Ionospheric tomography using GNSS reflections

In this paper, we report a preliminary analysis of the impact of Global Navigation Satellite System Reflections (GNSS-R) data on ionospheric monitoring over the oceans. The focus will be on a single polar Low Earth Orbiter (LEO) mission exploiting GNSS-R as well as Navigation (GNSS-N) and Occultation (GNSS-O) total electron content (TEC) measurements. In order to assess impact of the data, we have simulated GNSS-R/O/N TEC data as would be measured from the LEO and from International Geodesic Service (IGS) ground stations, with an electron density (ED) field generated using a climatic ionospheric model. We have also developed a new tomographic approach inspired by the physics of the hydrogen atom and used it to effectively retrieve the ED field from the simulated TEC data near the orbital plane. The tomographic inversion results demonstrate the significant impact of GNSS-R: three-dimensional ionospheric ED fields are retrieved over the oceans quite accurately, even as, in the spirit of this initial study, the simulation and inversion approaches avoided intensive computation and sophisticated algorithmic elements (such as spatio-temporal smoothing). We conclude that GNSS-R data over the oceans can contribute significantly to a Global/GNSS Ionospheric Observation System (GIOS). Index Terms Global Navigation Satellite System (GNSS), Global Navigation Satellite System Reflections (GNSS-R), ionosphere, Low Earth Orbiter (LEO), tomography.

A fast atom bombardment mass spectrometry study of tris (3, 6-dioxaheptyl) amine-alkali metal halide complexes and hydrogen bonded complexes

The objective of this thesis was to demonstrate the potential of fast atom bombardment mass spectrometry (FABMS) as a probe of condensed phase systems and its possible uses for the study of hydrogen bonding. FABMS was used to study three different systems. The first study was aimed at investigating the selectivity of the ligand tris(3,6-dioxaheptyl) amine (tdoha) for the alkali metal cations. FABMS results correlated well with infrared and nmr data. Systems where a crown ether competed with tdoha for a given alkali metal cation were also investigated by fast atom bombardment. The results were found to correlate with the cation affinity of tdoha and the ability of the crown ether to bind the cation. In the second and third studies, H-bonded systems were investigated. The imidazole-electron donor complexes were investigated and FABMS results showed the expected H-bond strength of the respective complexes. The effects of concentration, liquid matrix, water content, deuterium exchange, and pre-ionization of the complex were also investigated. In the third system investigated, the abundance of the diphenyl sulfone-ammonium salt complexes (presumably H-bonded) in the FABMS spectrum were found to correlate with qualitative considerations such as steric hindrance and strength of ion pairs.

HOW CAN ONE PROBE PODOLSKY ELECTRODYNAMICS?

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Optical interface based on a nanofiber atom-trap

In this thesis, I present the realization of a fiber-optical interface using optically trapped cesium atoms, which is an efficient tool for coupling light and atoms. The basic principle of the presented scheme relies on the trapping of neutral cesium atoms in a two-color evanescent field surrounding a nanofiber. The strong confinement of the fiber guided light, which also protrudes outside the nanofiber, provides strong confinement of the atoms as well as efficient coupling to near-resonant light propagating through the fiber. In chapter 1, the necessary physical and mathematical background describing the propagation of light in an optical fiber is presented. The exact solution of Maxwell’s equations allows us to model fiber-guided light fields which give rise to the trapping potentials and the atom-light coupling in the close vicinity of a nanofiber. Chapter 2 gives the theoretical background of light-atom interaction. A quantum mechanical model of the light-induced shifts of the relevant atomic levels is reviewed, which allows us to quantify the perturbation of the atomic states due to the presence of the trapping light-fields. The experimental realization of the fiber-based atom trap is the focus of chapter 3. Here, I analyze the properties of the fiber-based trap in terms of the confinement of the atoms and the impact of several heating mechanisms. Furthermore, I demonstrate the transportation of the trapped atoms, as a first step towards a deterministic delivery of individual atoms. In chapter 4, I present the successful interfacing of the trapped atomic ensemble and fiber-guided light. Three different approaches are discussed, i.e., those involving the measurement of either near-resonant scattering in absorption or the emission into the guided mode of the nanofiber. In the analysis of the spectroscopic properties of the trapped ensemble we find good agreement with the prediction of theoretical model discussed in chapter 2. In addition, I introduce a non-destructive scheme for the interrogation of the atoms states, which is sensitive to phase shifts of far-detuned fiber-guided light interacting with the trapped atoms. The inherent birefringence in our system, induced by the atoms, changes the state of polarization of the probe light and can be thus detected via a Stokes vector measurement.

