Browsing by Subject "spectroscopy"
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Item A Broadband Miniaturized Microwave Dielectric Spectroscopy System Based on Impedance Sensing(2013-01-07) Kabiri, Saman 1988-The main purpose of this thesis is to propose a broadband miniaturized spectroscopy system to detect dielectric constant and loss tangent of lossy organic materials at RF/Microwave frequencies. Complex permittivities of lossy liquids are measured using voltage variations across a sensing element embedded in a capacitive divider circuit. The methodology for characterization of complex permittivity of materials is explained in detail. The proposed method provides a unique detection algorithm to extract the dielectric constant and loss tangent of an unknown material exposed to the sensor. The complex permittivity of binary organic mixtures have been extracted to an accuracy better than 5% using sample volumes of 200-300 ?L within the frequency range of 1-2 GHz. The results obtained from the measurements are compared to the reported values, and their agreements are presented in this work. To the best of the authors? knowledge, this is the first work presented for broadband miniaturized self-sustained complex permittivity spectroscopy at microwave frequencies.Item Application and modeling of frequency-domain lifetime spectroscopy for microsphere-based optical glucose sensors(2009-05-15) Liang, FengA new glucose affinity sensor based on a homogeneous fluorescence resonance energy transfer (FRET) assay system was developed to monitor the competitive binding between concanavalin A (ConA) and dextran. The FRET quenching kinetics of the donor were analyzed from frequency-domain (FD) measurements as functions of both glucose and acceptor-protein concentrations using a F?rster-type decay kinetics model. The results showed that the FD measurements and donor decay kinetics can indicate quantitative changes in the presence of glucose at concentrations ranging from 0 to 224 mg/dL. The second set of experiments proved the feasibility of performing analyte sensing with FD lifetime spectroscopy using microsphere-based sensors in multiple scattering solutions. A well characterized pH-sensitive fluorophore was entrapped in poly(ethylene glycol) microspheres. The particles were then immersed in a buffered polystyrene solution of various pH. Measurements of phase shift and modulation of the generated and multiply scattered fluorescent light were acquired as the modulation frequency of the incident excitation light varied from 10 to 120 MHz. After the measured data were analyzed with the coupled diffusion equations, the obtained lifetimes from the scattering measurements matched values from non-scattering measurements. Lastly, a new two-speed Monte Carlo (MC) simulation was developed to predict light propagation through the sensors and thus was used to evaluate these sensors and to design these sensors for implantation. The model used random packing structure and considered geometric optics and two light propagation speeds. Experimental measurements of phase-shift and modulation of excitation light were made on a cubic phantom with non-fluorescent resin microspheres of 74 ?m diameter, and compared to those computed from the MC simulation. The results showed that the mean phase shift (PS) deviation was 0.736? and the mean amplitude deviation was 42%. Quantitative changes in detected fluorescence phase-shift and modulation were investigated for microsphere diameter, volume fraction, refractive index, and fluorophore lifetime. We also found that even though the sensitivity of PS change in the presence of scattering was the same as the value without scattering, the values of PS were magnified due to the scattering effects.Item Examining line broadening approximations using Xenomorph : a simulation line broadening program(2013-12) Gomez, Thomas Alexander; Winget, Donald Earl, 1955-White dwarfs are particularly interesting due to their broad application to the field of astronomy (cosmochronology, SN Ia progenitors, asteroseismology). Examining distributions of white dwarf masses and temperatures, it is evident that there is some flaw in our ability to make physical atmosphere models. Tremblay and Bergeron (2009) used an {\it ad hoc} treatment of line broadening and derived significantly different surface gravity and temperatures for white dwarfs, demonstrating the importance of the line broadneing treatment in determining stellar parameters for high surface gravity stars. This thesis presents a new line broadening program, Xenomorph, based on simulation techniques. Xenomorph is used to examine various approximations used in line broadening calculations used in white dwarf atmospheres. Some approximations, like including fine structure and lower state perturbations, have small, if detectable effects. Ion motions during a transition can make features commonly seen in Stark profiles less pronounced and leads to an increase in the FWHM of the lines. Including a more complete basis set at higher densities will result in extra features, including asymmetries that has been observed in many experiments.Item Helium charge exchange recombination spectroscopy on Alcator C-Mod Tokamak(2014-05) Liao, Kenneth Teh-Yong; Gentle, Kenneth W.; Rowan, William L.The Wide-View Charge Exchange Recombination Spectroscopy (CXRS) diagnostic at Alcator C-Mod, originally designed for measurement of boron, has