This thesis covers three different topics. The first part is a pedagogical review of the basic principles and recent advances in nonlinear optics. It was originally written as a chapter for the proceedings of the “International School of Physics (Enrico Fermi)” summer school on Photonics held in June, 2014. It is included to provide some background information about nonlinear optical processes in general, and is particularly relevant for the third part of this thesis which is based on the second-order nonlinear optical process of spontaneous parametric downconversion. The second part is based on original research, and deals with superradiance in plasmonic nanostructures. The process of superradiance, as introduced by Dicke in 1954, entails the shortening of the spontaneous emission lifetime of a collection of N quantum emitters as a consequence of the development of a macroscopic dipole moment. Specifically, the lifetime is shortened by a factor of 1/N, and the linewidth is broadened by a factor of N. Such a linewidth dependence has been previously observed in systems of several plasmonic ‘emitters’. However, a clear physical insight into this phenomenon and how it relates to Dicke superradiance has not been shown yet. In this part, we demonstrate by experiment, simulation, and a simple analytical model that Dicke’s superradiance can indeed be observed in a planar array of plasmonic nanoantennas, with a linewidth that scales linearly with the number of nanoantennas within a square wavelength. The third part is also based on original research, and is based on the scal- ing laws of spontaneous parametric downconversion (SPDC) for a type-I phase- matching configuration. The variation of bi-photon generation rate, heralding efficiency and radiance with parameters such as crystal length, pump focussing and collection waist sizes are examined for collinear and non-collinear emission. The results can be used to maximize the brightness of the SPDC source or increase the heralding efficiency depending on the application.

This thesis studies the different ways in which the localized plasmon heating effect of gold nanostructures -activated by plasmon excitation via visible and/or NIR irradiation- can be used to obtain different outcomes following the nanofabrication of applicable devices. Both spatial and temporal control were obtained for each one of the systems developed upon the incorporation of plasmonic gold nanostructures. Spatial control was enabled in hybrid mesoporous drug delivery systems fabricated in this thesis through the localized surface plasmon heating effect that allowed the modification of the dynamics of diffusion of the cargo being delivered, thus giving rise to different rates of release that can be controlled by plasmon excitation. At the same time, the plasmon heating effect proved to be capable of controlling the start of the release by dismantling thermo-responsive gates previously incorporated, thus enabling also a wavelength-controlled feature that enhances the versatility of these systems. Spatial control was also conferred to the photo-patterning applications presented in this dissertation by influencing the degree of motility of gold nanorods (AuNRs) embedded in polymer matrices allowing them to self-assemble when the longitudinal plasmon of the incorporated nanostructures was excited; the patterns generated were quite robust and persisted for extended periods of time. Finally, the feature of spatial heating control was also conferred to catalysis. The Friedel-Crafts alkylation of anisole by benzyl chloride using spherical gold nanoparticles (AuNPs) supported on Nb2O5-based catalysts was performed at bulk temperatures below those necessary for the reaction to occur when using bare or modified Nb2O5; this was the result of the combination of bulk and localized plasmon heating produced -both- via plasmon excitation. This also demonstrates the possibility of using plasmon excitation as an alternative heat source in this type of reactions. By combining the plasmonic properties of metallic nanostructures with those granted by mesoporous materials, polymer matrices and Nb2O5-based materials it was possible to obtain light-activated systems endowed also with temporal control and wavelength control while preserving the original properties of each systems' components. Overall, the content of this thesis describes in detail the practical aspects of combining gold nanostructures with different materials and the rationale behind the development of systems with customized and controllable properties.

