Thesis (M.Sc.)--York University, 2005. Graduate Programme in Earth and Space Science. / Typescript. Includes bibliographical references (leaves 139-147). Also available on the Internet. MODE OF ACCESS via web browser by entering the following URL: http://gateway.proquest.com/openurl?url%5Fver=Z39.88-2004&res%5Fdat=xri:pqdiss &rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&rft_dat=xri:pqdiss:MR11793

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Powerful optical spectroscopic and imaging tools have revolutionized many areas of science and technology. The detection sensitivity and chemical specificity are two major considerations when characterizing an optical technique. The fluorescence spectroscopy and microscopy provide excellent sensitivity down to single molecules. However, its reliance on probing the electronic transition limits the obtainable chemical information. In contrast, vibrational spectroscopy such as Raman scattering provides exquisite chemical specificity about the molecular structure, dynamics, and coupling with the environment. However, Raman scattering is intrinsically weak, and its cross sections are many orders of magnitudes smaller than those of fluorescence. The efforts that trying to bridge these two powerful methods can be traced back to the 1980s. But it was until our attempt in 2019, by carefully tuning the electronic pre-resonance and optimizing the excitation duration, the first successful Raman-featured fluorescence spectroscopy was demonstrated. This hybrid technique was named as stimulated Raman excited fluorescence (SREF). As expected, SREF combines both high sensitivity and exquisite chemical specificity, which enables the first all-far-field single-molecule Raman spectroscopy and imaging. This thesis is trying to provide a comprehensive interpretation of SREF, and at the same time serves as a practical guide for experiments and instrumentation. In chapter 1, the early (unsuccessful) attempts for SREF spectroscopy are reviewed. Additionally, I briefly summarize the basic theory for single- and multi-photon excitation process of a single fluorophore, from which the feasibility of SREF spectroscopy is explained. Chapter 2 is mainly focused on the instrumental details of the first successful SREF spectroscopy, and the basic spectroscopic features of SREF are summarized. The generality of SREF spectroscopy is systematically discussed in Chapter 3, and a rule-of-thumb criterion for successful SREF excitation based on the simple two-beam excitation strategy is proposed. Aimed at background-free SREF microscopy, a three-beam system based on nonlinear fiber optics and lock-in detection is illustrated in Chapter 4. In chapter 5, the first attempt to combine SREF and the stimulated emission depletion (STED) for an all-far-field super-resolution vibrational imaging is proposed. At last, as a simple application of SREF microscopy, SREF-based vibrational Stark spectroscopy on visualizing the electrostatic field at the water-oil interface of microdroplets is discussed(Chapter 6).

Ultracold bialkali polar molecules present a wealth of opportunities in quantum science research and technology; including fields such as quantum simulation, quantum chemistry, quantum metrology, precision measurement and quantum computation. A great deal of interest lies in their rich internal rotational and vibrational state structure and their large electric dipole moment. However, the additional complexity also provides significant challenges. To date, only a limited number of molecular species are available at ultracold temperatures below 1 microkelvin. The assembly of heteronuclear ground state molecules from ultracold atoms has emerged as a promising approach for creating ultracold molecules. In this thesis, I will present the creation of the first ultracold gases of NaCs ground state molecules. First, we produce an ultracold mixture of Na and Cs. Second, we associate weakly bound molecular pairs from the Na-Cs mixture. Finally, we apply a two-photon stimulated Raman adiabatic passage (STIRAP) pulse to transfer the weakly bound NaCs molecules into the deeply bound rovibrational ground state. I report on the construction of a new apparatus that produces ultracold mixtures of Na and Cs. We use this apparatus to assemble weakly bound NaCs molecules and successfully transfer up to 20,000 ultracold dipolar NaCs molecules to their rovibrational ground state in each experimental run. On the way to these results, we demonstrated a pathway towards creating the first quantum degenerate mixtures of Na and Cs. We identified and characterized an interspecies Feshbach resonance at 864.12(5) G, adiabatically sweeping across it to form weakly bound NaCs Feshbach molecules. We characterized the Feshbach molecule formation in various parameter regimes. Next, we performed a study of accessible NaCs excited states and identified a pathway to the rovibrational ground state using one- and two-photon spectroscopy. Finally, we demonstrated STIRAP to the rovibrational ground state, and investigated basic properties of the ground state molecules.

