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.

Title: Multifunctional biomolecular assemblies for parallelized analysis of biomolecular interactions Author: Markéta Bocková Department / Institute: Institute of Physics, Charles University Supervisor of the doctoral thesis: Prof. Jiří Homola, Ph.D., DSc., Institute of Photonics and Electronics, The Czech Academy of Sciences Abstract: Surface plasmon resonance (SPR) biosensors represent the most advanced optical method for the direct, real-time monitoring of biomolecular interactions without the need for labelling. This doctoral thesis aims to advance the SPR biosensor method and to expand its utility in the investigation of biomolecular interactions. This encompasses activities on two major fronts of SPR biosensor research - immobilization methods and biosensing methodologies. Methods for the immobilization of biomolecules were researched with the aim of enabling the immobilization of a broad range of biomolecules on the SPR biosensor surface in a spatially controlled manner. The development of novel biosensing methodologies was pursued in order to address the current limitations of SPR biosensors associated with non-specific adsorption and limited analyte transport, and thus to improve the accuracy and robustness of SPR biosensor measurements. Finally, advances in the development of immobilization...

Plasmonic nanocrystals have a unique ability to support localized surface plasmon resonances and exhibit rich and intriguing optical properties. Engineering plasmonic nanocrystals can maximize their potentials for specific applications. In this dissertation, we developed three unprecedented Au nanorod-based plasmonic nanocrystals through rational design of the crystal shape and/or composition, and successfully demonstrated their applications in light condensation, photothermal conversion, and surface-enhanced Raman spectroscopy (SERS). The “Au nanorod-Au nanosphere dimer” nanocrystal was synthesized via the ligand-induced asymmetric growth of a Au nanosphere on a Au nanorod. This dimeric nanostructure features an extraordinary broadband optical absorption in the range of 400‒1400nm, and it proved to be an ideal black-body material for light condensation and an efficient solar-light harvester for photothermal conversion. The “Au nanorod (core) @ AuAg alloy (shell)” nanocrystal was built through the epitaxial growth of homogeneously alloyed AuAg shells on Au nanorods by precisely controlled synthesis. The resulting core-shell structured, bimetallic nanorods integrate the merits of the AuAg alloy with the advantages of anisotropic nanorods, exhibiting strong, stable and tunable surface plasmon resonances that are essential for SERS applications in a corrosive environment. The “high-index faceted Au nanorod (core) @ AuPd alloy (shell)” nanocrystal was produced via site-specific epitaxial growth of AuPd alloyed horns at the ends of Au nanorods. The AuPd alloyed horns are bound with high-index side facets, while the Au nanorod concentrates an intensive electric field at each end. This unique configuration unites highly active catalytic sites with strong SERS sites into a single entity and was demonstrated to be ideal for in situ monitoring of Pd-catalyzed reactions by SERS. The synthetic strategies developed here are promising towards the fabrication of novel plasmonic nanocrystals with fascinating properties for nanoplasmonics and nanophotonics.

This Master’s dissertation focuses on engineering artificial nanostructures, namely, arrays of metamolecules on a substrate (metasurfaces), with the goal to achieve the desired linear and nonlinear optical responses. Specifically, a simple analytical model capable of predicting optical nonlinearity of an individual metamolecule has been developed. The model allows one to estimate the nonlinear optical response (linear polarizability and nonlinear hyperpolarizabilities) of a metamolecule based on the knowledge of its shape, dimensions, and material. In addition, a new experimental approach to measure hyperpolarizability has also been investigated. As another research effort, a 2D plasmonic metasurface with the collective behaviour of the metamolecules known as hybrid plasmonic-Fabry-Perot cavity and surface lattice resonances was designed, fabricated and optically characterized. We experimentally discovered a novel way of coupling the microcavity resonances and the diffraction orders of the plasmonic metamolecule arrays with the low-quality plasmon resonance to generate multiple sharp resonances with the higher quality factors. Finally, we experimentally observed and demonstrated a record ultra-high-Q surface lattice resonance from a plasmonic metasurface. These novel results can be used to render highly efficient nonlinear optical responses relying on high optical field localization, and can serve as the stepping stone towards achieving practical artificial nanophotonic devices with tailored linear and nonlinear optical responses.

