All living organisms must organize their genome so that it not only fits within the cell, but remains accessible for cellular processes. In bacteria, an arsenal of nucleoid-associated proteins contributes to chromosome condensation. A novel nucleoid-associated protein was recently discovered in actinobacteria, and is essential in Mycobacterium. It was classified as an integration host factor protein (IHF); however, it does not share sequence or structural homology with the well characterized Escherichia coli IHF. In this study, we characterize the structure and function of Streptomyces coelicolor IHF (sIHF). We have used a combination of biochemistry and structural biology to characterize the role of sIHF in DNA binding and DNA topology. We have solved crystal structures of sIHF bound to various double-stranded DNA substrates, and show that sIHF is able to contact DNA at multiple surfaces. Furthermore, sIHF inhibits the activity of TopA, impacting DNA topology in vitro. Our work demonstrates that sIHF is a novel nucleoid-associated protein with key roles in condensing DNA. We believe that sIHF performs its function by differentially using multiple nucleic-acid binding surfaces. Further characterization is required to confirm this hypothesis in vivo. Given that the Mycobacterium homolog of sIHF (mIHF) is essential, our studies lay the foundation to explore novel drug targets for Mycobacterium tuberculosis and Mycobacterium leprae. / Thesis / Master of Science (MSc) / Unconstrained, the bacterial genome exceeds the size of the cell by 1 000- 10 000 times; thus, compacting it into a condensed structure, known as the nucleoid, is essential for life. An arsenal of nucleoid-associated proteins contributes to this process. In this study, we characterize the structure and function of a novel nucleoid–associated protein from the soil dwelling organism Streptomyces coelicolor. We used a combination of genetics, biochemistry, and structural biology to characterize the role of this protein in DNA binding and nucleoid organization. Since this protein is also found in important human pathogens, this work lays the foundation to explore the use of nucleoid-associated proteins as antimicrobial drug targets.

<p>Metalloproteins, or proteins with a metal ion cofactor, are essential for biological function of both lower and higher level organisms. These proteins provide a multitude of functions from molecular transport, such as the hemoglobin transport of oxygen, to biologically important catalytic processes. As an example case, photosystem II (PSII) is studied as a representative metalloprotein. It was chosen based on the potential impact in the energy sector due to its ability to perform water oxidation using solar based energy. Understanding mechanisms by which the Mn₄Ca cluster inside PSII, also known as the oxygen evolving complex (OEC), can store energy as redox equivalents for splitting water will be essential for future development of analogous artificial systems. By using time resolved x-ray spectroscopy, the electron structure of the metal in the protein was probed through the catalytic cycle. While the applications mentioned herein are based on PSII from spinach, the developments in time-resolved x-ray spectroscopy techniques are also applicable to other metalloproteins.</p><p></p><p>By creating a new x-ray spectrometer we were able to capture the difference in x-ray emission spectra between two compounds differing in a single metal bound ligand, i.e. Mn^IV-OH and Mn^IV=O. This both establishes the functionality of the x-ray emission spectrometer and provides useful insight into the expected changes upon an oxygen double bond formation. This change in spectroscopic signal is discussed in context of the OEC which has been hypothesized to form a Mn^IV=O state.</p><p></p><p>A new sample delivery system and further developments to the x-ray spectrometer enabled both time-resolved x-ray absorption and time-resolved x-ray emission of PSII. These experiments show the potential of synchrotron sources for time-resolved x-ray spectroscopy. From our x-ray absorption measurements we were able to follow the electronic structure changes in time using a single incident photon energy. From the kinetic traces obtained, we show possible alternative interpretations of previous results showing a delay in reduction during the final step in water oxidation. From the x-ray emission spectroscopy (XES) measurements of PSII we were able to reproduce previous results within a limited collection time and give estimates for data size requirements for metalloproteins using this spectrometer. Between the results of both these measurements, we show the improved capability for time resolved measurements at synchrotrons.</p><p>The development of x-ray free electron lasers (XFELs) has also opened many opportunities for understanding faster electronic dynamics by providing femtosecond x-ray pulse durations with ~10¹² photons per pulse. While theoretical modeling of distortions to crystallographic data have been performed, little to no work has been done to understand under what conditions such an intense pulse will have on an impact on emission spectra. Here an atomistic model was developed, and data collected, to clarify the effects of sequential ionization, i.e. two single photons absorbed by the same atom at different times during a single pulse. Experimentally we found that XFELs easily achieve flux densities that invoke a different response than is classically observed for single photon absorption and emission for Mn^II which was used as a representative case for 3d transition metals in general. We also give parameters by which the onset of this damage can be predicted and an approximation to its effect on 3d transition metals. Additionally this work guides the work of future XFEL facilities as it shows that shorter pulses, currently believed to be able to escape x-ray induced distortions to crystallography data, is not a viable method for overcoming changes in x-ray emission spectra.</p><div><br></div>

