We investigate the propagation of light in different conditions that lead to exotic propagation of photons and use near-resonant light-matter interactions to enhance these effects. First, we study the propagation of light in a moving highly dispersive medium, namely rubidium atoms. Based on the special relativity the speed of light changes with the speed of the medium. However, this drag effect in a non-dispersive medium is very small and thus difficult to measure. We show that the drag effect is enhanced significantly when the moving medium is highly dispersive. Thus, with this enhancement even a slow motion can be detected. Next, we employ the large nonlinear response of rubidium atoms to accentuate the formation of optical caustics. Caustics are important as nature uses caustics to concentrate the energy of waves. Moreover, caustics can be formed in many physical systems such as water waves in oceans to amplify tsunamis or generate rogue waves. The connection of our study to these giant water waves is discussed. Finally, we explore light-matter interactions in plasmonic systems. We show that photons experience a significant phase jump as they couple into and out of a plasmonic structure. This coupling phase, also known as the scattering phase shift, is generic to all scattering events. We measure this coupling phase with a triple-slit plasmonic structure. Moreover, we use the near-field enhancement of the plasmonic structure to enhance the coupling between the slits. Consequently, the photons can take non-trivial trajectories that pass through all three slits. We measure such exotic trajectories for the first time that are seemingly in violation of the superposition principle. The application of the superposition principle and the validity of Born’s rule is discussed.

Les nanoparticules à base d’acide hyaluronique (AH) sont utilisées pour de nombreuses applications pharmaceutiques. Elles peuvent cibler les tumeurs par interaction avec le CD44,qui est un récepteur biologique surexprimé à la surface de certaines cellules cancéreuses. Dans ce projet nous explorons l’application potentielle de ces nanoparticules dans les domaines cosmétiques, car l’AH est aussi un ingrédient important pour l’hydratation et le renouvellement de la peau. Les copolymères à bloc à base de polypeptides et de polysaccharides ont été synthétisés par une combinaison de polymérisation par ouverture de cycle et de couplage par chimie « click ». Les nanoparticules ont été obtenues par l’auto assemblage de ces copolymères en utilisant un procédé de nano precipitation, dont la taille et la morphologie sont contrôlées par les paramètres expérimentaux. L’interaction entre les nanoparticules d’AH et le CD44 a été quantifiée par la résonance de plasmon de surface(RPS). En comparant avec l’AH libre en solution, les nanoparticules d’AH ont montré une interaction plus efficace avec le CD44, mettant ainsi en évidence un effet de multivalence des nanoparticules. Finalement, la dégradation enzymatique de ces nanoparticules d’AH a été évaluée avec deux types de hyaluronidases, HYAL1 et SPAM-1. La digestion des nanoparticules de l’AH a été significativement ralentie par rapport à l’AH libre. De manière très surprenante, ces nanoparticules de AH ont pu inhiber l’activité de l’enzyme HYAL1 et protéger l’AH libre dans la solution. Enfin, des ligands du récepteur TLR2 de type lipopeptide ont été synthétisés et leurs performances via TLR2 ont été évaluées par RPS. / Nanoparticles based on hyaluronic acid (HA) are widely used in pharmaceutics. They can target the tumor by the interaction with CD44, a biological receptor overexpressed in some cancer cells. In this project, we investigate the potential applications of these nanoparticles in cosmetics, since HA is also an important ingredient for the skin hydration and renewing. Block copolymers based on polypeptides and polysaccharides were synthesized using a combination of ring opening polymerization and “click chemistry”. The nanoparticles were formed by the self-assembly of these block copolymers using a nanoprecipitation process, and their size and morphology were controlled by the experimental conditions. The interaction between nanoparticles and CD44 were measured by surface plasmon resonance(SPR). Compared to free hyaluronic acid chains in solution, the HA-based nanoparticles could interact more efficiently with CD44, thus demonstrating a multivalent effect. The enzymatic degradation of these HA nanoparticles was then evaluated with twohyaluronidases: HYAL1 and SPAM-1. The digestion of the HA nanoparticles was significantly slower than that of free hyaluronic acid. Surprisingly, these HA nanoparticles could even inhibit the activity of the enzyme HYAL1 and protect free HA chains in the solution. Finally, lipopeptide-based ligands of the biological receptor TLR2 were also synthesized and their performances were evaluated by SPR.

