Nonlinear optical microscopy is a collection of very powerful imaging techniques. Linear optical microscopes probe the refractive index and absorption, which both stem from the first-order linear electric susceptibility. Especially in biological tissue, the variation in the refractive index is often small and the tissue is, in many cases, transparant. Nonlinear optical microscopes on the other hand probe the nonlinear higher-order susceptibilities, which can be chemically sensitive, leading to the capability to achieve label-free imaging. Nonlinear optical microscopes have been in development for more than thirty years and they are based on numerous nonlinear optical processes. The ones I will concentrate on in this thesis are second harmonic generation (SHG), coherent anti-Stokes Raman scattering (CARS), and stimulated Raman Scattering (SRS). The first technique is commonly used to image collagen as those molecules have a particularly large second-order nonlinear susceptibility due to their chiral structure. CARS and SRS on the other hand are often used because they resonantly target vibrational resonances in molecules, giving rise to the aforementioned label-free imaging. Deep understanding of the nonlinear imaging process is crucial to the interpretation of the images these techniques produce. Computational tools are exceptionally suited for this task as they allow studying the electromagnetic field anywhere in the sample as well as the far-field, and one can change any of the material properties to study their effect. One such tool is finite-difference time-domain (FDTD) that our group developed for nonlinear optical microscopy simulations. It is a direct discretization of Maxwell's equation. While computationally costly, it does allow any arbitrary shaped sample to be simulated. The sample can have frequency dependent refractive indexes, and also nonlinear media with third-order nonlinearities such as Kerr media and Raman-active media, but also second-order nonlinearities for SHG. The code is designed in such a way that it can run on thousands of CPUs on a wide variety of compute cluster which allows our group to obtain nanoscale resolution. Another computational tool I use is the free-space Green's function solution to the Helmholtz equation, which can be used to calculate the Hertz vector in the frequency domain, both in the near- and far-field, based on the induced nonlinear polarization. The electric field is then calculated from this Hertz vector. This technique is much faster then FDTD and also allows for arbitrary shapes of the nonlinear electric susceptibility in the sample. However, it assumes a homogeneous refractive index throughout the entire spatial domain and requires complete knowledge of the input beam or beams that induce the nonlinear polarization. In this thesis, I use these tools to study the image formation process of various nonlinear optical processes mentioned earlier. For example, I study the effect of an inhomogeneous refractive index on the images produced by these microscopes. In literature the index of refraction is almost always assumed to be homogeneous, because, as mentioned before, the inhomogeneity of the refractive index is often small. However, I show that these small differences in the index of refraction can have a significant effect on the measured far-field intensity signal. For example, in SRS and CARS images, the measured signal can increase by an order of magnitude depending on the index mismatch and structure of the sample. Additionally, significant shifts in perceived position occur. Even nonresonant nonlinear signals can be evoked purely through a mismatch in linear refractive index. Computational modelling can also help reveal additional detail. As SHG is a coherent process, subwavelength information can be inferred through the phase information. Our experimental collaborators built an interferometric SHG (I-SHG) microscope for exactly that purpose. We used this to image collagen fibrils, which are all aligned in a parallel fashion. However, because collagen fibrils have a chiral molecular structure, they can point either ``up'' or ``down''. Using my Green's function simulations of the SHG imaging process of collagen fibrils, I was able to predict the standard deviation in the measured phase and link it to the orientation of collagen fibrils in the focal spot of the probing laser beam, even though the diameters are far below the minimum resolvable capabilities of the microscope. We found that the ``upwards'' fibrils make up 46--53% of the sample. Even with a normal SHG microscope that does not measures phase, additional subresolution information is obtainable. With our collaborators we measured the ratio of the forward SHG intensity signal