Nanoplasmonics has opened up the gates for numerous innovations. Recent studies showed that metal nanoparticles, when introduced into the solar cells and organic light emitting diodes, would greatly enhance their efficiencies. Though these advances are promising, they require a tool for investigating the interactions occuring at the microscopic level to further optimize their performance. In that context, we are interested in understanding the energy transfer mechanism between molecules in the vicinity of metal nanoparticle. Time-resolved fluorescence intensity and anisotropy experiments on single and clusters of Silver-Silica core-shell nanoparticles coated with Rhodamine B(RB) dye molecules, (Ag-SiO2-RB) were performed. We witnessed the signature of the interaction between RB molecules and metal nanoclusters in the form of the enhanced fluorescence intensity decay rates. The fluorescence lifetime of RB in the vicinity of the nanoparticles was (600 +/- 100) ps, as compared to (2.4+/-0.3)ns in the absence of nanoparticle. While the anisotropy of RB molecules in the absence of nanoparticle has remained almost constant(0.075+/-0.029) over long times; anisotropy in the presence of particles showed wide range of values immediately after excitation. Surprisingly high anisotropy values, at about 10 ns after excitation, were observed with a mean of about (0.145+/-0.025). We interpret the high and low initial anisotropies of the clusters, relative to the case of RB alone, to be due to the interaction of dye molecules with collective plasmon modes of the clusters. / Thesis (Master, Physics, Engineering Physics and Astronomy) -- Queen's University, 2011-06-30 23:29:38.658

Arthur Ashkin's Nobel Prize-winning single-beam gradient force optical tweezers have revolutionized research in many fields of science. The invention has enabled various atomic and single molecular studies, proving to be an essential tool for observing and understanding nature at the nanoscale. This thesis showcases the uniqueness of single-beam gradient force traps and the advances necessary to overcome the limitations inherent in conventional techniques of optical trapping. With decreasing particle sizes, the power required for a stable trap increases and could potentially damage a particle. This is a significant limitation for studying biomolecules using conventional optical traps. Plasmonic nanoaperture optical trapping using double-nanohole apertures is introduced as a solution to overcoming these limitations. Achievements in double-nanohole optical trapping made possible by the pioneering work of Gordon et. al are highlighted as well. This thesis focuses on the advances in nanoaperture fabrication methods and improvements to experimental techniques adopted in single molecular optical trapping studies. The technique of colloidal lithography is discussed as a cost-effective high-throughput alternative method for nanofabrication. The limitation in using this technique for producing double-nanohole apertures with feature sizes essential for optical trapping is analyzed. Improvements to enable tuning of aperture diameter and cusp separation is one of the main achievements of the work detailed in this thesis. Furthermore, the thesis explains the modified fabrication process tailor-made for designing double-nanohole apertures optimized for optical trapping. Transmission characterization of various apertures fabricated using colloidal lithography is carried out experimentally and estimated by computational electrodynamics simulations using the finite-difference time-domain (FDTD) method. Optical trapping with double-nanohole apertures fabricated using colloidal lithography is demonstrated with distinct results revealing trapping of a single polystyrene molecule, a rubisco enzyme and a bovine serum albumin (BSA) protein. / Graduate

This research developed a biosensor for kinase drug discovery applications. In particular it combined electronic techniques with optical techniques to understand the phosphorylation of proteins. There are two major electronic characteristics of phosphorylation that aid in its detection and subsequently biosensor development: first is the release of a proton upon phosphorylation of a protein (change in pH) and second is the addition of negative charge to the protein upon its phosphorylation. The work in this thesis reports an electrolyte–insulator–semiconductor sensing structures to detect the pH changes associated with phosphorylation and metal–insulator–semiconductor structures to detect the charge change upon phosphorylation of proteins. Major application of the developed devices would be to screen inhibitors of kinase that mediate phosphorylation of proteins. Inhibitors of kinase act as drugs to prevent or cure diseases due to the phosphorylation of proteins. With the advancements in VLSI and microfluidics technology this method can be extended into arrays for high throughput screening for discovering drugs.

