Several methods for analysing materials and proteins use highly concentrated beams of X-rays, e.g. SAXS and X-ray crystallography. To evaluate the outgoing beam, it is of high importance to know the light distribution of the incoming beam. Previously, a method for this has been to focus the X-ray beam onto a pinhole in front of a photodiode, a so called pinhole measurement. Although this method gives information about the radial distribution of the beam, it is very time-consuming. In this report a faster alternative has been developed and evaluated. In this new method an image is taken with an X-ray camera in the focus of the beam. Algorithms are then used to replicate a pinhole measurement by applying virtual pinholes. Different pixels in an image act differently, referred to as spatial noise. This must be compensated for before information about the beam may be extracted. To do this, the camera noise was characterized and a calibration procedure developed for its minimization. It was shown that the spatial noise was greatly reduced, making the temporal shot noise the new largest noise source. Although the noise was successfully reduced, the calibration procedure failed to accurately remove all signal not originating from registered photons. Measurements done with low photon intensities, large exposure times or at high temperatures are therefore less accurate. The measured camera signal was transformed into incident photon intensity using a responsivity proportionality constant. This constant was estimated by comparing the results from real and virtual pinhole measurements for several photon intensities and pinholes. The results gave a responsivity proportionality constant of 0,03 DN/X-ph. Further measurements were done concerning the temperature dependence of the camera responsivity and to investigate possible bleaching. The results indicated that the responsivity was held constant under changing temperatures and that the camera remained unbleached during the 114h long measurement. Finally, real and virtual pinhole measurements were done for a series of pinholes and compared using the responsivity proportionality constant. A maximum relative deviation of 6% was measured between the two, indicating that virtual pinhole measurements give accurate results. The largest deviations of the measurement seem to occur when using small or large pinholes. These errors, however, have a high potential of being further minimized, resulting in higher accuracy.

Cadmium Zinc Telluride (CZT) has been one of the most promising semiconductor materials for many years. Due to its high atomic number, suitable band-gap energy and ability to function at room temperature, CdZnTe has become the material of choice to be used as a room temperature radiation detector for many applications in the fields of medical imaging, process monitoring and national security, where demands and specifications set by those applications require that these detectors can operate well at the extreme conditions while maintaining good resolution, high detection efficiency, good reliability and high throughput. In most applications, detectors are exposed to high flux of X-ray radiation. One of the most common issues is the degradation of these detectors due to the presence of extended and point defects, which can act as traps for the charge carriers. This charge trapping causes the build-up of space charge and disturbing the electric field, resulting incomplete charge collection and signal formation of the detectors. This thesis investigates the associated failure modes by identifying the types of defects that exist in the CZT crystal and studies their roles in the performance of X-ray radiation detectors using in-house diagnostic tools. The results from different screening methods are compared and studied in order to find meaningful relationships and correlations that will help researchers to better understand the underlying physics and provide information and means for corrections and improvements of the crystal quality. / Graduate

PhD - Science / Screening of asymptomatic women using X-ray mammography technique is very common in many parts of the world in view of the prevalence of breast cancer among women. Mammography X-ray procedures are well established; with radiation dose measurements usually carried out using air ionisation chamber despite its inherent disadvantages. In this study, the various parameters necessary for accurate dose calculations from mammography X-ray energies and their effect on the calculated dose values, the relationship between dose, breast size, image quality and X-ray tube parameters as well as an alternative method for dose measurements, were systematically investigated. A method is presented for calculating accurately the mass attenuation and mass-energy coefficients for any energy bin of interest in the photon energy region 1-20 keV from existing mass attenuation and mass-energy coefficients data. Data fitting procedure was used for the study using an established equation. The results of the study showed that when data points containing high and low energies such as 1 - 200 keV are fit together with a single set of parameters, an overestimation of about 20% at the lower energies with far greater deviations at higher energies can result. It