Lignin is one of the main components of wood and plants that acts as a kind of glue providing mechanical strength. It is a main polymer component composed from three phenolic structures, i.e. p-hydroxyphenyl (H), guaiacyl (G) and syringyl (S) units. It currently draws a lot of attention due to its eco-friendly. Recently, it has been shown that it is possible to produce lignin nanoparticles, small spherical particle that are composed out of lignin, that could possibly be used to replace the hazardous silver nanoparticles that are today used frequently in numerous applications. Lignin nanoparticles could potenitally also be used as functional coatings, as well as biologically degradable adhesives and float switches. Five samples, of nanoparticles, were investigated in this study. The first contained pure lignin nanoparticles, the second pure silver nanoparticles, and the three remaining samples contained lignin-coated silver nanoparticles, extracted from acetone, tetrahydrofuran (THF), and dimetylformamid (DMF) solvents. All samples were characterized using spectroscopic methods, e.g. infrared- and dark-field imaging, as well as UV-Vis-, fluorescence-, and Raman spectroscopy. In this thesis it was shown that lignin-coated silver nanoparticles exhibit surface plasmon resonance which induces a heat effect upon infrared irradiation. To identify the phenolic structures of lignin, UV-Vis spectroscopy was used. It was found that the spectra of the samples exhibited several intense bands. The objective of the UV-Vis spectroscopy was to examine the absorbance characteristics of the lignin-coated silver nanoparticles. Possible surface plasmon resonance wavelengths were determined, and two of the phenolic structures were identified. In this study, Raman spectroscopy was used to define characteristic bands of the samples. This was done to investigate if the lignin nanoparticles have the same characteristics as bulk lignin. Raman spectroscopy provide structural information of lignin. Furthermore, p-hydroxyphenyl, guaiacyl and syringyl structures could be identified with an excitation wavelength of 532nm. A comparison of the spectra of the lignin-containing samples indicated the the Raman features of the specimens were similar meanwhile almost no signs of silver were present, which might show that the particles were fully covered with lignin. Main lignin bands were identified and assigned. The fluorescent properties of the nanoparticles were investigated by obtaining emission spectra for blue-, green- and UV light excitation. The spectra were deconvoluted into their Gaussian components. Emission spectra were obtained for blue-, green- and UV light excitation. It was found that the fluorescence, after UV light exposure, increased with time of exposure. Dark-field microscopy was used to generate light scattering images of the particles. As a result, optical images with different colors (white, yellow, blue and red) could be revealed. The color information, that is related to the size of the particles, was used to estimate ratios of the different particle sizes. The lignin-coated silver nanoparticles, extracted from acetone, exhibited a strong surface plasmon resonance effect, which could be due to the absorbance at 463nm. The lignin-coated silver nanoparticles, extracted from DMF, exhibited a medium surface plasmon resonance effect, which could be due to the absorbance at 362nm. The lignin-coated silver nanoparticles, extracted from the THF solvent, exhibited a weak surface plasmon resonance effect, which could be due to the absorption at 379-380nm. The pure lignin- and silver nanoparticles merely showed bulk heating but no surface plasmon resonance effect could be detected. / Lignin är en av huvudbeståndsdelarna av trä och plantor som fungerar likt ett lim som ger mekanisk styrka. Lignin är en biopolymer, som består av tre fenylgrupper: p-hydroxifenyl (H), guaiacyl (G) och syringyl (S). På senaste tid har det visat sig att det är möjligt att tillverka lignin nanopartiklar, det är små sfäriska partiklar som är helt gjorda av lignin, som skulle kunna ersätta de miljöfarliga silver nanopartiklarna som i nuläget används i många olika tillämpningar. Lignin nanopartiklar kan potentiellt också användas som funktionella ytbeläggningar, såväl som biologiskt nedbrytbara lim och flottörer. Fem prover, av nanopartiklar, undersöktes i denna studie. Det första provet innehöll lignin nanopartiklar, det andra silver nanopartiklarna, och de tre återstående proverna innehöll ligninbelagda silver nanopartiklar, extraherade från aceton, tetrahydrofuran (THF) och dimetylformamid (DMF). Alla prover karakteriserades med hjälp av spektroskopiska metoder: infraröd- och mörkfältavbildning, liksom UV-Vis-, fluorescens- och Ramanspektroskopi. I denna avhandling visades att ligninbelagda silver nanopartiklar uppvisar ytplasmonsresonans, vilket inducerar en värmeeffekt vid infraröd bestrålning. För att identifiera ligninets fenylgrupper användes UV-Vis-spektroskopi. Det visade sig att spektra från proverna uppvisade flera intensiva band. Målet med UV-Vis-spektroskopin var att undersöka absorptionsegenskaperna hos de ligninbelagda silvernanopartiklarna. Möjliga ytplasmonresonansvåglängder bestämdes och två av fenylgrupperna identifierades. I denna studie användes Ramansspektroskopi för att definiera karakteristiska band för proverna. Detta gjordes för att undersöka om lignin nanopartiklarna har samma egenskaper som bulk lignin. Ramanspektroskopi ger information om ligninets struktur. Vidare identigierades p-hydroxifenyl-, guaiacyl- och syringylstrukturerna med en excitationsvåglängd på 532nm. En jämförelse av spektra för de lignininnehållande proverna indikerade att provernas Raman-kännetecken var liknande medan nästan inga tecken på silver fanns, vilket kan visa att partiklarna var täckta med lignin. Huvudsakliga ligninband kunde identifieras. Fluorescensegenskaperna, hos nanopartiklarna, undersöktes genom de erhållna emissionspektra efter exponering av blå-, grön- och UV-ljus. De erhållna spektra dekonvoluterades till dess gaussiska komponenter. Det visade sig att fluorescensen, efter exponering av UV-ljus, ökade med exponeringstiden. Mörkfältmikroskopi användes för att generera bilder på partiklarna. De resulterade i bilder med olika färger (vitt, gult, blått och rött) som motsvarade olika partikelstorlekar och geometrier. På så sätt kunde färhållandena mellan de olika partikelstorlekarna uppskattas. De ligninbelagda silver-nanopartiklarna, extraherade från aceton-lösningen, uppvisade en stark ytplasmonresonanseffekt, vilket kan bero på absorptionen (från absorptionsspektrat) vid 463nm. De ligninbelagda silver-nanopartiklarna, extraherade från DMF-lösningen, uppvisade en medelstark ytplasmonresonanseffekt, vilket kan bero på absorptionen vid 362nm. De ligninbelagda silver-nanopartiklarna, extraherade från THF-lösningen, uppvisade en svag ytplasmonresonanseffekt, vilket kan bero på absorptionen vid 379-380nm. De rena lignin- och silver-nanopartiklarna uppvisade endast uppvärmning men ingen ytplasmonresonanseffekt.