been modified to fit several different roles. By measuring the He¹⁺ (n = 4 [rightwards arrow] 3) emission line at 4686Å and surrounding spectra, we can measure ⁴He and ³He density, temperature, and velocity profiles and use this information to study turbulent impurity transport. The transport is characterized using a standard ansatz for the radial particle flux: [mathematical equation]. This effort is designated He CXRS. Also, direct measurement of ³He are used to test models of Ion Cyclotron Resonance Heating (ICRH). We look for evidence of fast ion production and the effect of the minority ion profile on fast wave heating. Several modifications were made to the hardware. Light is collected via two optical arrays: poloidal and toroidal. The toroidal array has been upgraded to increase throughput and spatial resolution, increasing the number of toroidal channels from 10 to 22. A new protective shroud was installed on the poloidal array. Additional diagnostics (a 11 channel beam duct view, neutralizer view, duct pressure monitor) were added to the Diagnostic Neutral Beam to improve DNB modeling for CXRS. This work includes investigation of plasmas where helium is at low concentration (<1%), acting passively, as well as scenarios with a large fraction (>~20%). Using the STRAHL code, time-dependent helium density profiles are used to obtain anomalous transport parameters. Thermodiffusion and curvature pinch terms are also estimated from experimental scaling studies. Results are compared with neoclassical results from the NCLASS code and calculations by the GENE gyrokinetic code. Another focus is verification of power deposition models which are crucially dependent on minority ion density, for which ³He is used. At low ³He fraction, direct absorption by ³He generates fast ions with anisotropic velocity-space distribution functions. At high ³He fraction, mode conversion heating of electrons is dominant. The minority distribution function and predicted wave deposition are simulated using AORSA and CQL3D. This work provides the first measurements of helium transport on C-Mod and expands our understanding of helium transport and fast wave heating.Item Investigation of an unusual metal-RNA cluster in the P5abc subdomain of the group I intron(Texas A&M University, 2006-04-12) Burns, Shannon NaomiThis dissertation focuses on the spectroscopic and thermodynamic characterization of the unusual metal-RNA cluster found in the P5abc subdomain of the Tetrahymena group I intron. The P5abc subdomain is a part of the P4-P6 domain found in the Tetrahymena thermophila group I intron selfsplicing RNA. From both X-ray crystal structures of the P4-P6 domain, a remarkable cluster of Mg2+ or Mn2+ ions was found in the P5abc subdomain (Cate et al. 1996; Juneau et al. 2001). It is believed that the metal ion core in the P5abc subdomain stabilizes the active conformation of the RNA (Cate et al. 1996). An understanding of the role of these metal ions in facilitating the correct structure of the P5abc subdomain provides insight into how metal ions help overcome the folding barriers of complex RNA structures. Under solution conditions, the properties of this uncommon metal ion core and its influence on the truncated P5abc subdomain structure have been investigated. Both EPR spectroscopy and thermal denaturation experiments have been employed to search for a spectroscopic signature of metal ion core formation and also determine the thermodynamic contribution of the metal ion core on the stability of the folded P5abc structure. A spectroscopic signature of metal ion core formation was assigned for the P5abc subdomain by EPR microwave power saturation studies. Power saturation studies of the P5abc subdomain, P4-P6 domain and corresponding mutants reveal that the addition of 5 equivalents of Mn2+ are required for the wild type P5abc subdomain to form the metal ion core under solution conditions in 0.1 M NaCl. Results from both domain and subdomain microwave power saturation studies suggest that this technique can be applied for detecting clustering of Mn2+ ions in other RNA structures. The thermodynamic consequence of this metal ion core was probed by thermal denaturation techniques including UV-Vis spectroscopy and differential scanning calorimetry (DSC). DSC experiments were utilized to directly determine the thermodynamic contribution of the metal ion core. This value was determined to be an average of ∆∆G of -5.3 kcal/mol and is consistent with ∆∆G values obtained for other RNA tertiary structures.Item Investigation of Cryo-Cooled Microcoils for MRI(2012-10-19) Godley, Richard FranklinWhen increasing magnetic resonance imaging (MRI) resolution into the micron scale, image signal-to-noise ratio (SNR) can be maintained by using small radiofrequency (RF) coils in close proximity to the sample being imaged. Micro-scale RF coils (microcoils) can be easily fabricated on chip and placed adjacent to a sample under test. However, the high series resistance of microcoils limits the SNR due to the thermal noise generated in the copper. Cryo-cooling is a potential technique to reduce thermal noise in microcoils, thereby recovering SNR. In this research, copper microcoils of two different geometries have been cryo-cooled using liquid nitrogen. Quality-factor (Q) measurements have been taken to quantify the reduction in resistance due to cryo-cooling. Image SNR has been compared between identical coils at room