Sample records for x-ray molecular structure

  1. Method and apparatus for molecular imaging using x-rays at resonance wavelengths

    DOEpatents

    Chapline, G.F. Jr.

    Holographic x-ray images are produced representing the molecular structure of a microscopic object, such as a living cell, by directing a beam of coherent x-rays upon the object to produce scattering of the x-rays by the object, producing interference on a recording medium between the scattered x-rays from the object and unscattered coherent x-rays and thereby producing holograms on the recording surface, and establishing the wavelength of the coherent x-rays to correspond with a molecular resonance of a constituent of such object and thereby greatly improving the contrast, sensitivity and resolution of the holograms as representations of molecular structures involving such constituent. For example, the coherent x-rays may be adjusted to the molecular resonant absorption line of nitrogen at about 401.3 eV to produce holographic images featuring molecular structures involving nitrogen.

  2. Method and apparatus for molecular imaging using X-rays at resonance wavelengths

    DOEpatents

    Chapline, Jr., George F.

    1985-01-01

    Holographic X-ray images are produced representing the molecular structure of a microscopic object, such as a living cell, by directing a beam of coherent X-rays upon the object to produce scattering of the X-rays by the object, producing interference on a recording medium between the scattered X-rays from the object and unscattered coherent X-rays and thereby producing holograms on the recording surface, and establishing the wavelength of the coherent X-rays to correspond with a molecular resonance of a constituent of such object and thereby greatly improving the contrast, sensitivity and resolution of the holograms as representations of molecular structures involving such constituent. For example, the coherent X-rays may be adjusted to the molecular resonant absorption line of nitrogen at about 401.3 eV to produce holographic images featuring molecular structures involving nitrogen.

  3. X-ray structure determination using low-resolution electron microscopy maps for molecular replacement

    DOE PAGES

    Jackson, Ryan N.; McCoy, Airlie J.; Terwilliger, Thomas C.; ...

    2015-07-30

    Structures of multi-subunit macromolecular machines are primarily determined by either electron microscopy (EM) or X-ray crystallography. In many cases, a structure for a complex can be obtained at low resolution (at a coarse level of detail) with EM and at higher resolution (with finer detail) by X-ray crystallography. The integration of these two structural techniques is becoming increasingly important for generating atomic models of macromolecular complexes. A low-resolution EM image can be a powerful tool for obtaining the "phase" information that is missing from an X-ray crystallography experiment, however integration of EM and X-ray diffraction data has been technically challenging.more » Here we show a step-by-step protocol that explains how low-resolution EM maps can be placed in the crystallographic unit cell by molecular replacement, and how initial phases computed from the placed EM density are extended to high resolution by averaging maps over non-crystallographic symmetry. As the resolution gap between EM and Xray crystallography continues to narrow, the use of EM maps to help with X-ray crystal structure determination, as described in this protocol, will become increasingly effective.« less

  4. xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures.

    PubMed

    McGreevy, Ryan; Singharoy, Abhishek; Li, Qufei; Zhang, Jingfen; Xu, Dong; Perozo, Eduardo; Schulten, Klaus

    2014-09-01

    X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of D-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally, via systematic refinement of a series of data from 3.6 to 7 Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP.

  5. Structural studies on choline-carboxylate bio-ionic liquids by x-ray scattering and molecular dynamics.

    PubMed

    Tanzi, Luana; Ramondo, Fabio; Caminiti, Ruggero; Campetella, Marco; Di Luca, Andrea; Gontrani, Lorenzo

    2015-09-21

    We report a X-ray diffraction and molecular dynamics study on three choline-based bio-ionic liquids, choline formate, [Ch] [For], choline propanoate, [Ch][Pro], and choline butanoate, [Ch][But]. For the first time, this class of ionic liquids has been investigated by X-ray diffraction. Experimental and theoretical structure factors have been compared for each term of the series. Local structural organization has been obtained from ab initio calculations through static models of isolated ion pairs and dynamic simulations of small portions of liquids through twelve, ten, and nine ion pairs for [Ch][For], [Ch][Pro], and [Ch][But], respectively. All the theoretical models indicate that cations and anions are connected by strong hydrogen bonding and form stable ion pairs in the liquid that are reminiscent of the static ab initio ion pairs. Different structural aspects may affect the radial distribution function, like the local structure of ion pairs and the conformation of choline. When small portions of liquids have been simulated by dynamic quantum chemical methods, some key structural features of the X-ray radial distribution function were well reproduced whereas the classical force fields here applied did not entirely reproduce all the observed structural features.

  6. Structural studies on choline-carboxylate bio-ionic liquids by x-ray scattering and molecular dynamics

    NASA Astrophysics Data System (ADS)

    Tanzi, Luana; Ramondo, Fabio; Caminiti, Ruggero; Campetella, Marco; Di Luca, Andrea; Gontrani, Lorenzo

    2015-09-01

    We report a X-ray diffraction and molecular dynamics study on three choline-based bio-ionic liquids, choline formate, [Ch] [For], choline propanoate, [Ch][Pro], and choline butanoate, [Ch][But]. For the first time, this class of ionic liquids has been investigated by X-ray diffraction. Experimental and theoretical structure factors have been compared for each term of the series. Local structural organization has been obtained from ab initio calculations through static models of isolated ion pairs and dynamic simulations of small portions of liquids through twelve, ten, and nine ion pairs for [Ch][For], [Ch][Pro], and [Ch][But], respectively. All the theoretical models indicate that cations and anions are connected by strong hydrogen bonding and form stable ion pairs in the liquid that are reminiscent of the static ab initio ion pairs. Different structural aspects may affect the radial distribution function, like the local structure of ion pairs and the conformation of choline. When small portions of liquids have been simulated by dynamic quantum chemical methods, some key structural features of the X-ray radial distribution function were well reproduced whereas the classical force fields here applied did not entirely reproduce all the observed structural features.