FGF2 (Fibroblast Growth Factor 2), o fundador da família FGF, tem funções regulatórias na mitogênese, diferenciação, morfogênese e reparo tecidual. Diversas espécies moleculares de FGF2 compartilham uma seqüência C-terminal comum de 155 aminoácidos, pois se originam de diferentes sítios de iniciação de leitura de um único mRNA. O menor, o FGF2-18kDa, é liberado extracelularmente para se ligar a receptores específicos (FGFRs) para disparar as funções parácrinas e autócrinas pelas quais este fator é conhecido. Por outro lado, as espécies maiores (FGF2-21, 22, 22,5 e 34kDa) são intracelulares se ligam a parceiros moleculares desconhecidos para exercer funções intrácrinas ainda indefinidas. O objetivo desta tese foi produzir espécies recombinantes do FGF2-18 e FGF2-22,5, na forma de proteínas de fusão, para analisar funções biológicas e mecanismos de sinalização. Nas células malignas Y1 de camundongo, os recombinantes de FGF2-18kDa (FGF2-18, His-FGF2-18 e His-FGF2-18-ProA) dispararam uma resposta antagônica estimulando as vias de sinalização mitogênica, mas bloqueando o ciclo celular. Nos fibroblastos não tumorigênicos Balb3T3, estes mesmos recombinantes de FGF2-18kDa dispararam apenas a resposta mitogênica clássica. Todos os efeitos biológicos destes recombinantes de FGF2-18kDa foram bloqueados pelo inibidor específico da proteína quinase de tirosina dos FGFRs, PD173074, demonstrando que são respostas intermediadas pelos FGFRs. Portanto, os domínios estruturais adicionados aos recombinantes de FGF2-18kDa não impediram que estas proteínas se ligassem e ativassem os FGFRs. Por outro lado, o recombinante His-FGF2-22,5 dispara apenas as vias de sinalização mitogênica em ambas as células Y1 e 3T3, mas este efeito biológico não é inibido por PD173074. Estes resultados sugerem que a seqüência N-terminal de 55 resíduos, rica em aminoácidos básicos, impede que o FGF2-22,5kDa se ligue e/ou ative os FGFRs. Entretanto, o recombinante His-FGF2-22,5ProA dispara a resposta antagônica característica do FGF2-18kDa. As implicações destes últimos resultados é que o domínio de ProA adicionado ao C-terminal torna o FGF2-22,5kDa um bom ligante dos FGFRs. A interação física entre ligante e receptor das formas recombinantes His-FGF2-18kDa (ou His-FGF2-18ProA) e FGF2-22,5kDa com os putativos FGFRs foi analisada através da técnica de SPR e os resultados mostram KDs aproximados (Kd18=21, 488.10-9 e Kd22,5=20,70393.10-9), enquanto que o número de sítios ligantes em vesículas microssomais das células é significantemente inferior para o FGF2-22,5kDa. Estes resultados são compatíveis com a existência de receptores diferentes para FGF2-18kDa e FGF2-22,5kDa, uma hipótese ainda a ser definitivamente corroborada. Em conclusão, o FGF2-18kDa, mesmo em formas recombinantes como proteína de fusão, dispara todos os efeitos biológicos descritos para FGF2, através dos FGFRs. Diferentemente, o FGF2-22,5kDa, como fator parácrino, só desencadeou a resposta mitogênica clássica de FGF2, provavelmente através de receptores diferentes dos FGFRs. Os resultados e conclusões desta tese têm um potencial indiscutivelmente relevante para a biologia molecular do câncer, com implicações possíveis em terapia oncológica / FGF2 (Fibroblast Growth Factor 2), the founder of the FGF family, has regulatory functions in mitogenesis, differentiation, morphogenesis and tissue repair. Multiple FGF2 molecular species, sharing a C-terminal sequence of 155 amino acids, are translated from different iniciation sites of the same mRNA. The smaller, the FGF2-18kD, is extracellularly released to bind to specific membrane receptors (FGFRs), performing paracrine and autocrine functions. On the other hand, the larger FGF2s (21, 22, 22.5 and 34kDa) are intracellular species that bind to unknown partners to play still undefined intracrine roles. The aim of this thesis was to produce recombinant species of FGF2-18kDa and FGF2-22,5kDa, in the form of fusion proteins, to analyze functions and signaling mechanisms. In mouse Y1 malignant cells, FGF2-18kD recombinants (FGF2-18kDa and His-FGF2-18kDaProA) triggered an antagonistic response activating mitogenic signaling pathways, but blocking the cell cycle. However, in non tumorigenic Balb3T3 fibroblasts, these same FGF2-18kD recombinants only elicited the classical mitogenic response. All biological effects of these FGF2-18kD recombinants were blocked by the specific inhibitor of FGFR-protein-tyrosine-kinases, PD173074, demonstrating that these responses are mediated by FGFRs. Therefore, the new peptide domains added to FGF2-18kD did not prevent these recombinant fusion proteins to bind and activate FGFRs. Conversely, the recombinant His-FGF2-22,5kDa triggered only mitogenic signaling pathways in both Y1 and Balb3T3 cells, a biological effect not inhibited by PD173074. These results suggested that the additional basic-rich N-terminal sequence of 55 amino acid residues, found in FGF2-22,5kDa, prevents this FGF2 species from binding and / or activate FGFRs. However, surprisingly, the recombinant His-FGF2-22kDaProA triggered the antagonistic response characteristic of FGF2-18kDa. These results imply that the ProA-domain added to the C-terminal end rendered the FGF2-22,5kDaProA a good ligand of FGFRs. The physical interaction between recombinants of both His-FGF2-18kD and His-FGF2-22kDa with putative FGFRs, analyzed by SPR, yielded close KD values (KD18=21, 5.10-9 e K D22,5=20,7.10-9), while the number of binding sites in cell microsomal vesicles were significantly lower for the His-FGF2-22,5kDa. These results are consistent with the existence of different receptors for FGF2 and FGF2-18kD-22,5kDa, a hypothesis that has yet to be definitively confirmed. In conclusion, FGF2-18kD, even as recombinant fusion proteins, triggered all biological effects of FGF2, through FGFRs. Conversely, the FGF2-22, 5kDa only triggered the classical mitogenic response, probably via receptors other than FGFRs. The results and conclusions of this thesis are potentially of great interest in cancer molecular biology, with implications in oncologic therapy.

