Plasmonic nanoparticles, specifically gold and silver nanoparticles, exhibit unique optical, physical, and chemical properties that are exploited in many biomedical applications. Due to their nanometer size, facile surface functionalization and enhanced optical performance, gold and silver nanoparticles can be used to investigate cellular biology. The work herein highlights a new methodology that has exploited these remarkable properties in order to probe various aspect of cancer cell biology, such as cell cycle progression, drug delivery, and cell death. Cell death mechanisms due to localized gold and silver nanoparticle exposure were also elucidated in this work. Chapter 1 introduces the reader to the synthesis and functionalization of gold and silver nanoparticles as well as reviews their implementation in biodiagnostic and therapeutic applications to provide a foundation for Chapters 3 and 4, where their use in spectroscopic and cytotoxic studies are presented. Chapter 2 provides the reader with detailed explanations of experimental protocols for nanoparticle synthesis and functionalization, in vitro cellular biology experiments, and live-cell Raman spectroscopy experiments that were utilized throughout Chapters 3 and 4. Chapter 3 presents the use of nuclear-targeted gold nanoparticles in conjunction with a Raman microscope modified to contain a live-cell imaging chamber to probe cancer cell cycle progression (Chapter 3.1), examine drug efficacy (Chapter 3.2), monitor drug delivery (Chapter 3.3), and detect apoptotic molecular events in real-time (Chapter 3.4). In Chapter 4, the intracellular effects of gold and silver nanoparticles are explored through live-cell Rayleigh imaging, cell cycle analysis and DNA damage (Chapter 4.1), as well as through the elucidation of cytotoxic cell death mechanisms after nanoparticle exposure (Chapter 4.2) and live cell imaging of silver nanoparticle treated cancer cell communities (Chapter 4.3).

The purpose of this study is to demonstrate the ability of surface enhanced Raman scattering (SERS) active particles to enable multiplexed immunoassays in a lateral flow format for point of care (POC) testing. The SERS particles used for this study are chemically active glass coated gold particles, containing tracer molecules which in principle can be chosen to provide Raman Spectra with unique features allowing multiple tracers to be simultaneously measured and distinguished without interference between each other. Lateral flow immunoassay technology is the important part of this study and can be conveniently packaged for the use of other than highly skilled technicians outside of the laboratory. A well-known (single channel - simplex) device for the pregnancy test is a typical example of the lateral flow assay. Similar formats have been/are being developed by others for a range of POC applications – but most diagnostic applications require simultaneous determination of a range of biomarkers and multiplexed assays are difficult to achieve without significant interference between the individual assays. This is where SERS particles may provide some advantages over existing techniques. Cardiac markers are the growing market for point of care technology therefore biomarkers of cardiac injury (Troponin, myoglobin and CRP) have been chosen as a model. The object of the study is to establish the proof of concept multiplexing assay using these chosen biomarkers. Thus, initially all different particles were characterised in single and mixture form. Also development of conjugate chemistry between antibodies for each analyte that have been purchased from commercial sources and SERS particles were analysed using different conditions like buffer, pH and antibody loading concentration to get the optimum intensity. The selected SERS particles and their conjugates were tested for size, aggregation and immune quality using a range of techniques: ultraviolet-visible (UV/Vis) absorption spectroscopy, dynamic light scattering (DLS) and lateral flow assay. These characterisations methodologies gave the understanding of optimum conditions of the each conjugates and individual’s behaviour in mixture conditions as well. After the characterisation all conjugates were tested singularly on the lateral flow assay using buffers and serum. The results of this single analyte immunoassay explained the individual’s bioactivity on the lateral flow strip. Further in study, multiplex assay have been demonstrated in serum. These outcomes have described each candidate characteristic in a mixture form on the lateral flow strip. In order to get the optimum Raman intensity from multiplex assay, the detection and capture antibodies loading concentrations were tuned in the assay. Later on different combinations (high, medium and low concentrations) of all three analytes were analysed and has found some interferences in multiplex assay. To investigate these issues various aspect were considered. First of all, different possibilities of non-specific interactions between the co-analytes and antibodies were tested. In addition, steric hindrance and optical interference investigations were performed via several assays and analysis using Scanning electron microscopy. The outcomes have confirmed related optical interferences. Therefore other assay (wound biomarkers) established to eliminate the interferences. In summary, the works reported here have built and test the equipment and necessary reagents for individual assays before moving on the more complicated task. In addition, the entire study has given a deep knowledge of multiplex assay on a single test line including the investigation of the issues for selected cardiac biomarkers and their applications in the future.