has been shown that grouping data into smaller energy regions when fitting would lead to accurate calculations of the mass attenuation or mass energy-absorption data. This is especially important if the data were to be used in low energy photon calculations such as would be the case for mammography beams. An investigation into the effect of pressure, temperature and humidity in air on photon fluence at a typical mammography, low bremsstrahlung energy (25 kVp), has been carried out. The results of the investigation showed that air kerma values from an X-ray spectrum that has significant lower energy components is likely to be more sensitive to changes in pressure, temperature and humidity than the air kerma from an X-ray spectrum with lower energy components less pronounced. Mean glandular dose (MGD) values had been calculated for various tube potentials and tube loadings (TL) using direct measurements of the incident entrance air kerma (ESAK) at the surface of a standard breast phantom and also from spectral measurements acquired with a solid-state detector. Detailed presentations of dose measurements from direct measurements and also from X-ray spectral data employing the established methods are given. Comparisons of the MGD values thus derived are presented and the relationship between MGD, phantom thickness, image quality and tube operating parameters is discussed. The possibility of evaluating radiation dose from mammography X-ray beams using constructed probes with diamond as the active radiation sensing material has been studied. Diamond has been used in the conduction mode whereby electrodes are connected to it and the resulting current from the interaction of the ionizing radiation with the diamond detected. Single crystal diamonds produced under high pressure and temperature (HPHT), as well as polycrystalline diamonds manufactured by the chemical vapour deposition (CVD) method were used. Suitable diamond stones were carefully selected for the study using various techniques. The probe was constructed entirely using tissue equivalent materials. In current practice diamond in the form of thin plates are used in the “flat-on” geometry, where the radiation beam to be monitored or measured, impinges on the flat face of the diamond. In this work it was found that using diamond plates in a side-on, or “edgeon”, geometry improves the collection efficiency of the diamond. The probe has been designed for radiation detection in both “edge-on” and “flat-on” sensor geometry profiles without having firstly to unseat the diamond sensor element from its original position within the probe housing before taking measurements. The study has shown that with the “edge-on” geometry configuration, radiation from impinging photons with energies below 30 keV can be made to deposit almost all (about 90%) of their energy into the sensor. The probe was designed for use in combination with commercially available electrometer systems. The response of the diamond probe to changes in radiation dose correlated well with that obtained from a secondary standard ionization chamber at the same X-ray tube settings.

Thesis (M.Phil.)--Chinese University of Hong Kong. / Bibliography: leaves 78-83.

Transition metals are crucial components of several metabolic pathways and are critical for DNA, RNA and protein synthesis. However, when found in excess, these metal ions are toxic. To maintain the physiological concentration of metal ions at non-toxic concentration, bacteria rely on members of the Ferric uptake regulator (Fur) family of metalloregulators. Intriguingly, despite being coined as “metalloregulator”, specific members of the Fur family activate and repress gene expression in presence or absence of regulatory metals. Based on these observations, we hypothesized that the ability of these transcription factors to adopt different structural conformations underlies their ability to display different functions in presence and absence of metal ions. To address this important question, we solved the crystal structure of apo-Fur protein from Campylobacter jejuni. Structural analysis revealed that the protein adopts a V-shaped conformation harboring an evolutionary conserved cluster of positively charged residues on the surface. Using an extensive library of mutants and electrophoretic mobility shift analysis, we found that substituting residues forming the positively charged surface is detrimental for Fur interaction with DNA. Furthermore, our in vivo studies suggest that these positively charged residues are important for the regulation of CjFur target genes and that different mechanisms modulate the activity of Fur family of metalloregulators depending on the number of occupied metal binding sites. We showed that the disruption of metal binding sites of CjFur significantly reduces DNA binding in vitro and is deleterious for the repression of Fur target genes and gut colonization by C. jejuni. Finally, based on initial findings that adding a tag at the N-terminus of CjFur significantly reduces its ability to incorporate regulatory metal ions and bind DNA, we developed a new protocol for the purification of a highly active untagged CjFur protein. Overall, our studies shed new lights on the mechanistic basis controlling Fur gene regulatory activity in C. jejuni.