to that in the backward direction and with my simulations, we are able to link this to the fibril diameters in collagen tissue. Thus we inferred that the fibril diameter increases as a function of tissue depth. Furthermore, a computational technique called ptychography is able to retrieve phase information without an interferometric reference beam. Additionally, it increases resolution to the theoretical limit, independent of the laser focal spot size, and corrects for distortions in the input beam as well. I have developed this technique for use with nonlinear optical microscopy and was able to show it is a viable alternative to I-SHG by imaging simulated rat tail tendon at the diffraction limit while retrieving the orientation of the fibrils through the phase of the SHG signal. I also implemented the algorithm for CARS, where the phase information can be used to greatly increase the signal-to-noise ratio by reducing the nonresonant background radiation that results from competing nonlinear optical processes. I showed an example of this by imaging a simulated fibroblast cell where the CARS process was tuned to the lipid droplets inside of the cell. I am currently in talk with experimentalists to apply this theoretical technique to experiments as that would further demonstrate the impact of my work. Finally, keeping in theme with the collagen fibrils, I show that the ratio of the forward SHG signal to the backward signal, the F/B ratio, is affected by a mismatch in the refractive index for fibrils larger than 100nm. This measure is an indicator of fibril diameter and thus important for making qualitative predictions. Single fibrils are generally too small to be significantly affected by near-field effects, but the bigger fibrils can be. Fibrils in rat tail tendon have a distribution of fibrils diameters and the large fibrils occur infrequent. However, I found that the large fibrils are largely responsible for the forward as well as backward signal, thus refractive index mismatches still affect the F/B ratio significantly despite their infrequency. The F/B ratio for a collection of fibrils placed in a n=1.47 medium was found to be 31.8±0.7% higher than for those in a n=1.33 medium. Our experimental colleagues have done preliminary measurements on mouse tail tendon where they found an increase of 40±20%, in line with the value of 28.1±0.6% that I found for simulations with mouse tail tendon. In conclusion, the theoretical tools I have used in my thesis have provided me with the ability to study nonlinear optical image formation processes with a level of detail that would be near-impossible to do experimentally. I have used this ability to show how refractive index mismatches, such as those found in biological tissue, can significantly distort the far-field intensity signals. I have shown this for SRS and CARS where the far-field intensity signal appeared an order-of-magnitude larger compared to the same sample without a refractive index mismatch with the background medium. Additionally, shifts in the perceived position of the object under investigation were observed and I showed the presence of a nonresonant background signal in AM-SRS. Likewise I showed that in the SHG imaging of collagen fibrils significant changes in the F/B ratio can occur. All of these effects have important implications as these types of images as biomedical researches rely on the correct interpretation of nonlinear optical microscopy images for both research and diagnostics. Apart from showing the effect of a refractive index mismatch, I have also shown that computation modelling can be used to infer subwavelength features in SHG imaging experiments of collagen fibril such as fibril orientation and fibril diameter. These methods have the potential to aid medical researchers as changes in the structure of collagen are often an early indicator of diseases such as osteoarthritis. Finally, I showed that the ptychography algorithm I developed for nonlinear optical microscopy is able to retrieve phase information of the nonlinear electric susceptibility in SHG and CARS imaging while also enhancing the resolution and correcting for distortions in the input beams. I can also use much larger laser spot sizes than in conventional experiments without compromising the obtained resolution, thus fewer measurements are required. The technique is not limited to SHG and CARS either; it will work for other nonlinear optical processes as well. Experimental verification of nonlinear ptychography will be done soon. This technique has to potential to significantly improve current imaging techniques since access to the phase information allows one to observe additional information about the sample as we showed with the I-SHG microscope.

