DBRs to calculate intrinsic losses (from open boundaries), and to photonic crystal-based waveguides to calculate intrinsic and extrinsic losses (due to fabrication errors). Our results show that a metal-clad surface plasmon-based laser in a cylindrical configuration requires more gain to lase than is available from a semiconductor gain region. However, the lowest order TE and HE guided modes exhibit less loss than the other modes, and hold the most promise for lasing. For photonic crystal-based structures, our matrix-free implementation of the planewave expansion method for calculating layer modes combined with mode-matching between layers using a few lower order modes is shown to be a computationally efficient and reliable method. This method is then used to introduce robust design concepts for designing photonic crystal-based structures in the presence of fabrication uncertainties. Accounting for fabrication uncertainties is shown to be particularly important in the regions of the device where the light exhibits very low group velocity (`slow light'). Finally, the modal discrimination properties of photonic crystal-based DBRs (Distributed Bragg Reflectors) are compared with the properties of conventional oxide-DBR combinations to analyze the contribution of out-of-plane diffraction losses to modal discrimination.

Until recently, the standard therapy for hepatitis C treatment has been interferon and ribavirin. Such treatment has only 50% efficacy and is not well tolerated. The emergence of new drugs has increased the treatment efficacy to 90%. Despite such an achievement, the success is limited since the virus mutates rapidly, causing the emergence of drug resistant forms. In addition, most new drugs were developed to treat genotype 1 infections. Thus, development of new potent antivirals is needed and drug discovery against hepatitis C is continued. In this thesis, a FRET-based protease assay was used to evaluate new pyrazinone based NS3 protease inhibitors that are structurally different to the newly approved and currently developing drugs. Several compounds in this series showed good potencies in the nanomolar range against NS3 proteases from genotype 1, 3, and the drug resistance variant R155K. We assume that these compounds can be further developed into drug candidates that possess activity against above mentioned enzyme variants. By using SPR technology, we analyzed interaction mechanisms and characteristics of allosteric inhibitors targeting NS5B polymerases from genotypes 1 and 3. The compounds exhibited different binding mechanisms and displayed a low affinity against NS5B from genotype 3. In order to evaluate the activity and inhibitors of the NS5B polymerase, we established an SPR based assay, which enables the monitoring of polymerization and its inhibition in real time. This assay can readily be implemented for the discovery of inhibitors targeting HCV. An SPR based fragment screening approach has also been established. A screen of a fragment library has been performed in order to identify novel scaffolds that can be used as a starting point for development of new allosteric inhibitors against NS5B polymerase. Selected fragments will be further elaborated to generate a new potent allosteric drug candidate. Alternative approaches have successfully been developed and implemented to the discovery of potential lead compounds targeting two important HCV drug targets.

abstract: Obtaining local electrochemical (EC) information is extremely important for understanding basic surface reactions, and for many applications. Scanning electrochemical microscopy (SECM) can obtain local EC information by scanning a microelectrode across the surface. Although powerful, SECM is slow, the scanning microelectrode may perturb reaction and the measured signal decreases with the size of microelectrode. This thesis demonstrates a new imaging technique based on a principle that is completely different from the conventional EC detection technologies. The technique, referred to as plasmonic-based electrochemical imaging (PECI), images local EC current (both faradaic and non-faradaic) without using a scanning microelectrode. Because PECI response is an optical signal originated from surface plasmon resonance (SPR), PECI is fast and non-invasive and its signal is proportional to incident light intensity, thus does not decrease with the area of interest. A complete theory is developed in this thesis work to describe the relationship between EC current and PECI signal. EC current imaging at various fixed potentials and local cyclic voltammetry methods are developed and demonstrated with real samples. Fast imaging rate (up to 100,000 frames per second) with 0.2×3µm spatial resolution and 0.3 pA detection limit have been achieved. Several PECI applications have been developed to demonstrate the unique strengths of the new imaging technology. For example, trace particles in