This project examines how the collective oscillation of electrons in optically excited metal nanoparticles ( diameter < 100 nm) is affected by the presence of different dielectric environments. When coupled with material polarization, these collective oscillations are known as a Surface Plasmon Polaritons (SPPs), which preferentially absorb and scatter light at a specific frequency satisfying the Local Surface Plasmon Resonance (LSPR) condition. Surface plasmons on metal nanoparticles are widely studied for use in optical labeling, ultrasensitive biodetection, and thermally activated tissue treatment. In general Mie theory can be used to accurately model the optical behavior of ideal spherical particles in a homogeneous environment. However, many experiments involving LSPRs deal with metal nanoparticles in inhomogeneous environments; a typical experimental procedure involves the deposition of a colloidal suspension of metal nanoparticles directly onto a substrate. This project explains how the LSPR of nanoparticles deposited onto planar substrates depends upon the polarization of incident radiation, and demonstrates evidence of resonance tuning by comparing the optical response in various dielectric environments.

Nanotechnology has advanced to the point that nanoparticles can now be fabricated in a broad variety of shapes from a wide range of materials, each with their own properties and uses. As the list of manufacturable particles continues to grow, a new frontier presents itself: assembling these existing nanoparticles into more complicated nanoscale structures. The primary objective of this thesis is to demonstrate and characterize one such method of nanoscale construction, the plasmonically directed self-assembly of gold nanospheres onto both silver nanospheroids and gold nanorods. At the heart of this research is a the use of a photocleavable ligand (1-(6-Nitrobenzo[d][1,3]dioxol-5-yl)ethyl(4-(1,2-Dithiolan-3-yl)butyl) carbamate), which is capable of forming a photoreactive self-assembly monolayer (SAM) on gold and silver surfaces. After photoactivation, this SAM becomes positively charged at low pH, allowing it to electrostatically bind with negatively charged gold nanospheres (or other negatively charged nanoparticles). In this thesis, I describe both a secondary photoreaction that this ligand is capable post-photocleavage, which removes the ligand's ability to bind to negatively charged gold nanospheres, allowing for, among other assembly methods, reverse photopatterning. I further show that this photocleavable ligand can be used in conjunction with gold nanospheres to create aligned, metal structures on silver nanospheroid surface by exposure to linearly polarized UV light. Similarly, I also demonstrate how the ligand can be used to preferentially bind gold nanospheres to the ends of gold nanorods with the use of ultrafast femtosecond pulsed 750 nm laser light, making use of multi-photon absorption. Both methods of self-assembly, as well as the secondary photoreaction, are dependent on the plasmonics of the metal nanoparticles. This thesis also goes into the backgrounds of plasmonics, plasmonically mediated catalysis, self-assembly, and photocleavable chemicals. / Ph. D. / Nanotechnology has advanced to the point that nanoparticles can now be fabricated in a broad variety of shapes from a wide range of materials, each with their own properties and uses. As the list of manufacturable particles continues to grow, a new frontier presents itself: assembling these existing nanoparticles into more complicated nanoscale structures. The ability to build and design such structures further advances the use of nanotechnology for medical and industrial applications. In this thesis, I describe and demonstrate a method of nanoparticle self-assembly developed by our group which uses the unique optical properties of metallic nanoparticles in conjunction with a light-activated binding chemical to control and direct the assembly of gold nanoparticles onto a silver nanosphere or gold nanorod base. The preliminary results for both of these techniques are highly promising, and I describe them in detail. I furthermore explore a secondary light-driven reaction our light-activated chemical is capable of. This secondary reaction can prevent particle binding, broadening the applications and techniques of the lightactivated binding chemical.

