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.

More than half a decade of X-ray astronomy with various balloon borne and space orbiting X-ray instruments, have led to discoveries and detailed studies of X-ray binaries. An important property of X-ray binaries is intensity variations of different magnitudes in a wide range of timescales from milliseconds (quasi-periodic oscillations, millisecond pulsations), to a few weeks (orbital and super-orbital modulations) or longer (outbursts etc). In this thesis, different types of variabilities of X-ray binaries are considered in X-ray binary population studies and to investigate certain aspects of some individual systems. In Chapter 1, we provide an introduction to various types of variabilities seen in different classes of X-ray binaries. We mention in detail the various periodic and aperiodic variabilities seen in X-ray binaries. In Chapter 2, we describe, in some detail, the various X-ray all sky monitors and X-ray observatories, data from which has been utilized in the work carried out in this thesis. We also describe the various data analysis techniques that we have used. The rest of the thesis is divided into two major sections: Variability studies of indi-vidual systems and X-ray binary population studies Variability studies of individual systems In Chapter 3, we report results from an investigation of energy resolved orbital in-tensity pro les and from exhaustive orbital phase resolved spectroscopic measurements of GX 301{2 with MAXI{GSC . The orbital variation of the spectral parameters, es-pecially the relation between the equivalent width of Fe line and the column density of absorbing matter are then utilized to examine the models for the mode of accretion onto the neutron star in GX 301{2: circumstellar disk model by Pravdo & Ghosh (2001), and the accretion stream model by Leahy & Kostka (2008). A very large equivalent width of the iron line along with a small value of the column density in the orbital phase range 0.10-0.30 after the periastron passage indicates an asymmetry in the distribution of the matter around the neutron star, strongly favoring the accretion stream model by Leahy & Kostka (2008). Presence of an eclipse in an X-ray binary can be useful in determining orbital param-eters like inclination and in estimating the orbital evolution by eclipse timing method, which is reported in Chapter 4. For the HMXB system IGR J16393{4643, we found a short eclipse in the Swift{BAT light-curve and utilized it to constrain the orbital in-clination of the system. We have also studied, for the rst time, broad-band pulsation and spectral characteristic of the system with a Suzaku observation, showing sub-orbital intensity variations. For another eclipsing and non-pulsing HMXB 4U 1700{37, the orbital evolution is studied using mid-eclipse times from observations with narrow eld instruments as well as from long term light-curves of X-ray all sky monitors. The orbital period decay rate is estimated to be 5 10 7 /yr, an order slower than a previous measurement by Rubin et al.(1996). Since no pulsations are detected in this system, it is difficult to estimate its orbital parameters, especially its eccentricity. Using mid-eclipse times from 10 years of Swift{BAT data, we have independently constrained the eccentricity of the binary system. X-ray binary population studies In Chapter 5, we report results from an analysis of the 16 years light-curves of X-ray binaries in 2-10 keV energy band of RXTE{ASM , used to construct the differential and integral probability distributions of count-rates. These distributions are then employed to construct multiple snapshots of X-ray binary luminosity functions of the Milky Way instead of averaging the luminosities, an improvement over previous analysis by Grimm et al. (2002). We found that the averaged luminosities of highly variable X-ray binaries do not represent their true positions in XLFs and the variability of X-ray binaries do indeed signi cantly affect the luminosity functions. In Chapter 6, the measurements of the averaged spectra of X-ray binaries using MAXI{GSC data are reported and are used for constructing the composite X-ray spec-trum. These composite X-ray binary spectra are useful in estimating the contribution of X-ray binaries in extra-galactic SEDs constructed from the simultaneous Chandra / XMM{Newton and NuSTAR observations of these galaxies. These SEDs will also serve as a useful input in estimating the contribution of X-ray binary heating at high redshift IGM during the Epoch of Re-ionization. In Chapter 7, we summarize the main conclusions of the work carried out in this thesis and discuss some future prospects related to this thesis.