  7. Probing molecular dynamics in solution with x-ray valence-to-core spectroscopy

    NASA Astrophysics Data System (ADS)

    Doumy, Gilles; March, Anne Marie; Tu, Ming-Feng; Al Haddad, Andre; Southworth, Stephen; Young, Linda; Walko, Donald; Bostedt, Christoph

    2017-04-01

    Hard X-ray spectroscopies are powerful tools for probing the electronic and geometric structure of molecules in complex or disordered systems and have been particularly useful for studying molecules in the solution phase. They are element specific, sensitive to the electronic structure and the local arrangements of surrounding atoms of the element being selectively probed. When combined in a pump-probe scheme with ultrafast lasers, X-ray spectroscopies can be used to track the evolution of structural changes that occur after photoexcitation. Efficient use of hard x-ray radiation coming from high brilliance synchrotrons and upcoming high repetition rate X-ray Free Electron Lasers requires MHz repetition rate lasers and data acquisition systems. High information content Valence-to-Core x-ray emission is directly sensitive to the molecular orbitals involved in photochemistry. We report on recent progress towards fully enabling this photon-hungry technique for the study of time-resolved molecular dynamics, including efficient detection and use of polychromatic x-ray micro-probe at the Advanced Photon Source. Work was supported by the U.S. Department of Energy, Office of Science, Chemical Sciences, Geosciences, and Biosciences Division.

  8. X-ray circular dichroism signals: a unique probe of local molecular chirality

    DOE PAGES

    Zhang, Yu; Rouxel, Jeremy R.; Autschbach, Jochen; ...

    2017-06-26

    Core-resonant circular dichroism (CD) signals are induced by molecular chirality and vanish for achiral molecules and racemic mixtures. The highly localized nature of core excitations makes them ideal probes of local chirality within molecules. Simulations of the circular dichroism spectra of several molecular families illustrate how these signals vary with the electronic coupling to substitution groups, the distance between the X-ray chromophore and the chiral center, geometry, and chemical structure. As a result, clear insight into the molecular structure is obtained through analysis of the X-ray CD spectra.

  9. X-ray circular dichroism signals: a unique probe of local molecular chirality

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhang, Yu; Rouxel, Jeremy R.; Autschbach, Jochen

    Core-resonant circular dichroism (CD) signals are induced by molecular chirality and vanish for achiral molecules and racemic mixtures. The highly localized nature of core excitations makes them ideal probes of local chirality within molecules. Simulations of the circular dichroism spectra of several molecular families illustrate how these signals vary with the electronic coupling to substitution groups, the distance between the X-ray chromophore and the chiral center, geometry, and chemical structure. As a result, clear insight into the molecular structure is obtained through analysis of the X-ray CD spectra.

  10. Structural studies on choline-carboxylate bio-ionic liquids by x-ray scattering and molecular dynamics

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Tanzi, Luana; Ramondo, Fabio, E-mail: fabio.ramondo@univaq.it; Caminiti, Ruggero

    2015-09-21

    We report a X-ray diffraction and molecular dynamics study on three choline-based bio-ionic liquids, choline formate, [Ch] [For], choline propanoate, [Ch][Pro], and choline butanoate, [Ch][But]. For the first time, this class of ionic liquids has been investigated by X-ray diffraction. Experimental and theoretical structure factors have been compared for each term of the series. Local structural organization has been obtained from ab initio calculations through static models of isolated ion pairs and dynamic simulations of small portions of liquids through twelve, ten, and nine ion pairs for [Ch][For], [Ch][Pro], and [Ch][But], respectively. All the theoretical models indicate that cations andmore » anions are connected by strong hydrogen bonding and form stable ion pairs in the liquid that are reminiscent of the static ab initio ion pairs. Different structural aspects may affect the radial distribution function, like the local structure of ion pairs and the conformation of choline. When small portions of liquids have been simulated by dynamic quantum chemical methods, some key structural features of the X-ray radial distribution function were well reproduced whereas the classical force fields here applied did not entirely reproduce all the observed structural features.« less

  11. X-ray crystal structure and small-angle X-ray scattering of sheep liver sorbitol dehydrogenase

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yennawar, Hemant; Møller, Magda; University of Copenhagen, DK-2100 Copenhagen

    The X-ray crystal structure and a small-angle X-ray scattering solution structure of sheep liver sorbitol dehydrogenase have been determined. The details of the interactions that enable the tetramer scaffold to be the functional biological unit have been analyzed. The X-ray crystal structure of sheep liver sorbitol dehydrogenase (slSDH) has been determined using the crystal structure of human sorbitol dehydrogenase (hSDH) as a molecular-replacement model. slSDH crystallized in space group I222 with one monomer in the asymmetric unit. A conserved tetramer that superposes well with that seen in hSDH (despite belonging to a different space group) and obeying the 222 crystalmore » symmetry is seen in slSDH. An acetate molecule is bound in the active site, coordinating to the active-site zinc through a water molecule. Glycerol, a substrate of slSDH, also occupies the substrate-binding pocket together with the acetate designed by nature to fit large polyol substrates. The substrate-binding pocket is seen to be in close proximity to the tetramer interface, which explains the need for the structural integrity of the tetramer for enzyme activity. Small-angle X-ray scattering was also used to identify the quaternary structure of the tetramer of slSDH in solution.« less

  12. Probing molecular orientations in thin films by x-ray photoelectron spectroscopy

    NASA Astrophysics Data System (ADS)

    Li, Y.; Li, P.; Lu, Z.-H.

    2018-03-01

    A great number of functional organic molecules in active thin-film layers of optoelectronic devices have highly asymmetric structures, such as plate-like, rod-like, etc. This makes molecular orientation an important aspect in thin-films as it can significantly affect both the optical and electrical performance of optoelectronic devices. With a combination of in-situ ultra violet photoelectron spectroscopy (UPS) and x-ray photoelectron spectroscopy (XPS) investigations for organic molecules having a broad range of structural properties, we discovered a rigid connection of core levels and frontier highest occupied molecular orbital levels at organic interfaces. This finding opens up opportunities of using X-ray photoemission spectroscopy as an alternative tool to UPS for providing an easy and unambiguous data interpretation in probing molecular orientations.

  13. X-ray absorption spectroscopy: EXAFS (Extended X-ray Absorption Fine Structure) and XANES (X-ray Absorption Near Edge Structure)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Alp, E.E.; Mini, S.M.; Ramanathan, M.