Cette thèse considère de nouvelles architectures prometteuses des métamatériaux plasmoniques pour biosensing, comprenant: (I) des réseaux périodiques 2D de nanoparticules d'Au, qui peuvent supporter des résonances des réseaux de surface couplées de manière diffractive; (II) Reseaux 3D à base de cristaux plasmoniques du type d'assemblage de bois. Une étude systématique des conditions d'excitation plasmonique, des propriétés et de la sensibilité à l'environnement local dans ces géométries métamatérielles est présentée. On montre que de tels réseaux peuvent combiner une très haute sensibilité spectrale (400 nm / RIU et 2600 nm / RIU, ensemble respectivement) et une sensibilité de phase exceptionnellement élevée (> 105 deg./RIU) et peuvent être utilisés pour améliorer l'état actuel de la technologie de biosensing the-art. Enfin, on propose une méthode de sondage du champ électrique excité par des nanostructures plasmoniques (nanoparticules uniques, dimères). On suppose que cette méthode aidera à concevoir des structures pour SERS (La spectroscopie du type Raman à surface renforcée), qui peut être utilisée comme une chaîne d'information supplémentaire à un biocapteur de transduction optique. / This thesis consideres novel promissing architechtures of plasmonic metamaterial for biosensing, including: (I) 2D periodic arrays of Au nanoparticles, which can support diffractively coupled surface lattice resonances; (II) 3D periodic arrays based on woodpile-assembly plasmonic crystals, which can support novel delocalized plasmonic modes over 3D structure. A systematic study of conditions of plasmon excitation, properties and sensitivity to local environment is presented. It is shown that such arrays can combine very high spectral sensitivity (400nm/RIU and 2600 nm/RIU, respectively) and exceptionally high phase sensitivity (> 105 deg./RIU) and can be used for the improvement of current state-of-the-art biosensing technology. Finally, a method for probing electric field excited by plasmonic nanostructures (single nanoparticles, dimers) is proposed. It is implied that this method will help to design structures for SERS, which will later be used as an additional informational channel for biosensing.

La gammopathie monoclonale IgM est une polyneuropathie démyélinisante sensorielle et motrice. Il a été montré qu'elle est associée à des anticorps contre des glycoprotéines associées à la myéline (MAG/SGPG). L'épitope HNK-1 est un résidu 3-sulfo-glucuronyle lié à des structures lactosamine et il est présent aussi bien dans MAG que dans SGPG (SO4-3-GlcA(β1-3)Gal-(β1-4)GlcNAc(β1-3)Gal-(β1-4)Glcβ(1-1′)Cer). Il est exprimé principalement dans le système nerveux et joue un rôle important dans la réinnervation motrice préférentielle. Toutefois, l'épitope HNK-1 est difficile à isoler et à synthétiser et les essais diagnostiques cliniques ne sont pas toujours reproductibles et fiables.Le but de notre étude est d'identifier un outil synthétique simple de diagnostic (peptide ou monosaccharide), mimétique de l'épitope HNK-1, capable de reconnaître les anticorps dans les sera des neurogammapathies par Surface Plasmon Resonance (SPR) afin qu'il soit utilisé chez des patients à l'état précoce et qu'il puisse éventuellement permettre le suivi de l'évolution de la maladie. Pour cela, nous avons essayé de synthétiser ce trisaccharide, puis nous avons réalisé la synthèse de ses monosaccharides terminaux avec différents groupements fonctionnels (glucopyranoside d'octyle, acide 1-O-octylglucuronique, acide 1-O-octyl-3-O-sulfoglucuronique et acide 8-aminooctyl-3-O-sulfo-glucuronique).Puis 10 peptides linéaires et cycliques mimant conformationellement et/ou structuralement le HNK-1 ont également été synthétisés (LSETTI, LSETTl, cyclo(-TTILSE-), cyclo(-TTlLSE-), cyclo(-TKTlLSE-), cyclo(-TETKlLSE-), TYTKlLSE, TY(SO3)TKlLSE, cyclo(-TYTKlLSE-) et cyclo(-TY(SO3)TKlLSE-)). Les cinétiques d'affinité de ces mimes sucres et peptides ont été étudiées avec un anticorps anti HNK-1 commercial en utilisant le Biacore. De plus, les mimes avec les plus fortes affinités ont été choisis pour des études d'interaction antigène-anticorps dans des sera de patients atteints de gammapathie IgM. / IgM monoclonal gammopathy is a common age-related demyelinating sensory and motor polyneuropathy. It has been shown to be associated with antibodies against myelin-associated glycoproteins (MAG/SGPG). The HNK-1 carbohydrate epitope is a terminal 3-sulfo-glucuronyl residue attached to lactosamine structures and it is shared both in MAG and SGPG (SO4-3-GlcA(β1-3)Gal-(β1-4)GlcNAc(β1-3)Gal-(β1-4)Glcβ(1-1′)Cer). It is mostly expressed in the nervous system and plays an important role in preferential motor reinnervation. Nevertheless, the HNK-1 epitope is difficult to be isolated and synthesized and diagnostic assays used in the clinics are not always reproducible and reliable. Therefore in our study, our goal is to identify a simple synthetic diagnostic tool (peptide or monosaccharide), mimetic of the HNK-1 epitope, able to recognize antibodies in neurogammopathies sera by Surface Plasmon Resonance to be used in earlier stage patients and possibly to monitor disease activity. For this reason, we firstly tried to synthesize this trisaccharide and then we achieved the synthesis of its terminal monosaccharides with different function groups (octyl glucopyranoside, octyl glucuronic acid, octyl 3-O-sulfo-glucuronic acid and 8-amino octyl 3-O-sulfo-glucuronic acid). Then 10 linear and cyclic peptides conformationally and/or structurally mimicking HNK-1 were also synthesized (LSETTI, LSETTl, cyclo(-TTILSE-), cyclo(-TTlLSE-), cyclo(-TKTlLSE-), cyclo(-TETKlLSE-), TYTKlLSE, TY(SO3)TKlLSE, cyclo(-TYTKlLSE-) and cyclo(-TY(SO3)TKlLSE-)). The SPR kinetic binding affinities of all these sugar and peptide mimics were studied with commercial anti HNK-1 antibody using Biacore. Moreover, mimics with highest binding affinities were chosen for antigen-antibody interaction study in IgM gammopathy patients' serum.