This thesis presents analytic and computational advances in the prediction of perturbative nonlinear optical spectroscopies. The contributions of this thesis are packaged together in an open source, freely available piece of software called ultrafast spectroscopy suite (UFSS). It is designed to automatically simulate nonlinear optical spectroscopies for any phase-matching or phase-cycling condition, including finite pulse effects. UFSS includes an algorithm called the diagram generator (DG) that automates the process of writing out all of the Feynman diagrams that contribute to a desired phase-matching or phase-cycling condition, and includes all pulse overlap diagrams when relevant, paving the way toward automation of perturbative calculations. Further, many diagrams can be automatically combined into composite diagrams, giving an exponential decrease in computation time of high-order calculations. Composite diagrams even allow for the efficient study of Rabi oscillations as a function of pulse amplitude, by summing many orders of perturbation theory. The perturbative calculations are done using a novel algorithm presented in this thesis called Ultrafast Ultrafast spectroscopy (UF2). UF2 is an efficient method for determining diagrammatic contributions to spectra including arbitrary (whether analytical or experimentally measured) pulse shapes. It uses the speed of the fast Fourier transform to be as much as 500 times faster than direct propagation techniques for small model Hamiltonians (for Hamiltonian dimension of 100 or less). UF2 outperforms direct propagation techniques for a wide range of model systems, with the speed boost diminishing as the dimension of the model Hamiltonian increases. UF2 can predict spectra for any model system whose relevant Hilbert space that can be described using a finite basis and that can be diagonalized numerically, and users are free to specify their own model. UFSS includes a model generator that generates Hamiltonians and Liouvillians of vibronic systems, allowing users to easily simulate NLOSs for a wide range of model system parameters. UFSS is a fully functional piece of software for simulating any NLOS, to any desired order in perturbation theory.

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A magnetic resonance imaging (MRI) compatible near infrared spectrometer (NIRS) system was developed and evaluated for continuous-wave diffuse optical spectroscopy (DOS) and concurrent functional MRI measurements of human muscle. Phantom and in-vivo experiments using the system’s fiber bundle suggested that an isolation distance greater than 8 mm needs to exist between adjacent illumination-detection channels. Using single and probe-pair arrangements (inter-fiber separations of 80 µm and 5 mm, respectively), in-vivo DOS point-measurements (total=20 images) were performed on 1) the antecubital vein and a reference tissue area and 2) the lower leg at the medial (MG) and lateral gastrocnemius (LG) under isokinetic exercise. Mean spectral morphological differences and relative mean intensity changes at Hemoglobin key wavelengths were found, namely reduced mean pixel intensity (~30%) for the vessel-area and a signal change of ~1-4% between the rest and the recovery condition at both muscle locations for the single-probe configuration. Subsequent work is necessary to evaluate the oxygenation assessment capabilities of this system. Lastly, experiments were performed in which two volunteers had concurrent measurement of optical and blood oxygen level dependent (BOLD) MRI, before and following exercise. The same probe arrangement was used for DOS measurements for this experiment. The BOLD signal was studied for manually-derived ROIs. BOLD recovery curves corresponding to the LG followed routine temporal progression where immediate post-exercise signal is hypointense, followed with a sigmoidal-shaped recovery. A decrease ranging between ~0.1-20% was found in the normalized mean spectral signal (20 images) for recovery with reference to the rest condition at both muscle locations for single-probe measurements and for one probe-pair measurement (for 800,808 and 850 nm). The specific trend of the measured decrease in the mean spectral curves during recovery was not consistent among these trials. Future steps include repeatable phantom experiments, increased optical power delivery, enhanced skin contact and improved reflectance measurements / Thesis / Master of Applied Science (MASc)