The exploitation of the soft x-ray/extreme ultra-violet (EUV) region of the electromagnetic spectrum is possible mainly due to the development of multilayer (ML) mirrors. This region of the electromagnetic spectrum offers great opportunities in both science and technology. The shorter wavelength allows one to see smaller features in microscopy and write finer features in lithography. High reflectivity with moderate spectral bandwidth at normal/near-normal incidence can be achieved in soft x-ray/ EUV spectral range using these ML mirrors, where natural crystals with the required large periodicity are not available. These MLs are generally artificial Bragg’s reflectors, which consist of alternative high and low density materials with periodicity in the nanometer range. The main advantages of ML optics stem from the tunability of layer thickness, composition, lateral gradient, and the gradient along the normal to the substrate; these can be tailored according to the desired wavelength regime. They have the great advantage of being adaptable to figured surfaces, enabling their use as reflective optics in these spectral regions, for focusing and imaging applications. Broadband reflectivity and wavelength tunability are also possible by using MLs with normal and lateral gradient, respectively. However, fabrication of these ML mirrors requires the capability to deposit uniform, ultra-thin (a few angstroms-thick) films of different materials with thickness control on the atomic scale. Thus, one requires a proper understanding of substrate surfaces, individual layers, chemical reactivity at interfaces and, finally, of the ML structures required for particular applications. The performance of these MLs is limited by (the lack of) contrast in optical constants of the two materials, interfacial roughness, the chemical reactivity of two materials and, finally, errors in the thickness of individual layers. Soft x-ray/extreme ultra-violet ML mirrors have found a wide range of applications in synchrotron radiation beam lines, materials science, astronomy, x-ray microscopy, x-ray laser, x-ray lithography, polarizers, and plasma diagnostics. The Indus–1 synchrotron radiation (SR) source is an operational 450 MeV machine, which produces radiation up to soft x-rays. Indus-2 is a 2.5 GeV machine, which has been commissioned recently to produce hard x-rays (E > 25 keV). The combination of Indus-1 and Indus-2 will cover a broad energy spectrum from IR to hard x-rays. Therefore, there is a significant need and opportunity to study MLs of different pairs of materials, with different parameters such as periodicity and optimum thickness of individual layers. The goal of the present thesis is to fabricate MLs for soft x-ray optics and to study their physics for application as polarizers in the wavelength range from 67 Å to 160 Å on the Indus-1 synchrotron source. To accomplish this task, a UHV electron beam evaporation system has been developed indigenously for the fabrication of MLs. Three different ML systems viz., Mo/Si, Fe/B4C and Mo/Y have been fabricated, and their surfaces and interfaces were investigated thoroughly for the polarizer application. X-ray reflectivity (XRR) has been used extensively in the investigations of these MLs. This is because XRR is a highly sensitive non-destructive technique for the characterization of buried interfaces, and gives microscopic information (at atomic resolution) over a macroscopic length scale (a few microns). Numerical analysis of XRR data has been carried out using computer programs. Depth-graded x-ray photoelectron spectroscopy (XPS) has been used for compositional analysis at interfaces for some of the ML structures, as a technique complementary to XRR. The performance of some of these MLs has been tested in the soft x-ray region, using the Indus-1 synchrotron radiation (SR) source. Prior to studying the MLs, a detailed study of the surfaces and interfaces of thin films, bi-layers, and tri-layers was carried out using XRR and the glancing incidence fluorescence technique. The discontinuous-to-continuous transition and the mode of film growth, which are vital to the optimization of layer thickness (basically for the high-atomic number or high-Z layer) in the ML structures, were also investigated using in situ sheet resistance measurement method. Indus-1 is a soft x-ray SR source that covers atomic absorption edges of many low-Z materials. The present work demonstrates the possibilities of characterizing low-Z thin films and multilayers using soft x-ray resonant reflectivity. In one case, we have shown for first time that soft x-ray resonant reflectivity can be employed as a non-destructive technique for the determination of interlayer composition. In a second study using the Indus-1 SR source, we have shown, by observing the effect of the anomalous optical constant on reflectivity pattern when photon energy is tuned across the atomic absorption edge of the constituent low-Z element, that soft x-ray resonant reflectivity is an element-specific technique. This thesis is organized into 7 chapters. A brief summary of individual chapters is presented below. Chapter 1 gives a brief general introduction to x-ray ML optics. This is followed by a discussion of the importance of the soft x-ray region of electromagnetic radiation. The optical properties of x-rays are reviewed and optical constants are calculated for some of the important materials used for x-ray MLs. The refractive index in the x-ray region being less than unity (except absorption edges), the consequent limitation of conventional transmission lenses is discussed. The limitation of glancing angle incidence optics is presented, motivating the need for ML optics, which is discussed along with a theoretically calculated reflectivity profile. The procedure for materials for the MLs for application in different spectral regions is discussed, along with a survey of literature related to the present thesis. The importance of the quality of surfaces and interfaces on the performance of ML structures has been shown through simulations. The applications of soft x-ray MLs are discussed with emphasis on polarization. This is followed by a review of different modes of growth of thin films. Finally, the scope of the present work is highlighted. Chapter 2 provides brief descriptions of the experimental techniques used in the present investigations and of the numerical methods employed for quantitative data analysis. The XRR technique is discussed elaborately because it has been used extensively. Detailed calculations of x-ray reflectivity from single surfaces, thin films and bi-layers are presented, along with simulated values. The effect of critical angle and Brewster’s angle is also discussed. Data