<p><font face="Arial"> <p align="left">In this study, the capabilities of Neutron Radiography (NRad) and -Tomography (NTomo), as well as X-ray Radiography (XRad) to investigate chlorides and chlorides corrosion effects within steel reinforced laboratory concrete samples are practically explored. Capabilities of Scanning Electron Microscopy (SEM), Prompt Gamma Neutron Activation Analysis (PGNAA), Particle Induced X-ray Emission (PIXE), Small-Angle Neutron Scattering (SANS), Neutron Diffraction (NDIFF) and X-ray Diffraction (XDIFF) analytical techniques are also explored through review of literature.</p> </font></p>

Rare earths and copper systems were studied using X-ray absorption spectroscopy (XAS) and resonant inelastic X-ray scattering (RIXS). The use of monochromased synchrotron radiation and improved energy resolution for RIXS made possible to obtain valuable information on the electronic structure in 4f, 5f and 3d systems. Experimental results for rare-earths (Ho, Gd, Cm,U, Np, Pu) were analyzed by atomic multiplet theory based on the Hartree-Fock calculations. The inelastic scattering structures in RIXS spectra at 5d edge of actinides found to be sensitive to actinide oxidation states in different systems. Comparison of experimental and calculated Cm 5d RIXS spectra gave direct information about valency of the 248-curium isotope in oxide. Scientific understanding of processes that control chemical changes of radioactive species from spent fuel is improved by studying interactions of actinide ions (U, Np, Pu) with corroded iron surfaces. RIXS measurements at the actinide 5d edge indicate the reduction of U(VI), Np (V) and Pu (VI) to U(IV), Np(IV) and Pu (IV) by presence of iron ions. This thesis is also addressed to the study of changes in the electronic structure of copper films during interaction with synthetic groundwater solutions. The surface modifications induced by chemical reactions of oxidized 100Å Cu films with Cl−, SO42− and HCO3– ions in aqueous solutions with various concentrations were studied in-situ using XAS. It was shown that the pH value, the concentration of Cl− ion and presence of HCO3– ion in the solutions strongly affect the speed of the corrosion reaction. The Cu 2p RIXS was used to distinguish between the species present on the copper surface while in contact with groundwater solution.

Human immunodeficiency virus type 1 (HIV-1), the pathogen responsible for the onset of acquired immuno-deficiency syndrome (AIDS) in humans has reached pandemic proportions. To this day, no cure is available for infection with this virus and the only treatment option for this chronic infection is the life-long adherence to anti-retroviral therapy. Efforts in the quest to control the worldwide AIDS pandemic include the search for an effective anti-HIV-1 vaccine. Providing hope in this endeavor are a few monoclonal antibodies possessing broad neutralizing characteristics (bnmAbs) that have been isolated from the sera of rare patients that have a delayed progression to AIDS. In this thesis, one of these bnmAbs, 2F5 is extensively characterized at the atomic level to better understand its binding and neutralization mechanism. In total, 27 crystal structures of the 2F5 Fab’ in complex with various peptides representing its linear gp41 membrane proximal external region (MPER) epitope are presented. Furthermore, expression of the 2F5 Fab in a bacterial system allowed to design mutants of the 2F5 Fab and therefore investigate the implication of specific domains of 2F5 in mediating binding and neutralization. Atomic level characterization of this immune complex revealed a somewhat promiscuous recognition of 2F5 for its 664DKW666 epitope as long as the following characteristics were conserved: the aspartate’s negative charge, the hydrophobic alkyl-pi stacking arrangement between the beta-turn lysine and tryptophan, and the positive charge of the former. Moreover, it was demonstrated that 2F5 has an elongated and flexible complementary determining region 3 loop of the heavy chain (CDR H3), which is required for neutralization and is involved in secondary binding interactions other than to its core linear epitope. These contributions will significantly help in guiding the structure-based design of an HIV-1 vaccine looking to elicit 2F5-like antibody responses.