La structuration laser femtoseconde (fs) de verres d’oxydes est un domaine de larecherche en pleine expansion. L’interaction laser-matière est utilisée pour sa facilité de miseen oeuvre et les nombreuses applications découlant de la fabrication des composantsphotoniques. En effet, un faisceau d’impulsions ultra-courtes focalisé dans un matériautransparent atteint une intensité suffisante pour modifier en 3D la matière à des échelles microetnanométrique. Ce mémoire se compose de deux volets. Le premier volet traite del’interaction laser fs en surface de verres menant à une auto organisation périodique de lamatière. L’influence du dopage ions photosensibles et des paramètres d’irradiation laser sontétudiées afin d’appuyer le modèle d’incubation pour la formation de nanoréseaux. À travers uneapproche innovante, il a été permis le contrôle de ces structures nanométriques périodiquespour de futures applications. Le second volet traite de cristallisation localisée de volume.Plusieurs matrices vitreuses, avec différents dopages en ion argent, ont été étudiées pourcomprendre les mécanismes de précipitation de nanoparticules d’argent (Ag-NPs). Ce travaildémontre le lien entre la physicochimie des verres et le caractère hors équilibrethermodynamique de l’interaction qui influence les conditions de nucléation/croissances des Ag-NPs. Les résultats sont comparés aux modélisations de la réponse optique du plasmon desurface des Ag-NPs. Les nombreuses perspectives de ce travail ouvrent sur de nouvellesapproches quant à la caractérisation, aux applications et à la compréhension de l’interactionlaser fs pour l’inscription de briques photoniques dans des verres d’oxydes. / Femtosecond direct laser writing (fs-DLW) of oxide glasses is a growing researchand development area. It is also increasingly used in the high-tech industry thanks to its simpleimplementation and numerous possible applications emerging from the photonic componentsmanufacture. Indeed, an ultra-short focused beam in a transparent material reaches a sufficientintensity to 3D modify the material on micro- or nanometer scale. However, the fs-DLW regimesat such high intensity are not completely understood, and the materials, already used, are notperfectly adapted for new photonics applications. This research work aims to provide answersto those open questions. This thesis is based on two thrusts. The first one addresses the issueof the glass surface DLW with fs pulses which lead to self organized periodic structures. Theinfluence of photosensitive doping ions and irradiation parameters are studied to support theincubation model for nanogratings surface formation. This study allows the control of theseperiodic nanostructures for further applications. The second thrusts deals with localized volumecrystallization. Several glassy matrices with various silver oxide doping have been studied tounderstand the mechanisms of silver nanoparticles (Ag-NPs) precipitation. This workdemonstrates the link between the physical chemistry of the glass and the non-equilibriumthermodynamic state during fs-DLW to influence nucleation and growth conditions of Ag-NPs.These results are compared to models that describe the optical responses of plasmonicbehavior. This research opens on new approaches and prospects for applications andunderstandings of fs-DLW of novel photonic bricks.

