Doctor of Philosophy / Department of Chemistry / Christine M. Aikens / Gold and silver particles with dimensions less than a nanometer possess unique characteristics and properties that are different from the properties of the bulk. They demonstrate a non–zero HOMO–LUMO gap that can reach up to 3.0 eV. These differences arise from size quantization effects in the metal core due to the small number of atoms. These nanoparticles have attracted great interest for decades both in fundamental and applied research. Small gold clusters protected by various types of ligands are of interest because ligands allow obtaining gold nanoclusters with given sizes, shapes and properties. Three main families of organic ligands are usually used for stabilization of gold nanoclusters: phosphine ligands, thiolate ligands and DNA. Usually, optical properties of these NPs are studied using optical absorption spectroscopy. Unfortunately, sometimes this type of spectrum is poorly resolved and tends to appear very similar for different complexes. In these cases, circular dichroism (CD) and magnetic circular dichroism (MCD) spectroscopy can be applied. However, the interpretation of experimental CD and MCD spectra is a complicated process. In this thesis, theoretically simulated CD and MCD spectra were combined with optical absorption spectra to study optical activity for octa– and nona– and undecanuclear gold clusters protected by mono– and bidentate phosphine ligands. Additionally, optical properties of bare and DNA protected silver NPs were studied. Theoretical CD spectra were examined to learn more about the origin of chirality in chiral organometallic complexes, and to contribute to the understanding of the difference in chiroptical activity of gold clusters stabilized by different phosphine ligands and DNA–stabilized silver clusters. Furthermore, optical properties of the small centered gold clusters Au₈(PPh₃)₈²⁺ and Au₉(PPh₃)₈³⁺ were examined by optical absorption and MCD spectra using TDDFT. Theoretical MCD spectra were also used to identify the plasmonic behavior of silver nanoparticles. These results showed that CD and MCD spectroscopy yield more detailed information about optical properties and electronic structure of the different chemical systems than optical absorption spectroscopy alone. Theoretical simulation of the CD and MCD spectra together with optical absorption spectra can be used to assist in the understanding of empirically measured CD and MCD and provide useful information about optical properties and electronic structure.

Cette thèse se concentre sur la caractérisation d'assemblages organisés de nanoparticules plasmoniques appelés supracristaux. Les nanoparticules utilisées mesurent entre 5 et 11 nm de diamètre et possèdent une distribution en taille étroite permettant leur organisation à trois dimensions. Une fois les supracristaux obtenus, nous avons mesuré les spectres d'absorbance de supracristaux individuels constitués de différentes nanoparticules : cuivre, argent et or. Un modèle théorique simple a été utilisé pour calculer les spectres d'absorbance à partir de données disponibles dans la littérature. Nous avons ensuite montré que les supracristaux de nanoparticules d'argent ou d'or constituent de nouveaux substrats présentant un grand intérêt pour des applications en Spectroscopie Raman Exaltée de Surface (SERS). Les tailles des nanoparticules utilisées sont en effet beaucoup plus petites que celles reportées dans la littérature, d'où un nombre plus important de points chauds et donc une grande sensibilité. En vue d'applications couplées électrochimie/Raman, nous avons également mesuré les spectres de réflectance sous potentiel. De plus, des mesures par AFM conducteur et par microscopie électrochimique montrent que la conductivité des assemblages est faible mais autorise néanmoins des transferts d'électrons entre les supracristaux les plus fins et une sonde redox en solution. Enfin, des expériences de microscopie holographique ont permis de suivre la formation de ces édifices en solution. / This thesis focuses on the characterization of organized assemblies of plasmonic nanoparticles called supracrystals. The nanoparticles have a diameter ranging from 5 to 11 nm diameter and a narrow size distribution allowing their organization at three dimensions. Once the supracrystals were obtained, we measured the absorbance spectrum of individual supracrystals made of various nanoparticles: copper, silver or gold. A simple theoretical model was used to calculate the absorbance spectrum from available data in the literature. We then demonstrated that the supracrystals made of silver or gold nanoparticles are suitable substrates for Surface Enhanced Raman Spectroscopy applications. The sizes of the nanoparticles we use are indeed much smaller than in the literature, so that the number of hot spots and thus the sensitivity are increased. In view of coupling electrochemistry and Raman spectroscopy for future applications, we also measured the reflectance spectrum under potential control. Moreover, conductive AFM and Scanning ElectroChemical Microscopy measurements demonstrate that even if the conductivity of the supracrystals is weak, electron transfers between thin supracrystals and a redox probe in solution are nevertheless possible. Finally, holographic microscopy experiments allowed to follow the formation of these structures inside the solution.

