Developments in the Theory of X-ray Absorption and Compton Scattering.

Thesis (Ph.D.)--University of Washington, 2016-06

Using a non-invasive stable isotope tracer to measure the absorption of water in humans

The development of solutions that prevent dehydration or promote adequate re-hydration play a vital role in preventing fatigue during exercise, however, the methods commonly used to assess the hydration ability of such solutions are invasive and often assess the components of absorption separately. This paper describes using a non-invasive deuterium tracer technique that assesses gastric emptying and intestinal absorption simultaneously to evaluate the uptake of water during rest and exercise. The kinetics of absorption are further examined by mathematical modelling of the data generated. For the rest group, 0.05 g/kg of body weight of deuterium, contained in gelatine capsules, was ingested with ordinary tap water and saliva samples were collected every 5 min for one hour while the subject remained seated. The deuterium was administered as above for the exercise group but sample collection was during one hour of exercise on a treadmill at 55% of the subject's maximum heart rate. The enrichment data for each subject were mathematically modelled and the parameters obtained were compared across groups using an independent samples t-test. Compared with the rest condition, the exercise group showed delayed absorption of water as indicated by significant differences for the modelling parameters t(2), t(1/2), maximum absorption rate and solution absorption amount at t(1). Labelling with a deuterium tracer is a good measure of the relative rate ingested fluids are absorbed by the body. Mathematical modelling of the data generates rates of maximum absorption and allows calculation of the percentage of the solution that is absorbed at any given time during the testing period. Copyright (C) 2004 John Wiley Sons, Ltd.

Time-resolved spectroscopy of the metal-to-metal charge transfer excited state in dinuclear cyano-bridged mixed-valence complexes

Visible pump-probe spectroscopy has been used to identify and characterize short-lived metal-to-metal charge transfer (MMCT) excited states in a group of cyano-bridged mixed-valence complexes of the formula [(LCoNCMII)-N-III(CN)(5)](-), where L is a pentadentate macrocyclic pentaamine (L-14) or triamine-dithiaether (L-14S) and M is Fe or Ru. Nanosecond pump-probe spectroscopy on frozen solutions of [(LCoNCFeII)-Co-14-N-III(CN)(5)](-) and [(LCoNCFeII)-Co-14S-N-III(CN)(5)](-) at 11 K enabled the construction of difference transient absorption spectra that featured a rise in absorbance in the region of 350-400 nm consistent with the generation of the ferricyanide chromophore of the photoexcited complex. The MMCT excited state of the Ru analogue [(LCoNCRuII)-Co-14-N-III(CN)(5)](-) was too short-lived to allow its detection. Femtosecond pump-probe spectroscopy on aqueous solutions of [(LCoNCFeII)-Co-14-N-III(CN)(5)](-) and [(LCoNCFeII)-Co-14S-N-III(CN)(5)](-) at room temperature enabled the lifetimes of their Co-II-Fe-III MMCT excited states to be determined as 0.8 and 1.3 ps, respectively.

Study of optical properties of electropolymerized melanin films by photopyroelectric spectroscopy

Photopyroelectric (PPE) spectroscopy, in the 350-1,075 nm wavelength range, was used to study the optical properties of electropolymerized melanin films on indium tin oxide (ITO) coated glass. The PPE intensity signal as a function of the wavelength lambda, V (n)(lambda) and its phase F (n)(lambda) were independently measured. Using the PPE signal intensity and the thermal and optical properties of the pyroelectric detector, we were able to calculate the optical absorption coefficient beta of melanin in the solid-state. We believe this to be the first such measurement of its kind on this material. Additionally, we found an optical gap in these melanin films at 1.70 eV.

Time-resolved photoluminescence spectroscopy of ligand-capped PbS nanocrystals

PbS nanocrystals are synthesized using colloidal techniques and have their surfaces capped with oleic acid. The absorption band edge of the PbS nanocrystals is tuned between 900 and 580 nm. The PbS nanocrystals exhibit tuneable photoluminescence with large non-resonant Stokes shifts of up to 500 mcV. The magnitude of the Stokes shift is found to be dependent upon the size of PbS nanocrystals. Time-resolved photoluminescence spectroscopy of the PbS nanocrystals reveals that the photouminescence has an extraordinarily long lifetime of 1 mus. This long fluorescence lifetime is attributed to the effect of dielectric screening similar to that observed in other IV-VI semiconductor nanocrystals.