Imaging and modeling of pore scale processes in porous media using X-ray computed tomography and lattice Boltzmann solver

In der Erdöl– und Gasindustrie sind bildgebende Verfahren und Simulationen auf der Porenskala im Begriff Routineanwendungen zu werden. Ihr weiteres Potential lässt sich im Umweltbereich anwenden, wie z.B. für den Transport und Verbleib von Schadstoffen im Untergrund, die Speicherung von Kohlendioxid und dem natürlichen Abbau von Schadstoffen in Böden. Mit der Röntgen-Computertomografie (XCT) steht ein zerstörungsfreies 3D bildgebendes Verfahren zur Verfügung, das auch häufig für die Untersuchung der internen Struktur geologischer Proben herangezogen wird. Das erste Ziel dieser Dissertation war die Implementierung einer Bildverarbeitungstechnik, die die Strahlenaufhärtung der Röntgen-Computertomografie beseitigt und den Segmentierungsprozess dessen Daten vereinfacht. Das zweite Ziel dieser Arbeit untersuchte die kombinierten Effekte von Porenraumcharakteristika, Porentortuosität, sowie die Strömungssimulation und Transportmodellierung in Porenräumen mit der Gitter-Boltzmann-Methode. In einer zylindrischen geologischen Probe war die Position jeder Phase auf Grundlage der Beobachtung durch das Vorhandensein der Strahlenaufhärtung in den rekonstruierten Bildern, das eine radiale Funktion vom Probenrand zum Zentrum darstellt, extrahierbar und die unterschiedlichen Phasen ließen sich automatisch segmentieren. Weiterhin wurden Strahlungsaufhärtungeffekte von beliebig geformten Objekten durch einen Oberflächenanpassungsalgorithmus korrigiert. Die Methode der „least square support vector machine” (LSSVM) ist durch einen modularen Aufbau charakterisiert und ist sehr gut für die Erkennung und Klassifizierung von Mustern geeignet. Aus diesem Grund wurde die Methode der LSSVM als pixelbasierte Klassifikationsmethode implementiert. Dieser Algorithmus ist in der Lage komplexe geologische Proben korrekt zu klassifizieren, benötigt für den Fall aber längere Rechenzeiten, so dass mehrdimensionale Trainingsdatensätze verwendet werden müssen. Die Dynamik von den unmischbaren Phasen Luft und Wasser wird durch eine Kombination von Porenmorphologie und Gitter Boltzmann Methode für Drainage und Imbibition Prozessen in 3D Datensätzen von Böden, die durch synchrotron-basierte XCT gewonnen wurden, untersucht. Obwohl die Porenmorphologie eine einfache Methode ist Kugeln in den verfügbaren Porenraum einzupassen, kann sie dennoch die komplexe kapillare Hysterese als eine Funktion der Wassersättigung erklären. Eine Hysterese ist für den Kapillardruck und die hydraulische Leitfähigkeit beobachtet worden, welche durch die hauptsächlich verbundenen Porennetzwerke und der verfügbaren Porenraumgrößenverteilung verursacht sind. Die hydraulische Konduktivität ist eine Funktion des Wassersättigungslevels und wird mit einer makroskopischen Berechnung empirischer Modelle verglichen. Die Daten stimmen vor allem für hohe Wassersättigungen gut überein. Um die Gegenwart von Krankheitserregern im Grundwasser und Abwässern vorhersagen zu können, wurde in einem Bodenaggregat der Einfluss von Korngröße, Porengeometrie und Fluidflussgeschwindigkeit z.B. mit dem Mikroorganismus Escherichia coli studiert. Die asymmetrischen und langschweifigen Durchbruchskurven, besonders bei höheren Wassersättigungen, wurden durch dispersiven Transport aufgrund des verbundenen Porennetzwerks und durch die Heterogenität des Strömungsfeldes verursacht. Es wurde beobachtet, dass die biokolloidale Verweilzeit eine Funktion des Druckgradienten als auch der Kolloidgröße ist. Unsere Modellierungsergebnisse stimmen sehr gut mit den bereits veröffentlichten Daten überein.