This thesis presents the experimental work performed on the spectrin protein. The aim of the work was to study the direct interactions of spectrin, the cytoskeleton of RBCs, with membrane lipid to determine its effects on the mechanical properties of the lipid bilayer. Motivation for this work came from a lack of unanimity in the field of spectrin, and the hypothesized potential of the protein to perforate giant unilamellar vesicles. The work aimed to investigate and determine how spectrin-lipid interactions influence membrane mesoscopic morphology and biophysics in ways that could ultimately be important to cellular function. For this purpose, a protocol was implemented to take into account the different aspects of the binding. Direct visualisation of the spectrin-lipid interaction and distribution was achieved using confocal fluorescence microscopy. Changes in the mechanical properties of the membrane were investigated using the micropipette aspiration technique. Finally the thermodynamics of the interaction were considered with isothermal titration calorimetry experiments. This allowed evaluation of the protein-lipid interaction in a complete and coherent manner. Experiments were also performed on another elastic protein, alpha-elastin, for comparison. In addition to its similarities with spectrin (both possess hydrophobic domains and entropy elasticity), elastin is auto-fluorescent which makes it an attractive model protein. Elastin was also used as a sample model to implement new techniques using nonlinear optics microscopy.

In some high-field laser-plasma experiments, it is advantageous to accompany the main high-energy (~1 J) laser with a second high-energy pulse (~0.1 J) which has been frequency-shifted by ~10-20%. Such a pulse-pair would have a low walk-off velocity while remaining spectrally distinct for use in two-color pump-probe experiments. Moreover, by shifting the second pulse by ~plasma frequency, it is theoretically possible to exercise some amount of control over a variety of laser-plasma instabilities, including forward Raman scattering, electromagnetic cascading, and relativistic self-focusing. Alternatively, the two pulses may be counter-propagated so that the collide in the plasma and create a slowly-propagating beatwave which can be used to inject electrons into a laser wakefield accelerator. The design, characeterization, and performance of a hybrid chirped-pulse Raman amplifier (CPRA)/Ti-Sapphire amplifier are reported and discussed. This hybrid system allows for the generation of a high-energy (>200 mJ), broadband (15-20 nm bandwidth FWHM), short duration (>100 fs duration) laser sideband. When amplified and compressed, the Raman beam's power exceeds 1 TW. This sideband is combined with the primary laser system to create a bi-color terawatt laser system which is capable of performing two-color high-field experiments. This two-color capability can be added to any commercial terawatt laser system without compromising the energy, duration or beam quality of the primary system. Preliminary two-color laser-plasma experiments are also discussed. / text

Die vorliegende Arbeit befasst sich mit der Untersuchung von weitbandlückigen Halbleitern mittels Raman-Spektroskopie. Diese wurde vorwiegend unter Verwendung von Licht einer Wellenlänge von 325 nm im ultravioletten Spektralbereich angeregt. Damit konnten zum einen aufgrund eines erhöhten Streuquerschnittes Messungen zur Probencharakterisierung durchgeführt werden, die mit Anregung im sichtbaren Spektralbereich nicht möglich gewesen wären. Zum anderen wurden bei dieser Anregungswellenlänge auftretende Resonanzeffekte untersucht. Dabei werden zwei verschiedene Materialsysteme behandelt: zum einen Kristalle mit Wurtzitstruktur und zum anderen binäre und ternäre Sesquioxide mit Metallionen der III. Hauptgruppe. An den Kristallen mit Wurtzitstruktur wurde die Streuung des Anregungslichts mit Energie oberhalb der Bandlücke an longitudinal-optischen (LO) Phononen untersucht. Die Streuung an einzelnen LO-Phononen wird unter diesen Anregungsbedingungen von einem Prozess dominiert, der eine elastische Streuung beinhaltet, durch die die Impulserhaltung verletzt wird. Es wurde ein Modell aufgestellt, dass zwischen einer elastischen Streuung an der Oberfläche und an Punktdefekten unterscheidet, und mit Hilfe von Experimenten verifiziert. Weiterhin wurde der Einfluss von Ladungsträgern auf die Energie der LO-Phononen untersucht und es wird eine Anwendung dieser Erkenntnisse zur Charakterisierung der Oberfläche von Zinkoxid vorgestellt. An den binären Oxiden des Galliums und Indiums wurden die Energien der Phononenmoden ermittelt und die resonante Verstärkung bei der verwendeten Anregungswellenlänge untersucht. Für das Galliumoxid wurde dabei insbesondere die Anisotropie des Materials berücksichtigt. Für das Indiumoxid wird dargestellt, dass durch die resonante Anregung alle Phononenmoden beobachtet werden können, was insbesondere auch die Bestimmung der Phononenmoden von Dünnschichtproben ermöglicht. Weiterhin waren Mischkristalle des Galliumoxids Untersuchungsgegenstand, in denen das Gallium teilweise durch Indium oder Aluminium ersetzt wurde. Die Phononenenergien wurden in Abhängigkeit der Zusammensetzung ermittelt und der Einfluss von strukturellen Eigenschaften darauf sowie das Auftreten von Phasenübergängen untersucht.