temperature and liquid nitrogen temperature. The relationship between the drop in series resistance and the increase in image SNR has been analyzed, and these measurements compared to theory. While cryo-cooling can bring about dramatic increases in SNR, the extremely low temperature of liquid nitrogen is incompatible with living tissue. In general, the useful imaging region of a coil is approximately as deep as the coil diameter, thus cryo-cooling of coils has been limited in the past to larger coils, such that the thickness of a conventional cryostat does not put the sample outside of the optimal imaging region. This research utilizes a scheme of microfluidic cooling (developed in the Texas A&M NanoBio Systems Lab), which greatly reduces the volume of liquid nitrogen required to cryo-cool the coil. Along with a small gas phase nitrogen gap, this eliminates the need for a bulky cryostat. This thesis includes a review of the existing literature on cryo-cooled coils for MRI, as well as a review of planar pair coils and spiral microcoils in MR applications. Our methods of fabricating and testing these coils are described, and the results explained and analyzed. An image SNR improvement factor of 1.47 was achieved after cryo-cooling of a single planar pair coil, and an improvement factor of 4 was achieved with spiral microcoils.Item Skin cancer detection by oblique-incidence diffuse reflectance spectroscopy(2009-05-15) Smith, Elizabeth BrooksSkin cancer is the most common form of cancer and it is on the rise. If skin cancer is diagnosed early enough, the survival rate is close to 90%. Oblique-incidence diffuse reflectance (OIR) spectroscopy offers a technology that may be used in the clinic to aid physicians in diagnosing both melanoma and non-melanoma skin cancers. The system includes a halogen light source, a fiber optic probe, an imaging spectrograph, a charge coupled device (CCD) camera, and a computer. Light is delivered to the skin surface via optical fibers in the probe. After interacting with the skin, the light is collected and sent to the spectrograph that generates optical spectra. Images and histopathological diagnoses were obtained from 250 lesions at the University of Texas M.D. Anderson Cancer Center (Melanoma and Skin Center). To classify OIR data, an image processing algorithm was developed and evaluated for both pigmented and non-pigmented lesions. The continuous wavelet transform and the genetic algorithm were employed to extract optimal classification features. Bayes decision rule was used to categorize spatiospectral images based on the selected classification features. The overall classification accuracy for pigmented melanomas and severely dysplastic nevi is 100%. The overall classification accuracy for non-pigmented skin cancers and severely dysplastic nevi is 93.33%. Oblique-incidence diffuse reflectance spectroscopy and the developed algorithms have high classification rates and may prove useful in the clinic as the process is fast, noninvasive and accurate.Item Spectroscopic Investigations of Selected Cyclic and Bicyclic Molecules(2010-10-12) McCann, Kathleen RaeSeveral cyclic molecules along with two bicyclic molecules were investigated using infrared (IR), Raman, ultraviolet (UV) absorption, fluorescence excitation (FES), and single vibronic level fluorescence (SVLF) spectroscopies. The laser-induced fluorescence spectra (both fluorescence excitation and single vibronic level fluorescence) of jet-cooled 1,3-benzodioxan (13BZN) along with its ultraviolet absorption spectra have been recorded and analyzed in order to determine the vibrational quantum levels in both the ground and S1(pi,pi*) electronic excited states. A detailed energy map was established and utilized to better understand the structural and conformational differences between the ground and excited electronic states. Ab initio and DFT calculations were also carried out to complement the experimental work. The data allowed one-dimensional potential energy functions in terms of the ring-twisting coordinate to be calculated. A complete study of all of the vibrations of 13BZN in both its S0 ground and S1(pi,pi*) excited state was done utilizing several types of spectral data including infrared and Raman spectra. The vibrational frequencies of 13BZN were compared to those of the very similar 1,4-benzodioxan. The Raman and infrared spectra of dipicolinic acid (DPA), a component of anthrax spores, and dinicotinic acid (DNic) and their salts (CaDPA, Na2DPA, and CaDNic) have been recorded and the spectra have been assigned. Ab initio and DFT calculations were carried out to predict the structures and vibrational spectra and were compared to the experimental results. Theoretical calculations were also carried out for DPA dimers and DPA+2H2O to better understand the intermolecular interactions. 