Cone-beam computed tomography-guided stereotactic liver punctures: a phantom study

PURPOSE Images from computed tomography (CT), combined with navigation systems, improve the outcomes of local thermal therapies that are dependent on accurate probe placement. Although the usage of CT is desired, its availability for time-consuming radiological interventions is limited. Alternatively, three-dimensional images from C-arm cone-beam CT (CBCT) can be used. The goal of this study was to evaluate the accuracy of navigated CBCT-guided needle punctures, controlled with CT scans. METHODS Five series of five navigated punctures were performed on a nonrigid phantom using a liver specific navigation system and CBCT volumetric dataset for planning and navigation. To mimic targets, five titanium screws were fixed to the phantom. Target positioning accuracy (TPECBCT) was computed from control CT scans and divided into lateral and longitudinal components. Additionally, CBCT-CT guidance accuracy was deducted by performing CBCT-to-CT image coregistration and measuring TPECBCT-CT from fused datasets. Image coregistration was evaluated using fiducial registration error (FRECBCT-CT) and target registration error (TRECBCT-CT). RESULTS Positioning accuracies in lateral directions pertaining to CBCT (TPECBCT = 2.1 ± 1.0 mm) were found to be better to those achieved from previous study using CT (TPECT = 2.3 ± 1.3 mm). Image coregistration error was 0.3 ± 0.1 mm, resulting in an average TRE of 2.1 ± 0.7 mm (N = 5 targets) and average Euclidean TPECBCT-CT of 3.1 ± 1.3 mm. CONCLUSIONS Stereotactic needle punctures might be planned and performed on volumetric CBCT images and controlled with multidetector CT with positioning accuracy higher or similar to those performed using CT scanners.

Imaging adenoviral-directed reporter gene expression in living animals with positron emission tomography

We are developing quantitative assays to repeatedly and noninvasively image expression of reporter genes in living animals, using positron emission tomography (PET). We synthesized positron-emitting 8-[18F]fluoroganciclovir (FGCV) and demonstrated that this compound is a substrate for the herpes simplex virus 1 thymidine kinase enzyme (HSV1-TK). Using positron-emitting FGCV as a PET reporter probe, we imaged adenovirus-directed hepatic expression of the HSV1-tk reporter gene in living mice. There is a significant positive correlation between the percent injected dose of FGCV retained per gram of liver and the levels of hepatic HSV1-tk reporter gene expression (r2 > 0.80). Over a similar range of HSV1-tk expression in vivo, the percent injected dose retained per gram of liver was 0–23% for ganciclovir and 0–3% for FGCV. Repeated, noninvasive, and quantitative imaging of PET reporter gene expression should be a valuable tool for studies of human gene therapy, of organ/cell transplantation, and of both environmental and behavioral modulation of gene expression in transgenic mice.

Ancilla-assisted quantum process tomography

Complete and precise characterization of a quantum dynamical process can be achieved via the method of quantum process tomography. Using a source of correlated photons, we have implemented several methods, each investigating a wide range of processes, e.g., unitary, decohering, and polarizing. One of these methods, ancilla-assisted process tomography (AAPT), makes use of an additional ancilla system, and we have theoretically determined the conditions when AAPT is possible. Surprisingly, entanglement is not required. We present data obtained using both separable and entangled input states. The use of entanglement yields superior results, however.