The number of skin cancer cases reported in the United States is increasing every year and nearly equals the total cancer cases detected from every other part of the body. Current detection strategies of skin cancers include a visual examination followed by a tissue biopsy. This procedure is subjective, invasive and time-consuming. Therefore, considering the number of cancer cases reported and the number biopsies performed, there is a critical need for a non-invasive diagnostic aid to help clinicians reduce the significantly large numbers of unnecessary biopsies. This dissertation presents a quantitative method based on optical spectroscopy for performing a non-invasive ‘optical biopsy’ of melanoma and non-melanoma skin cancers. We have developed the hardware, software and optical algorithms necessary to implement such a device. First, we present a novel lookup table-based model for determining the optical properties of tissue that is valid for fiber-based probe geometries with close source-detector separations and in highly absorbing tissue. These optical properties are quantitative parameters that can be correlated with the physiology of tissue. Second, we present experimental validation of the effects of microvasculature pigment packaging on diffuse reflectance spectra. We have conducted experiments using microfluidic devices over a physiologically relevant range of optical properties and blood vessel sizes. Third, we present the development of a probe-based portable and clinically compatible instrument capable of in vivo spectral measurements. The instrument combines two modalities – diffuse reflectance and intrinsic fluorescence spectroscopy – to provide complementary information regarding tissue morphology, function and biochemical composition. Finally, we present the results of a pilot clinical study using our portable instrument to determine the accuracy of spectral diagnosis of non-melanoma skin cancers. Our results show that the mean optical properties and fluorophore contributions of normal skin and non-melanoma skin cancers are significantly different from each other and can potentially be used as biomarkers for non-invasive diagnosis of skin cancer. / text

The nonlinear modeling capabilities of artificial neural networks (ANN’s) are renowned in the field of artificial intelligence (Al) for capturing knowledge that can be very difficult to understand otherwise. Their ability to be trained on representative data within a particular problem domain and generalise over a set of data make them efficient predictive models. One problem domain that contains complex data that would benefit from the predictive capabilities of ANN’s is that of optical emission spectra (OES). OES is an important diagnostic for monitoring plasma species within plasma processing. Normally, OES spectral interpretation requires significant prior expertise from a spectroscopist. One way of alleviating this intensive demand in order to quickly interpret OES spectra is to interpret the data using an intelligent pattern recognition technique like ANN’s. This thesis investigates and presents MLP ANN models that can successfully classify chemical species within OES spectral patterns. The primary contribution of the thesis is the creation of deployable ANN species models that can predict OES spectral line sizes directly from six controllable input process parameters; and the implementation of a novel rule extraction procedure to relate the real multi-output values of the spectral line sizes to individual input process parameters. Not only are the trained species models excellent in their predictive capability, but they also provide the foundation for extracting comprehensible rules. A secondary contribution made by this thesis is to present an adapted fuzzy rule extraction system that attaches a quantitative measure of confidence to individual rules. The most significant contribution to the field of Al that is generated from the work presented in the thesis is the fact that the rule extraction procedure utilises predictive ANN species models that employ real continuously valued multi-output data. This is an improvement on rule extraction from trained networks that normally focus on discrete binary outputs

Over the past several decades, rapid progress has been made toward the accurate characterization and control of atoms, made possible largely by the development of narrow-linewidth lasers and techniques for trapping and cooling at ultracold temperatures. Extending this progress to molecules will have exciting implications for chemistry, condensed matter physics, and precision tests of physics beyond the Standard Model. These possibilities are all consequences of the richness of molecular structure, which is governed by physics substantially different from that characterizing atomic structure. This same richness of structure, however, increases the complexity of any molecular experiment manyfold over its atomic counterpart, magnifying the difficulty of everything from trapping and cooling to the comparison of theory with experiment. This thesis describes work performed over the past six years to establish the state of the art in manipulation and quantum control of ultracold molecules. Our molecules are produced via photoassociation of ultracold strontium atoms followed by spontaneous decay to a stable ground state. We describe a thorough set of measurements characterizing the rovibrational structure of very weakly bound (and therefore very large) ⁸⁸Sr₂ molecules from several different perspectives, including determinations of binding energies; linear, quadratic, and higher order Zeeman shifts; transition strengths between bound states; and lifetimes of narrow subradiant states. The physical intuition gained in these experiments applies generally to weakly bound diatomic molecules, and suggests extensive applications in precision measurement and metrology. In addition, we present a detailed analysis of the thermally broadened spectroscopic lineshape of molecules in a non-magic optical lattice trap, showing how such lineshapes can be used to directly determine the temperature of atoms or molecules in situ, addressing a long-standing problem in ultracold physics. Finally, we discuss the measurement of photofragment angular distributions produced by photodissociation, leading to an exploration of quantum-state-resolved ultracold chemistry.