analysis methods for computing x-ray reflectivity from multilayer structures, based on dynamical and kinematical models, have been discussed. The effect of roughness on XRR has been discussed based on the recursion formalism of dynamical theory. Simulations of XRR and experimental XRR data fitting are carried out using computer programs. The XRR experimental set up is also outlined. A theoretical background is given for the electrical measurements on thin films. This is followed by a brief overview of x-ray photoelectron spectroscopy (XPS) and interpretation of spectra. Finally, the glancing incidence x-ray fluorescence (GIXRF) technique is outlined. Chapter 3 describes in detail the ultra-high vacuum electron beam evaporation system developed in house especially for the fabrication of thin films and x-ray multilayer optics. At the outset, a brief overview of different deposition techniques commonly used for the fabrication of x-ray optical elements is presented. Design, fabrication, and assembly of different accessories are discussed. The control of thickness and uniformity of the films deposited has been checked through the experiments, whose results are provided. The results obtained for ML test structures are presented to show the capability of system in carrying out fabrication of high quality x-ray ML structures. Finally, the versatility of evaporation system incorporating in situ characterization facilities such as -situ electrical measurements for different substrate temperatures is illustrated. Chapter 4 presents a study of the growth of ultra-thin Mo films at different substrate temperatures using in situ sheet resistance measurements. First, a theoretical background is given on the different stages of island growth and on factors affecting thin film growth, followed by a discussion of the possible electrical conduction phenomena in continuous and discontinuous metal films. The nature of thin film growth and a detailed microscopic picture at different growth stages are derived from a modeling of sheet resistance data obtained in situ. The various conduction mechanisms have been identified in different stages of growth. In the island growth stage, the isotropic and anisotropic growth of Mo islands is identified from the model. In the insulator-metal transition region, experimentally determined values of critical exponent of conductivity agrees well with theoretically predicted values for a two-dimensional (2D) percolating system, revealing that Mo films on float glass substrate is predominantly a 2D structure. The minimum thickness for which Mo films becomes continuous is obtained as 1.8 nm and 2.2 nm for Mo deposited at substrate temperatures 300 K and 100 K, respectively. An amorphous-to- crystalline transition is also observed, and discussed. Chapter 5 covers the detailed study of the surfaces and interfaces studies in three different ML structures viz., Mo/Si, Fe/B4C and Mo/Y, meant for the polarizer application in the wavelength range of 67 Å to 160 Å. Multilayers with varying periodicity, varying number of layer pairs, and different ratios of high-Z layer thickness to the period, were fabricated using the electron beam system. Initially, a brief overview of the design aspects of ML structures is given, along with the theoretically calculated reflectivity at Brewster’s angle from the best material combinations. In Mo/Si MLs, the interlayer formed at the interfaces due to interdiffusion of the two elements is asymmetric in thickness, i.e., Mo-on-Si interlayer is thicker than the Si-on-Mo interlayer. To take account of these interlayers in XRR data fitting, a four layer model is considered. The effect of interlayers on reflectivity pattern was studied using simulations, and differences with respect to roughness are also discussed. The mechanism of formation of asymmetric interlayers is also discussed. The interlayer composition has determined using depth-graded XPS. The results reveal the formation of the MoSi2 composition at both the interfaces. The experimental results agree well with theoretical calculations based on solid-state amorphization reaction, which is a result of large heat of mixing. The effective heat of formation model reveals the formation of MoSi2 as the first phase. The soft x-ray reflectivity performance of the Mo/Si ML structure at Brewster’s angle is tested using Indus-1 synchrotron radiation (SR). Using XRR and GIXFR, a study of the surfaces and interfaces of bilayers of B4C-on-Fe and Fe-on- B4C, and tri-layers of Fe-B4C-Fe was carried out, with a systematic variation of Fe and B4C layer thicknesses. A sharp interface was observed in Fe-on-B4C, whereas a low density (w.r.t. Fe) interlayer is observed at the B4C-on-Fe interface. The interlayer properties fluctuates w.r.t. the bottom Fe layer thickness and is independent of the top B4C layer thickness. The nature of fluctuations has been discussed in detail. A study of the surfaces and interfaces of Fe/B4C MLs is described. Finally, a study of the surfaces and interfaces of bilayers, tri-layers, and MLs of the Mo/Y system is discussed in detail. Chapter 6 describes the application of soft x-ray resonant reflectivity for the characterization of low-Z thin films and interfaces in multilayer structures. Initially, a discussion of the energy dependence of atomic scattering factors and hence of optical constants is provided with simulations, with emphasis on the atomic absorption edge. Then, a brief overview of synchrotron radiation, with particular emphasis on the parameters of the Indus-1 synchrotron source is given. The possibilities of determining the composition of the buried interlayer with sub-nanometer scale sensitivity using soft x-ray resonant reflectivity are discussed. The methodology has been applied to study the Mo/Si interface both by simulations and by experiments on the Indus-1 SR, by tuning the photon energy to the Si L-absorption edge. Finally, direct evidence of elemental specificity of soft x-ray resonant reflectivity through the observation of the effect of anomalous optical constants on the reflectivity pattern is discussed. We demonstrate the method through simulations and experiments on the B4C material in B4C thin films and Fe/ B4C bi-layers, using Indus-1 SR tuned to the boron Kedge. Chapter 7 summarizes the main findings of the present work, and provides an outlook for further investigations in the field.