<p>Nonlinear optical microscopy serves as a great tool for biomedical imaging due to its high resolution, deep penetration, inherent three dimensional optical sectioning capabilities and superior performance in scattering media. Conventional nonlinear optical microscopy techniques, e.g. two photon fluorescence and second harmonic generation, are based on detecting a small light signal emitted at a new wavelength that is well separated from the excitation light. However, there are also many other nonlinear processes, such as two-photon absorption and self-phase modulation, that do not generate light at new wavelengths and that have not been extensively explored for imaging. This dissertation extends the accessible mechanisms for contrast to the later nonlinear optical processes by combining femtosecond laser pulse shaping and homodyne detection. We developed a rapid pulse shaper with a relatively simple and compact instrument design that modifies the spectrum of individual laser pulses from an 80 MHz mode-locked laser. The pulse shaper enables simultaneous two-photon absorption and self-phase modulation imaging of various nanoparticles in-vitro with high sensitivity. We also applied this imaging technique to study the nonlinear optical response in graphene. Because our technology detects the nonlinear signature encoded within the laser pulse itself, we achieve intrinsic contrast of biological and non-biological samples in highly scattering media. These capabilities have significant implications in biomedical imaging and nanophotonics.</p> / Dissertation

Applying linear programming (LP) to spectroscopy techniques, such as IR, Raman and SFG, is a new approach to extract the molecular orientation information at surfaces. In Hung’s previous research, he has shown how applying LP results in the computational gain from O(n!) to O(n). However, this LP approach does not always return the known molecular orientation distribution information when mock spectral information is used to build the instance of the model. The first goal of our study is to figure out the cause for the failed LP instances. After that, we also want to know for different cases with what spectral information, can the correct molecular orientation be expected when using LP. To achieve these goals, a simplified molecular model is designated to study the nature of our LP model. With the information gained, we further apply the LP approach to various test cases in order to verify whether it can be systematically applied to different circumstances. We have achieved the following conclusions: with the help of simplified molecular model, the inability to extract a sufficient data set from the given spectral information to build the LP instances is the reason that the LP solver does not return the target composition. When candidates coming from one same molecule, even combining all three spectral information of IR, Raman and SFG, the data set extracted is still not sufficient in order to obtain the target composition for most cases. When candidates are coming from different molecules, Raman or SFG spectral information alone contains sufficient data set to obtain the target composition when candidates of each molecule expanded in [0◦, 90◦) on θ. When candidates of each molecule expanded in [0◦, 180◦] on θ, excluding 90◦, SFG spectral information needs to combine with IR or Raman in order to obtain the sufficient data set to obtain the target composition. When the slack variable is introduced to each spectral technique, for the case of candidates coming from different molecules, when candidates expanded in [0◦, 90◦) on θ, Raman spectral information carries sufficient data set to obtain the target composition. When candidates expanded in [0◦, 180◦] on θ, excluding 90◦, SFG and Raman spectral information together carries sufficient data set in order to obtain the target composition. / Graduate / chenfei.cp@gmail.com