Chronic arsenic poisoning due to arsenic contamination of groundwater is a serious public health problem in Bangladesh and neighboring countries. Severe health effects associated with chronic exposure to arsenic include melanosis and several kinds of cancer. It is now generally agreed that the arsenic contamination of groundwater in Bangladesh is of geological origin. Arsenic naturally present in aquifers may be mobilized into drinking water by microbial action.<p> The formation of a novel arsenic-selenium compound: seleno-bis (S-glutathionyl) arsinium ion, [(GS)2AsSe]-, and its subsequent excretion in rabbit bile has been demonstrated previously. This molecular basis for the in vivo antagonism between arsenic and selenium was discovered using X-ray absorption spectroscopy. There is growing evidence that, in Bangladeshi people who are suffering long term chronic lowlevel arsenic poisoning, this antagonism is causing a selenium deficiency. Administering selenium supplements might provide a simple but highly effective treatment of the Bangladeshi arsenic poisoning.<p> In order to examine the disposition of [(GS)2AsSe]-, a set of rabbits were intravenously injected with selenite, arsenite or both. Whole blood, red blood cell and plasma samples were collected at different time intervals within 2hrs after injection and cecotrope samples 24hr after injection. Samples were examined using X-ray absorption spectroscopy and both arsenic and selenium K-near edge spectra were recorded.<p> iii Speciation of arsenic and selenium will be discussed in this thesis. Results indicate that [(GS)2AsSe]- is formed in blood very rapidly after injection of both arsenite and selenite, and then is removed from blood stream within 2hrs post injection. Results also show that [(GS)2AsSe]- is assembled in red blood cells, with no [(GS)2AsSe]- detected in plasma samples. [(GS)2AsSe]- is also found in cecotrope samples after injection of both arsenite and selenite.<p> The results of this study in rabbits will contribute to the understanding of chronic arsenic poisoning in humans.

<p>Couplers are one of the most frequently used passive devices in microwave circuitry. The main function of a coupler is to divide (or combine) a radio frequency signal into (from) two separate signals by a specific ratio and phase difference. With the need for smaller electronic devices, a reduction in the area of a distributed coupler would prove to be valuable. The purpose of this research is to develop, simulate, fabricate and test high aspect ratio microstructure couplers that are smaller in area than existing distributed couplers, and have comparable or better performance. One method used to reduce the area of a distributed coupler is to replace single or multiple transmission lines with lumped element equivalent circuits. One category of lumped elements that has not been extensively implemented is high aspect ratio lumped elements. High aspect ratio lumped elements fabricated with deep X-ray lithography are able to take advantage of using the vertical dimension, and reduce their planar area. In this thesis high aspect ratio lumped elements are used in the design of 3-dB microstructure couplers that show significant area reduction compared to equivalent distributed couplers.</p> <p>The designs of the microstructure couplers were based on the lumped element equivalent circuits of a 3-dB branch-line and a 3-dB rat-race distributed coupler. Simulations were performed to determine the lumped element values that would provide the largest 3-dB bandwidth while still maintaining close to ideal coupling and through values, return loss bandwidth, isolation bandwidth, and phase. These lumped element values were then implemented in the microstructure coupler designs as high aspect ratio microstructure lumped elements. 3-D electromagnetic simulations were performed which verified that the structures behaved electrically as couplers. The microstructure couplers were designed to be 220 &#x00B5;m tall nickel structures with capacitance gap widths of 6 µm.</p> <p>Fabrication of the microstructure couplers using deep X-ray lithography was performed by the microfabrication group at IMT/KIT in Karlsruhe, Germany. Before testing, detailed visual inspection and the etching of the structures was performed at the Canadian Light Source.</p> <p>A total of five microstructure couplers were tested. Four of the tested couplers were based on the 3-dB branch-line coupler, and the fifth coupler was based on the 3-dB rat-race coupler. The microstructure branch-line design that had the best overall results was fabricated on quartz glass substrate and had an operation frequency of 5.3 GHz. The 3-dB bandwidth of the coupler was measured to be better than 75.5% and extrapolated to be 95.0%. At the centre frequency the through and coupled values were -4.32 dB and -4.44 dB. The phase difference between the couplers output ports was designed to be 90.0° and was measured to be 95.8°. The ±5° phase bandwidth was measured to be 12.7% and the isolation bandwidth was 28.8%. The measured results from the other couplers were comparable to simulation results.</p> <p>The main advantage of the microstructure coupler designs over existing distributed couplers is that the microstructure couplers show a significant area reduction. The branch-line microstructure designs were at least 85% smaller in area than their distributed equivalent on quartz glass. The rat-race microstructure design showed an area reduction of 90% when compared to its distributed equivalent on quartz glass.</p>

The thesis presented here describes the steps that were taken in an attempt to solve the protein structure of MenD via molecular replacement and multiple wavelength anomalous dispersion. The introduction provides background on menaquinone biosynthesis and the role of MenD in this metabolic pathway. Also, a detailed discussion of the DC Family of enzymes, a subgroup of ThDP dependent enzymes, which MenD is a part of, is included.<p> Utilizing various software packages a 1.9 Å data set was processed and analyzed in an attempt to provide a molecular replacement result. When molecular replacement was deemed incapable of solving the phase problem of the data set, the production of SeMet protein was attempted to allow for MAD phasing.<p> A homology model of MenD was produced using the program Modeller with benzaldehyde lyase as a template. A structure based sequence alignment was done with all DC Family enzymes with structures published. Then a second structure based sequence alignment was done to compare the same set to the Modeller model. This was done to gain a deeper understanding of MenD and how it interacts with its cofactors ThDP and Mg2+. Furthermore, these results were used to implicate potential active site residues.