Strong light matter interactions in metallic nanoparticles (NPs), especially those made of noble metals such as Gold and Silver is at the heart of much ongoing research in nanoplasmonics. Individual NPs can support collective excitations (Plasmon’s) of the electron plasma at certain wavelengths, known as the localized surface Plasmon resonance (LSPR) which provides a powerful platform for various sensing, imaging and therapeutic applications. For a collection of NPs their optical properties can be signify cannily different from isolated particles, an effect which originates in the electromagnetic interactions between the localised Plasmon modes. An interesting aspect of such interactions is their strong dependence on the geometry of NP collection and accordingly new optical properties can arise. While this problem has been well considered in one and two dimensions with periodic as well as with random arrays of NPs, three dimensional systems are yet to be fully explored. In particular, there are challenges in the successful de-sign and fabrication of three dimensional (3D) plasmonic metamaterials at optical frequencies. In the work presented in this thesis we present a detail investigation of the theoretical and experimental aspects of plasmonic interactions in two geometrically different three dimensional plasmonic nanostructured systems - a chiral system consisting of achiral plasmonic nanoparticles arranged in a helical geometry and an achiral system consisting of achiral plasmonic nanoparticle arrays stacked vertically into three dimensional geometry. The helical arrangement of achiral plasmonic nanoparticles were realised using a wafer scale technique known as Glancing Angle Deposition (GLAD). The measured chiro-optical response which arises solely from the interactions of the individual achiral plasmonic NPs was found to be one of the largest reported value in the visible. Semi analytical calculation based on couple dipole approximation was able to model the experimental chiro-optical response including all the variabilities present in the experimental system. Various strategies based on antiparticle spacing, oriented elliptical nanoparticles, dielectric constant value of the dielectric template were explored such as to engineer a strong and tunable chiro-optical response. A key point of the experimental system despite the presence of variabilities, was that the measured chiro-optical response showed less than 10 % variability along the sample surface. Additionally we could exploit the strong near held interactions of the plasmonic nanoparticles to achieve a strongly nonlinear circular differential response of two photon photoluminescent from the helically arranged nanoparticles. In addition to these plasmonic chiral systems, our study also includes investigation of light matter interactions in purely dielectric chiral systems of solid and core shell helical geometry. The chiro-optical response was found to be similar for both the systems and depend strongly on their helical geometry. A core-shell helical geometry provides an easy route for tuning the chiro-optical response over the entire visible and near IR range by simply changing the shell thickness as well as shell material. The measured response of the samples was found to be very large and very uniform over the sample surface. Since the material system is based entirely on dielectrics, losses are minimal and hence could possibly serve as an alternative to conventional plasmonic chiro-optical materials. Finally we demonstrated the used of an achiral three dimensional plasmonic nanostructure as a SERS (surface enhance Raman spectroscopy) substrate. The structure consisted of porous 3D metallic NP arrays that are held in place by dielectric rods. For practically important applications, the enhancement factor, as well as the spatial density of the metallic NPs within the laser illumination volume, arranged in a porous 3D array needs to be large, such that any molecule in the vicinity of the metal NP gives rise to an enhanced Raman signal. Having a large number of metallic NPs within the laser illumination volume, increases the probability of a target molecule to come in the vicinity of the metal NPs. This has been achieved in the structures reported here, where high enhancement factor (EF) in conjunction with large surface area available in a three dimensional structure, makes the 3D NP arrays attractive candidates as SERS substrates.