    1990-04-01

    The x-ray absorption spectroscopy (XAS) had been an essential tool to gather spectroscopic information about atomic energy level structure in the early decades of this century. It has also played an important role in the discovery and systematization of rare-earth elements. The discovery of synchrotron radiation in 1952, and later the availability of broadly tunable synchrotron based x-ray sources have revitalized this technique since the 1970's. The correct interpretation of the oscillatory structure in the x-ray absorption cross-section above the absorption edge by Sayers et. al. has transformed XAS from a spectroscopic tool to a structural technique. EXAFS (Extended X-raymore » Absorption Fine Structure) yields information about the interatomic distances, near neighbor coordination numbers, and lattice dynamics. An excellent description of the principles and data analysis techniques of EXAFS is given by Teo. XANES (X-ray Absorption Near Edge Structure), on the other hand, gives information about the valence state, energy bandwidth and bond angles. Today, there are about 50 experimental stations in various synchrotrons around the world dedicated to collecting x-ray absorption data from the bulk and surfaces of solids and liquids. In this chapter, we will give the basic principles of XAS, explain the information content of essentially two different aspects of the absorption process leading to EXAFS and XANES, and discuss the source and samples limitations.« less

  14. Fast automatic segmentation of anatomical structures in x-ray computed tomography images to improve fluorescence molecular tomography reconstruction.

    PubMed

    Freyer, Marcus; Ale, Angelique; Schulz, Ralf B; Zientkowska, Marta; Ntziachristos, Vasilis; Englmeier, Karl-Hans

    2010-01-01

    The recent development of hybrid imaging scanners that integrate fluorescence molecular tomography (FMT) and x-ray computed tomography (XCT) allows the utilization of x-ray information as image priors for improving optical tomography reconstruction. To fully capitalize on this capacity, we consider a framework for the automatic and fast detection of different anatomic structures in murine XCT images. To accurately differentiate between different structures such as bone, lung, and heart, a combination of image processing steps including thresholding, seed growing, and signal detection are found to offer optimal segmentation performance. The algorithm and its utilization in an inverse FMT scheme that uses priors is demonstrated on mouse images.

  15. Bone structure studies with holographic interferometric nondestructive testing and x-ray methods

    NASA Astrophysics Data System (ADS)

    Silvennoinen, Raimo; Nygren, Kaarlo; Rouvinen, Juha; Petrova, Valentina V.

    1994-02-01

    Changes in the biomechanics and in the molecular texture and structure of isolated radioulnar bones of subadult European moose (Alces alces L.) collected in various environmentally polluted areas of Finland were investigated by means of holographic interferometric non- destructive testing (HNDT), radiological, morphometrical, and x-ray diffraction methods. By means of small caudal-cranial bending forces, the surface movements of the lower end (distal epiphysis) of the radial bone were recorded with the HNDT method. To study bone molecular texture and structure changes under external compressing forces, the samples for x-ray diffraction analysis were taken from the upper end of the ulnar bone (olecranon tip). Results showed that the bones obtained from the Harjavalta area and those of North Karelian moose showing malnutrition and healing femoral fractures produced different HNDT pictures compared with the four normally developed North Karelian moose. In the x-ray diffraction, the Harjavalta samples showed changes in molecular texture and structure compared with the samples from the apparently normal North Karelian animals.

  16. Structural studies of homoisoflavonoids: NMR spectroscopy, X-ray diffraction, and theoretical calculations

    NASA Astrophysics Data System (ADS)

    Sievänen, Elina; Toušek, Jaromír; Lunerová, Kamila; Marek, Jaromír; Jankovská, Dagmar; Dvorská, Margita; Marek, Radek

    2010-08-01

    In this article we present a detailed structural investigation for five homoisoflavonoids, molecules important from the pharmacological point of view. For studying the electron distribution as well as its influence on the physicochemical properties, NMR spectroscopy, X-ray diffraction, and theoretical calculations have been used. Nuclear magnetic shieldings obtained by using DFT calculations for optimized molecular geometries are correlated with the experimentally determined chemical shifts. The theoretical data are well in agreement with the experimental values. The single crystal X-ray structures of homoisoflavonoid derivatives 1, 3, and 4 have been solved. The molecular geometries and crystal packing determined by X-ray diffraction are used for characterizing the intermolecular interactions. Electron distribution is crucial for the stability of radicals and hence the antioxidant efficiency of flavonoid structures. The hydrogen bonding governs the formation of complexes of homoisoflavonoids with biological targets.

  17. Role of Molecular Structure on X-ray Diffraction in Thermotropic Uniaxial and Biaxial Nematic Liquid Crystal Phases

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Acharya, Bharat R.; Kang, Shin-Woong; Prasad, Veena

    2009-08-27

    X-ray diffraction is one of the most definitive methods to determine the structure of condensed matter phases, and it has been applied to unequivocally infer the structures of conventional calamitic and lyotropic liquid crystals. With the advent of bent-core and tetrapodic mesogens and the discovery of the biaxial nematic phase in them, the experimental results require more careful interpretation and analysis. Here, we present ab-initio calculations of X-ray diffraction patterns in the isotropic, uniaxial nematic, and biaxial nematic phases of bent-core mesogens. A simple Meier-Saupe-like molecular distribution function is employed to describe both aligned and unaligned mesophases. The distribution functionmore » is decomposed into two, polar and azimuthal, distribution functions to calculate the effect of the evolution of uniaxial and biaxial nematic orientational order. The calculations provide satisfactory semiquantitative interpretations of experimental results. The calculations presented here should provide a pathway to more refined and quantitative analysis of X-ray diffraction data from the biaxial nematic phase.« less

  18. Role of Molecular Structure on X-ray Diffraction in Uniaxial and Biaxial Phases of Thermotropic Liquid Crystals

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Acharya, Bharat R.; Kang, Shin-Woong; Prasad, Veena

    2009-04-29

    X-ray diffraction is one of the most definitive methods to determine the structure of condensed matter phases, and it has been applied to unequivocally infer the structures of conventional calamitic and lyotropic liquid crystals. With the advent of bent-core and tetrapodic mesogens and the discovery of the biaxial nematic phase in them, the experimental results require more careful interpretation and analysis. Here, we present ab-initio calculations of X-ray diffraction patterns in the isotropic, uniaxial nematic, and biaxial nematic phases of bent-core mesogens. A simple Meier-Saupe-like molecular distribution function is employed to describe both aligned and unaligned mesophases. The distribution functionmore » is decomposed into two, polar and azimuthal, distribution functions to calculate the effect of the evolution of uniaxial and biaxial nematic orientational order. The calculations provide satisfactory semiquantitative interpretations of experimental results. The calculations presented here should provide a pathway to more refined and quantitative analysis of X-ray diffraction data from the biaxial nematic phase.« less