In this thesis by articles, I propose and demonstrate the full design, fabrication and characterization of optical biosensors based on (Bloch) Long Range Surface Plasmon Polaritons (LRSPPs). Gold waveguides embedded in CYTOP with an etched microfluidic channel supporting LRSPPs and gold waveguides on a one-dimensional photonic crystal (1DPC) supporting Bloch LRSPPs are exploited for biosensing applications. Straight gold waveguides embedded in CYTOP supporting LRSPPs as a biosensor, are initially used to measure the kinetics constants of protein-protein interactions. The kinetics constants are extracted from binding curves using the integrated rate equation. Linear and non-linear least squares analysis are employed to obtain the kinetics constants and the results are compared. The device is also used to demonstrate enhanced assay formats (sandwich and inhibition assays) and protein concentrations as low as 10 pg/ml in solution are detected with a signal-to-noise ratio of 20 using this new optical biosensor technology. CYTOP which has a refractive index close to water is the fluoropolymer of choice in current state of the art waveguide biosensors. CYTOP has a low glass transition temperature which introduces limitations in fabrication processes. A truncated 1D photonic crystal can replace a low-index polymer cladding such as CYTOP, to support Bloch LRSPPs within the bandgap of the 1DPC over a limited ranges of wavenumber and wavelength. Motivated by quality issues with end facets, we seek to use grating couplers in a broadside coupling scheme where a laser beam emerging from an optical fiber excites Bloch LRSPPs on a Au stripe on a truncated 1D photonic crystal. Adiabatic and non-adiabatic flared stripes accommodating wide gratings size-matched to an incident Gaussian beam are designed and compared to maximise the coupling efficiency to LRSPPs. The gratings are optimized, initially, through 2D modelling using the vectorial finite element method (FEM). Different 3D grating designs were then investigated via 3D modelling using the vectorial finite difference time domain (FDTD) method. Given their compatibility with planar technologies, gratings and waveguides can be integrated into arrays of biosensors enabling multi-channel biosensing. A multi-channel platform can provide, e.g., additional measurements to improve the reliability in a disease detection problem. Thus, a novel optical biosensor based on Bloch LRSPPs on waveguide arrays integrated with electrochemical biosensors is presented. The structures were fabricated on truncated 1D photonic crystals comprised of 15 period stack of alternating layers of SiO2/Ta2O5. The optical biosensors consist of Au stripes supporting Bloch LRSPPs and integrate grating couplers as input/output means. The Au stripes also operate as a working electrode in conjunction with a neighboring Pt counter electrode to form an electrochemical sensor. The structures were fabricated using bilayer lift-off photolithography and the gratings were fabricated using overlaid e-beam lithography. The planar waveguides are integrated into arrays capable of multichannel biosensing. The wafer is covered with CYTOP as the upper cladding with etched microfluidic channels, and wafer-bonded to a borofloat silica wafer to seal the fluidic channels and enable side fluidic interfaces. The proposed device is capable in principle of simultaneous optical and electrochemical sensing and could be used to address disease detection problems using a multimodal strategy.