Various nanostructured materials display unique and interesting optical properties. Specific nanoscale objects discussed in an experimental perspective in this dissertation include optical metamaterials, surface plasmon sensors, and two-dimensional materials. These nanoscale objects were fabricated, investigated optically, and their applications are assessed. First, one-dimensional magnetic gratings were studied, followed by their two-dimensional analog, the so-called "fishnet." Both were fabricated, characterized, and their properties, such as waveguiding modes, are examined. Interestingly, these devices can exhibit optical magnetism and even negative refraction; however, their general characterization at oblique incidence is challenging due to diffraction. Here, a new method of optical characterization of metamaterials which takes into account diffraction is presented. Next, surface plasmon resonance (SPR) was experimentally used in two schemes, for the first time, to determine the transition layer characteristics between a metal and dielectric. The physics of interfaces, namely the singularity of electric permittivity and how it can be electrically shifted, becomes clearer owing to the extreme sensitivity of SPR detection mechanisms. Finally, ultra-thin two-dimensional semiconducting materials had their radiative lifetime analyzed. Their lifetimes are tuned both by number of atomic layers and applied voltage biasing across the surface, and the changes in lifetime are suspected to be due to quenching or enhancement of non-radiative process rates.

Surface-plasmon-resonance (SPR) sensors are widely used in biological, chemical, medical, and environmental sensing. This dissertation describes the design and development of dual-mode, self-referencing SPR sensors supporting two surface-plasmon modes (long- and short-range) which can differentiate surface binding interactions from bulk index changes at a single sensing location. Dual-mode SPR sensors have been optimized for surface limit of detection (LOD). In a wavelength interrogated optical setup, both surface plasmons are simultaneously excited at the same location and incident angle but at different wavelengths. To improve the sensor performance, a new approach to dual-mode SPR sensing is presented that offers improved differentiation between surface and bulk effects. By using an angular interrogation, both surface plasmons are simultaneously excited at the same location and wavelength but at different angles. Angular interrogation offers at least a factor of 3.6 improvement in surface and bulk cross-sensitivity compared to wavelength-interrogated dual-mode SPR sensors. Multi-mode SPR sensors supporting at least three surface-plasmon modes can differentiate a target surface effect from interfering surface effects and bulk index changes. This dissertation describes a tri-mode SPR sensor which supports three surface plasmon resonance modes at one single sensing position, where each mode is excited at a different wavelength. The tri-mode SPR sensor can successfully differentiate specific binding from the non-specific binding and bulk index changes.

Widefield surface plasmon resonance (WSPR) microscopy provides high resolution imaging of interfacial interactions. We report the application of the WSPR imaging system in the study of the interaction between keratinocytes and liquid crystals (LC). Imaging of fixed keratinocytes cultured on gold coated surface plasmon substrates functionalized with a thin film of liquid crystals was performed in air using a 1.45NA objective based system. Focal adhesion of the cells adhered to glass and LC were further studied using immunofluorescence staining of the vinculin. The imaging system was also simulated with 2x2 scattering matrix to investigate the optical reflection of the resonant plasmonic wave via the glass/gold/cell and glass/gold/LC/cell layers. WSPR imaging indicated that keratinocytes are less spread and formed distinct topography of cell-liquid crystal couplings when cultured on liquid crystal coated substrates. The simulation indicates that glass/LC shifted the surface plasmon excitation angle to 75.39 degrees as compared to glass/air interface at 44 degrees . The WSPR microcopy reveals that the cells remodelled their topography of adhesion at different interfaces.

Plasmonics techniques, such as surface plasmon resonance (SPR) and surface-enhanced Raman scattering (SERS), have been widely used for chemical and biochemical sensing applications. One approach to excite surface plasmons is through the coupling of light into metallic grating nanostructures. Those grating nanostructures can be fabricated using state-of-the-art nanofabrication methods. Laser interference lithography (LIL) is one of those methods that allow the rapid fabrication of nanostructures with a high-throughput. In this thesis, LIL was combined with other microfabrication techniques, such as photolithography and template stripping, to fabricate different types of plasmonic sensors. Firstly, template stripping was applied to transfer LIL-fabricated patterns of one-dimensional nanogratings onto planar supports (e.g., glass slides and plane-cut optical fiber tips). A thin adhesive layer of epoxy resin was used to facilitate the transfer. The UV-Vis spectroscopic response of the nanogratings supported on glass slides demonstrated a strong dependency on the polarization of the incident light. The bulk refractive index sensitivities of the glass-supported nanogratings were dependent on the type of metal (Ag or Au) and the thickness of the metal film. The described methodology provided an efficient low-cost fabrication alternative to produce metallic nanostructures for plasmonic chemical sensing applications. Secondly, we demonstrated a versatile procedure (LIL either alone or combined with traditional laser photolithography) to prepare both large area (i.e. one inch2) and microarrays (μarrays) of metallic gratings structures capable of supporting SPR excitation (and SERS). The fabrication procedure was simple, high-throughput, and reproducible, with less than 5 % array-to-array variations in geometrical properties. The nanostructured gold μarrays were integrated on a chip for SERS detection of ppm-level of 8-quinolinol, an emerging water-borne pharmaceutical contaminant. Lastly, the LIL-fabricated large area nanogratings have been applied for SERS detection of the mixtures of quinolone antibiotics, enrofloxacin, an approved veterinary antibiotic, and one of its active metabolite, ciprofloxacin. The quantification of these analytes (enrofloxacin and ciprofloxacin) in aqueous mixtures were achieved by employing chemometric analysis. The limit of quantification of the method described in this work is in the ppm-level, with <10 % SERS spatial variation. Isotope-edited internal calibration method was attempted to improve the accuracy and reproducibility of the SERS methodology. / Graduate / 2018-02-17