  19. Molecular environment and an X-ray study of the double-shell supernova remnant Kes 79

    NASA Astrophysics Data System (ADS)

    Zhou, Ping; Chen, Yang; Safi-Harb, Samar; Ming, Sun

    Kes 79 is a remarkable middle-age supernova remnant (SNR) with double shells in radio band and many structures in X-rays, harbouring a CCO and with a transient magnetar to the south. We have performed new 12CO J=1-0, 13CO J=1-0, 12CO J=2-1 observations towards this remnant to investigate its molecular environment. SNR Kes 79 is found to be associated with the molecular cloud in LSR velocity 100-115 km/s, which deformed the SNR's shell in the east. The inner radio shell appears to be well confined by a molecular shell at V_{LSR}˜113 km/s. We also revisited the 380 ks XMM-Newton data of Kes 79, which reveal many bright filamentary structures well coincident with infrared features and an X-ray faint halo confined by the outer radio shell. We performed a spatially resolved spectroscopic analysis for the X-ray filaments and the halo emission. We also studied the spatial distribution of the overabundant metal species that may be related to the asymmetric ejecta. Finally, we will discuss the evolution of Kes 79 combining the molecular line and X-ray properties.

  20. X-ray Intermolecular Structure Factor ( XISF ): separation of intra- and intermolecular interactions from total X-ray scattering data

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Mou, Q.; Benmore, C. J.; Yarger, J. L.

    2015-05-09

    XISFis a MATLAB program developed to separate intermolecular structure factors from total X-ray scattering structure factors for molecular liquids and amorphous solids. The program is built on a trust-region-reflective optimization routine with the r.m.s. deviations of atoms physically constrained.XISFhas been optimized for performance and can separate intermolecular structure factors of complex molecules.

  1. Imaging Molecular Motion: Femtosecond X-Ray Scattering of an Electrocyclic Chemical Reaction

    NASA Astrophysics Data System (ADS)

    Minitti, M. P.; Budarz, J. M.; Kirrander, A.; Robinson, J. S.; Ratner, D.; Lane, T. J.; Zhu, D.; Glownia, J. M.; Kozina, M.; Lemke, H. T.; Sikorski, M.; Feng, Y.; Nelson, S.; Saita, K.; Stankus, B.; Northey, T.; Hastings, J. B.; Weber, P. M.

    2015-06-01

    Structural rearrangements within single molecules occur on ultrafast time scales. Many aspects of molecular dynamics, such as the energy flow through excited states, have been studied using spectroscopic techniques, yet the goal to watch molecules evolve their geometrical structure in real time remains challenging. By mapping nuclear motions using femtosecond x-ray pulses, we have created real-space representations of the evolving dynamics during a well-known chemical reaction and show a series of time-sorted structural snapshots produced by ultrafast time-resolved hard x-ray scattering. A computational analysis optimally matches the series of scattering patterns produced by the x rays to a multitude of potential reaction paths. In so doing, we have made a critical step toward the goal of viewing chemical reactions on femtosecond time scales, opening a new direction in studies of ultrafast chemical reactions in the gas phase.

  2. Imaging Molecular Motion: Femtosecond X-Ray Scattering of an Electrocyclic Chemical Reaction.

    PubMed

    Minitti, M P; Budarz, J M; Kirrander, A; Robinson, J S; Ratner, D; Lane, T J; Zhu, D; Glownia, J M; Kozina, M; Lemke, H T; Sikorski, M; Feng, Y; Nelson, S; Saita, K; Stankus, B; Northey, T; Hastings, J B; Weber, P M

    2015-06-26

    Structural rearrangements within single molecules occur on ultrafast time scales. Many aspects of molecular dynamics, such as the energy flow through excited states, have been studied using spectroscopic techniques, yet the goal to watch molecules evolve their geometrical structure in real time remains challenging. By mapping nuclear motions using femtosecond x-ray pulses, we have created real-space representations of the evolving dynamics during a well-known chemical reaction and show a series of time-sorted structural snapshots produced by ultrafast time-resolved hard x-ray scattering. A computational analysis optimally matches the series of scattering patterns produced by the x rays to a multitude of potential reaction paths. In so doing, we have made a critical step toward the goal of viewing chemical reactions on femtosecond time scales, opening a new direction in studies of ultrafast chemical reactions in the gas phase.

  3. X-ray Intermolecular Structure Factor (XISF): separation of intra- and intermolecular interactions from total X-ray scattering data

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Mou, Q.; Benmore, C. J.; Yarger, J. L.

    2015-06-01

    XISF is a MATLAB program developed to separate intermolecular structure factors from total X-ray scattering structure factors for molecular liquids and amorphous solids. The program is built on a trust-region-reflective optimization routine with the r.m.s. deviations of atoms physically constrained. XISF has been optimized for performance and can separate intermolecular structure factors of complex molecules.

  4. Insights into Photosystem II from Isomorphous Difference Fourier Maps of Femtosecond X-ray Diffraction Data and Quantum Mechanics/Molecular Mechanics Structural Models.

    PubMed

    Wang, Jimin; Askerka, Mikhail; Brudvig, Gary W; Batista, Victor S

    2017-02-10

    Understanding structure-function relations in photosystem II (PSII) is important for the development of biomimetic photocatalytic systems. X-ray crystallography, computational modeling, and spectroscopy have played central roles in elucidating the structure and function of PSII. Recent breakthroughs in femtosecond X-ray crystallography offer the possibility of collecting diffraction data from the X-ray free electron laser (XFEL) before radiation damage of the sample, thereby overcoming the main challenge of conventional X-ray diffraction methods. However, the interpretation of XFEL data from PSII intermediates is challenging because of the issues regarding data-processing, uncertainty on the precise positions of light oxygen atoms next to heavy metal centers, and different kinetics of the S-state transition in microcrystals compared to solution. Here, we summarize recent advances and outstanding challenges in PSII structure-function determination with emphasis on the implementation of quantum mechanics/molecular mechanics techniques combined with isomorphous difference Fourier maps, direct methods, and high-resolution spectroscopy.

