This thesis reports work in three areas of X-ray crystallography. An initial chapter describes the structure of a protein, the methods based on the use of X-rays and computer analysis of diffraction patterns to determine crystal structure, and the subsequent derivation of the structure of part or all of a protein molecule. Work to determine the structure of the protein cytokine receptor-like factor 3 (CRLF3) leading to the successful generation of a structural model of a significant part of this molecule is then described in Chapter 2. A variety of techniques had to be deployed to complete this work, and the steps undertaken are described. Analysis was performed principally using phaser, using maximum likelihood methods. Areas for improvement in generating non-crystallographic symmetry (NCS) operators in existing programmes were identified and new and modified algorithms implemented and tested. Searches based on improved single sphere algorithms, and a new two-sphere approach, are reported. These methods showed improvements in many cases and are available for future use. In Chapter 4, work on determining the relative importance of low resolution and high intensity data in molecular replacement solutions is described. This work has shown that high intensity data are more important than the low resolution data, dispelling a common perception and helping in experimental design.

X-ray microscopy is a well-established technique for nanoscale imaging. Zone plates are used as microscope objectives and provide high resolution, approaching 10 nm, currently limited by fabrication issues. This Thesis presents zone plate optics that achieve either high resolution or phase contrast in x-ray microscopy. The high-resolution optics use high orders of the zone plate, which alleviates the demands on fabrication, and the phase-contrast optics are single-element diffractive optical elements that produce contrast by Zernike or differential-interference contrast methods. The advantage of phase contrast in x-ray microscopy is shorter exposure times, and is crucial in the hard x-ray regime. Microscopy in the absorption‑contrast region of the water-window (2.34 - 4.37 nm) also benefits from these optics. The development of the optics for a laboratory soft x-ray microscope spans from theoretical and numerical analysis of coherence and stray light to experimental implementation and testing. The laboratory microscope uses laser-produced plasma-sources in the water-window and is unique in its design and performance. It will be shown that the laboratory microscope in its current form is a user-oriented and stable instrument, and has been used in a number of applications. The implementation of a cryogenic sample stage for tomographic imaging of biological samples in their natural environment has enabled applications in biology, and 3D x-ray microscopy of cells was performed for the first time with a laboratory instrument. / QC 20101130

This thesis summarizes the present status of the nanofabrication of diffractive optics, i.e. zone plates, and test objects for soft x-ray microscopy at KTH. The emphasis is on new and improved fabrication processes for nickel and germanium zone plates. A new concept in which nickel and germanium are combined in a zone plate is also presented. The main techniques used in the fabrication are electron beam lithography for the patterning, followed by plasma etching and electroplating for the structuring of the optical materials. The process for fabricating nickel zone plates has been significantly improved. The reproducibility of the electroplating step has been increased by the implementation of an in-situ rate measurement and an end-point detection method. We have also shown that pulse plating can be used to obtain zone plates with a uniform height profile. New plating mold materials have been introduced and electron-beam curing of the molds has been investigated and implemented to increase their mechanical stability so that pattern collapse in the electroplating step can be avoided. The introduction of cold development has improved the achievable resolution of the process. This has enabled the fabrication of zone plates with outermost zone widths down to 16 nm. The nickel process has also recently been adapted to fabrication of gold structures intended for test objects and hard x-ray zone plates. For the fabrication of germanium zone plates we developed a highly anisotropic plasma-etch process using Cl2 feed and sidewall passivation. Germanium zone plates have been fabricated with zone widths down to 30 nm. The diffraction efficiency is comparable to that of nickel zone plates, but the process does not involve electroplating and thus has for potential for highyield fabrication. The combination of nickel and germanium is a new fabrication concept that provides a means to achieve high diffraction efficiency even for thin nickel. The idea is to fabricate a nickel zone plate on a germanium film. The nickel zone plate itself is then used as etch mask for a highly selective CHF3- plasma etch into the germanium layer. Proof of principle experiments showed an efficiency increase of about a factor of two for nickel zone plates with a 50- nm nickel thickness. / QC 20100728

Thesis (Ph.D.) -- University of Western Sydney, 2002. / "Submitted in fulfilment of the requirements for the degree of Doctor of Philosophy, University of Western Sydney" Bibliography.

<p>In this Thesis studies of highly excited states in gas-phase atoms and molecules (He, Ne, N₂, O₂, N₂O and CO₂) using a variety of synchrotron-radiation based techniques are presented. The three techniques used most frequently are X-ray-emission-threshold-electron coincidence (XETECO), X-ray emission spectroscopy (XES) and X-ray photoelectron spectroscopy (XPS) and they are all given a brief introduction. </p><p>The fluorescence yield (FY) from doubly excited states in helium near the N=2 threshold(s) has been investigated in weak static external magnetic and electric fields, but also in a field free environment. The FY spectra in weak static magnetic fields show the importance of including the diamagnetic interaction in the theoretical models. The presence of weak static electric fields shows that even weak fields (as low as 44 V/cm) has a great impact on the observed FY spectra. Resonant XES spectra from some of the first doubly excited states in helium has been recorded in a field free environment, and compared to theory.</p><p>The XETECO technique is presented and the first XETECO results from Ne, N₂, O₂, CO₂ and N₂O are shown, together with interpretations of possible threshold dynamics. I show that XETECO can be interpreted as threshold photoelectron spectra free from post collision interaction, and can hence be compared to above threshold XPS measurements. The observed below-threshold structures in the XETECO spectra are discussed and given a tentative explanation. The results from the analysis of the N₂O XETECO spectrum lead to further investigations using XPS. Results showing the vibrational parameters and vibrationally resolved cross-sections and asymmetry parameters for N₂O are presented together with theoretical predictions.</p>