Para melhorar a visualização das pequenas estruturas anatômicas importantes para o diagnóstico do câncer de mama e otimizar o processamento das mamografias pelos sistemas computadorizados de auxílio ao diagnóstico (CAD), foi desenvolvido um dispositivo, baseado na tecnologia slit, que melhora a aquisição dos mamogramas. Este dispositivo reduz a radiação espalhada e o tamanho do foco e foi projetado a partir de um modelo computacional. O modelo adotado permite quantificar o valor desses parâmetros para qualquer sistema radiológico, qualquer espessura de tecidos moles radiografada e qualquer tensão aplicada ao tubo de raios-X. O dispositivo foi implementado e testado, quantificando as melhorias obtidas. As imagens geradas foram comparadas com as fornecidas pelos sistemas mamográficos convencionais. O modelo serviu para estudar também a interferência do espalhamento sobre o desempenho dos algoritmos usados nos sistemas de diagnóstico auxiliado por computador (CAD). / In order to improve the visualization of the small and important anatomical structures for breast cancer diagnosis and to optimize the image processing of mammograms by the computer aided diagnosis systems (CAD), a device that comes from slit technology was developed to improve the acquisition of mammograms. This device reduces the amount of scattered radiation and the focus size and it can be projected from a computational model. This model allows quantifying the value of those parameters, scattered radiation and the focus size, for any radiological system, any X-rayed soft tissue thickness and any tension applied to the X-ray tube. The device was implemented and tested quantifying the obtained improvements. The generated images were compared to the supplied for conventional mammography systems. The model was also good for studying interference on the algorithms used in the computer aided diagnosis systems (CAD).

Les otolithes, croissances aragonitiques de l'oreille interne des poissons téléostéens, peuvent être utilisés comme traceurs des variations de l’environnement rencontrées par un individu au cours de sa vie. Un ensemble d’otolithes de Sciaenidae et d’Ariidae archéologiques et modernes a été étudié dans le but d'améliorer les méthodes de reconstruction paléo-environnementale utilisant les otolithes et les autres biominéraux carbonatés stratifiés. L'incorporation du strontium, l'élément lié à l'environnement le plus facilement accessible, a été étudiée par analyses ponctuelles et par cartographie de spectroscopie d'absorption des rayons X (XAS). Une approche multivariée de cartographie rapide de l'environnement chimique a été mise en place pour déterminer le mode d’incorporation du Sr sur une superficie de 0,25 mm² avec une résolution micrométrique. Ces résultats démontrent pour la première fois avec une résolution latérale micrométrique sur des distances millimétriques que le Sr se substitue aléatoirement au calcium dans le réseau de l'aragonite, indépendamment de la concentration en Sr, de l’âge de l’individu ou de la période géologique. D’autre part, des cartes élémentaires sur des zones atteignant 2,6 mm² ont été collectées à des résolutions latérales micrométriques avec plusieurs techniques d'émission de rayons X (émissions provoquées par les particules des rayons X (PIXE) et fluorescence des rayons X par rayonnement synchrotron (SR-µXRF)). Ces cartes permettent l'examen détaillé de l'histoire de la vie d'un individu et de la taphonomie de l'échantillon avec une haute résolution temporelle, tout en identifiant les défauts ou les éléments abiogéniques. Enfin, la diffraction des rayons X par rayonnement synchrotron (SR-XRD) a été utilisée pour cartographier la texture cristalline sur des sections complètes d'otolithes afin d’approfondir notre connaissance de la structure interne et de la croissance des otolithes. Ces développements fournissent des outils précieux pour de futures études des biominéraux, mais plus généralement pour les sciences des matériaux. La sélection et la mise en œuvre de ces méthodes ont été réalisées dans le but d’exploiter au maximum leur fort potentiel pour l'étude des biocarbonates stratifiés, tout en tenant compte des approches existantes et en cherchant à en améliorer certains aspects tels que la profondeur d'information, la résolution latérale, la sensibilité, et les dégâts d’irradiation provoqués par les faisceau. Ce travail démontre la stabilité et l'homogénéité de l'incorporation du Sr par substitution aléatoire au Ca dans l’aragonite biogénique des otolithes modernes et archéologiques. Des cartes multi-élémentaires ont été collectées à l'aide de la SR-µXRF dans un temps raisonnable de quelques heures, et permettent de distinguer une contamination ou des défauts dans l'échantillon, mais également de corréler les cartes obtenues à des observations microscopiques des sections pour fournir une résolution temporelle. Les orientations préférentielles des cristallites composant les sections d'otolithes ont été analysées par la méthode d’acquisition rapide « flyscan », permettant de réduire le temps de mesure à quelques minutes au lieu des quelques heures nécessaires auparavant. / Otoliths, aragonitic growths in the inner ear of teleost fishes, can be used as proxies for the water conditions experienced by an individual over its lifetime. A set of archaeological Sciaenidae and Ariidae otoliths and modern counterparts was studied with the objective of improving palaeoenvironmental reconstruction methodologies using otoliths and other incremental carbonate biominerals. The incorporation of strontium, the most accessible environment-related element, was studied by X-ray absorption spectroscopy (XAS) point analyses and mapping. A fast multivariate chemical environment mapping approach was implemented to