3-Methylindole (3MI), which serves as a structural model for the tryptophan side chain in proteins, has been investigated using vapor phase Raman spectroscopy. The vapor phase spectrum of 3MI complements previously reported Raman studies of 3MI solutions and related tryptophan derivatives. The analysis of the Raman spectrum of 3MI vapor was also supported here with newly obtained vapor phase infrared data and ab initio calculation to refine previous vibrational assignments. The present results provide an improved basis for assessing the dependence on the indoyl Raman signature on the local environment of the tryptophan side chain of proteins.Item Spectroscopic investigations of the vibrational potential energy surfaces in electronic ground and excited states(Texas A&M University, 2007-09-17) Yang, JuanThe vibrational potential energy surfaces in electronic ground and excited states of several ring molecules were investigated using several different spectroscopic methods, including far-infrared (IR), Raman, ultraviolet (UV) absorption, fluorescence excitation (FES), and single vibronic level fluorescence (SVLF) spectroscopies. Based on new information obtained from SVLF and millimeter wave spectra, the far-IR spectra of coumaran were reassigned and the one-dimensional ring-puckering potential energy functions for several vibrational states in the S0 ground state were determined. The barrier was found to be 154 cm-1 and the puckering angles to be ???? 25????, in good agreement with the millimeter wave barrier of 152 cm-1 and puckering angles of ???? 23????. Moreover, the UV absorption and FES spectra of coumaran allowed the one-dimensional ring-puckering potential energy functions in the S1 excited state to be determined. The puckering barrier is 34 cm-1 for the excited state and the puckering angles are ???? 14????. Several calculations with different basis sets have been carried out to better understand the unusual vibrational frequencies of cyclopropenone. It was shown that there is strong interaction between the C=O and symmetric C-C stretching vibrations. These results differ quantitatively from a previous normal coordinate calculation and interpretation. The vapor-phase Raman spectrum of 3,7-dioxabicyclo[3.3.0]oct-1,5-ene was analyzed and compared to the predicted spectrum from DFT calculations. The spectrum further shows it has D2h symmetry, in which the skeletons of both rings are planar. The infrared and Raman spectra of vapor-phase and liquid-phase 1,4-benzodioxan and 1,2,3,4-tetrahydronaphthalene were collected and the complete vibrational assignments for both molecules were made. Theoretical calculations predicted the barriers to planarity to be 4809 cm-1 for 1,2,3,4-tetrahydonaphthalene and 4095 cm-1 for 1,4-benzodioxan. The UV absorption, FES, and SVLF spectra of both molecules were recorded and assigned. Both one and two-dimensional potential energy functions of 1,4-benzodioxan for the ring-twisting and ring-bending vibrations were carried out for the S0 and S1(????,????*) states, and these were consistent with the high barriers calculated for both states. The low-frequency spectra of 1,2,3,4-tetrahydronaphthalene in both S0 and S1(????,????*) states were also analyzed.Item Spectroscopical Analysis of Mechano-chemically Activated Surfaces(2012-10-19) Cooper, RodrigoMechano-chemical activation is fundamentally different than chemical activation in that energy is added to alter the state of bond energy instead of exciting electrons to produce a chemical reaction. Mechano-chemical activation has demonstrated to alter the chemical reaction and rates. There remains no development of a model to quantify the changes in reactions due to mechano-chemical activation. This research aims in expanding our understanding of the influence of mechanochemical activation methods. The dynamics and kinetics of mechano-chemically activated surfaces will be studied using x-ray spectroscopy methods. Mechano-chemical interactions can be quantified through the study of electron energies. X-ray spectroscopy is a useful method of analyzing and quantifying electron energy states. X-ray absorbance is used to study the valence state electron shells of iron undergone activation through sliding friction of naturally produced wax. In-situ x-ray photoemission spectroscopy is employed to instantaneously characterize single crystal tantalum samples of each principal crystallographic orientation during oxidation. Sliding friction of the naturally produced wax resulted in a reduction in the binding energy of the iron 2p electrons by approximately one electron-volt. This reduction in binding energy is attributed to ferrocene which is an organo-metallic alloy, Fe(C5H5)2. Mechanical strain of the crystal lattices of tantalum resulted in altered activation energies. Activation energy increased with the application of lattice strain. At increasing strain, oxide properties become more dependent on the lattice strain than the crystal orientation and temperature. A model system is developed incorporating mechanical strain into the prediction of activation energy and rates.Item Tubulin in vitro, in vivo and in silico(Texas A&M University, 2005-02-17) Mershin, AndreasTubulin, microtubules and associated proteins were studied theoretically, computationally and experimentally in vitro and in vivo in order to elucidate the possible role these play in cellular information processing and storage. Use of the electric dipole moment of tubulin as the basis for binary switches (biobits) in nanofabricated circuits was explored with surface plasmon resonance, refractometry and dielectric spectroscopy. The effects of burdening the microtubular cytoskeleton of olfactory associative memory neurons with excess microtubule associated protein TAU in Drosophila fruitflies were determined. To investigate whether tubulin may be used as the substrate for quantum computation as a bioqubit, suggestions for experimental detection of quantum coherence and entanglement among tubulin electric dipole moment states were developed.