  5. X-ray diffraction-based electronic structure calculations and experimental x-ray analysis for medical and materials applications

    NASA Astrophysics Data System (ADS)

    Mahato, Dip Narayan

    This thesis includes x-ray experiments for medical and materials applications and the use of x-ray diffraction data in a first-principles study of electronic structures and hyperfine properties of chemical and biological systems. Polycapillary focusing lenses were used to collect divergent x rays emitted from conventional x-ray tubes and redirect them to form an intense focused beam. These lenses are routinely used in microbeam x-ray fluorescence analysis. In this thesis, their potential application to powder diffraction and focused beam orthovoltage cancer therapy has been investigated. In conventional x-ray therapy, very high energy (˜ MeV) beams are used, partly to reduce the skin dose. For any divergent beam, the dose is necessarily highest at the entry point, and decays exponentially into the tissue. To reduce the skin dose, high energy beams, which have long absorption lengths, are employed, and rotated about the patient to enter from different angles. This necessitates large expensive specialized equipment. A focused beam could concentrate the dose within the patient. Since this is inherently skin dose sparing, lower energy photons could be employed. A primary concern in applying focused beams to therapy is whether the focus would be maintained despite Compton scattering within the tissue. To investigate this, transmission and focal spot sizes as a function of photon energy of two polycapillary focusing lenses were measured. The effects of tissue-equivalent phantoms of different thicknesses on the focal spot size were studied. Scatter fraction and depth dose were calculated. For powder diffraction, the polycapillary optics provide clean Gaussian peaks, which result in angular resolution that is much smaller than the peak width due to the beam convergence. Powder diffraction (also called coherent scatter) without optics can also be used to distinguish between tissue types that, because they have different nanoscale structures, scatter at different angles

  6. Covering complete proteomes with X-ray structures: A current snapshot

    DOE PAGES

    Mizianty, Marcin J.; Fan, Xiao; Yan, Jing; ...

    2014-10-23

    Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtainedmore » through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-ray structure determination were determined.« less

  7. Molecular environment and X-ray study of the metal-rich thermal composite supernova remnant Kes 79

    NASA Astrophysics Data System (ADS)

    Zhou, Ping; Chen, Yang; Safi-Harb, Samar; Sun, Ming

    2015-08-01

    Kes 79 is a thermal composite SNR hosting a central compact object (anti-magnetar) and with a transient magnetar in the south. The SNR has an intriguing double radio shell structure and the nature of the centrally-filled X-ray morphology is still unclear. We have performed 13CO 1-0, 12CO 1-0, 12CO 2-1, and 12CO 3-2 study towards this remnant to investigate the molecular environment. SNR Kes 79 is found to be associated with the molecular cloud in LSR velocity 100-120 km/s. The inner radio shell appears to be well confined by a molecular shell at VLSR˜113 km/s. We also revisited the 380 ks XMM-Newton data of Kes 79, which reveals many bright filamentary structures well coincident with 24 um infrared filaments and an X-ray faint halo confined by the outer radio shell. We performed a spatially resolved spectroscopic analysis for the X-ray filaments and the halo emission. We also study the overabundant metal species Mg, Si, S and Ar, and show their asymmetric distribution across the remnant. The broadband observations suggest that the centrally filled X-ray morphology is a projection effect. Finally, we will discuss the progenitor star of Kes 79 based on the molecular line and X-ray properties.

  8. Probing Galactic Center Cosmic-Rays in the X-ray Regime

    NASA Astrophysics Data System (ADS)

    Zhang, Shuo; Baganoff, Frederick K.; Bulbul, Esra; Miller, Eric D.; Bautz, Mark W.

    2017-08-01

    The central few hundred parsecs of the Galaxy harbors 5-10% of the molecular gas mass of the entire Milky Way. This central molecular zone exhibits 6.4 keV Fe Kα line and continuum X-ray emission with time-variability. The time-variable X-ray emission from the gas clouds is best explained by light echoes of past X-ray outbursts from the central supermassive black hole Sgr A*. However,MeV-GeV cosmic-ray particles may also contribute to a constant X-ray emission component from the clouds, through collisional ionization and bremsstrahlung. Sgr B2 is the densest and most massive cloud in the central molecular zone. It is the only known gas cloud whose X-ray emission has kept fading over the past decade and will soon reach a constant X-ray level in 2017/2018, and thus serves as the best probe for MeV-GeV particles in the central 100 pc of the Galaxy. At the same time, the Fe Kα emission has also been discovered from molecular structures beyond the central molecular zone, extening to ~1 kpc from the Galactic center. The X-ray reflection scenario meets challenges this far from the Galactic center, while the MeV-GeV cosmic-ray electrons serve as a more natural explanation. Our studies on Sgr B2 and the large-scale moleuclar structures will for the first time constrain the MeV-GeV particles in the Galactic center, and point to their origin: whether they rise from particle acceleration or dark matter annihilation.

  9. X-ray lasers for structural and dynamic biology

    NASA Astrophysics Data System (ADS)

    Spence, J. C. H.; Weierstall, U.; Chapman, H. N.

    2012-10-01

    Research opportunities and techniques are reviewed for the application of hard x-ray pulsed free-electron lasers (XFEL) to structural biology. These include the imaging of protein nanocrystals, single particles such as viruses, pump-probe experiments for time-resolved nanocrystallography, and snapshot wide-angle x-ray scattering (WAXS) from molecules in solution. The use of femtosecond exposure times, rather than freezing of samples, as a means of minimizing radiation damage is shown to open up new opportunities for the molecular imaging of biochemical reactions at room temperature in solution. This is possible using a ‘diffract-and-destroy’ mode in which the incident pulse terminates before radiation damage begins. Methods for delivering hundreds of hydrated bioparticles per second (in random orientations) to a pulsed x-ray beam are described. New data analysis approaches are outlined for the correlated fluctuations in fast WAXS, for protein nanocrystals just a few molecules on a side, and for the continuous x-ray scattering from a single virus. Methods for determining the orientation of a molecule from its diffraction pattern are reviewed. Methods for the preparation of protein nanocrystals are also reviewed. New opportunities for solving the phase problem for XFEL data are outlined. A summary of the latest results is given, which now extend to atomic resolution for nanocrystals. Possibilities for time-resolved chemistry using fast WAXS (solution scattering) from mixtures is reviewed, toward the general goal of making molecular movies of biochemical processes.