Hop (Hsp70-Hsp90 Organizing Protein) is a co-chaperone of two major molecular chaperones, Hsp70 and Hsp90, and acts by transferring substrates from Hsp70 to Hsp90. Although under normal conditions Hop is predominantly localized within the cytosol, Hop has been detected in the nucleus under certain conditions including cell cycle arrest. A putative nuclear localization signal (NLS) has been identified within Hop, which overlaps with the TPR2A domain (previously shown to be critical for Hop-Hsp90 interactions). Hop is phosphorylated in vitro by two cell cycle kinases, namely, casein kinase II (CKII) at S189 and cdc2-kinase at T198; both residues are found upstream of the putative NLS and TPR2A domain. Mimicking phosphorylation at either phosphorylation site appeared to affect the subcellular localization of Hop. The aim of this study was to characterize Hop with respect to its phosphorylation status in vivo, as well as its subcellular localization pattern under heat stress and determine how these properties affected its interaction with Hsp90 as a co-chaperone. Dephosphorylation of proteins under normal and heat shock conditions changed the isoform composition of Hop, providing strong evidence that Hop was phosphorylated in vivo. Surface plasmon resonance (SPR) and glutatione-S-transferase (GST) co-precipitation studies showed that a cdc2-kinase phosphorylated mimic of Hop disrupted Hop-Hsp90 binding. A full length Hop-EGFP construct, as well as substitution mutants of the predicted NLS residues within the Hop-EGFP construct, were transfected into baby hamster kidney (BHK)-21 cells in order to establish the subcellular localization of Hop under heat stress and to test whether predicted residues were critical for nuclear localization of Hop. Under normal conditions, both Hop-EGFP and the NLS mutants were predominantly cytosolic, but when the cells were subjected to heat stress, Hop and its NLS-mutants were localized to both the cytosol and the nucleus. SPR and GST co-precipitation studies showed that substitution of the residues within the major arm of the putative NLS abrogated Hop-Hsp90 interactions. The data obtained from this study, showed for the first time, that Hop was phosphorylated in vivo and suggested that phosphorylation of Hop by cdc2-kinase could inhibit Hop-Hsp90 interactions. Moreover, these results suggested that the subcellular localization of Hop was dependent on stress levels of the cell, particularly heat stress. We propose that the nuclear localization of Hop may be primarily regulated by stress and secondarily by cell cycle arrest. The major arm of the putative NLS did not affect the localization of Hop directly, but was shown to be critical for Hop-Hsp90 binding in vitro. The results of this study suggested that binding of Hop to Hsp90 sequestered Hop within the cytosol and that Hsp90 acted as a cytosolic retention factor for Hop. Both phosphorylation of Hop, and its subcellular localization, appeared to be intimately related to its interaction with Hsp90 as a co-chaperone.

Hybridization of quantum emitters and plasmonic nanostructures has attracted much attention over the last years, due to their potential use as plasmon-based nanolasersor to achieve long-range quantum bit entanglement. Recent theoretical studies suggest that the plasmonic field can induce efficient cross-talking between emitters and lead to the formation of collective superradiant states. In this thesis, we developed a theoretical modelable to analyse collective effects in large ensemble of dipoles coupled by an electromagnetic nanoresonator. We experimentally investigated the plasmon-mediated superradiance of organic emitters grafted at a well-controlled distance from a metal nanosphere at room temperature. We report on the measured decay rates of these hybrid structures at the ensemble and single object levels. We find that the decay rate increases i) with the number ofemitters and ii) as the spacing between the emitters and the metal core decreases, a direct and clear evidence of plasmonic superradiance. This trend was observed for two types of hybrid structures, differing both by the size of the metal core and the type of organic dye used as emitter. The observation of plasmonic superradiance at room temperature opens questions about the robustness of these collective states against decoherence mechanisms.This robustness is of major interest for potential applications of quantum systems at room temperature. / Placer des nanostructures plasmoniques à proximité d’émetteurs quantiques est une approche prometteuse pour concevoir des nanolasers plasmoniques ou réaliser l’intrication de bits quantiques à longue distance. Des études théoriques récentes suggèrent que le champ plasmonique peut induire un couplage efficace entre émetteurs et mener à la formationd’états collectifs superradiants. Dans ce travail de thèse, nous avons développé un modèle théorique afin d’analyser les effets collectifs pour un ensemble de dipoles couplés à un nanorésonateur électromagnétique. Nous avons étudié expérimentalement la superradiance plasmonique d’émetteurs organiques greffés à une distance contrôlée d’une nanosphère metallique,à température ambiante. Nous avons mesuré le taux de relaxation de ces structures hybrides, en ensemble et à l’échelle de l’objet unique. Nous observons que le taux de relaxation augmente i) avec le nombre d’émetteurs et ii) lorsque la distance entre les émetteurs et le coeur métallique diminue, une preuve directe et claire de la superradiance plasmonique.Cette tendance a été observée pour deux types de structure hybride, différentes par la taille du coeur métallique et par le type de molécule utilisée comme émetteur. L’observation de la superradiance plasmonique à température ambiante ouvre des questions sur la robustesse d’un état superradiant contre des mécanismes de décohérence. Cette robustesse présente un intérêt majeur pour des applications potentielles de systèmes quantiques à température ambiante.