Multilevel coherence effects in a two-level atom driven by a trichromatic field

We study the absorption and dispersion properties of a weak probe field monitoring a two-level atom driven by a trichromatic field. We calculate the steady-state linear susceptibility and find that the system can produce a number of multilevel coherence effects predicted for atoms composed of three and more energy levels. Although the atom has only one transition channel, the multilevel effects are possible because there are multichannel transitions between dressed states induced by the driving field. In particular, we show that the system can exhibit multiple electromagnetically induced transparency and can also produce a strong amplification at the central frequency which is not attributed to population inversion in both the atomic bare states and in the dressed atomic states. Moreover, we show that the absorption and dispersion of the probe field is sensitive to the initial relative phase of the components of the driving field. In addition, we show that the group velocity of the probe field can be controlled by changing the initial relative phases or frequencies of the driving fields and can also be varied from subluminal to superluminal. (C) 2003 Elsevier Science B.V. All rights reserved.

Clinical translation of a hand-held optical imager for breast cancer diagnostics: In vitro and in vivo tomography studies

Optical imaging is an emerging technology towards non-invasive breast cancer diagnostics. In recent years, portable and patient comfortable hand-held optical imagers are developed towards two-dimensional (2D) tumor detections. However, these imagers are not capable of three-dimensional (3D) tomography because they cannot register the positional information of the hand-held probe onto the imaged tissue. A hand-held optical imager has been developed in our Optical Imaging Laboratory with 3D tomography capabilities, as demonstrated from tissue phantom studies. The overall goal of my dissertation is towards the translation of our imager to the clinical setting for 3D tomographic imaging in human breast tissues. A systematic experimental approach was designed and executed as follows: (i) fast 2D imaging, (ii) coregistered imaging, and (iii) 3D tomographic imaging studies. (i) Fast 2D imaging was initially demonstrated in tissue phantoms (1% Liposyn solution) and in vitro (minced chicken breast and 1% Liposyn). A 0.45 cm3 fluorescent target at 1:0 contrast ratio was detectable up to 2.5 cm deep. Fast 2D imaging experiments performed in vivo with healthy female subjects also detected a 0.45 cm3 fluorescent target superficially placed ∼2.5 cm under the breast tissue. (ii) Coregistered imaging was automated and validated in phantoms with ∼0.19 cm error in the probe’s positional information. Coregistration also improved the target depth detection to 3.5 cm, from multi-location imaging approach. Coregistered imaging was further validated in-vivo , although the error in probe’s positional information increased to ∼0.9 cm (subject to soft tissue deformation and movement). (iii) Three-dimensional tomography studies were successfully demonstrated in vitro using 0.45 cm3 fluorescence targets. The feasibility of 3D tomography was demonstrated for the first time in breast tissues using the hand-held optical imager, wherein a 0.45 cm3 fluorescent target (superficially placed) was recovered along with artifacts. Diffuse optical imaging studies were performed in two breast cancer patients with invasive ductal carcinoma. The images showed greater absorption at the tumor cites (as observed from x-ray mammography, ultrasound, and/or MRI). In summary, my dissertation demonstrated the potential of a hand-held optical imager towards 2D breast tumor detection and 3D breast tomography, holding a promise for extensive clinical translational efforts.

Temperature measurement of cold atoms using transient absorption of a resonant probe through an optical nanofibre

Optical nanofibres are ultrathin optical fibres with a waist diameter typically less than the wavelength of light being guided through them. Cold atoms can couple to the evanescent field of the nanofibre-guided modes and such systems are emerging as promising technologies for the development of atom-photon hybrid quantum devices. Atoms within the evanescent field region of an optical nanofibre can be probed by sending near or on-resonant light through the fibre; however, the probe light can detrimentally affect the properties of the atoms. In this paper, we report on the modification of the local temperature of laser-cooled 87Rb atoms in a magneto-optical trap centred around an optical nanofibre when near-resonant probe light propagates through it. A transient absorption technique has been used to measure the temperature of the affected atoms and temperature variations from 160 μk to 850 μk, for a probe power ranging from 0 to 50 nW, have been observed. This effect could have implications in relation to using optical nanofibres for probing and manipulating cold or ultracold atoms.