We study theoretically graphene-like plasmonic metamaterials, in particular a honeycomb structured array of identical metallic nanoparticles, and examine the collective plasmonic modes that arise due to the near-field dipolar coupling between the localised surface plasmons of each individual nanoparticle. An analysis of the band structure of these eigenmodes reveals a phenomenal tunability granted by the polarisation of the dipole moments associated with the localised surface plasmons. As a function of the dipole orientation we uncover a rich phase diagram of gapped and gapless phases, where remarkably every gapless phase is characterised by the existence of collective plasmons that behave as massless chiral Dirac particles, in analogy to electrons in graphene. We consider lattices beyond the perfect honeycomb structure in two ways. Firstly, we break the inversion symmetry which leads to collective plasmons described as massive chiral modes with an energy dependent Berry phase. Secondly, we break the three-fold rotational symmetry and investigate generic bipartite lattices. In this scenario we progressively shift one sublattice away from the original honeycomb arrangement and observe a sequence of topological phase transitions in the phase diagram, as well as the merging and annihilation of Dirac points in the dispersions. After examining the purely plasmonic response we wish to address the true eigenmodes responsible for transporting electromagnetic radiation. For this reason we examine plasmon polaritons that arise from the strong light-matter coupling between the collective plasmons in a honeycomb array of metallic nanoparticles and the fundamental photonic mode of an enclosing cavity. Here we identify that the Dirac point remains robust and fixed in momentum space, irrespective of the light-matter coupling strength. Moreover, we demonstrate a qualitative modification of the polariton properties through modulation of the photonic environment, including order-of-magnitude renormalisation of the group velocity and the intriguing ability to invert the chirality of Dirac polaritons.

In our modern society, we are surrounded by numerous sensors, constantly feeding us information about our physical environment. From small, wearable sensors that monitor our physiological status to large satellites orbiting around the earth, detecting global changes. Although, the performance of these sensors have been significantly improved during the last decades there is still a demand for faster and more reliable sensing systems with improved sensitivity and selectivity. The rapid progress in nanofabrication techniques has made a profound impact for the development of small, novel sensors that enables miniaturization and integration. A specific area where nanostructures are especially attractive is biochemical sensing, where the exceptional properties of nanomaterials can be utilized in order to detect and analyze biomolecular interactions.  The focus of this thesis is to investigate plasmonic nanoparticles composed of gold or silver and optimize their performance as signal transducers in optical biosensors. Metal nanoparticles exhibit unique optical properties due to excitation of localized surface plasmons, which makes them highly sensitive probes for detecting small, local changes in their surrounding environment, for instance the binding of a biomolecule to the nanoparticle surface. This is the basic principle behind nanoplasmonic sensing based on refractometric detection, a sensing scheme that offers real-time and label-free detection of molecular interactions.  This thesis shows that the sensitivity for detecting local refractive index changes is highly dependent on the geometry of the metal nanoparticles, their interaction with neighboring particles and their chemical composition and functionalization. An increased knowledge about how these parameters affects the sensitivity is essential when developing nanoplasmonic sensing devices with high performance based on metal nanoparticles.