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Tam Yi Mei. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2004. / Includes bibliographical references. / Abstracts in English and Chinese. / Abstract --- p.ii / 摘要 --- p.iii / Acknowledgement --- p.iv / Table of Contents --- p.v / List of Figures --- p.ix / List of Tables --- p.xii / Chapter Chapter 1 --- Background of study --- p.1 / Chapter 1.1 --- Introduction --- p.1 / Chapter 1.2 --- Theoretical background of XPS --- p.2 / Chapter 1.2.1 --- Principle of XPS --- p.2 / Chapter 1.2.2 --- Surface sensitivity --- p.6 / Chapter 1.2.3 --- Inelastic Mean Free Path (IMFP) --- p.6 / Chapter 1.3 --- XPS spectral features --- p.7 / Chapter 1.3.1 --- Chemical shift --- p.8 / Chapter 1.3.2 --- Spin orbital splitting (SOS) --- p.8 / Chapter 1.4 --- Quantitative analysis in XPS --- p.10 / Chapter 1.4.1 --- Atomic concentration --- p.10 / Chapter 1.4.2 --- Layer thickness determination --- p.11 / Chapter 1.5 --- The new XPS analysis technique in the present study --- p.14 / Chapter 1.5.1 --- Ion sputtering --- p.14 / Chapter 1.5.1.1 --- Sputtering-induced defects --- p.16 / Chapter 1.5.1.2 --- Effects of ion incident angle --- p.17 / Chapter 1.5.1.3 --- Depth resolution --- p.17 / Chapter 1.5.2 --- Perpendicular detection --- p.19 / Chapter 1.6 --- Objectives of present study --- p.23 / References for Chapter1 --- p.24 / Chapter Chapter 2 --- Instrumentation --- p.28 / Chapter 2.1 --- Introduction --- p.28 / Chapter 2.2 --- X-ray Photoelectron Spectroscopy --- p.28 / Chapter 2.2.1 --- XPS used in the present study --- p.28 / Chapter 2.2.2 --- Vacuum requirements --- p.29 / Chapter 2.2.3 --- X-ray source --- p.29 / Chapter 2.2.4 --- Charge Neutralizer --- p.33 / Chapter 2.2.5 --- Ion sputtering gun --- p.34 / Chapter 2.2.6 --- Electron energy analyzer --- p.36 / Chapter 2.2.6.1 --- Energy resolution --- p.38 / Chapter 2.2.6.2 --- Pass energy --- p.38 / Chapter 2.2.7 --- Electron detector / Multiplier --- p.39 / Chapter 2.3 --- Other analysis techniques for verification --- p.42 / Chapter 2.3.1 --- Energy Dispersive X-ray detector in Scanning Electron Microscope (SEM-EDX) --- p.42 / Chapter 2.3.2 --- X-ray Fluorescence Spectrometer (XRF) --- p.42 / Chapter 2.3.3 --- Rutherford Backscattering Spectrometer (RBS) --- p.43 / Chapter 2.3.4 --- Differential Scanning Calorimeter (DSC) --- p.44 / References for Chapter2 --- p.45 / Chapter Chapter 3 --- Determination of the thickness of the damaged layer --- p.46 / Chapter 3.1 --- Introduction --- p.46 / Chapter 3.2 --- Experimentation --- p.46 / Chapter 3.2.1 --- Instrumentation --- p.46 / Chapter 3.2.1.1 --- Work function calibration --- p.48 / Chapter 3.2.1.2 --- Sputtering ion beam calibration --- p.49 / Chapter 3.2.2 --- Sample preparation --- p.49 / Chapter 3.2.3 --- XPS measurements --- p.51 / Chapter 3.3 --- Results and discussion --- p.53 / Chapter 3.3.1 --- Spectral analysis and peak fitting --- p.53 / Chapter 3.3.2 --- Modeling and damaged layer thickness determination --- p.59 / Chapter 3.3.3 --- TRIM simulation --- p.62 / Chapter 3.4 --- Conclusion --- p.65 / References for Chapter3 --- p.68 / Chapter Chapter 4 --- Applications of the new XPS technique to different materials --- p.70 / Chapter 4.1 --- Introduction --- p.70 / Chapter 4.2 --- Analysis of ceramic --- p.70 / Chapter 4.2.1 --- Experimentation --- p.71 / Chapter 4.2.2 --- XPS results and comparison with other analysis techniques --- p.74 / Chapter 4.3 --- Analysis of metal alloys --- p.77 / Chapter 4.3.1 --- Experimentation for the tin-lead solder bump analysis --- p.78 / Chapter 4.3.2 --- Calibration of XPS sensitivity --- p.78 / Chapter 4.4 --- Development of XPS analysis method for the tin-silver solder bump measurement --- p.82 / Chapter 4.4.1 --- Experimentation --- p.83 / Chapter 4.4.2 --- XPS results --- p.83 / Chapter 4.5 --- Analysis of polymer (Polyacrylic acid) --- p.84 / Chapter 4.5.1 --- XPS results --- p.84 / Chapter 4.6 --- Analysis of Indium Phosphide --- p.90 / Chapter 4.6.1 --- XPS results --- p.92 / Chapter 4.7 --- Analysis of Gallium Arsenide --- p.96 / Chapter 4.8 --- Conclusion --- p.100 / References for Chapter4 --- p.101 / Chapter Chapter 5 --- Conclusions --- p.102

In this thesis, we present the optical to X-ray scaling relations from the XMM Cluster Survey (XCS) and the red-sequence Matched-filter Probabilistic Percolation cluster finding algorithm (redMaPPer) cluster catalogs. XCS finds galaxy clusters in the XMM-Newton public archive and redMaPPer uses optical data from the Sloan Digital Sky Survey eighth data release (SDSS-DR8) and the Dark Energy Survey first year data release (DES Y1). redMaPPer catalogs provide reliable photometric redshift estimations that have been calibrated with spectroscopic redshifts. The XCS temperature and luminosity pipelines need redshift information to calculate the X-ray observables. We introduced third generation of the XCS Post Processing Pipeline (XCS3P). A description of the previous versions is given, highlighting the modifications made for XCS3P-v3. This methodology was validated by comparing the LX - TX relation obtained from XCS3Pv1, XCS3P-v2 and the current version, the results are similar to XCS3P-v2 finding a self similar evolution. Samples of clusters are defined after several control filters, each cluster has optical and X-ray follow up, the sample has 327 unique clusters that span a redshift range of 0:08 < z < 0:8. Optical to X-ray scaling relations are obtained for the samples XCS-RM (SDSS DR8), XCS-RM (DES Y1) and XCS-RM (SDSS+DES Y1). Obtaining as a result, the most comprehensive examination of the TX - λ and LX - λ relations up to date, showing a clear correlation between the observables. This work confirms that it is possible to relate optical properties with the underlying mass. Cluster observables like the X-ray temperature, X-ray luminosity and the optical richness are well known mass tracers. The XCS3P-v3 methodology and the process followed to obtain the scaling relations are validated using four non-redMaPPer cluster catalogs, two from the optical (CAMIRA and GMBCG) and two from the millimiter (SPT and Planck). The results show a clear correlation between X-ray and optical and millimeter observables. This analysis is not a robust as for redMaPPer, thus further work is needed to present this results to the scientific community.

by Feng Xue. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1996. / Includes bibliographical references (leaves 76-84). / ACKNOWLEDGMENTS --- p.I / ABSTRACT --- p.II / TABLE OF CONTENTS --- p.III / LIST OF TABLES --- p.V / LIST OF FIGURES --- p.VI / Chapter CHAPTER 1: --- INTRODUCTION --- p.1 / Chapter 1. --- supramolecular chemistry --- p.1 / Chapter 2. --- Infinite multi-dimensional architecture --- p.10 / Chapter 3. --- Chemistry of pseudohalides --- p.15 / Chapter 4. --- Chemistry of hexamethylenetetramine --- p.20 / Chapter 5. --- Objectives of the present research --- p.24 / Chapter CHAPTER 2: --- EXPERIMENTAL --- p.25 / Chapter 1. --- Preparation --- p.25 / Chapter 1.1 --- Materials --- p.25 / Chapter 1.2 --- Preparation of the compounds --- p.25 / Chapter 2. --- X-ray crystallography --- p.26 / Chapter CHAPTER 3: --- DESCRIPTION OF CRYSTAL STRUCTURES --- p.28 / Chapter 1. --- isostructural compounds K2[FEII(CN)6] ´Ø 