  10. The structure of PX3 (X = Cl, Br, I) molecular liquids from X-ray diffraction, molecular dynamics simulations, and reverse Monte Carlo modeling.

    PubMed

    Pothoczki, Szilvia; Temleitner, László; Pusztai, László

    2014-02-07

    Synchrotron X-ray diffraction measurements have been conducted on liquid phosphorus trichloride, tribromide, and triiodide. Molecular Dynamics simulations for these molecular liquids were performed with a dual purpose: (1) to establish whether existing intermolecular potential functions can provide a picture that is consistent with diffraction data and (2) to generate reliable starting configurations for subsequent Reverse Monte Carlo modelling. Structural models (i.e., sets of coordinates of thousands of atoms) that were fully consistent with experimental diffraction information, within errors, have been prepared by means of the Reverse Monte Carlo method. Comparison with reference systems, generated by hard sphere-like Monte Carlo simulations, was also carried out to demonstrate the extent to which simple space filling effects determine the structure of the liquids (and thus, also estimating the information content of measured data). Total scattering structure factors, partial radial distribution functions and orientational correlations as a function of distances between the molecular centres have been calculated from the models. In general, more or less antiparallel arrangements of the primary molecular axes that are found to be the most favourable orientation of two neighbouring molecules. In liquid PBr3 electrostatic interactions seem to play a more important role in determining intermolecular correlations than in the other two liquids; molecular arrangements in both PCl3 and PI3 are largely driven by steric effects.

  11. In situ surface/interface x-ray diffractometer for oxide molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Lee, J. H.; Tung, I. C.; Chang, S.-H.; Bhattacharya, A.; Fong, D. D.; Freeland, J. W.; Hong, Hawoong

    2016-01-01

    In situ studies of oxide molecular beam epitaxy by synchrotron x-ray scattering has been made possible by upgrading an existing UHV/molecular beam epitaxy (MBE) six-circle diffractometer system. For oxide MBE growth, pure ozone delivery to the chamber has been made available, and several new deposition sources have been made available on a new 12 in. CF (ConFlat, a registered trademark of Varian, Inc.) flange. X-ray diffraction has been used as a major probe for film growth and structures for the system. In the original design, electron diffraction was intended for the secondary diagnostics available without the necessity of the x-ray and located at separate positions. Deposition of films was made possible at the two diagnostic positions. And, the aiming of the evaporation sources is fixed to the point between two locations. Ozone can be supplied through two separate nozzles for each location. Also two separate thickness monitors are installed. Additional features of the equipment are also presented together with the data taken during typical oxide film growth to illustrate the depth of information available via in situ x-ray techniques.

  12. In situ surface/interface x-ray diffractometer for oxide molecular beam epitaxy.

    PubMed

    Lee, J H; Tung, I C; Chang, S-H; Bhattacharya, A; Fong, D D; Freeland, J W; Hong, Hawoong

    2016-01-01

    In situ studies of oxide molecular beam epitaxy by synchrotron x-ray scattering has been made possible by upgrading an existing UHV/molecular beam epitaxy (MBE) six-circle diffractometer system. For oxide MBE growth, pure ozone delivery to the chamber has been made available, and several new deposition sources have been made available on a new 12 in. CF (ConFlat, a registered trademark of Varian, Inc.) flange. X-ray diffraction has been used as a major probe for film growth and structures for the system. In the original design, electron diffraction was intended for the secondary diagnostics available without the necessity of the x-ray and located at separate positions. Deposition of films was made possible at the two diagnostic positions. And, the aiming of the evaporation sources is fixed to the point between two locations. Ozone can be supplied through two separate nozzles for each location. Also two separate thickness monitors are installed. Additional features of the equipment are also presented together with the data taken during typical oxide film growth to illustrate the depth of information available via in situ x-ray techniques.

  13. X-ray Constrained Extremely Localized Molecular Orbitals: Theory and Critical Assessment of the New Technique.

    PubMed

    Genoni, Alessandro

    2013-07-09

    Following the X-ray constrained wave function approach proposed by Jayatilaka, we have devised a new technique that allows to extract molecular orbitals strictly localized on small molecular fragments from sets of experimental X-ray structure factors amplitudes. Since the novel strategy enables to obtain electron distributions that have quantum mechanical features and that can be easily interpreted in terms of traditional chemical concepts, the method can be also considered as a new useful tool for the determination and the analysis of charge densities from high-resolution X-ray experiments. In this paper, we describe in detail the theory of the new technique, which, in comparison to our preliminary work, has been improved both treating the effects of isotropic secondary extinctions and introducing a new protocol to halt the fitting procedure against the experimental X-ray scattering data. The performances of the novel strategy have been studied both in function of the basis-sets flexibility and in function of the quality of the considered crystallographic data. The tests performed on four different systems (α-glycine, l-cysteine, (aminomethyl)phosphonic acid and N-(trifluoromethyl)formamide) have shown that the achievement of good statistical agreements with the experimental measures mainly depends on the quality of the crystal structures (i.e., geometry positions and thermal parameters) used in the X-ray constrained calculations. Finally, given the reliable transferability of the obtained Extremely Localized Molecular Orbitals (ELMOs), we envisage to exploit the novel approach to construct new ELMOs databases suited to the development of linear-scaling methods for the refinement of macromolecular crystal structures.

  14. Excited state X-ray absorption spectroscopy: Probing both electronic and structural dynamics

    NASA Astrophysics Data System (ADS)

    Neville, Simon P.; Averbukh, Vitali; Ruberti, Marco; Yun, Renjie; Patchkovskii, Serguei; Chergui, Majed; Stolow, Albert; Schuurman, Michael S.