La découverte de la photoluminescence du silicium sous sa forme nanométrique a ouvert la voie de l’utilisation du silicium dans les composants optoélectroniques. Cependant cette photoluminescence reste trop peu efficace et de nombreuses recherches portent aujourd’hui sur l’amélioration des propriétés optiques du silicium. Ce travail de thèse s’intéresse particulièrement à l’utilisation de plasmons de surface localisés afin d’améliorer les propriétés optiques de nanocristaux de silicium. Grâce au contrôle de tous les paramètres géométriques des nanocristaux de silicium et des nanoparticules métalliques lors de la fabrication des échantillons, il a été possible d’étudier les phénomènes physiques du couplage entre ces deux objets. Une modification de l’émission des nanocristaux de silicium en fonction de la distance, de la taille et de la nature des nanoparticules métalliques a été étudiée. Grâce au développement de différentes techniques de caractérisation optique, il a été possible de montrer que la photoluminescence des nanocristaux de silicium était modifiée à la fois spectralement et spatialement par les plasmons de surface localisés. Ce travail montre que grâce aux plasmons de surface localisés il est possible de grandement améliorer la photoluminescence des nanocristaux de silicium et ainsi il est possible d’imaginer de nouveaux composants optoélectroniques à base de silicium et de plasmons / The discovery of photoluminescence of nanometric silicon paves the way to use silicon in optoelectronic devices. However this photoluminescence remains low and a lot of works aim at improving silicon optical properties. In this dissertation we study localized surface plasmons to improve optical properties of silicon nanocrystals. Thanks to the control of all geometrical parameters of silicon nanocrystals and metallic nanoparticles during the fabrication process, the coupling process between these two objects has been studied. The modification of silicon nanocrystals emission as a function of the distance, the size and the nature of metallic nanoparticles has been investigated. Thanks to the development of experimental optical characterization techniques we showed that silicon nanocrystals photoluminescence is modified both spectrally and spatially by localized surface plasmons. This work shows that it’s possible to enhance silicon’s optical properties and thus to devise optoelectronic devices with silicon and plasmons

Long-range surface plasmon-polaritons are transverse-magnetic polarized optical surface waves formed through the interaction of photons with free electrons at the surface of metal slabs or stripes. They play important roles in a variety of field such as integrated optics, amplifiers and lasers, optical sensing, modulation, etc. Due to their longer propagation length and deeper penetration depth compared to those of single-interface surface plasmon-polaritons, they have become increasingly promising in optical sensing. In sensing applications, it is necessary to reduce the noise level in order to obtain a lower detection limit. One way to achieve this is to use dual- or triple-output Mach-Zehnder interferometers so that the common perturbations among the outputs can be suppressed. The objective of this thesis is to provide deeper insights on the performances of dual- and triple-output Mach-Zehnder interferometers in thermo-optic and optical bulk sensing applications, theoretically and experimentally, and to demonstrate their ability to suppress common perturbations and lower the detection limit. On the theoretical side, the objective is approached by constructing a model for the transfer characteristic. For dual-output Mach-Zehnder interferometers, the plane-wave model is used to develop a general model for thermo-optic sensing and an unbalanced model for optical bulk sensing. For triple-output ones, local normal mode theory is used with modal analysis for the 3×3 coupler portion of the structure. Quantitative methods to analyze and compare different detection schemes are developed. The minimum detectable phase shift is determined for the case of thermo-optic sensing while the detection limit is determined for optical bulk sensing. On the experimental side, the objective is approached by providing a direct experimental demonstration of the transfer characteristics at an optimized operating wavelength for the coupler portion of the device, then comparing to theory. Time traces are carried out and various detection schemes are applied to suppress common perturbations among the outputs, and to improve the minimum detectable phase shift or the detection limit.