In this Thesis studies of highly excited states in gas-phase atoms and molecules (He, Ne, N2, O2, N2O and CO2) using a variety of synchrotron-radiation based techniques are presented. The three techniques used most frequently are X-ray-emission-threshold-electron coincidence (XETECO), X-ray emission spectroscopy (XES) and X-ray photoelectron spectroscopy (XPS) and they are all given a brief introduction. The fluorescence yield (FY) from doubly excited states in helium near the N=2 threshold(s) has been investigated in weak static external magnetic and electric fields, but also in a field free environment. The FY spectra in weak static magnetic fields show the importance of including the diamagnetic interaction in the theoretical models. The presence of weak static electric fields shows that even weak fields (as low as 44 V/cm) has a great impact on the observed FY spectra. Resonant XES spectra from some of the first doubly excited states in helium has been recorded in a field free environment, and compared to theory. The XETECO technique is presented and the first XETECO results from Ne, N2, O2, CO2 and N2O are shown, together with interpretations of possible threshold dynamics. I show that XETECO can be interpreted as threshold photoelectron spectra free from post collision interaction, and can hence be compared to above threshold XPS measurements. The observed below-threshold structures in the XETECO spectra are discussed and given a tentative explanation. The results from the analysis of the N2O XETECO spectrum lead to further investigations using XPS. Results showing the vibrational parameters and vibrationally resolved cross-sections and asymmetry parameters for N2O are presented together with theoretical predictions.

Soft x-ray microscopy in the water-window (λ = 2.28 nm – 4.36 nm) is based on zone-plate optics and allows high-resolution imaging of, e.g., cells and soils in their natural or near-natural environment. Three-dimensional imaging is provided via tomographic techniques, soft x-ray cryo tomography. However, soft x-ray microscopes with such capabilities have been based on large-scale synchrotron x‑ray facilities, thereby limiting their accessibility for a wider scientific community. This Thesis describes the development of the Stockholm laboratory soft x-ray microscope to three-dimensional cryo tomography and to new optics-based contrast mechanisms. The microscope relies on a methanol or nitrogen liquid-jet laser-plasma source, normal-incidence multilayer or zone-plate condenser optics, in-house fabricated zone-plate objectives, and allows operation at two wavelengths in the water-window, λ = 2.48 nm and λ = 2.48 nm. With the implementation of a new state-of-the-art normal-incidence multilayer condenser for operation at λ = 2.48 nm and a tiltable cryogenic sample stage the microscope now allows imaging of dry, wet or cryo-fixed samples. This arrangement was used for the first demonstration of laboratory soft x-ray cryo microscopy and tomography. The performance of the microscope has been demonstrated in a number of experiments described in this Thesis, including, tomographic imaging with a resolution of 140 nm, cryo microscopy and tomography of various cells and parasites, and for studies of aqueous soils and clays. The Thesis also describes the development and implementation of single-element differential-interference and Zernike phase-contrast zone-plate objectives. The enhanced contrast provided by these optics reduce exposure times or lowers the dose in samples and are of major importance for harder x-ray microscopy. The implementation of a high-resolution 50 nm compound zone-plate objective for sub-25-nm resolution imaging is also described. All experiments are supported by extensive numerical modelling for improved understanding of partially coherent image formation and stray light in soft x-ray microscopes. The models are useful tools for studying effects of zone plate optics or optical design of the microscope on image formation and quantitative accuracy in soft x-ray tomography. / QC 20110221

An inspection system was required in order to eliminate the difficulties which appear during the inspection of the vehicles according to specific criteria at Turkish Custom Border in a short time and effectively. In this thesis, we performed experiments on such a system to obtain the overall performance of its inspection quality. We firstly give with reasons, why the source of beam is selected as X-ray source. The subsystems of the main system are the accelerator subsystem and detector subsystem. Their structures and working principles are studied in detail by comparing them with their alternatives. Series of experiments are carried out to verify the general performance of system in terms of radiation security and quality of images produced by the system. These experiments were classified as general scan experiment, inspection performance experiment, image quality indicator experiment, radiation safety experiment and general performance experiment. The container inspection system studied and experimented in this thesis is now used effectively in Turkish Customs Boarder, Edirne Kapikule and Edirne ipsala.

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Digitized by Kansas State University Libraries