determine the mode of Sr incorporation over an area of 0.25 mm² with micrometric resolution. XAS results demonstrate for the first time with a micrometric lateral resolution over millimetric distances that strontium randomly substitutes for calcium in the aragonite lattice, independent of strontium concentration, or individual or geological age. Elemental maps on areas up to 2.6 mm² were produced with micrometric lateral resolution X-ray emission techniques (Particle-induced X-ray emission (PIXE) and synchrotron X-ray fluorescence (SR-µXRF)). These maps permit the detailed examination of an individual’s life history and sample taphonomy with a high temporal resolution while also identifying defects or abiogenic elements. Synchrotron X-ray diffraction (SR-XRD) was used to map the crystal texture on complete otolith sections and may deepen understanding of otolith internal structure and growth processes, as well as providing a valuable tool for future studies of biominerals and advanced materials. The selection and implementation of methods were carried out with a view to maximise the potential contribution to the study of stratified biocarbonates, considering and seeking to complement existing approaches in aspects including information depth, lateral resolution, sensitivity, and beam damage. This work demonstrates the stability and homogeneity of Sr incorporation by random substitution for Ca in biogenic aragonite in both modern and archaeological otoliths. Multielemental maps were collected using SR-µXRF in a reasonable time scale of a few to several hours, with the ability to distinguish contamination and defects in the sample, as well as to correlate the maps to microscopic observations of the sections to provide temporal resolution. The preferential orientations of crystallites composing the otolith sections were analysed using the rapid acquisition ‘flyscan’ method, which reduces measurement time to minutes rather than hours.

<p>This thesis addresses the electronic structure of vanadium and copper oxides using soft X-ray absorption (SXA) spectroscopy and resonant inelastic X-ray scattering (RIXS) at high brightness synchrotron radiation sources. In RIXS incident photons, tuned to the energy of specific absorption resonances, are inelastically scattered leaving behind a low energy valence excitation in the system studied. Effects of electron localization are reflected by the occurrence of low-energy excitations in form of dd- and charge-transfer excitations that are modelled by cluster calculations. Band-like states are dominating when the intermediate core excited state is delocalized.</p><p>RIXS at V 2p and O 1s resonances has been used to study the electronic structure of the monovalent vanadium oxides VO₂ and V₂O₃, and of the mixed valence compounds, NaV₂O₅ and V₆O₁₃. For NaV₂O₅ and V₆O₁₃ significant contributions from localized low-energy excitations reflect the partly localized character of their valence band electronic structure, whereas VO₂ and V₂O₃ appear mostly as band-like. Effects of carrier doping are addressed for the case of Mo doping into VO₂ and reveal a quasi-rigid band behavior. In the cases of VO₂ and V₆O₁₃ the temperature dependent metal-insulator transition could be monitored by following the spectral evolution of bands originating from V 3d and V 3d - O2p hybridized states. For Na₂V₃O₇ nanotubes it was possible to selectively probe states from the apical and the basal oxygen sites of VO₅ pyramids that constitute these nanotubes. Furthermore, the RIXS technique has been demonstrated to be highly valuable in characterizing the charge transfer processes that accompany lithium insertion into vanadium oxide battery cathodes. Finally, for insulating cuprates RIXS at O 1s, Cu 3p and Cu 3s resonances has been recorded at high-resolution for the detailed investigation of crystal field excitations.</p>

This thesis addresses the electronic structure of vanadium and copper oxides using soft X-ray absorption (SXA) spectroscopy and resonant inelastic X-ray scattering (RIXS) at high brightness synchrotron radiation sources. In RIXS incident photons, tuned to the energy of specific absorption resonances, are inelastically scattered leaving behind a low energy valence excitation in the system studied. Effects of electron localization are reflected by the occurrence of low-energy excitations in form of dd- and charge-transfer excitations that are modelled by cluster calculations. Band-like states are dominating when the intermediate core excited state is delocalized. RIXS at V 2p and O 1s resonances has been used to study the electronic structure of the monovalent vanadium oxides VO2 and V2O3, and of the mixed valence compounds, NaV2O5 and V6O13. For NaV2O5 and V6O13 significant contributions from localized low-energy excitations reflect the partly localized character of their valence band electronic structure, whereas VO2 and V2O3 appear mostly as band-like. Effects of carrier doping are addressed for the case of Mo doping into VO2 and reveal a quasi-rigid band behavior. In the cases of VO2 and V6O13 the temperature dependent metal-insulator transition could be monitored by following the spectral evolution of bands originating from V 3d and V 3d - O2p hybridized states. For Na2V3O7 nanotubes it was possible to selectively probe states from the apical and the basal oxygen sites of VO5 pyramids that constitute these nanotubes. Furthermore, the RIXS technique has been demonstrated to be highly valuable in characterizing the charge transfer processes that accompany lithium insertion into vanadium oxide battery cathodes. Finally, for insulating cuprates RIXS at O 1s, Cu 3p and Cu 3s resonances has been recorded at high-resolution for the detailed investigation of crystal field excitations.