fingerprint is detected by PECI, a capability that cannot be achieved with the conventional EC technologies. Another example is PECI imaging of EC reaction and interfacial impedance of graphene of different thicknesses. In addition, local square wave voltammetry capability is demonstrated and applied to study local catalytic current of platinum nanoparticle microarray. This thesis also describes a related but different research project that develops a new method to measure surface charge densities of SPR sensor chips, and micro- and nano-particles. A third project of this thesis is to develop a method to expand the conventional SPR detection and imaging technology by including a waveguide mode. This innovation creates a sensitive detection of bulk index of refraction, which overcomes the limitation that the conventional SPR can probe only changes near the sensor surface within ~200 nm. / Dissertation/Thesis / Video for Figure 3.2 C to H / Video for Figure 3.5 / Video for Figure 5.5 / Video for Figure 6.7 / Video for Figure 6.11 / Ph.D. Electrical Engineering 2011

L ’intérêt des nano-particules pour le domaine de l ’optique visible a été suscité lors du premier rapport rédigé par Faraday en 1857 et qui a initié les bases de la production de nanoparticules métalliques en vue de leur propriété optiques inattendues (coloration des solutions). Plus récemment, le contrôle et le guidage de la lumière basés sur l’excitation de résonance plasmon dans les nanostructures a permis beaucoup d’applications liées à la vie quotidienne et impliquant la lumière. La résonance plasmonique de structures métalliques estun phénomène essentiel qui conduit à des propriétés optiques uniques à travers l’interaction de la lumière avecles électrons libres du métal. L’excitation de la résonance plasmon localisé (LSPR) permet d’exalter localement l’énergie électromagnétique comme dans le cas des nano-antennes mais aussi d’acheminer la lumière à travers des canaux de dimensions sub-l sur de grandes distances distances grâce à l’excitation du Plasmonde Surface Propagatif (PSP). Au cours de cette thèse, nous avons étendu un algorithme existant afin de calculer la réponse optique (sections efficaces de diffusion et d’absorption) de NPs ayant une forme géométrie quelconque. Ce type de NP anisotrope (vis-à-vis de la polarisation incidente) peut présenter à la résonance plasmonique une section efficace de diffusion 25 fois supérieure à celle géométrique. De plus, une étude systématique importante a été effectuée afin d’optimiser la géométrie de tels Nps.En ce qui concerne la PSP qui est impliqué dans la transmission exaltée à travers les matrices d’ouvertures annulaires AAA, nous avons entrepris une étude systématique des propriétés de l’excitation du mode particul particulier sans coupure de ces nano - guides. Il s’agit du mode Transverse Electrique et Magnétique (TEM). Une étude numérique complète est alors effectuée pour correctement concevoir la structure avant qu’elle ne soit expérimentalement fabriquée et caractérisée. Pour palier certaines contraintes expérimentale, une structure inclinée est proposée et étudiée dans le cas d’un métal parfaitement conducteur. Nous avons démontrée numériquement et analytiquement certaines propriétés intrinsèques de la structure montrant un coefficient de d’au moins 50% d’un faisceau incident non polarisé indépendamment des conditions d’éclairage (polarisation,angle et plan d’incidence). Lorsque le mode TEM est excité, le flux laminaire de l’énergie à travers la structure présente une déviation géante sur de très petites distances inférieures à la longueur d’onde. Les résultats présentés dans cette thèse pourraient être considérés comme une contribution importante à la compréhension du phénomène de transmission exaltée basé sur l’excitation de ce type de mode guidé. / The release of the rst report by Faraday in 1857 set the foundation of the production of metal nanoparticlesand their unexpected optical properties (coloring). More recently, controlling and guiding light via plasmonicresonance in nanostructures enable a lot of applications affecting everyday life that involves light. Plasmonresonance of metallic structures is a key phenomenon that allows unique optical properties through the interactionof light with the free electrons of the metal. The excitation of Localized Surface Plasmon Resonance(LSPR) leads to turn-on large local enhancements of electromagnetic energy as within antennas or to routelight as waveguide to desired region with high transmission through the excitation of Propagating SurfacePlasmon (PSP). During this thesis, we have developed an existing algorithm in order to calculate the opticalresponse of NPs of any shape. We have especially determined the localized energy enhancement factor interm of optical response of nano-antenna. This anisotropic (polarization dependent) NPs type can feature, atplasmon resonance, scattering efciency factor