<p>In this study the formation of supported membranes onto planar solid supports has been investigated. The stability and activity of reconstituted membrane receptors has been studied. The potential use of such preparations in biosensor applications is discussed.</p><p>The lipid films were made by the Langmuir Blodgett and by the liposome fusion techniques. These supported films were characterised by ellipsometry, atomic force microscopy, surface plasmon resonance (SPR) and resonant mirror techniques. The thickness of the films was in agreement with that of a cell membrane. The kinetics of formation of the lipid films was studied and discussed.</p><p>The proteins, bacteriorhodopsin, cytochrome oxidase, acetylcholinesterase and the nicotinic acetylcholine receptor were reconstituted into the supported membrane. The subsequent analysis showed that the proteins were individually distributed and that the activity was retained, in some cases for several weeks after immobilisation.</p><p>The glycolipids, GM1, GM2, GD1b, asialo-GM1, globotriaosylceramide, lactosylceramide and galactosylceramide, were also reconstituted into the supported membranes. Their specific interaction with the toxin ricin or with its B-chain was examined using SPR. The affinity of intact toxin and of its B-chain differed markedly and was pH dependent. The carbohydrate chain length and charge density of the glycolipids also influenced the affinity.</p>

<p>The study and understanding of molecular interactions is fundamentally important in today's field of life sciences and there is a demand for well designed surfaces for biosensor applications. The biosensor has to be able to detect specific molecular interactions, while non-specific binding of other substances to the sensor surface should be kept to a minimum.                                                                                                                                                                                The objective of this master´s thesis was to design sensor surfaces based on self-assembled monolayers (SAMs) and evaluate their structural characteristics as well as their performance in Biacore systems. By mixing different oligo (ethylene glycol) terminated thiol compounds in the SAMs, the density of functional groups for bimolecular attachment could be controlled.  Structural characteristics of the SAMs were studied using Ellipsometry, Contact Angle Goniometry, IRAS and XPS. Surfaces showing promising results were examined further with Surface Plasmon Resonance in Biacore instruments.<p>Mixed SAM surfaces with a tailored degree of functional COOH groups could be prepared. The surfaces showed promising characteristics in terms of stability, immobilization capacity of biomolecules, non-specific binding and kinetic assay performance, while further work needs to be dedicated to the improvement of their storage stability. In conclusion, the SAM based sensor surfaces studied in this thesis are interesting candidates for Biacore applications.</p></p>

<p>Gold nanoparticles exhibit remarkable optical properties and could prove useful in sensitive biosensing applications. Upon illumination gold nanoparticles produce localized surface plasmons, which influence nearby fluorophores and an enhancement in their fluorescence intensity can be observed. This property makes gold nanoparticles attractive for enhancing optical signals.</p><p>In this project gold nanoparticles were functionalized with an antibody and immobilized to the surface of an existing biochip platform based on fluorescence. The aim was to investigate the possibility of obtaining an increased fluorescence signal from the gold nanoparticles. Two different conjugation procedures were investigated, direct physisorption and covalent attachment of the antibodies to the particles. Activity of bound antibodies was confirmed in both cases.</p><p>The on-chip fluorescence intensity produced by the different conjugates was monitored by use a specialized fluorescence reader designed for point-of-care use. AFM and SEM were used to determine the surface concentration of particles. A correlation between the produced fluorescence intensity and the surface concentration could be seen.</p>