X-ray binaries are binary stellar systems containing a compact object and a normal companion star which are gravitationally bound and rotate about a common center of mass. The compact object accretes matter from the companion star. The accreted matter may have a high angular momentum and hence follow a Keplarian orbit about the compact object. It slowly spirals inward as its angular momentum is redistributed via viscous forces and forms an accreting disk before being finally accreted onto the compact object. The compact object that is accreting matter may either be a neutron star or a black hole. X-ray binaries can be broadly classified into two classes depending on the mass of the companion star. Low Mass X-ray Binaries (LMXBs) have companion star masses and accrete mass via Roche lobe overflow of the companion star. High Mass X-ray Binaries (HMXBs) have companion star masses and in these systems the compact object accretes matter from the high velocity stellar winds of the companion star. For the work and results that are presented in the thesis we have studied the orbital evolution, apsidal motion and long term flux variations in High mass X-ray binaries which have a neutron star compact object with very high magnetic field of the order of B ~ 1012 G. Due to the high magnetic field, the accretion disk is disrupted at the Alfven radius where the magnetic field pressure equals the ram pressure of the infalling matter. From that boundary, the flow of the infalling matter will be guided by the magnetic field lines. The infalling matter will follow these lines, finally falling onto the magnetic poles with velocity nearly equal to the free fall velocity and form an accretion column over the magnetic poles. A hot spot is formed at both the magnetic poles and high energy photons are emitted from these regions. Inverse Compton scattering of these photons by high energy electrons in the accretion column can produce hard X-rays. If the optical depth of the accretion column is low, the radiation comes along the magnetic axis forming a pencil beam whereas if the optical depth is high, radiation escapes tangential to the accretion column forming a fan beam. Since the neutron star is rotating about its rotation axis, the radiation beam directed along magnetic axis non-aligned with the rotation axis will sweep across the sky. Whenever this beam of rotating radiation is aligned with the line of sight, a pulse of X-ray radiation is detected. Hence these systems are also called X-ray Binary Pulsars (XBP). These pulses are emitted at equal intervals of time, where the time between the emission of two pulses is the spin period of the neutron star. But since the neutron star is in a binary orbit, the arrival time of pulses as recorded by an observer will be delayed or advanced due to the motion of the neutron star. When the neutron star is moving towards the observer, the pulses arrive faster and when the neutron star is moving away from the observer, the pulses are delayed. These delays or advances of the arrival time of pulses can be measured accurately which allows us to measure the orbital elements (ax sin i, Porb, e, ω, Tω ) of the neutron star orbit. The neutron star orbit may evolve with time due to mass loss from the system, mass transfer from the companion star onto the neutron star and due to tidal interaction between the neutron star and the companion star. Gravitational wave radiation may also cause orbital evolution. However, in HMXBs this effect is likely to be much weaker compared to the effect of mass loss, mass exchange and tidal interaction. Rossi X-ray Timing Explorer (RXTE) is an X-ray astronomy satellite launched in 1995 by NASA. It has two pointed instruments, the Proportional Counter Array (PCA) and the High Energy X-ray Timing Experiment (HEXTE). PCA has a large effective area of 6500 sq cm and works in the energy range of 2-60 keV. It has a very good time resolution of 1 microsec. HEXTE observes in the energy range of 15-250 keV and has a time resolution of 8 microsec. RXTE also has an All Sky Monitor (ASM) which scans 80% of the sky in 90 minutes. We have used RXTE-PCA data for timing and spectral studies and ASM data for the long term flux variation studies of Cen X-3. The thesis presents details of our work, the analysis of the data, results of the analysis and our conclusions from these results. The first chapter of the thesis gives an overview of X-ray binaries, their orbital evolution and the instrument details of RXTE. In the second chapter we have presented our work of timing analysis of three persistent sources, namely Cen X-3, SMC X-1 and 4U 1538–52. For the SMC X-1 system, we have for the first time measured the eccentricity and the angle of periastron (ω). We found that the accuracy of pulse timing analysis is limited by the dependence of pulse profile on orbital phase. The new measurement of the orbit ephemeris of Cen X-3 when combined with the previous measurements of orbit ephemeris obtained by observations from other X-ray missions, gave an improved measurement of the rate of orbital decay P˙orb/Porb ~ -1.8 x 10−6yr−1 . A long observation of SMC X-1 made by RXTE in 2000 during the high state of SMC X-1 allowed us to measure the very small orbit eccentricity e ~ 0.00021 in this system. SMC X-1 was again observed for a long time by RXTE during 2003 during its low state. The SMC X-1 pulse fraction depends on the flux state of the source such that the pulse fraction decreases with decrease in the source flux. Thus the 2003 observations of SMC X-1 have higher error in measurement of pulse arrival times compared to the 2000 observations and could not be used to measure the eccentricity of the orbit. But combining the orbital ephemeris of SMC X-1 measured using the 2000 and the 2003 observation with the epoch history allowed us to improve the measurement of rate of orbit decay by an order of magnitude compared to previous observations P˙orb/Porb ~ - 3.4 x 10−6yr−1 . We observed 4U 1538–52 with RXTE under the guest observer program to measure the orbital evolution of this system. From observations of this system with BeppoSAX , a circular orbit similar to the SMC X-1 system was inferred. 