Indiana University-Purdue University Indianapolis (IUPUI) / Designing and developing a diagnostic technology that is capable of highly sensitive and specific, multiplexed, high-throughput, and quantitative biomarker assays for disease diagnosis and progression is of the upmost importance in modern medicine and patient care. Current diagnostic assays capable of multiplexed and high-throughput analysis include mass spectrometry, electrochemistry, polymerase chain reaction (PCR), and fluorescence-based techniques, however, these techniques suffer from a lack in sensitivity, false responses, or extensive sample processing that are detrimental to clinical diagnostics. To overcome these sensitivity challenges, the field of nanoplasmonics has become utilized when developing diagnostic assays. Plasmonic-based diagnostic tests utilize the unique optical, chemical, and physical property of nanoparticles to increase the sensitivity of the assay. In this dissertation, novel diagnostic platforms that utilize nanoparticles and their localized surface plasmon resonance (LSPR) property will be introduced. LSPR is an optical property in noble metallic nanoparticles that is referred to as the collective oscillation of free electrons upon light irradiation. It is highly dependent on the shape, size, and dielectric constant (refractive index) of the surrounding medium of the nanoparticle and LSPR sensing is based on a change in these properties. In this dissertation, the LSPR property is utilized to fabricate nanoplasmonic-based diagnostic platforms that are capable of multiplexed and high-throughput biomarker assays, with high sensitivity and specificity. The work presented in this dissertation is presented as six chapters, (1) Introduction. (2) Methods, (3) Fabrication of a LSPR-based multiplexed and high-throughput biosensor platform and its application in performing microRNA assays for the diagnosis of bladder cancer. In this chapter, the advancement of single-plex solid state LSPR-based biosensors into a multiplexed and high-throughput diagnostic biosensor platform is reported for the first time. The diagnostic biosensor platform is first fabricated utilizing different gold nanoparticles (spherical nanoparticles, nanorods, and triangular nanoprisms), and then with the gold triangular nanoprisms as the nanoparticle of choice, microRNA assays were performed. The developed biosensor platform is capable of assaying five different types of microRNAs simultaneously at an attomolar limit of detection. Additionally, five microRNA were assayed in 20-bladder cancer patient plasma samples. (4) Development/optimization of the biosensor platform presented in Chapter 3 for the detection of COVID-19 biomarkers. In this chapter, the biosensor platform utilized in Chapter 3 was designed to assay 10 different COVID-19 specific biomarkers from three classes (six viral nucleic acid gene sequences, two spike protein subunits, and two antibodies) with limit of detections in the attomolar range and with high specificity. The high-throughput capability of the biosensor platform was advanced, with the platform performing analysis of a single biomarker in 92 patient samples simultaneously. Additionally, the biomarker platform was utilized to assay all 10 biomarkers in a total of 80 COVID-19 patient samples. (5) Further optimization of the biosensor platform for the development of a highly specific antibody detection test for COVID-19. During the COVID-19 pandemic, knowledge was gained on the specificity of antibodies produced against COVID-19. In this chapter, that knowledge was applied towards the optimization of the biosensor platform presented in Chapter 4 in order to assay SARS-CoV-2 neutralizing antibody IgG. The optimization of the biosensor platform included the size of the gold triangular nanoprisms and the receptor molecule of choice. The biosensor platform assayed this highly specific COVID-19 IgG antibody with a limit of detection as low as 30.0 attomolar with high specificity and no cross reactivity. Additionally, as a proof of concept, the biosensor platform was utilized in a high-throughput format to assay SARS-CoV-2 IgG in a large cohort of 121 COVID-19 patient samples simultaneously. (6) Advancement of the biosensor platform from a 96-well plate to a 384-well plate and its application in assaying microRNA for early diagnosis of pancreatic cancer. In this chapter, the high-throughput capabilities of the biosensor platform presented in Chapters 3-5 was expanded by increasing the sensor amount in one platform from 92 to 359. The 384-well plate biosensor platform was designed, optimized, and utilized to perform microRNA assays for early-stage pancreatic cancer diagnosis. The optimization of the biosensor platform included the manipulation of LSPR-based parameters and the -ssDNA receptor molecule in order to obtain low limit of detections (high sensitivity). Additionally, the biosensor platform assayed two microRNA in a large cohort (n=110) of pancreatic cancer and chronic pancreatitis patient samples.

This thesis focuses on the physics of nanoplasmonic systems for dispersive and lossy media. Gold nanoparticles in P3HT (poly(3-hexylthiophene)) and PMMA (poly(methyl methacrylate)) are analyzed both theoretically and experimentally. It is found in both cases that the presence of P3HT narrows the linewidth of the gold plasmon peak. This is a counter-intuitive result, and this narrowing of the linewidth by a lossy material is analyzed in detail. It is found that dispersion in both the real and imaginary parts of the permittivity of the surrounding medium can significantly affect the linewidth. Another plasmonic phenomena was also researched. An atomic energy level model of erbium was constructed and used to solve a rate equation to calculate the far-field emission enhancement from an erbium atom nearby a gold nanorod when the dark mode is excited. Normally a small emission enhancement is expected in the far field since dark modes do not couple strongly to radiation, but in experiments this dark field emission enhancement was seen to be significant. The results of the calculation were compared to this previous experimental result. Although the incident power dependence of the calculated 980 nm emission line agreed with experiments, the 650 nm emission line power dependence and the calculated emission enhancement did not, and so more work needs to be done with this model to explain the experimental results. / Graduate