X-ray medical imaging provides invaluable medical information, while subjecting patients to hazardous ionizing radiation. The dosage that the patient is exposed to may be reduced, at the cost of image resolution. A technology that promises lower dosage for a given resolution is direct conversion digital imaging, typically based on amorphous Selenium semiconductor. Sufficient exposure should be used for the first exposure to avoid subsequent exposures; a challenge is then to reduce the necessary exposure for a suitable image. To quantify how little radiation the detector can reliably discriminate, one needs an analysis of the variance that 1/f and white noise contribute to the signal of such detectors. An important consideration is that the dark current, which varies with time, is subtracted from the photo-current, to reduce the spurious spatial variance in the image. In this thesis, the variance that 1/f noise contributes to integrating detectors is analysed, for a very general integrating detector. Experiments were performed to verify the theoretical results obtained for the 1/f noise variance contribution.

An overview of synchrotrons and synchrotron radiation is presented, along with the theory and practical considerations behind several types of X-ray spectroscopy. The theory and practical considerations of density functional theory are also given, with direct reference to some specific software packages.<p> Some synchrotron-excited X-ray spectroscopy measurements and density functional theory calculations of selenium and arsenic-doped selenium films are then outlined. The physical structure of crystalline and amorphous selenium and the electronic structure of amorphous selenium are discussed and comparison is made to the experimental results.<p> A weak feature in the conduction band is identified as a "fingerprint" of the degree of crystallization in amorphous selenium from X-ray absorption measurements. Similarly, a weak feature corresponding to lone-pairs in the valence band is identified as a "fingerprint" of the arsenic concentration from X-ray emission measurements.<p> Finally a detailed model of the structure of amorphous selenium is explained, and compared to experiment. This model is tested both by direct calculations and by a reverse Monte Carlo approach. The implications of this model with respect to the structure of amorphous and arsenic-doped amorphous selenium are discussed. Calculations suggest that simply randomizing the arrangement of "perfect" trigonal selenium is unable to reproduce the measurements of amorphous selenium; a moderate variation in the bond angle of "perfect" trigonal selenium is also necessary.

The desire for low cost electronics has led to a huge increase in research focused on organic materials. These materials are appealing due to their unique electrical and material-processing properties and are rapidly being adopted in old and new electronic applications. To create practical devices requires a further understanding of the charge transport properties of the unique anisotropic molecular crystal structures. This work looks at how doping with the transition-metal element manganese can alter the electronic structure of the organic material pentacene. It has been found that using manganese as a dopant provides novel physical characteristics previously not encountered in organic field effect transistors based on pentacene. These organic thin films were characterized using X-ray absorption spectroscopy and the results compared to computational density functional theory analysis.

The sensitivity reduction or ghosting mechanism of x-ray photoconductor is studied based on Monte Carlo simulation techniques. We have calculated the sensitivity reduction for different detector operating conditions (applied electric field, x-ray spectrum and photoconductor thickness) and for different levels of carrier trapping. We have analyzed the effect of photoconductor biasing (positive or negative) on ghosting. The following effects are taken into account in modeling the ghosting phenomena: (i) recombination between trapped and oppositely charged drifting carriers, (ii) trap filling, (iii) nonuniform electric field, (iv) detrapping of trapped holes, and (v) x-ray induced trap generation. Our calculation shows that not only the recombination between trapped and oppositely charged drifting carriers but the x-ray induced trap generation is also responsible for ghosting in photoconductor based x-ray image detectors. Moreover not all the trapped carriers take part in recombination; rather only a fraction of the trapped carriers are involved in recombination. Electric field also plays an important role in ghosting calculations via the electron hole pair generation mechanism. Trap filling has also non trivial effects on ghosting. The simulation results show that the amount of ghosting strongly depends on the applied electric field. Ghosting increases with decreasing applied electric field and vice versa. It is observed that ghosting is higher at high carrier trapping level than at low trapping level. Again ghosting is more pronounced in chest radiographic detector than mammographic detector. In chest radiographic detector, carrier trapping is high due to greater thickness hence recombination and electric field effects are prominent in chest radiographic detector. Biasing dependent ghosting depends on the carrier mobility lifetime product. For positively biased detectors, ghosting is less if the mobility lifetime product of hole is higher than that of electron and vice versa for negatively biased detectors. It also appears that the use of only recombination to calculate ghosting, as believed the primary source of ghosting in some literatures, will lead to significant error in the calculation of ghosting.