4U1538–52 was observed with RXTE again in 1997 and analysis of this observation showed it to have eccentric orbit with a marginal evidence for an orbital decay. Our analysis carried out using the 2003 RXTE observation data confirmed that the orbit is eccentric with e ~ 0.18. But the new orbital ephemeris measured clearly shows that the orbit is not evolving with time as reported earlier. We have derived an upper limit on the rate of change of orbital period of this system to be P˙orb/Porb = 2.5 x 10−6yr−1 . 4U 1538–52 is similar to SMC X-1 in many respects, both have similar orbital period of Porb(SMC X -1) = 3.89 days and Porb(4U1538 - 52) = 3.72 days and companion star mass. But tidal interactions between the neutron star and the companion star have almost circularised the orbit of SMC X-1 where as the orbit of 4U 1538–52 is quite eccentric. Therefore we conclude that 4U 1538–52 is a young system and hence the orbit has not circularised by tidal interaction. The neutron star orbit also precesses due to tidal interaction and rotation of the companion star, which causes the longitude of periastron ω to change with time. The rate of change of ω can be measured by comparing the orbital elements of the neutron star orbit measured at different epochs of time. This rate of change of ω is directly related to the mass distribution of the companion star and hence the apsidal motion constant that are predicted by the theoretical models for stellar structure. Therefore measuring ˙ω will be a direct test for the stellar structure models. But ω can be measured only when the orbit is eccentric and for this purpose the Be-star/X-ray binary pulsars are the most suitable objects. The Be-star/X-ray binary pulsars are transient systems and have wide eccentric orbits of Porb > 10 days. The Be-stars are fast rotating stars with rotational velocity near to the break-up velocity. They eject matter along their equator in a circumstellar disk. When the neutron star intercepts this circumstellar disk during its periastron passage, the rate of mass accretion increases and the system becomes bright in X-rays. These short outburst are called the type-I X-ray bursts. The Be-star also has episodes of high mass ejection when the neutron star may accrete a larger amount of matter and can be seen over several binary orbits. These long duration outbursts are called type-II X-ray bursts. In the third chapter of the the thesis we have reported the analysis and results of three Be-/X-ray binary pulsars we have studied, namely 4U 0115+62, V0332+52 and 2S 1417-624 which were observed by RXTE during their respective type-II bursts. The X-ray pulse profiles of the Be-/X-ray systems evolve as a function of the source flux. Generally a simple single peaked pulse profile is seen during the onset of the outburst, which evolves into a more complex multiple peaked pulse profile as the source flux increases. The pulse profile again returns to the simple single peaked profile as the outburst fades off and the source flux decreases to persistent X-ray flux levels. Also due to varying mass accretion rate, the spin period evolves during the outburst. Both these factors together reduce the accuracy of measuring the arrival time of pulses. Hence we have used the instantaneous spin period measurements to deduce the orbital parameters of these system. The apparent spin period (Pspin) of the neutron star is modified by the radial velocity of the neutron star due to Doppler effect. The radial velocity of neutron star is dependant on the neutron star orbit and hence measurement of the spin period of the neutron star at different orbital phases allows us to determine the orbital elements. 4U 0115+63 was observed with the RXTE during two of its recent type II outbursts in 1999 and 2004. We measured the orbital parameters during both these outbursts independently. We combined the previous measurements of ω with our two measurements and measure the rate of apsidal motion of the system to be ˙ω ~ 0o .06 yr−1. V0332+52 was seen in outburst during 2004. During its previous outburst of 1983 only nine spin period measurements had been obtained and the orbital parameters measured from them were erroneous. We have measured the orbital parameters of this system accurately and determined the correct projected semi-major axis ax sin i and orbital period. The new orbit parameters can now be used to compare with future orbital element measurements to estimate any apsidal motion and/or orbital evolution in this system. We also used the 1999 outburst of 2S 1417–624 to accurately measure the orbital parameters of this system. We have also investigated the long term flux variations in the X-ray light curves of X-ray Binaries. Our studies on the flux variations observed in Cen X-3 are described in the fourth chapter of the thesis. Long term light curves of X-ray binaries show variations due to many reasons. Periodic variations of few milliseconds to a few hours in the light curve are seen due to spin of the neutron star. Light curves show variations due to motion of the neutron star in its orbit at timescales of few minutes to several days. Many sources also show quasi periodic variations in their X-ray light curves at timescales smaller than the neutron star orbital period which are believed to arise due to some material inhomogeneity orbiting the neutron star. These variations are called quasi periodic oscillations (QPOs). QPOs in X-ray binaries are observed between a frequency range of few millihertz to a few kilohertz. Long term X-ray light curves of many sources also reveal flux variations at time scales greater than the respective orbital period of the source. These variations are called superorbital variations. Systems like Her X-1, LMC X-4, 2S0114+650, SS 433, XTE J1716–389, 4U 1820–303 and Cyg X-1 show periodic superorbital variations whereas other systems like SMC X-1, GRS 1747-312, Cyg X2, LMC X-3 and the Rapid Burster show quasi periodic superorbital flux variations. These superorbital flux variations are understood as arising either due to a changing mass accretion rate which could be aperiodic in nature or as due to obscuration of the central X-ray source by a tilted, warped and precessing accretion disk. Many theoretical models have been proposed to explain the disk precession. The long term flux variations in the X-ray light curves of bright persistent X-ray binaries like Her X-1, SMC X-1 and LMC X-4 have been