One in 3,000 people in the US are born with cystic fibrosis (CF), a genetic disorder affecting the reproductive system, pancreas, and lungs. Lung disease caused by chronic bacterial and fungal infections is the leading cause of morbidity and mortality in CF. Identities of the microbes are traditionally determined by culturing followed by phenotypic and biochemical assays. It was first thought that the bacterial infections were caused by a select handful of bacteria such as S. aureus, H. influenzae, B. cenocepacia, and P. aeruginosa. With the advent of PCR and molecular techniques, the polymicrobial nature of the CF lung became evident. The CF lung contains numerous bacteria and the communities are diverse and unique to each patient. The total complexity of the bacterial infections is still being determined. In addition, only a few members of the fungal communities have been identified. Much of the fungal community composition is still a mystery. This dissertation addresses this gap in knowledge. A snap shot of CF sputa bacterial community was obtained using the length heterogeneity-PCR community profiling technique. The profiles show that south Florida CF patients have a unique, diverse, and dynamic bacterial community which changes over time. The identities of the bacteria and fungi present were determined using the state-of-the-art 454 sequencing. Sequencing results show that the CF lung microbiome contains commonly cultured pathogenic bacteria, organisms considered a part of the healthy core biome, and novel organisms. Understanding the dynamic changes of these identified microbes will ultimately lead to better therapeutical interventions. Early detection is key in reducing the lung damage caused by chronic infections. Thus, there is a need for accurate and sensitive diagnostic tests. This issue was addressed by designing a bacterial diagnostic tool targeted towards CF pathogens using SPR. By identifying the organisms associated with the CF lung and understanding their community interactions, patients can receive better treatment and live longer.

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第22452号 / 工博第4713号 / 新制||工||1736(附属図書館) / 京都大学大学院工学研究科材料化学専攻 / (主査)教授 田中 勝久, 教授 三浦 清貴, 教授 藤田 晃司 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

An infrared radiometry setup has been developed based on a commercially available FTIR spectrometer for measuring mid-infrared thermal radiation. The setup was calibrated with a lab-built blackbody source. The setup was tested with a grating structure with 4-micron periodicity. Periodic microstructures using nickel and gold are fabricated on elastomeric substrates by use of strain-induced buckling of the nickel layer. The intrinsically low emissivity of gold in the mid-infrared regime is selectively enhanced by the surface plasmonic resonance at three different mid-infrared wavelengths, 4.5 µm, 6.3 µm, and 9.4 µm. As the thermal emission enhancement effect exists only for the polarization perpendicular to the orientation of the microstructures, substantially polarized thermal emission with an extinction ratio of close to 3 is demonstrated. Moreover, the elastically deformed plasmonic thermal emitters demonstrate strain-dependent emission peaks, which can be applied for future mechano-thermal sensing and dynamic thermal signature modulation.

The immunoglobulin superfamily (IgSF) is a large protein superfamily of membrane and soluble proteins that influence recognition, binding, and adhesion. Among members of this family are cell adhesion molecules (CAMs), which form cell-cell contact points that play key roles in development, cell polarization, and cellular fate. Cadherins (CADs) are calcium-dependent proteins of the adherens junction (AJ), and polarize epithelium and endothelium. The tight junction (TJ) is a multiprotein junctional complex whose function is to control the permeability of the paracellular pathway. At the membrane level, TJs are composed of three types of proteins: claudins (CLDNs), occludin (OCLN) and junctional adhesion molecules (JAMs). JAMs are members of the IgSF while CLDN and OCLN are 4-α-helix membrane proteins. Although JAMs are part of the TJ and reside in the same ultrastructure, they are similar to CADs in their secondary, tertiary, and quaternary protein structure. Crystallographic studies of CADs in the presence of calcium yielded trans interactions that resulted in cell-cell contacts. In the absence of calcium, CADs form cis interactions that do not form cell-cell interactions. The crystal structure of JAM-A, has a quaternary organization of a cis dimer. In spite of the many similarities, a link between CADs and JAMs remains unclear. Beyond this point, the association between JAMs, CLDNs, and OCLN in the TJ is vaguely understood. The JAM family (JAM-A, -B, -C and 4) and their tissue-specific distribution indicate that they are key to understanding the TJ’s function and the interplay with the AJ. JAM-A has been used as a prototype for the other three members of the family, but based on current evidence we hypothesized that these proteins may display unique properties to support TJ’s function in a given tissue. Are JAMs affected by calcium just as CADs? Do CLDNs and OCLN make direct contact with JAMs? Do JAMs coordinate the interplay between TJ and AJ? We designed a strategy based on recombinant proteins and biophysical methods to answer these questions. First, we fused the extracellular domain of each JAM to maltose-binding protein (MBP). Our results indicate that JAM proteins have similar secondary structures, but unique tertiary structures. Surface Plasmon Resonance experiments showed that JAM proteins favored heterotypic compared to homotypic interactions. Second, we addressed the effects of cations (Ca2+, Mg2+, Cu2+, Fe2+, Fe3+, and Zn2+) on JAM-A. The exposure of JAM-A to the resulted in changes in its secondary, tertiary structure, and homotypic binding affinity. Finally, we addressed whether cations had an effect on the other TJ components and if there is an interplay with E-CAD. We determined that in the assembly of a simple TJ and AJ, JAM-A and E-CAD are calcium-dependent, while CLDN1 and OCLN are calcium independent. We conclude that TJ components such as CLDN1 and OCLN may work as anchors to maintain cell-cell interactions while JAM-A and E-CAD would be regulated by cations in order to accommodate other homeostatic functions.