Local structures around Y and Ce cations in 10 mol% Y2O3 doped ceria ceramics by EXAFS spectroscopy

Local structures around host Ce and dopant Y cations in 10 mol% Y2O3 doped ceria solid solutions have been investigated by room and high temperature EXAFS spectroscopy. The results show that the local structures around the Cc cation in doped ceria samples are similar to that in the fluorite CeO2 structure though the coordination numbers of Ce-O tend to be smaller than 8. The local structures around Y cation, however, are significantly different from those around Ce cation, and show more resemblance to that around Y cation in the C-type Y2O3 Structure. A more accurate description of the local structures around Y cation in doped ceria was given by analyzing Y-K edge EXAFS spectra based on the C-type Y2O3 structure. (c) 2006 Elsevier B.V. All rights reserved.

The development of attenuation compensation models of fluorescence spectroscopy signals

This study examines the effect of blood absorption on the endogenous fluorescence signal intensity of biological tissues. Experimental studies were conducted to identify these effects. To register the fluorescence intensity, the fluorescence spectroscopy method was employed. The intensity of the blood flow was measured by laser Doppler flowmetry. We proposed one possible implementation of the Monte Carlo method for the theoretical analysis of the effect of blood on the fluorescence signals. The simulation is constructed as a four-layer skin optical model based on the known optical parameters of the skin with different levels of blood supply. With the help of the simulation, we demonstrate how the level of blood supply can affect the appearance of the fluorescence spectra. In addition, to describe the properties of biological tissue, which may affect the fluorescence spectra, we turned to the method of diffuse reflectance spectroscopy (DRS). Using the spectral data provided by the DRS, the tissue attenuation effect can be extracted and used to correct the fluorescence spectra.

In vivo tissue diagnosis for myocardial infarction using optical spectroscopy with novel spectral interpretation algorithms

In recent decades, the rapid development of optical spectroscopy for tissue diagnosis has been indicative of its high clinical value. The goal of this research is to prove the feasibility of using diffuse reflectance spectroscopy and fluorescence spectroscopy to assess myocardial infarction (MI) in vivo. The proposed optical technique was designed to be an intra-operative guidance tool that can provide useful information about the condition of an infarct for surgeons and researchers. ^ In order to gain insight into the pathophysiological characteristics of an infarct, two novel spectral analysis algorithms were developed to interpret diffuse reflectance spectra. The algorithms were developed based on the unique absorption properties of hemoglobin for the purpose of retrieving regional hemoglobin oxygenation saturation and concentration data in tissue from diffuse reflectance spectra. The algorithms were evaluated and validated using simulated data and actual experimental data. ^ Finally, the hypothesis of the study was validated using a rabbit model of MI. The mechanism by which the MI was induced was the ligation of a major coronary artery of the left ventricle. Three to four weeks after the MI was induced, the extent of myocardial tissue injury and the evolution of the wound healing process were investigated using the proposed spectroscopic methodology as well as histology. The correlations between spectral alterations and histopathological features of the MI were analyzed statistically. ^ The results of this PhD study demonstrate the applicability of the proposed optical methodology for assessing myocardial tissue damage induced by MI in vivo. The results of the spectral analysis suggest that connective tissue proliferation induced by MI significantly alter the characteristics of diffuse reflectance and fluorescence spectra. The magnitudes of the alterations could be quantitatively related to the severity and extensiveness of connective tissue proliferation.^

(Table 1) Salinity, dissolved organic carbon and absorption characteristics of surface river waters around Hudson Bay

Composition and concentration of colored dissolved organic matter (CDOM) have been determined in Hudson Bay and Hudson Strait by excitation emission matrix spectroscopy (EEM) and parallel factor analysis (PARAFAC). Based on 63 surface samples, PARAFAC identified three fluorescent components, which were attributed to two humic- and one protein-like components. One humic-like component was identified as representing terrestrial organic matter and showed a conservative behaviour in Hudson Bay estuaries. The second humic-like component, traditionally identified as peak M, originated both from land and produced in the marine environment. Component 3 had spectra resembling protein-like material and thought to be plankton-derived. The distribution and composition of CDOM were largely controlled by water mass mixing with protein-like component being the least affected. Distinctive fluorescence patterns were also found between Hudson Bay and Hudson Strait, suggesting different sources of CDOM. The optically active fraction of DOC (both absorbing and fluorescing) was very high in the Hudson Bay (up to 89%) suggesting that fluorescence and absorbance can be used as proxies of the DOC concentration.

Surface-Enhanced Raman Spectroscopy as a Probe of the Surface Chemistry of Nanostructured Materials

Surface-enhanced Raman spectroscopy (SERS) is now widely used as a rapid and inexpensive tool for chemical/biochemical analysis. The method can give enormous increases in the intensities of the Raman signals of low-concentration molecular targets if they are adsorbed on suitable enhancing substrates, which are typically composed of nanostructured Ag or Au. However, the features of SERS that allow it to be used as a chemical sensor also mean that it can be used as a powerful probe of the surface chemistry of any nanostructured material that can provide SERS enhancement. This is important because it is the surface chemistry that controls how these materials interact with their local environment and, in real applications, this interaction can be more important than more commonly measured properties such as morphology or plasmonic absorption. Here, the opportunity that this approach to SERS provides is illustrated with examples where the surface chemistry is both characterized and controlled in order to create functional nanomaterials.