Nanoplasmonics has provided a way to control light with extremely high precision, into nanoscale volumes. In many circumstances, the nanoplasmonic devices which can be realised are fabricated using processing techniques which rely on planar technologies. This thesis provides a general method to make nanoplasmonic devices on a flexible membrane structure, which can be free standing, extremely thin (less than the wavelength of visible light), but retains the ability to be manipulated without loss of optical function. These devices are very pliant and conformable. Flexibility allows the integration of nanoplasmonic devices into many new applications where curved surfaces or the ability to conform to another object is required, as well as providing a route for post-fabrication tunability. Two specific applications are considered: lab-on-fibre technology and surface enhanced Raman spectroscopy. Lab-on-fibre technologies have been advancing the ability to miniaturise experiments which would normally require a whole laboratory. Fabricating a membrane and then later applying it to the fibre decouples the choice of fibre from the design of the device. Surface enhanced Raman spectroscopy is a powerful diagnostic tool which can uniquely identify an optical fingerprint of different molecules. The technique has been held back from widespread clinical adoption because of the difficulty of reproducibility of the substrates used. A repeatable and reliable rigid substrate is demonstrated, which can identify the concentration of a three component mixture of physiologically relevant biomolecules. This same design is then shown in a flexible form factor, which is applied to a non-planar landscape where it can identify the locations where a molecule of interest has been deposited. This thesis details the development of the fabrication protocol, the construction of experimental apparatus for characterisation, and the use of numerical modelling to advance the flexible nanoplasmonic membrane platform.