Cette thèse porte sur les mélanges d’onde non linéaires qui peuvent avoir lieu dans le champ évanescent de nanofibres de silice. Nous nous sommes plus particulièrement intéressés à la diffusion Raman stimulée qui est obtenue par l’interaction du champ évanescent très intense et un liquide non linéaire dans lequel baigne la nanofibre. Afin de mettre en évidence la diffusion Raman stimulée« évanescente », nous avons développé un modèle de simulation non linéaire dont le but est de déterminer les caractéristiques des nanofibres à réaliser. Le gain Raman modal est calculé afin de trouver le rayon optimal des nanofibres pour chaque liquide ou mélange de liquides possible. En considérant la puissance critique et le seuil de dommage de nos nanofibres, nous avons déduit la longueur minimale d’interaction. Les conditions d’adiabacité des parties évasées menant à la nanofibre sont également discutées. Ces spécifications nous ont amenés à développer une plateforme de tirage de nanofibres spécifiquement dédiée à ces expériences de non-linéarités évanescentes. Cette palteforme nous permet de tirer des nanofibres de diamètre allant jusqu’à 200 nm sur des longueurs de 10 cm, avec plus de 90% de transmission. Avec ces nanofibres, nous avons mis en évidence le premier ordre Stokes de l’éthanol dans le champ évanescent d’une nanofibre, ainsi que les premier et second ordres Stokes du toluène. Ces premières expériences sont en très bon accord avec nos simulations et ouvrent la voie à de nombreuses expériences en optique non linéaire. / The present PhD thesis explored nonlinear wave mixing with the strong evanescent field of nanofibers. The focus has been on the effect of stimulated Raman scattering which is activated by the interaction between such a strong evanescent field and the nonlinear liquid surrounding the nanofiber. In order to observe the stimulated Raman scattering, we investigated the nonlinear modeling to determine the needed characteristics of the nanofibers. The modal Raman gain was calculated to determine the optimal radius of nanofibers for each possible liquid. Considering the critical power and the damage threshold of our nanofibers, we found the minimum required interaction length. The condition of adiabacity of the tapers was also described. These specifications of nanofibers guide us towards the design of a proper pulling system. Several pulling systems and techniques are investigated for the fabrication of our specific nanofibers. We now are able to fabricate low loss uniform nanofibers of up to 10 cm long, a diameter down to 200 nm, with two identical low loss tapers by using our own designed translation stage pulling platform and implemented with the “variable heat brush” technique. With the achieved nanofibers, the Raman effect induced in the evanescent field was observed in both pure (ethanol) and binary mixture (toluene in ethanol) liquids. These first measurements are in good agreement with our simulation even without any fitting parameters in the modeling.

[pt] Este trabalho visa estabelecer na prática a estatística do ganho dependente da polarização (PDG-Polarization Dependent Gain) em sistemas ópticos com amplificação Raman. A amplificação Raman depende fortemente da polarização relativa entre os fótons de bombeio e de sinal, que tem que ser paralelas para máximo ganho [1]. Portanto, a birrefringência é um importante limitador de desempenho de sistemas de longa distância amplificados por esta técnica visto que modifica os estados de polarização de forma diferente para cada comprimento de onda. A birrefringência varia aleatoriamente de acordo com as flutuações do ambiente onde está a fibra óptica, dando origem à dispersão dos modos de polarização, efeito este conhecido pela sigla PMD. Alguns experimentos recentes mostraram que o amplificador Raman não só depende do estado de polarização do sinal de entrada, mas também que o valor da dependência do ganho com a polarização (PDG- Polarization Dependent Gain) flutua devido a natureza aleatória da PMD [4,5]. É importante conhecer a estatística da PDG, sua relação com a PMD e como a PDG pode ser reduzida a níveis aceitáveis. Nesse trabalho será medida experimentalmente a distribuição estatística da PDG em fibras de dispersão deslocada e os resultados comparados com as previsões teóricas dadas por [2]. / [en] Raman amplifiers are very attractive because they provide a large and relatively flat gain over a wide bandwidth while maintaining a small noise figure, and they can be made using regular silica fiber. However, the Raman Gain coefficient is polarization sensitive and can be up to ten times higher when the signal and pump polarization states are parallel rather than perpendicular [1]. Usually fibers present some degree of residual asymmetry - because the fiber core is slightly out-of-round, or because of mechanical stress on the deployed fiber - and this causes polarization mode dispersion. The light traveling along one polarization axis moves slower or faster than the light polarized along the other axis. This effect distorts the signal and causes polarization fluctuations along the fiber. As the Raman gain is higher when the signal and pump polarization states are parallel these fluctuations of the relative polarization between signal and pump vary the instantaneous value of the Raman gain. So the Polarization Dependence Gain (PMG) is directly related to the PMD. Several experimental studies have shown not only that the gain of raman amplifiers depends on the state of polarization of the input signal but also that this polarization-dependent gain (PDG) fluctuates over a wide range because of the random nature of polarization mode dispersion (PMD) [4,5]. It is important to know the statistics of PDG, its relationship to the PMD, and how the PDG can be reduced to acceptable low levels. In this letter we will demonstrate experimentally the statistical distribution of the PDG given by [2]. This In this work the polarization dependent gain (PDG) fluctuations due to PMD in Raman amplified optical transmissions is experimentally demonstrated.