understood to be due to a periodic (in case of Her X-1 and LMC X-4) or a quasi periodic (for SMC X-1) precession of a warped accretion disk. We analysed the light curves of Cen X-3 obtained with the RXTE-ASM. The Cen X-3 light curves show aperiodic X-ray flux variations in all the energy bands of 1.5-3, 3-5 and 5-12 keV. The high and low states last for a few to upto a hundred days. The source also shows two spectral modes during the observations carried out with the ASM. The source was in a hard state during December 2000 to April 2004. At first look the aperiodic variations seen in Cen X-3 light curves seem to be arising due to a changing mass accretion rate. To investigate the cause of these aperiodic flux variations of Cen X-3 we studied the orbital modulation and the pulsed fraction as a function of source flux state. In the high state, the eclipse ingress and egress are found to be sharp whereas in the intermediate state, the transitions are more gradual. In the low state, instead of eclipse ingress and egress, the light curve shows a smooth intensity variation with orbital phase. The orbital modulation of the X-ray light curve in the low state shows that the X-ray emission observed in this state is from an extended object. The intensity dependent orbital modulations indicate that the different intensity states of Cen X-3 are primarily due to varying degree of obscuration. Measurements of the pulsed fraction in different intensity states are consistent with the X-ray emission of Cen X-3 having two components, one highly varying component with a constant pulsed fraction and a relatively stable component that is unpulsed and in the low state, the unpulsed component becomes dominant. The observed X-ray emission in the low state is likely to be due to scattering of X-rays from the stellar wind of the companion star. Though we can not ascertain the origin and nature of the obscuring material that causes the aperiodic long term intensity variation, we point out that a precessing accretion disk driven by radiative forces is a distinct possibility. We also studied the QPOs in Cen X-3 that are seen at 40 mHz. The QPOs are explained by the Beat Frequency Model (BFM) as arising due to the beat between the Keplarian frequency of the inner accretion disk and the spin of the neutron star. Thus when the mass accretion rate is high the inner disk radius decreases, increasing the Keplarian frequency and hence the observed QPO frequency and vise versa when the mass accretion rate decreases. Thus if the flux variations of Cen X-3 were due to a changing mass accretion rate then the observed QPO frequency should have a positive correlation with the observed X-ray flux of the source. But we find in our study that the QPO frequency does not have any correlation with the observed X-ray flux and the QPO frequencies does not follow the Frequency-Flux relation as expected in the Beat frequency model. Thus the QPO behaviour is in agreement that the observed X-ray flux does not indicate the true X-ray intensity state and hence the mass accretion rate in Cen X-3. Therefore, we conclude that X-ray variations of Cen X-3 are not due to changing mass accretion rate but due to varying obscuration of the central X-ray source, possibly by an accretion disk which precesses aperiodically. The conclusions from our studies presented in chapter 2, 3 and 4 of the thesis are summarised in the final chapter. The improved measurements of the rate of change of orbital periods from our work can now help us to detect any small departures from a constant period derivative in the persistent HMXB systems. The improved measurements of the orbital elements of Be-/X-ray binaries can now be used to study orbital evolution and apsidal motion in these system. New outbursts of the transient systems observed by future satellites providing good timing accuracy and large effective area, like LAXPC (Large Area X-ray Proportional Counter) of the ASTROSAT mission will facilitate such studies. The long term X-ray light curves study as done for Cen X-3 can be extended to other X-ray binary systems observed by All Sky Monitor. The method of source flux state dependent studies developed to study the Cen X-3 system can be easily extended to other systems that show long term superorbital flux variations. These kind of studies can be done by future proposed X-ray missions like ASTROSAT which will have a Sky Monitor similar to ASM dedicated to monitor X-ray sources. More sensitive measurements of long term X-ray light curves with the MAXI mission will allow similar studies of a large number of X-ray binaries and we will be able to see if aperiodically precessing accretion disk is present in many X-ray binaries.

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The main focus of this thesis is ab initio modeling of core level spectra with a high-level quantum chemical description both of the chemical interactions and of local atomic multiplet effects. In particular, the combination of calculations and synchrotron-based core-level spectroscopy aims at understanding the local structure of the electronic valence in transition metal complexes, and the details of the solvation mechanisms of electrolyte solutions, systems relevant for the dye-sensitized solar cell. Configurational sampling in solution is included through molecular dynamics simulations. Transition metal complexes are studied with x-ray absorption (XA) and resonant inelastic scattering (RIXS) spectroscopy, characterizing excited states with atomic site specificity. The theoretical multiconfigurational method, applying an active-space partitioning of the molecular orbitals (RASSCF), is used to assign the transitions observed in spectra of hydrated Ni2+ explicitly, including charge transfer and multiplet effects. Furthermore, the solvent-induced binding energy properties of the I- and I3- anions in aqueous, ethanol, and acetonitrile solutions are analyzed using photoelectron spectroscopy (XPS). The study shows that specific ion–solvent interactions are important for the core-level binding energy shifts in solution. The special case with I3- dissolved in water, where hydrogen bonding causes breaking of the molecular symmetry, is treated and proves that the geometry changes influence the photoelectron spectrum of aqueous I3- directly.