Endoscopic optical coherence tomography : design and application

This thesis presents an investigation on endoscopic optical coherence tomography (OCT). As a noninvasive imaging modality, OCT emerges as an increasingly important diagnostic tool for many clinical applications. Despite of many of its merits, such as high resolution and depth resolvability, a major limitation is the relatively shallow penetration depth in tissue (about 2∼3 mm). This is mainly due to tissue scattering and absorption. To overcome this limitation, people have been developing many different endoscopic OCT systems. By utilizing a minimally invasive endoscope, the OCT probing beam can be brought to the close vicinity of the tissue of interest and bypass the scattering of intervening tissues so that it can collect the reflected light signal from desired depth and provide a clear image representing the physiological structure of the region, which can not be disclosed by traditional OCT. In this thesis, three endoscope designs have been studied. While they rely on vastly different principles, they all converge to solve this long-standing problem.

A hand-held endoscope with manual scanning is first explored. When a user is holding a hand- held endoscope to examine samples, the movement of the device provides a natural scanning. We proposed and implemented an optical tracking system to estimate and record the trajectory of the device. By registering the OCT axial scan with the spatial information obtained from the tracking system, one can use this system to simply ‘paint’ a desired volume and get any arbitrary scanning pattern by manually waving the endoscope over the region of interest. The accuracy of the tracking system was measured to be about 10 microns, which is comparable to the lateral resolution of most OCT system. Targeted phantom sample and biological samples were manually scanned and the reconstructed images verified the method.

Next, we investigated a mechanical way to steer the beam in an OCT endoscope, which is termed as Paired-angle-rotation scanning (PARS). This concept was proposed by my colleague and we further developed this technology by enhancing the longevity of the device, reducing the diameter of the probe, and shrinking down the form factor of the hand-piece. Several families of probes have been designed and fabricated with various optical performances. They have been applied to different applications, including the collector channel examination for glaucoma stent implantation, and vitreous remnant detection during live animal vitrectomy.

Lastly a novel non-moving scanning method has been devised. This approach is based on the EO effect of a KTN crystal. With Ohmic contact of the electrodes, the KTN crystal can exhibit a special mode of EO effect, termed as space-charge-controlled electro-optic effect, where the carrier electron will be injected into the material via the Ohmic contact. By applying a high voltage across the material, a linear phase profile can be built under this mode, which in turn deflects the light beam passing through. We constructed a relay telescope to adapt the KTN deflector into a bench top OCT scanning system. One of major technical challenges for this system is the strong chromatic dispersion of KTN crystal within the wavelength band of OCT system. We investigated its impact on the acquired OCT images and proposed a new approach to estimate and compensate the actual dispersion. Comparing with traditional methods, the new method is more computational efficient and accurate. Some biological samples were scanned by this KTN based system. The acquired images justified the feasibility of the usage of this system into a endoscopy setting. My research above all aims to provide solutions to implement an OCT endoscope. As technology evolves from manual, to mechanical, and to electrical approaches, different solutions are presented. Since all have their own advantages and disadvantages, one has to determine the actual requirements and select the best fit for a specific application.

Atomic-level structure and deformation in metallic glasses

Metallic glasses (MGs) are a relatively new class of materials discovered in 1960 and lauded for its high strengths and superior elastic properties. Three major obstacles prevent their widespread use as engineering materials for nanotechnology and industry: 1) their lack of plasticity mechanisms for deformation beyond the elastic limit, 2) their disordered atomic structure, which prevents effective study of their structure-to-property relationships, and 3) their poor glass forming ability, which limits bulk metallic glasses to sizes on the order of centimeters. We focused on understanding the first two major challenges by observing the mechanical properties of nanoscale metallic glasses in order to gain insight into its atomic-level structure and deformation mechanisms. We found that anomalous stable plastic flow emerges in room-temperature MGs at the nanoscale in wires as little as ~100 nanometers wide regardless of fabrication route (ion-irradiated or not). To circumvent experimental challenges in characterizing the atomic-level structure, extensive molecular dynamics simulations were conducted using approximated (embedded atom method) potentials to probe the underlying processes that give rise to plasticity in nanowires. Simulated results showed that mechanisms of relaxation via the sample free surfaces contribute to tensile ductility in these nanowires. Continuing with characterizing nanoscale properties, we studied the fracture properties of nano-notched MGnanowires and the compressive response of MG nanolattices at cryogenic (~130 K) temperatures. We learned from these experiments that nanowires are sensitive to flaws when the (amorphous) microstructure does not contribute stress concentrations, and that nano-architected structures with MG nanoribbons are brittle at low temperatures except when elastic shell buckling mechanisms dominate at low ribbon thicknesses (~20 nm), which instead gives rise to fully recoverable nanostructures regardless of temperature. Finally, motivated by understanding structure-to-property relationships in MGs, we studied the disordered atomic structure using a combination of in-situ X-ray tomography and X-ray diffraction in a diamond anvil cell and molecular dynamics simulations. Synchrotron X-ray experiments showed the progression of the atomic-level structure (in momentum space) and macroscale volume under increasing hydrostatic pressures. Corresponding simulations provided information on the real space structure, and we found that the samples displayed fractal scaling (r^d ∝ V, d < 3) at short length scales (< ~8 Å), and exhibited a crossover to a homogeneous scaling (d = 3) at long length scales. We examined this underlying fractal structure of MGs with parallels to percolation clusters and discuss the implications of this structural analogy to MG properties and the glass transition phenomenon.