<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>

Given the wide range of properties and applications of intermetallic compounds, it is important to achieve a detailed understanding of their structure and bonding. X-ray photoelectron spectroscopy (XPS) and X-ray absorption near-edge spectroscopy (XANES) were used to study the electronic structure of several types of pnictides (compounds containing Pn = P, As). ZrAs2, forming a PbCl2-type structure, has been established to be a genuine binary phase that is strictly stoichiometric. At 900 °C, it supports extensive solubility of Ge to form the ternary extension Zr(GexAs1−x)As (0 ≤ x ≤ 0.4). XPS analysis and band structure calculations confirmed that the Ge and As atoms are anionic in character and that the substitution of Ge for As is driven by a depopulation of anion–anion antibonding states. ZrCuSiPn and REMAsO are important representatives of ZrCuSiAs-type materials. The small magnitudes of the binding energy shifts in the XPS spectra of ZrCuSiPn suggest significant covalent character in the Zr–Si, Zr–Pn, and Cu–Pn bonds, consistent with a three-dimensional structure. On progressing from ZrCuSiP to ZrCuSiAs, the charge transfer from metal to Pn atoms becomes less pronounced, as indicated by changes in the intensity of the Cu K-edge and Zr K, L-edge XANES spectra. Binding energy shifts and satellite features of the XPS spectra of REMAsO indicated that bonding in the [REO] layer is ionic, whereas bonding in the [MAs] layer is strongly covalent. Altering the electronic structure of one layer (by M or RE substitution) does not affect the electronic structure of the other layer, consistent with a two-dimensional structure in REMAsO. Metal-rich phosphides M2P (forming Cr2P-, Fe2P-, and Co2P-type structures) and M3P (forming Ni3P-type structures) were examined by XPS and XANES. The P 2p3/2 binding and P K-edge absorption energies decrease with greater ionic character of the M−P bonding and indicate the presence of anionic phosphorus. Interatomic effects play a more important role in affecting the energy shifts in these metal-rich phosphides than in the monophosphides, becoming more pronounced with higher metal concentration. Surprisingly, intraatomic effects dominate in mixed-metal phosphides (Ni1-xMx)2P despite evidence of metal-to-metal charge transfer from the Ni XANES spectra and Ni 2p XPS satellite features.

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

In this thesis, we have performed systematical study of anomalous electric and magnetic behaviors of the 3d transition metal oxides; colossal magnetoresistance (La1−xRxMnO3 where R is a divalent alkaline earth ion) and Multiferroic (Ho1-xLaxMn2O5) systems by X-ray and Neutron scattering techniques. In our study, the enhancement of the transfer temperature for La0.8Ba0.2MnO3 under strain effect from the SrTiO3 substrate could be possible due to two reasons which one is Sr diffusion from SrTiO3 substructure, and other one is the octahedral MnO6 high symmetry are increasing. We focus the intrinsic strain effect on La0.67Ca0.33MnO3 and La0.8Ba0.2MnO3 films, and findings show that due to the different ionic sizes of doped Ca or Ba ions, the strain effect acts differently in the way it deforms. The interfacial strain effect produces opposite influences on the lattice symmetry, the average Mn¡VO bond lengths, the average oxygen disorders, the coupling symmetries inside and in the vicinity of the MnO6 octahedrons, as well as producing an opposing trend in metal-insulator and magnetic transition temperatures of the strained La0.67Ca0.33MnO3 and La0.8Ba0.2MnO3 films. The strain effects on the electronic structures of La0.67Ca0.33MnO3 and La0.8Ba0.2MnO3 thin films have been studied by O K-edge x-ray absorption near edge structure (XANES) spectroscopy. For La0.67Ca0.33MnO3, the first-principles calculations reveal that the features in the XANES spectra are associated with hybridized states between O 2p and Mn minority-spin 3d t2g and eg, La 5d/Ca 3d, and Mn 4s/Ca 4p states. An analysis of these features shows that the tensile strain decreases substantially La¡VO and Ca¡VO hybridization and TC for La0.67Ca0.33MnO3. For La0.8Ba0.2MnO3, the small compressive strain enhances slightly La¡VO and Ba¡VO hybridization and TC. In this thesis, the influence of the local structure distortion on the magnetic transition in La doped HoMn2O5 Multiferroics has been investigated systematically. The orthorhombic crystal structure of Ho1−xLaxMn2O5 is maintained up to x¡Ø0.2 but decomposed into multiphase for x¡Ù0.25. By doping La ions to a concentration of 0.1¡Øx¡Ø0.2, the formation of the RMnO3 1(13) phase can be suppressed and single-phase Ho1−xLaxMn2O5 (0.1¡Øx¡Ø0.2) compounds can be formed under 1 atm flowing oxygen. For x=0.2, a ferromagnetic FM transition at 150 K is superimposed on the paramagnetic background, which implies that the compound undergoes a ferromagnetic to antiferromagnetic (AFM) transition. This unique FM to AFM transition is observed for the first time. The FM transition is attributed to the formation of magnetic clusters in a host paramagnetic matrix. The anomalous magnetic clusters phenomena observed in Ho0.8La0.2Mn2O5 can be directly attributed to the different properties between Ho and La ions, and the differences of Ho and La ions are not only in the ionic radius but also in the electron negativity. During 90~150K, X-ray scattering diffraction presented the new addition peaks indicates the new electric density distribution, and the Neutron powder scattering diffraction (NPD) refining results show that the local structure of R-O (R: La, Ho) is un-symmetry which is conflict to the La Extended X-ray absorption fine structure (EXAFS) (which shows that the local structure of La-O becomes more symmetry than H-O. Since the refining values of the NPD are an average of entire crystal, such that it cannot tell the local changes. X-ray absorption spectrum (XAS) and EXAFS, in contrarily, can provide the local information. They implies that the temperature evolutions of the coupling strength with O 2p or unoccupied density state are opposite for the Ho and La ions in our Ho0.8La0.2Mn2O5 sample. Therefore, local change of ions position and charge redistribution happens in this specific temperature range.