higher than 25. Moreover, an important systematic study hasbeen performed in order to optimize design of such NPs.Concerning the PSP that are involved in the enhanced transmission through Annular Aperture Arrays (AAAs),we systematically study the properties of the excitation of the peculiar Transverse ElectroMagnetic (TEM) guidedmode inside such nano-apertures. A complete numerical study is performed to correctly design the structurebefore it is experimentally characterized. For reasons associated to fabrication constraints and efciency,a slanted AAA made in perfectly conducting metal is proposed and studied. We numerically and analyticallydemonstrate some intrinsic properties of the structure showing a transmission coefcient of at least 50%ofan un-polarized incident beam independently of the illumination configuration (polarization, angle, and planeof incidence). At the TEM peak transmission, the laminar flow of the energy through the structure can exhibitgiant deviation over very small distances ( ). The results presented in this thesis could be considered as animportant contribution to the understanding of the enhanced transmission phenomenon based on the excitationof guided modes

As visual display technologies move closer to producing true three dimensional displays, pixel technologies need to be ever smaller and more functional to keep pushing the boundaries. Plasmonic metasurfaces have been shown to control the phase, amplitude and/or polarisation of incoming electromagnetic radiation. Nano-fabrication advancements have resulted in the fabrication of the building blocks of such metasurfaces at nano-scale dimensions, allowing the surfaces to interact with visible light, opening up applications in visual displays. As pixel sizes shrink, smaller colour filters will be required. The excitation of plasmonic resonances in metallic nano-structure arrays have resulted in colour filters an order of magnitude smaller than what is currently commercially available. As colour filters, plasmonic metasurfaces offer numerous advantages over pigment-based colour filters used in modern commercial liquid crystal (LC) displays, including environmental, size and longevity factors. Furthermore, exploiting the wavelength and polarisation dependant scattering of nano-structures, optical components, including lenses, waveplates and holograms containing sub-wavelength pixels have been demonstrated in the visible wavelength spectrum. The metasurfaces are able to mould optical wavefronts into arbitrary shapes with sub-wavelength resolution by introducing spatial variations in the optical response of the light scatterers. The applications demonstrated so far are, on the whole, static devices, that is to say their optical properties may not be altered post fabrication. To realise the full potential of plasmonic metasurfaces to visual applications the devices must be made active. By activating structural colour surfaces, not only may pixel densities potentially be increased simply by removing the need for separate red, green and blue filters, but a new class of high definition ultra-thin display devices may be accessible, whilst the dynamic manipulation of the wavelength and polarisation properties of nano-scattering elements would open up the possibilities to create sub-wavelength holographic pixels. This thesis investigates ways to activate static metasurfaces for colour, flat optic, and holographic applications. First, methods of dynamic control of the structural colour of plasmonic nano-hole arrays are investigated. By combining nano-hole arrays with liquid crystals, transmissive electrically tunable LC-nanohole pixels operating across the visible spectrum with un-polarised input light are experimentally demonstrated. An output analyser in combination with a nematic LC layer enables pixel colour to be electronically controlled through an applied voltage across the device, where LC re-orientation leads to tunable mixing of the relative contributions from the plasmonic colour input. Furthermore, exploiting the strong surface anchoring effects between an aluminium surface and LC molecules a twisted nematic LC cell, using a metallic grating as a combined colour filter, electrode and alignment layer, was shown to act a variable amplitude colour filter. The colour of these pixels was improved greatly utilising a grating-insulator-grating structure unique to this work. Second, a new process for fabricating aluminium nano-rod structures embedded in an elastomeric medium, with high spatial accuracy, is presented. The process is used to create nano-rod plasmonic resonator arrays whose optical properties may be altered by mechanical deformation. The pattern transfer process is further utilised to create dynamic optical elements, including nano-rod arrays for colour filters, tunable focal length Fresnel zone plates and photon sieves, and stretchable holograms with dynamic replay fields.