No description available.

Les nanocristaux semi-conducteurs colloïdaux possèdent des propriétés photo-physiques qui en font des objets de choix pour des applications variées, comme le marquage biologique, le photovoltaïque ou encore l’optique quantique. Leur interaction avec une structure photonique peut modifier leurs propriétés d’émission (durée de vie, intensité…). Le microscope optique de champ proche est un outil privilégié pour venir sonder ces modifications à l’échelle nanométrique.Cette thèse porte sur la réalisation d’une sonde active de champ proche réalisée à partir d’un nanocristal cœur/coquille CdSe/CdS greffé à l’apex d’une fibre optique amincie. Cette sonde est utilisée pour cartographier, dans les 3 dimensions de l’espace et à l’échelle nanométrique, les variations de durée de vie de l’émetteur. Elle permet de rendre compte des variations des modes photoniques sur la surface.Une partie de cette thèse porte sur la réalisation de la sonde active elle-même. Grâce à cette sonde les études sont alors développées sur un réseau de trous dans un film mince d’or. Des simulations FDTD ont été réalisées dans le but de déterminer les paramètres pertinents du réseau et d’analyser leur réponse en champ proche.Les résultats expérimentaux des durées de vie en divers points de différents réseaux, obtenus avec la sonde active, sont confrontés aux résultats numériques. / Colloidal semiconductor nanocrystals have photo-physical properties that make them objects of choice for various applications, such as biological marking, photovoltaics or quantum optics. Their interaction with a photonic structure can modify their emission properties (lifetime, intensity, etc.). The near-field optical microscope is a privileged tool to probe these changes at the nanoscale.This thesis deals with the realization of an active near-field probe made from a CdSe / CdS core / shell nanocrystal grafted to the apex of a thinned optical fiber. This probe is used to map, in the 3 dimensions of the space and on the nanometric scale, the variations in the lifetime of the emitter. It makes it possible to account for variations in photonic modes on the surface.A part of this thesis concerns the realization of the active probe itself. Thanks to this probe the studies are then developed on a hole grating made in a thin film of gold. FDTD simulations were performed to determine relevant grating parameters and to analyze their near field response.The experimental results of the lifetimes at various points of different gratings, obtained with the active probe, are compared with the numerical results.

A system was developed to perform real-time biological threat agent (BTA) detection with a small autonomous unmanned aerial vehicle (UAV). Biological sensors just recently reached a level of miniaturization and sensitivity that made UAV integration a feasible task. A Surface Plasmon Resonance (SPR) biosensor was integrated for the first time into a small UAV platform, allowing the UAV platform to collect and then quantify the concentration of an aerosolized biological agent in real-time. A sensor operator ran the SPR unit through a groundstation laptop and was able to wirelessly view detection results in real time. An aerial sampling mechanism was also developed for use with the SPR sensor. The collection system utilized a custom impinger setup to collect and concentrate aerosolized particles. The particles were then relocated and pressurized for use with the SPR sensor. The sampling system was tested by flying the UAV through a ground based plume of water soluble dye. During a second flight test utilizing the onboard SPR sensor, a sucrose solution was autonomously aerosolized, collected, and then detected by the combined sampling and SPR sensor subsystems, validating the system\'s functionality. The real-time BTA detection system has paved the way for future work quantifying biological agents in the atmosphere and performing source localization procedures. / Master of Science