L'objectif principal de cette thèse est de concevoir, fabriquer et caractériser les dispositifs plasmoniques basés sur les cavités métalliques bidimensionnelles monocristallines pour le transfert d'information et la réalisation d'opérations logiques. Les fonctionnalités ciblées émergent de l'ingénierie spatiale et spectrale de résonances plasmon d'ordre supérieur supportées par ces cavités prismatiques. Les nouveaux éléments étudiés dans cette thèse ouvrent la voie à de nouvelles stratégies de transfert et de traitement de l'information en optique intégrée et miniaturisée. Dans un premier temps, nous caractérisons la réponse optique des nanoplaquettes d'or ultra-fines et de taille submicronique (400 à 900 nm) par spectroscopie en champ sombre. La dispersion des résonances plasmoniques d'ordre supérieur de ces cavités est mesurée et comparée avec un bon accord aux simulations obtenues par la méthode des dyades de Green (GDM). En outre, nous présentons une analyse par décomposition lorentzienne des réponses spectrales de ces nanoprismes déposés sur des minces substrats métalliques. Nous avons, par ailleurs systématiquement étudié les effets qui pourraient modifier les résonances plasmoniques par microscopie de luminescence non-linéaire, qui s'est avérée un outil efficace pour observer la densité d'états locale des plasmons de surface (SPLDOS). En particulier, nous montrons que les caractéristiques spectrale et spatiale des résonances plasmoniques d'ordre supérieur peuvent être modulées par la modification du substrat (diélectrique ou métallique), par l'insertion contrôlée d'un défaut dans la cavité ou par le couplage électromagnétique, même faible, entre les deux cavités. L'ingénierie rationnelle de la répartition spatiale des résonances confinées 2D a été appliquée à la conception de dispositifs à transmittance accordable entre deux cavités connectées. Les géométries particulières sont produites par gravure au faisceau d'ions focalisé sur des plaquettes cristallines d'or. Les dispositifs sont caractérisés par cartographie de luminescence non-linéaire en microscopie confocale et en microscopie de fuites. Cette dernière méthode offre un moyen unique d'observer la propagation du signal plasmon dans la cavité. Nous démontrons la dépendance en polarisation de la transmission plasmonique dans les composants à symétrie et géométrie adéquates. Les résultats sont fidèlement reproduits par notre outil de simulation GDM adapté à la configuration de transmission. Enfin, notre approche est appliquée à la conception et à la fabrication d'une porte logique reconfigurable avec plusieurs entrées et sorties. Nous démontrons que dix des douze portes logiques possibles à 2 entrées et 1 sortie sont activable sur une même structure en choisissant les trois points d'entrée et de sortie et en ajustant le seuil de luminescence non-linéaire pour le signal de sortie. / The main objective of this PhD work is to design, fabricate and characterize plasmonic devices based on highly crystalline metallic cavities for the two-dimensional information transfer and logic gate operations. First, we thoroughly characterize the optical response of ultra-thin gold colloidal cavities of sub-micronic size (400 to 900 nm) by dark- field spectroscopy (Fig. 1a). The dispersion of the high order plasmonic resonances of the cavities is measured and compared with a good agreement to simulations obtained with a numerical based on the Green Dyadic Method (GDM). We further extend our experiments to systematically tune the spectral responses of these colloidal nanoprisms in vicinity of metallic thin film substrates. A comprehensive study of these sub-micronic size cavity in bowtie antenna configuration is performed. We show a polarization-dependent field enhancement and a nanoscale field confinement at specific locations in these bowtie antennas. We systematically study the effects that could potentially affect the plasmonic resonances by non-linear photon luminescence microscopy, which has proved to be an efficient tool to observe the surface plasmon local density of states (SPLDOS). Inparticular, we show that an effective spatially and spectrally tuning of the high order plasmonic resonances can be achieved by the modification of the substrate (dielectric or metallic), by the controlled insertion of a defect inside a cavity or by the weak electromagnetic coupling between two adjacent cavities. The rational tailoring of the spatial distribution of the 2D confined resonances was applied to the design of devices with tunable plasmon transmittance between two connected cavities. The specific geometries are produced by focused ion milling crystalline gold platelets. The devices are characterized by non-linear luminescence mapping in confocal and leakage radiation microscopy techniques. The latter offers a unique way to observe propagating SPP signal over a 2D plasmonic cavity. We demonstrate the polarization-dependent mode-mediated transmittance for devices withadequate symmetry. The results are faithfully reproduced with our simulation tool based on Green dyadic method. Finally, we extend our approach to the design and fabrication of a reconfigurable logic gate device with multiple inputs and outputs. We demonstrate that 10 out of the possible 12 2-input 1-output logic gates can be implemented on the same structure by choosing the two input and the one output points. We also demonstrate reconfiguration of the device by changing polarization of the incident beam, set of input locations and threshold of the non-linear luminescence readout signal.

abstract: Extracellular vesicles (EVs) are membranous particles that are abundantly secreted in the circulation system by most cells and can be found in most biological fluids. Among different EV subtypes, exosomes are small particles (30 – 150 nm) that are generated through the double invagination of the lipid bilayer membrane of cell. Therefore, they mirror the cell membrane proteins and contain proteins, RNAs, and DNAs that can represent the phenotypic state of their cell of origin, hence considered promising biomarker candidates. Importantly, in most pathological conditions, such as cancer and infection, diseased cells secrete more EVs and the disease associated exosomes have shown great potential to serve as biomarkers for early diagnosis, disease staging, and treatment monitoring. However, using EVs as diagnostic or prognostic tools in the clinic is hindered by the lack of a rapid, sensitive, purification-free technique for their isolation and characterization. Developing standardized assays that can translate the emerging academic EV biomarker discoveries to clinically relevant procedures is a bottleneck that have slowed down advancements in medical research. Integrating widely known immunoassays with plasmonic sensors has shown the promise to detect minute amounts of antigen present in biological sample, based on changes of ambient optical refractive index, and achieve ultra-sensitivity. Plasmonic sensors take advantage of the enhanced interaction of electromagnetic radiations with electron clouds of plasmonic materials at the dielectric-metal interface in tunable wavelengths. / Dissertation/Thesis / Doctoral Dissertation Biomedical Engineering 2020