Les cellules dendritiques jouent un rôle primordial dans le système immunitaire. En effet, ces cellules sont à l'interface entre l'immunité innée et adaptative par leur capacité de reconnaissance, d'internalisation et de dégradation de pathogènes afin de présenter des antigènes aux lymphocytes. La capacité de reconnaissance est engendrée par l'expression de différents récepteurs à la surface de ces cellules. Parmi ces récepteurs, deux grandes familles permettent la reconnaissance d'un large panel de différents pathogènes, comme les TLRs (« Toll-Like Receptors) et les lectines de type-C. Ces récepteurs sont utilisés comme marqueurs des différents sous-types de cellules dendritiques. Par exemple, parmi les lectines de type-C, DC-SIGN est majoritairement exprimée dans les cellules dendritiques dermiques alors que la Langérine est, quand à elle, fortement exprimée par les cellules dendritiques épidermiques, les cellules de Langerhans. Ces deux sous-types de cellules dendritiques divergent par leur réponse à l'infection par le VIH (« virus d'immunodéficience humain »). En effet, le virus utilise DC-SIGN pour détourner le rôle de ces cellules afin d'infecter les lymphocytes T alors que la reconnaissance du VIH par la Langérine, dans les cellules de Langerhans, conduit à la clairance de virus par son internalisation dans le granule de Birbeck. Cet organite est spécifique des cellules de Langerhans et nécessite l'expression de la Langérine. Ce travail de thèse s'est donc focalisé sur la caractérisation structurale et fonctionnelle de la Langérine. Il a permis de mettre en évidence l'importance de la structure tertiaire du domaine CRD et de la structure quaternaire de la protéine pour la formation et la bonne structuration du granule de Birbeck. Ensuite, l'étude fonctionnelle de cette lectine, notamment par résonance plasmonique de surface, nous a conduit à identifier une nouvelle spécificité de reconnaissance de la Langérine pour les glycosaminoglycanes dans un site d'interaction différent du site canonique. Enfin, nous avons caractérisé une spécificité de reconnaissance du site canonique pour les monosaccharides sulfatés de type glucosamine en utilisant la résonance plasmonique de surface et la cristallographie. / Dendritic cells play a crucial role in the immune system. Indeed, these cells are at the interface between innate and acquired immunity by their capacities of recognition, internalisation and pathogen degradation to present antigens to T lymphocytes. The recognition capacity is generated by the expression of diverse receptors onto the cell surface. Among these receptors, two large families allow the recognition of a large panel of different pathogens, as TLRs (“Toll-Like Receptor) and C-type lectins. These receptors are used as markers of different dendritic cells subtypes. For example, and among the C-type lectins, DC-SIGN is mainly expressed onto dermic dendritic cells contrary to langerin, which is highly expressed onto epidermic dendritic cells, called Langerhans cells. These two subtypes of dendritic cells differ in their response of HIV infection. Indeed, the virus recognition by DC-SIGN enables hijacking the dendritic cell to infect T lymphocyte contrary to langerin recognition, in Langerhans cells, which allows the clearance of the virus by its internalisation into Birbeck granules. This organite is specific of Langerhans cells and requires langerin expression. This work is focused on structural and functional characterisation of langerin. It highlights the importance of the CRD tertiary structure and the quaternary structure of the protein for the formation and the structure of Birbeck granules. Then, functional study by surface plasmon resonance enabled us to identify a new binding site of langerin for glycosaminoglycans. Finally, we have characterised a recognition specificity of langerin for sulphated monosaccharide of glucosamine type using surface plasmon resonance and crystallography.