<p>In this thesis, the structure and stability of globular proteins adsorbed onto nanometer-sized hydrophilic silica particles were investigated using differential scanning calorimetry (DSC), hydrogen/deuterium exchange (HDX), and mass spectrometry (MS). The adsorption process itself was characterized with fluorescence and absorption spectroscopy and surface plasmon resonance (SPR). The combination of these methods offered a unique insight into adsorption-induced changes within proteins related to their adsorption characteristics. DSC contributed with thermodynamic information on the overall structural stability within the protein population. HDX in combination with MS contributed information on the structure and stability of adsorbed proteins with focus on changes within the secondary structure elements. In order to increase the structural resolution in this part of the investigation, proteolysis was performed prior to the MS analyzing step. Knowledge on the protein adsorption process was utilized in a practical approach called ligand fishing. In this approach, SPR was used to monitor the chip-based affinity purification of a protein with MS used for protein identification.</p><p>Adsorption isotherms revealed that electrostatic interactions play an important role in the adsorption of proteins to hydrophilic surfaces. DSC investigation revealed that the thermal stability of proteins reduces with increasing electrostatic attraction between the protein and the surface and that this effect diminishes at higher surface coverage. The mass-increase due to exchange between protein hydrogen atoms and deuterium atoms in solution was investigated as a function of time. This gave insight into adsorption-induced changes in the structural stability of proteins. By combining DSC and HDX-MS, it was possible to differentiate between adsorption-induced changes in the secondary and tertiary structure. Additionally, if limited proteolysis was performed, the investigations gave insight into the orientation and protein segment specific changes in the stability of proteins adsorbed to silica surfaces. The adsorption of proteins to silica particles also provided the basis for a new experimental design that allows handling of minute amounts of proteins in a ligand fishing application, as used in the field of functional proteomics.</p>

My doctoral research has focused on the development of surface plasmon resonance (SPR) reflectance imaging technique to detect near-field transport properties such as concentration, temperature, and salinity in micro/nano fluidic phenomena in label-free, real-time, and full-field manner. A label-free visualization technique based on surface plasmon resonance (SPR) reflectance sensing is presented for real-time and full-field mapping of microscale concentration and temperature fields. The key idea is that the SPR reflectance sensitivity varies with the refractive index of the near-wall region of the test mixture fluid. The Fresnel equation, based on Kretschmann’s theory, correlates the SPR reflectance with the refractive index of the test medium, and then, the refractive index correlates with the mixture concentration or temperature. The basic operation principle is summarized and the laboratory-developed SPR imaging/analyzing system is described with the measurement sensitivity, uncertainties and detection limitations of the implemented SPR reflectance imaging. Total five proposed uses of SPR reflectance imaging technique are presented: (1) micromixing concentration field development of ethanol penetrating into water contained in a micro-channel, (2) full-field detection of the near-wall salinity profiles for convective/diffusion of saline droplet into water, (3) full-field and real-time surface plasmon resonance imaging thermometry, (4) correlation of near-field refractive index of nanofluids with surface plasmon resonance reflectance, and (5) unveiling hidden complex cavities formed during nanocrystalline self-assembly.

In this study the formation of supported membranes onto planar solid supports has been investigated. The stability and activity of reconstituted membrane receptors has been studied. The potential use of such preparations in biosensor applications is discussed. The lipid films were made by the Langmuir Blodgett and by the liposome fusion techniques. These supported films were characterised by ellipsometry, atomic force microscopy, surface plasmon resonance (SPR) and resonant mirror techniques. The thickness of the films was in agreement with that of a cell membrane. The kinetics of formation of the lipid films was studied and discussed. The proteins, bacteriorhodopsin, cytochrome oxidase, acetylcholinesterase and the nicotinic acetylcholine receptor were reconstituted into the supported membrane. The subsequent analysis showed that the proteins were individually distributed and that the activity was retained, in some cases for several weeks after immobilisation. The glycolipids, GM1, GM2, GD1b, asialo-GM1, globotriaosylceramide, lactosylceramide and galactosylceramide, were also reconstituted into the supported membranes. Their specific interaction with the toxin ricin or with its B-chain was examined using SPR. The affinity of intact toxin and of its B-chain differed markedly and was pH dependent. The carbohydrate chain length and charge density of the glycolipids also influenced the affinity.