In der vorliegenden Dissertation werden verschiedene plasmonisch aktive Kern/Schale- Nanopartikel synthetisiert, experimentell und theoretisch charakterisiert und in analytischen Anwendungen der oberflächenverstärkten Raman-Spektroskopie (engl. surface-enhanced Raman scattering, SERS) eingesetzt. Es werden die optischen Eigenschaften von Gold/Silber-Nanoschalen mit durchstimmbaren Plasmonbanden behandelt. Motivation dafür ist die Frage nach optimalen SERS-Markern für die rote Laseranregung (λ = 632.8 nm). In SERS-Anwendungen gibt es die Möglichkeit mehrere Marker-Moleküle auf die Oberfläche der Nanopartikel aufzubringen, um so eine erhöhte Multiplexing-Kapazität zu generieren. Diese Option der gemischten Monolagen wird in der vorliegenden Arbeit untersucht. Es werden SERS-Marker-Konzepte für die rote Laseranregung basierend auf einzelnen Nanopartikeln gezeigt. Außerdem wird dargestellt, inwieweit sich durch die Anordnung von Nanopartikeln in allen drei Raumdimensionen neue SERS-Marker- Konzepte mit sehr guten plasmonischen Eigenschaften realisieren lassen. In den oben beschriebenen Kapiteln übernehmen Nanopartikel die Rolle des SERS-Substrats für den selektiven Nachweis eines bestimmten Zielmoleküls (z.B. Antigens). Neben diesen Anwendungen können Nanopartikel jedoch auch noch als SERS-Substrat für die markierungsfreie Detektion von Analytmolekülen eingesetzt werden. In dieser Dissertation wird die Herstellung, Charakterisierung und der Einsatz eines integrierten SERS-Substrats für die kombinierte Festphasensynthese und Analytik mittels plamonisch aktiver Gold/Glas-Kern/Schale-Nanopartikel auf Harz-Mikrokugeln behandelt.

Metallic nanostructures supporting surface plasmon modes can concentrate optical fields, and enhance luminescence processes from the metal surface at plasmonic hotspots. Such nanoplasmonic metal luminescence contributes to the spectral background in surface-enhanced Raman spectroscopy (SERS) measurements and is helpful in bioimaging, nano-thermometry, and chemical reaction monitoring applications. Despite increasing interest in nanoplasmonic metal luminescence, little attention has been paid to investigating its dependence on voltage modulation. Also, the hyphenated electrochemical surface-enhanced Raman spectroscopy (EC-SERS) technique typically ignores voltage-dependent spectral background information associated with nanoplasmonic metal luminescence due to limited mechanistic understanding and poor measurement reproducibility. In this thesis, we combine the experimental observations and theoretical study on dynamic Faradaic & non-Faradaic modulated nanoplasmonic metallic luminescence and molecular vibrational Raman from hotspots at the electrode-electrolyte interfaces using multiple novel nano-optoelectrodes. Our work represents a critical step toward the general application of nanoplasmonic metal luminescence signals in optical voltage biosensing, hybrid optical-electrical signal transduction, and interfacial electrochemical monitoring. / Master of Science / Understanding the non-Faradaic and Faradaic process pathway is crucial for unraveling reaction mechanisms, developing efficient catalysts, designing bionsensing methodology, energy conversion and cellular stimulator (1-7). Advances in spectroscopic techniques( 8, 9) and computational models (3, 10) have facilitated the investigation of the non-Faradic and Faradaic processes. Unlike bulk reactions, interfacial electrochemical reactions occur in nanometer-thin layers (3, 11), necessitating highly sensitive detection methods. A significant challenge is background interference from bulk electrolytes and electrodes, often obscuring weak signals from the interfacial region – traditional spectroelectrochemistry struggles to match the high temporal resolution requirement due to noise (12, 13). Surface plasmons have become a promising solution for enhancing the sensitivity of spectroelectrochemical techniques (14, 15). Surface plasmons are collective oscillations of electrons at the metal-dielectric interface, which can focus and intensify optical fields at the nanoscale (16), boosting diverse nonlinear emission signals, including fluorescence, Raman scattering, and harmonic generation (17-23). By utilizing surface plasmons, spectroelectrochemistry techniques have shown promise in detecting interfacial activities with high sensitivity. In this thesis, we introduce a pioneering dual-channel in situ EC-SERS methodology, which harnesses the synergy between plasmon-enhanced vibrational Raman scattering (PE-VRS) and plasmon-enhanced electronic Raman scattering (PE-ERS) interfacial signals to monitor and analyze the Faradaic and non-Faradaic process at the electrode-electrolyte interfaces.

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