VLT FORS2 comparative transmission spectroscopy: Detection of Na in the atmosphere of WASP-39b from the ground

We present transmission spectroscopy of the warm Saturn-mass exoplanet WASP-39b made with the Very Large Telescope (VLT) FOcal Reducer and Spectrograph (FORS2) across the wavelength range 411-810nm. The transit depth is measured with a typical precision of 240 parts per million (ppm) in wavelength bins of 10nm on a V = 12.1 magnitude star. We detect the sodium absorption feature (3.2-sigma) and find evidence for potassium. The ground-based transmission spectrum is consistent with Hubble Space Telescope (HST) optical spectroscopy, strengthening the interpretation of WASP-39b having a largely clear atmosphere. Our results demonstrate the great potential of the recently upgraded FORS2 spectrograph for optical transmission spectroscopy, obtaining HST-quality light curves from the ground.

Energy level decay and excited state absorption processes in erbium-doped tellurium glass

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Insight into Biological Small-Molecule Activation from Enzymes, Model Complexes, and X-ray Spectroscopy

Thesis (Ph.D.)--University of Washington, 2016-08

Using Surface Spectroscopy to Help Interpret STM Images of Chemisorbed Molecules: Application to the Study of the Hydrogenation of Ketones and a-Ketoesters on Pt

Depuis que la haute énantiopureté est nécessaire dans l’industrie pharmaceutique, les études visant à découvrir les mécanismes pour l’hydrogénation énantiosélective de cétones ou céto-esters sur les surfaces, et à rechercher de nouveaux et plus performants catalyseurs asymétriques, sont d’une grande importance. La microscopie à effet tunnel (STM), la spectroscopie infrarouge de réflexion-absorption, la spectroscopie de désorption à température programmée et la spectrométrie de photoélectrons induits par rayons X sont des méthodes performantes facilitant la compréhension des mécanismes de réaction. En plus de nous permettre de comprendre les mécanismes réactionnels, les études peuvent fournir des informations sur la dynamique des réactions en catalyse hétérogène ainsi que sur le développement de la théorie de la fonctionnelle de la densité (DFT) afin de calculer des interactions faibles dans les processus de surface. D’autres parts, les calculs DFT fournissent une aide essentielle à l’interprétation des données de STM et spectroscopie de surface. Dans cette thèse, certains cétones et céto-esters sur la surface de platine sont étudiées par les techniques sophistiquées mentionnées ci-dessus. Mes études démontrent que la combinaison de l’utilisation de la spectroscopie de routine, des nanotechnologies et de nombreux calculs élaborés, est une méthode efficace pour étudier les réactions à la surface car ces techniques explorent les différents aspects de la surface ainsi que s’entraident mutuellement lors de certaines interprétations.

Studies of Protein-Protein and Protein-Water Interactions by Small Angle X-Ray Scattering, Terahertz Spectroscopy, ASMOS, And Computer Simulation

The protein folding problem has been one of the most challenging subjects in biological physics due to its complexity. Energy landscape theory based on statistical mechanics provides a thermodynamic interpretation of the protein folding process. We have been working to answer fundamental questions about protein-protein and protein-water interactions, which are very important for describing the energy landscape surface of proteins correctly. At first, we present a new method for computing protein-protein interaction potentials of solvated proteins directly from SAXS data. An ensemble of proteins was modeled by Metropolis Monte Carlo and Molecular Dynamics simulations, and the global X-ray scattering of the whole model ensemble was computed at each snapshot of the simulation. The interaction potential model was optimized and iterated by a Levenberg-Marquardt algorithm. Secondly, we report that terahertz spectroscopy directly probes hydration dynamics around proteins and determines the size of the dynamical hydration shell. We also present the sequence and pH-dependence of the hydration shell and the effect of the hydrophobicity. On the other hand, kinetic terahertz absorption (KITA) spectroscopy is introduced to study the refolding kinetics of ubiquitin and its mutants. KITA results are compared to small angle X-ray scattering, tryptophan fluorescence, and circular dichroism results. We propose that KITA monitors the rearrangement of hydrogen bonding during secondary structure formation. Finally, we present development of the automated single molecule operating system (ASMOS) for a high throughput single molecule detector, which levitates a single protein molecule in a 10 µm diameter droplet by the laser guidance. I also have performed supporting calculations and simulations with my own program codes.