    2016-10-01

    We investigate the sensitivity of X-ray absorption spectra, simulated using a general method, to properties of molecular excited states. Recently, Averbukh and co-workers [M. Ruberti et al., J. Chem. Phys. 140, 184107 (2014)] introduced an efficient and accurate L 2 method for the calculation of excited state valence photoionization cross-sections based on the application of Stieltjes imaging to the Lanczos pseudo-spectrum of the algebraic diagrammatic construction (ADC) representation of the electronic Hamiltonian. In this paper, we report an extension of this method to the calculation of excited state core photoionization cross-sections. We demonstrate that, at the ADC(2)x level of theory, ground state X-ray absorption spectra may be accurately reproduced, validating the method. Significantly, the calculated X-ray absorption spectra of the excited states are found to be sensitive to both geometric distortions (structural dynamics) and the electronic character (electronic dynamics) of the initial state, suggesting that core excitation spectroscopies will be useful probes of excited state non-adiabatic dynamics. We anticipate that the method presented here can be combined with ab initio molecular dynamics calculations to simulate the time-resolved X-ray spectroscopy of excited state molecular wavepacket dynamics.

  15. Tracking reaction dynamics in solution by pump-probe X-ray absorption spectroscopy and X-ray liquidography (solution scattering).

    PubMed

    Kim, Jeongho; Kim, Kyung Hwan; Oang, Key Young; Lee, Jae Hyuk; Hong, Kiryong; Cho, Hana; Huse, Nils; Schoenlein, Robert W; Kim, Tae Kyu; Ihee, Hyotcherl

    2016-03-07

    Characterization of transient molecular structures formed during chemical and biological processes is essential for understanding their mechanisms and functions. Over the last decade, time-resolved X-ray liquidography (TRXL) and time-resolved X-ray absorption spectroscopy (TRXAS) have emerged as powerful techniques for molecular and electronic structural analysis of photoinduced reactions in the solution phase. Both techniques make use of a pump-probe scheme that consists of (1) an optical pump pulse to initiate a photoinduced process and (2) an X-ray probe pulse to monitor changes in the molecular structure as a function of time delay between pump and probe pulses. TRXL is sensitive to changes in the global molecular structure and therefore can be used to elucidate structural changes of reacting solute molecules as well as the collective response of solvent molecules. On the other hand, TRXAS can be used to probe changes in both local geometrical and electronic structures of specific X-ray-absorbing atoms due to the element-specific nature of core-level transitions. These techniques are complementary to each other and a combination of the two methods will enhance the capability of accurately obtaining structural changes induced by photoexcitation. Here we review the principles of TRXL and TRXAS and present recent application examples of the two methods for studying chemical and biological processes in solution. Furthermore, we briefly discuss the prospect of using X-ray free electron lasers for the two techniques, which will allow us to keep track of structural dynamics on femtosecond time scales in various solution-phase molecular reactions.

  16. X-ray scattering data and structural genomics

    NASA Astrophysics Data System (ADS)

    Doniach, Sebastian

    2003-03-01

    High throughput structural genomics has the ambitious goal of determining the structure of all, or a very large number of protein folds using the high-resolution techniques of protein crystallography and NMR. However, the program is facing significant bottlenecks in reaching this goal, which include problems of protein expression and crystallization. In this talk, some preliminary results on how the low-resolution technique of small-angle X-ray solution scattering (SAXS) can help ameliorate some of these bottlenecks will be presented. One of the most significant bottlenecks arises from the difficulty of crystallizing integral membrane proteins, where only a handful of structures are available compared to thousands of structures for soluble proteins. By 3-dimensional reconstruction from SAXS data, the size and shape of detergent-solubilized integral membrane proteins can be characterized. This information can then be used to classify membrane proteins which constitute some 25% of all genomes. SAXS may also be used to study the dependence of interparticle interference scattering on solvent conditions so that regions of the protein solution phase diagram which favor crystallization can be elucidated. As a further application, SAXS may be used to provide physical constraints on computational methods for protein structure prediction based on primary sequence information. This in turn can help in identifying structural homologs of a given protein, which can then give clues to its function. D. Walther, F. Cohen and S. Doniach. "Reconstruction of low resolution three-dimensional density maps from one-dimensional small angle x-ray scattering data for biomolecules." J. Appl. Cryst. 33(2):350-363 (2000). Protein structure prediction constrained by solution X-ray scattering data and structural homology identification Zheng WJ, Doniach S JOURNAL OF MOLECULAR BIOLOGY , v. 316(#1) pp. 173-187 FEB 8, 2002

  17. X-ray Binaries and the Galaxy Structure in Hard X-rays

    NASA Astrophysics Data System (ADS)

    Lutovinov, Alexander

    The Galaxy structure in the hard X-ray energy band (¿20 keV) was studied using data of the INTEGRAL observatory. A deep and nearly uniform coverage of the galactic plane allowed to increase significantly the sensitivity of the survey and discover several dozens new galac-tic sources. The follow-up observations with XMM-Newton and CHANDRA observatories in X-rays and ground-based telescopes in optical and infrared wavebands gave us a possibility to determine optical counterparts and distances for number of new and already known faint sources. That, in turn, allowed us to build the spatial distribution of different classes of galactic X-ray binaries and obtain preliminary results of the structure of the further part of the Galaxy.

  18. Ultrafast molecular processes mapped by femtosecond x-ray diffraction

    NASA Astrophysics Data System (ADS)

    Elsaesser, Thomas

    2012-02-01

    X-ray diffraction with a femtosecond time resolution allows for mapping photoinduced structural dynamics on the length scale of a chemical bond and in the time domain of atomic and molecular motion. In a pump-probe approach, a femtosecond excitation pulse induces structural changes which are probed by diffracting a femtosecond hard x-ray pulse from the excited sample. The transient angular positions and intensities of diffraction peaks give insight into the momentary atomic or molecular positions and into the distribution of electronic charge density. The simultaneous measurement of changes on different diffraction peaks is essential for determining atom positions and charge density maps with high accuracy. Recent progress in the generation of ultrashort hard x-ray pulses (Cu Kα, wavelength λ=0.154 nm) in laser-driven plasma sources has led to the implementation of the powder diffraction and the rotating crystal method with a time resolution of 100 fs. In this contribution, we report new results from powder diffraction studies of molecular materials. A first series of experiments gives evidence of a so far unknown concerted transfer of electrons and protons in ammonium sulfate [(NH4)2SO4], a centrosymmetric structure. Charge transfer from the sulfate groups results in the sub-100 fs generation of a confined electron channel along the c-axis of the unit cell which is stabilized by transferring protons from the adjacent ammonium groups into the channel. Time-dependent charge density maps display a periodic modulation of the channel's charge density by low-frequency lattice motions with a concerted electron and proton motion between the channel and the initial proton binding site. A second study addresses atomic rearrangements and charge dislocations in the non-centrosymmetric potassium dihydrogen phosphate [KH2PO4, KDP]. Photoexcitation generates coherent low-frequency motions along the LO and TO phonon coordinates, leaving the average atomic positions unchanged