No presente trabalho é feito um estudo sistemático do efeito do campo cristalino nas propriedades ópticas do íon Er3+. Para tal propósito utilizamos três diferentes sistemas cristalinos dopados com Er3+: Ortovanadato de cálcio [Ca3(VO4)2], Niobato de lítio [LiNb03] e Titanato de bismuto [Bi12TiO20]. Os cristais foram crescidos no formato de fibras, pela técnica LHPG (Laser Heated Pedestal Growth). O uso deste método de crescimento permitiu não apenas o estudo do efeito do campo cristalino da matriz no Er3+ como também, a influência de diferentes condições crescimento. As composições dos cristais foram determinadas através de EDX (Energy Dispersive X Ray), XPS (X Ray Photoelectron Spectroscopy) e microscopia Auger. As amostras também foram investigadas através de absorção óptica e emissão, incluindo a determinação de seus índices de refração, gap óptico, identificação e análise de várias transições, medidas de emissão dependentes do tempo e da temperatura. A estrutura de todos os cristais foram investigadas pelas técnicas de difração de raios X e espalhamento Raman. Baseados nos resultados experimentais foi possível inferir sobre as regras impostas pelas condições de crescimento nas propriedades finais das fibras cristalinas de Ca3(VO4)2, LilNbO3 e Bi12Ti020 dopados com Er3+. Especificamente relacionado com as fibras cristalinas de Ca3(VO4)2 e LiNBbO3 dopadas com Er3+, a inserção de diferentes pressões de oxigênio molecular, durante o crescimento, induz mudanças significativas na sua estrutura cristalina. A inserção de íons Er3+ na matiz Bi12Ti020 produz uma luminescência fraca, quando comparada a do Ca3(VO4)2 e LiNbO3, porém esta luminescência apresenta um aumento considerável quando as amostras são co-dopada com íons Ga3+ / In this work we performed a systematic study of the crystal field effect on the optical properties of the Er3+ ion. For such a purpose we used three different crystalline Er3+ doped systems: calcium orthovanadate [Ca3(VO4)2, lithium niobate [LiNbO3] and bismuth titanate [Bi12TiO20]. The crystals were grown in the shape of fibers by the Laser Heated Pedestal Growth (LHPG) technique. By using this growth technique it was possible to explore not only the effects of different crystal fields on the Er3+ ion but also, the influence of different growth conditions. The composition of each fiber was determined from EDX (Energy, Dispersive X Ray , analysis), XPS (X Ray Photoelectron Spectroscopy) and Auger microprobe. The fibers were also optically investigated through optical absorption and emission and included the determination of their index of refraction, optical band gap, the identification and analysis of several different transitions, temperature and time-dependent measurements, etc. The structure of all crystals were investigated by X ray diffraction and Raman scattering techniques. Based on these experimental results it was possible to infer the role played by the growth technique and conditions on the final properties of these Er3+ -doped Ca3(VO4)2, LiNbO3 and Bi12Ti020 crystalline fibers. Specifically related to the Er3+ -doped Ca3(VO4)2 and LiNbO3 fibers, different pressures of molecular oxygen, during the groNvt.h., induces significant changes on their atomic (and electronic) structure. The insertion of Er3+ ions in the Bi12Ti020 matrix produces a small photoluminescence intensity, when compared with Ca3(VO4)2 and LINbO3, which is considerably increased by co-doping with Ga3+ ions