La leishmaniose est causée par un parasite protozoaire du genre Leishmania. Cette maladie infecte environ 12 millions de personnes dans le monde et en menace 350 millions dans 98 pays. Il existe trois formes majeures de leishmaniose : cutanée, mucocutanée et viscérale. L'infection se produit par le dépôt des parasites sous forme de promastigotes dans la peau de l'hôte mammifère via la piqûre d’un phlébotome. Les parasites peuvent migrer au sein de la matrice extracellulaire avant d’infecter les macrophages. Bien que la plupart des études réalisées jusqu’ici aient été consacrées aux interactions des parasites Leishmania avec leurs cellules cibles, quelques interactants extracellulaires ont déjà été identifiés. Dans cette étude, nous avons étudié pour la première fois le répertoire d’interactions de 24 souches de promastigotes intacts, vivants (6 espèces aux différents tropismes) avec environ ~70 biomolécules de la matrice extracellulaire de l’hôte à l’échelle moléculaire en utilisant des puces à protéines et à glycosaminoglycanes et la résonance plasmonique de surface en mode imagerie. Nous avons identifié 27 nouveaux partenaires (23 protéines et 4 glycosaminoglycanes) des promastigotes de Leishmania. Les souches partagent des partenaires communs tels que le plasminogène, TEM-8 et la tropoélastine, qui est dégradée in vitro par la majorité des souches. Les Leishmania se lient à plusieurs régulateurs de l’angiogenèse et à des glycosaminoglycanes. Dans une seconde partie, nous avons cloné deux protéines de L. major, l’énolase et la superoxyde dismutase, toutes deux identifiées dans le sécrétome de Leishmania, afin d’étudier leur répertoire d’interactions. L’énolase possède un répertoire d’interactions (13 partenaires) supérieur à celui de la superoxyde dismutase (6 partenaires) mais toutes deux interagissent également avec le plasminogène, l’ectodomaine de TEM-8, l’endostatine et l’héparine. Enfin, dans une troisième partie, nous avons créé une base de données, LeishMatrixDB, qui recense toutes les interactions des parasites Leishmania, ou leurs molécules, avec les composants de la matrice extracellulaire de l’hôte décrites dans la littérature / Leishmaniasis is a vector-borne disease caused by parasitic protozoa of the genus Leishmania. 12 million people are presently infected worldwide and the disease threatens 350 million people in 98 countries around the world. There are three main types of the disease: cutaneous, mucocutaneous and visceral. Infection occurs by the deposition of promastigote form into the mammalian skin via the bite of phlebotomine sandflies within the extracellular matrix proteins prior infecting macrophages. Most studies have focused on the interaction of Leishmania promastigotes with their cellular targets, some extracellular partners have been identified. In this study, we investigated for the first time the interplay between 24 strains of intact, live, parasites (6 species of different tropisms) and ~70 biomolecules of the host extracellular matrix at the molecular level using protein and glycosaminoglycan arrays probed by surface plasmon resonance imaging. We have identified 27 new partners (23 proteins and 4 glycosaminoglycans) of Leishmania promastigotes. All strains tested shared 3 common partners such as plasminogen, TEM-8 and tropoelastin, which is degraded in vitro by most Leishmania tested. Leishmania bound to several regulators of angiogenesis and to glycosaminoglycans. In a second part, we cloned two L. major proteins, enolase and superoxyde dismutase, both identified in Leishmania secretome in order to study their interaction repertoire. Enolase had a larger interaction repertoire (13 partners) than superoxide dismutase (6 partners) but both bound to plasminogen, ectodomain of TEM-8, endostatin and heparin. In a third part, we have created a database, LeishMatrixDB, which lists all the interactions of Leishmania, or their molecules, with host extracellular components from the literature