Nous montrons comment des dimères de nanoparticules d'or, assemblés sur un brin d'ADN unique présentant un site de reconnaissance spécifique, fournissent une réponse optique macroscopique dépendant de leur environnement chimiqueLa séparation électrophorétique nous permet de préparer des suspensions purifiées de dimères de nanoparticules d'or de diamètre allant de 8 à 60 nm, et possédant différentes chimies de surface, avec une pureté pouvant atteindre 90%. L'échafaudage d'ADN contient une structure tige-boucle permettant de modifier réversiblement la structure du dimère en présence d'un brin d'ADN cible. Les distances interparticules (D), estimées en TEM cryogénique, peuvent varier de façon réversible jusqu'à un facteur 3 pour des sphères d'or de 8 nm de diamètre.Afin de traduire le changement conformationnel de l'échafaudage d'ADN en un signal optique mesurable, nous mesurons les spectres de diffusion de dimères uniques de nanoparticules d'or de 40 ou 60 nm de diamètre, en chambre microfluidique.Nous avons pu, en augmentant la concentration saline locale, diminuer progressivement D à l'échelle nanométrique, de 20 à 1 nm, ce qui se traduit par un décalage spectral de la résonance vers le rouge. La bonne corrélation entre les réponses spectrales de dimères uniques, estimées avec un spectromètre ou une caméra CCD couleur, nous permet de démontrer une méthode de détection en champ large et à bas coût, de la déformation nanométrique de ces nanostructures. L'utilisation de ligands amphiphiles nous a permis d'optimiser la stabilité colloïdale des dimères de particules d'or pour minimiser leur sensibilité à la force ionique locale et aux changements de température. / We demonstrate how gold nanoparticle dimers assembled around a single DNA template exhibiting a specific recognition site, provide a macroscopic optical signal depending on their chemical environment. Electrophoresis enables us to produce purified suspensions of gold nanoparticle dimers, with particle diameters ranging from 8 to 60 nm, with different surface chemistries and sample purities as high as 90%. The DNA template features a hairpin loop in order to switch its shape reversibly when binding a target DNA strand. Interparticle distances are estimated using cryo-electron microscopy and indicate a reversible change of the surface-to-surface distance by a factor of 3 in the case of 8 nm diameter gold particles. In order to translate the dynamic switching of a single DNA scaffold in a measurable optical signal, we study the scattering cross-sections of single 40 nm or 60 nm diameter gold nanoparticle dimers, in microfluidic conditions. We are able to progressively decrease the interparticle distance, at the nanometer scale, by increasing the local salt concentration. This deformation results in a spectral shift of the resonance (up to 100 nm) corresponding to a decrease of the interparticle distance from 20 to 1 nm. Moreover, the good correlation between the spectral responses of individual dimers, estimated using a spectrometer or a CCD color camera, enables us to demonstrate a wide-field low-cost detection method of the nanometric deformation of these nanostructures. Using amphiphilic ligands enables us to optimize the colloidal stability of gold nanoparticle dimers in order to minimize their sensitivity to the local ionic strength and temperature changes.

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(理学) / 甲第22240号 / 理博第4554号 / 新制||理||1654(附属図書館) / 京都大学大学院理学研究科物理学・宇宙物理学専攻 / (主査)准教授 松田 和博, 教授 田中 耕一郎, 教授 佐々 真一 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM

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.

Influence optical response on underetching of plasmonic antennas is observed in this thesis. When light falls with resonant wavelength on the optical antennas, the electromagnetic field is amplified near this antennas. The resonant wavelength depends on the length of the antenna and on effective refractive index given by the ambient properties around the antenna. The contact surface with substrate (dielectric) is reduced by underetching the antenna and the effective refractive index is changed and thus the optical response of the antenna is changed.

The human bone marrow vasculature constitutively expresses both E-selectin and P-selectin where they interact with the cell-surface glycan moiety, sialyl Lewis x, on circulating hematopoietic stem/progenitor cells (HSPCs) to mediate the essential tethering/rolling step. Although several E-selectin glycoprotein ligands (E-selLs) have been identified, the importance of each E-selL on human HSPCs is debatable and requires additional methodologies to advance their specific involvement. The first objective was to fill the knowledge gap in the in vitro characterization of the mechanisms used by selectins to mediate the initial step in the HSPCs homing by developing a real time immunoprecipitation-based assay on a surface plasmon resonance chip. This novel assay bypass the difficulties of purifying ligands, enables the use of natively glycosylated forms of selectin ligands from any model cell of interest and study its binding affinities under flow. We provide the first comprehensive quantitative binding kinetics of two well-documented ligands, CD44 and PSGL-1, with E-selectin. Both ligands bind monomeric E-selectin transiently with fast on- and off-rates while they bind dimeric E-selectin with remarkably slow on- and off-rates with the on-rate, but not the off-rate, is dependent on salt concentration. Thus, suggest a mechanism through which monomeric selectins mediate initial fast-on and -off binding to capture the circulating cells out of shear-flow; subsequently, tight binding by dimeric/oligomeric selectins is enabled to slow rolling significantly. The second objective is to fully identify and characterize E/P-selectin ligand candidates expressed on CD34+ HSPCs which cause enhanced migration after intravenous transplantation compared to their CD34- counterparts. CD34 is widely recognized marker of human HSPCs but its natural ligand and function on these cells remain elusive. Proteomics identified CD34 as an E-selL candidate on human HSPCs, whose binding to E-selectin was confirmed using some static and flow-based assays. E-selectin binds to CD34 with an affinity comparable to the well-described E-selLs CD44/HCELL and PSGL-1. CD34 knockdown resulted in faster-rolling velocities compared to control cells especially at and above three dyne/cm2. CD34 is the first selectin ligand since PSGL-1 reported to bind E-/P-/L-selectins and likely plays a key role in directing the migration of human HSPCs to the bone marrow.