Applications Of Visual Evoked Potentials And Fourier-domain Optical Coherence Tomography In Parkinson's Disease: A Controlled Study.

The goal of this cross-sectional observational study was to quantify the pattern-shift visual evoked potentials (VEP) and the thickness as well as the volume of retinal layers using optical coherence tomography (OCT) across a cohort of Parkinson's disease (PD) patients and age-matched controls. Forty-three PD patients and 38 controls were enrolled. All participants underwent a detailed neurological and ophthalmologic evaluation. Idiopathic PD cases were included. Cases with glaucoma or increased intra-ocular pressure were excluded. Patients were assessed by VEP and high-resolution Fourier-domain OCT, which quantified the inner and outer thicknesses of the retinal layers. VEP latencies and the thicknesses of the retinal layers were the main outcome measures. The mean age, with standard deviation (SD), of the PD patients and controls were 63.1 (7.5) and 62.4 (7.2) years, respectively. The patients were predominantly in the initial Hoehn-Yahr (HY) disease stages (34.8% in stage 1 or 1.5, and 55.8 % in stage 2). The VEP latencies and the thicknesses as well as the volumes of the retinal inner and outer layers of the groups were similar. A negative correlation between the retinal thickness and the age was noted in both groups. The thickness of the retinal nerve fibre layer (RNFL) was 102.7 μm in PD patients vs. 104.2 μm in controls. The thicknesses of retinal layers, VEP, and RNFL of PD patients were similar to those of the controls. Despite the use of a representative cohort of PD patients and high-resolution OCT in this study, further studies are required to establish the validity of using OCT and VEP measurements as the anatomic and functional biomarkers for the evaluation of retinal and visual pathways in PD patients.

Effects Of Misalignments In The Retinal Nerve Fiber Layer Thickness Measurements With Spectral Domain Optical Coherence Tomography.

Purpose. To investigate misalignments (MAs) on retinal nerve fiber layer thickness (RNFLT) measurements obtained with Cirrus(©) SD-OCT. Methods. This was a retrospective, observational, cross-sectional study. Twenty-seven healthy and 29 glaucomatous eyes of 56 individuals with one normal exam and another showing MA were included. MAs were defined as an improper alignment of vertical vessels in the en face image. MAs were classified in complete MA (CMA) and partial MA (PMA), according to their site: 1 (superior, outside the measurement ring (MR)), 2 (superior, within MR), 3 (inferior, within MR), and 4 (inferior, outside MR). We compared RNFLT measurements of aligned versus misaligned exams in all 4 sectors, in the superior area (sectors 1 + 2), inferior area (sectors 3 + 4), and within the measurement ring (sectors 2 + 3). Results. RNFLT measurements at 12 clock-hour of eyes with MAs in the superior area (sectors 1 + 2) were significantly lower than those obtained in the same eyes without MAs (P = 0.043). No significant difference was found in other areas (sectors 1 + 2 + 3 + 4, sectors 3 + 4, and sectors 2 + 3). Conclusion. SD-OCT scans with superior MAs may present lower superior RNFLT measurements compared to aligned exams.