2[(CH2)6n4H] ´Ø 4H2 O(1) and K2[FEIII(CN)6] ´Ø [(CH2)6N4H] ´Ø [(CH2)6N4] ´Ø 4H2O (2) --- p.28 / Chapter 2. --- Crystal structure of NA2[FEIII(CN)6] ´Ø [(CH2)6N4H] ´Ø [(CH2)6N4] ´Ø 5H2O (3) --- p.33 / Chapter 3. --- Crystal structure of K3[FEIII(CN)6] ´Ø 2[(CH2)6N4] ´Ø 4H2O (4) --- p.37 / Chapter 4. --- Crystal Structure of ferricyanic acid-HMT adduct H3[FEIII(CN)6] ´Ø 2[(CH2)6N4] ´Ø 2H2O (5) --- p.43 / Chapter 5. --- "Crystal structure of cadmium chloride-HMT adduct, Cd2[C6H12N4H2]Cl6´Ø 3H2O (6)" --- p.48 / Chapter 6. --- "Crystal structure of cadmium bromide-HMT adduct, CdBr2 ´Ø 2[(CH2)6N4] ´Ø 2H2O (7)" --- p.53 / Chapter 7. --- "Crystal structure of cadmium iodide-HMT adduct, 3CdI2 ´Ø 2[(CH2)6N4] ´Ø 4H2O (8)" --- p.57 / Chapter 8. --- Crystal structure of cadmium thiocyanate-HMT adduct Cd(SCN)2 ´Ø 1(CH2)6N4] ´Ø MeOH (9) --- p.61 / Chapter 9. --- Crystal structure of cobalt cyanate-HMT adduct Co(NCO)2 ´Ø [(CH2)6N4] ´Ø 2H2O (10) --- p.67 / Chapter CHAPTER 4: --- SUMMARY AND DISCUSSIONS --- p.72 / REFERENCES --- p.76 / TABLE A1 Crystallographic data for compounds 1 ~5 --- p.85 / TABLE A2 Crystallographic data for compounds 6~10 --- p.86 / APPENDIX 1 Atomic Coordinates (Ax 104) and Equivalent Isotropic Thermal Parameters (A 2x103) --- p.87 / APPENDIX 2 Anisotropic thermal parameters (A2x 103) --- p.92 / APPENDIX 3 H-atom coordinates (x 104) and isotropic thermal parameters (A2x 103) --- p.96

Soft x-ray microscopy is a powerful technique for natural-contrast, high-resolution imaging of organic materials. This Thesis describes new instrumentational and new image-processing methods to improve the image quality of the compact x-ray microscope at the Biomedical &amp; X-Ray Physics division at KTH. The microscope is based on a laser-plasma source combined with different condenser optics, either multilayer mirrors or zone plates. Imaging is performed by micro zone plates. The microscope works in the water window (\lambda = 2.3-4.4 nm), where the attenuation lengths of oxygen and carbon differ strongly, providing high natural contrast for carbon-containing specimens in an aqueous environment. By optimizing the properties of the laser-plasma source and fabricating multilayer mirrors with high, uniform reflectivity, the performance of the microscope's illumination system could be improved and exposure times decreased significantly to about 2 min for imaging dry samples and 5 min for imaging wet samples. For imaging of wet samples, a wet-specimen chamber was developed, which is vacuum-compatible. Since it is horizontally mounted in the microscope, it offers advantages for investigations in polymer and soil science. To improve the quality of images taken by the compact x-ray microscope an image-restoration algorithm was developed. Denoising is performed by a filtering algorithm based on the discrete wavelet transform. This algorithm shows advantages compared to Fourier-based algorithms, since the filtering of spatial frequencies is done locally. An improvement in exposure time by a factor of about 2 could be realized without loss of image information. To stimulate experiments on functional imaging in x-ray microscopy an image-analysis algorithm for identifying colloidal-gold particles was developed. This algorithm is based on a combination of a threshold with respect to the local absorption and a shape discrimination, realized by fitting a Gaussian profile to the potential particles. The algorithm was evaluated and optimized on images taken by the transmission x-ray microscope at BESSY II. The size-selective identification and localization of single gold particles down to a diameter of 50 nm was demonstrated. / QC 20100920