  19. Acemetacin cocrystal structures by powder X-ray diffraction.

    PubMed

    Bolla, Geetha; Chernyshev, Vladimir; Nangia, Ashwini

    2017-05-01

    Cocrystals of acemetacin drug (ACM) with nicotinamide (NAM), p -aminobenzoic acid (PABA), valerolactam (VLM) and 2-pyridone (2HP) were prepared by melt crystallization and their X-ray crystal structures determined by high-resolution powder X-ray diffraction. The powerful technique of structure determination from powder data (SDPD) provided details of molecular packing and hydrogen bonding in pharmaceutical cocrystals of acemetacin. ACM-NAM occurs in anhydrate and hydrate forms, whereas the other structures crystallized in a single crystalline form. The carboxylic acid group of ACM forms theacid-amide dimer three-point synthon R 3 2 (9) R 2 2 (8) R 3 2 (9) with three different syn amides (VLM, 2HP and caprolactam). The conformations of the ACM molecule observed in the crystal structures differ mainly in the mutual orientation of chlorobenzene fragment and the neighboring methyl group, being anti (type I) or syn (type II). ACM hydrate, ACM-NAM, ACM-NAM-hydrate and the piperazine salt of ACM exhibit the type I conformation, whereas ACM polymorphs and other cocrystals adopt the ACM type II conformation. Hydrogen-bond interactions in all the crystal structures were quantified by calculating their molecular electrostatic potential (MEP) surfaces. Hirshfeld surface analysis of the cocrystal surfaces shows that about 50% of the contribution is due to a combination of strong and weak O⋯H, N⋯H, Cl⋯H and C⋯H interactions. The physicochemical properties of these cocrystals are under study.

  20. Acemetacin cocrystal structures by powder X-ray diffraction

    PubMed Central

    Bolla, Geetha

    2017-01-01

    Cocrystals of acemetacin drug (ACM) with nicotinamide (NAM), p-aminobenzoic acid (PABA), valerolactam (VLM) and 2-pyridone (2HP) were prepared by melt crystallization and their X-ray crystal structures determined by high-resolution powder X-ray diffraction. The powerful technique of structure determination from powder data (SDPD) provided details of molecular packing and hydrogen bonding in pharmaceutical cocrystals of acemetacin. ACM–NAM occurs in anhydrate and hydrate forms, whereas the other structures crystallized in a single crystalline form. The carboxylic acid group of ACM forms theacid–amide dimer three-point synthon R 3 2(9)R 2 2(8)R 3 2(9) with three different syn amides (VLM, 2HP and caprolactam). The conformations of the ACM molecule observed in the crystal structures differ mainly in the mutual orientation of chlorobenzene fragment and the neighboring methyl group, being anti (type I) or syn (type II). ACM hydrate, ACM—NAM, ACM–NAM-hydrate and the piperazine salt of ACM exhibit the type I conformation, whereas ACM polymorphs and other cocrystals adopt the ACM type II conformation. Hydrogen-bond interactions in all the crystal structures were quantified by calculating their molecular electrostatic potential (MEP) surfaces. Hirshfeld surface analysis of the cocrystal surfaces shows that about 50% of the contribution is due to a combination of strong and weak O⋯H, N⋯H, Cl⋯H and C⋯H interactions. The physicochemical properties of these cocrystals are under study. PMID:28512568

  1. In situ surface/interface x-ray diffractometer for oxide molecular beam epitaxy

    DOE PAGES

    Lee, J. H.; Tung, I. C.; Chang, S. -H.; ...

    2016-01-05

    In situ studies of oxide molecular beam epitaxy by synchrotron x-ray scattering has been made possible by upgrading an existing UHV/molecular beam epitaxy (MBE) six-circle diffractometer system. For oxide MBE growth, pure ozone delivery to the chamber has been made available, and several new deposition sources have been made available on a new 12 in. CF (ConFlat, a registered trademark of Varian, Inc.) flange. X-ray diffraction has been used as a major probe for film growth and structures for the system. In the original design, electron diffraction was intended for the secondary diagnostics available without the necessity of the x-raymore » and located at separate positions. Deposition of films was made possible at the two diagnostic positions. And, the aiming of the evaporation sources is fixed to the point between two locations. Ozone can be supplied through two separate nozzles for each location. Also two separate thickness monitors are installed. Finally, additional features of the equipment are also presented together with the data taken during typical oxide film growth to illustrate the depth of information available via in situ x-ray techniques.« less

  2. Relativistic effects on x-ray structure factors

    NASA Astrophysics Data System (ADS)

    Batke, Kilian; Eickerling, Georg

    2016-04-01

    Today, combined experimental and theoretical charge density studies based on quantum chemical calculations and x-ray diffraction experiments allow for the investigation of the topology of the electron density at subatomic resolution. When studying compounds containing transition metal elements, relativistic effects need to be adequately taken into account not only in quantum chemical calculations of the total electron density ρ ({r}), but also for the atomic scattering factors employed to extract ρ ({r}) from experimental x-ray diffraction data. In the present study, we investigate the magnitude of relativistic effects on x-ray structure factors and for this purpose {F}({{r}}*) have been calculated for the model systems M(C2H2) (M = Ni, Pd, Pt) from four-component molecular wave functions. Relativistic effects are then discussed by a comparison to structure factors obtained from a non-relativistic reference and different quasi-relativistic approximations. We show, that the overall effects of relativity on the structure factors on average amount to 0.81%, 1.51% and 2.78% for the three model systems under investigation, but that for individual reflections or reflection series the effects can be orders of magnitude larger. Employing the quasi-relativistic Douglas-Kroll-Hess second order or the zeroth order regular approximation Hamiltonian takes these effects into account to a large extend, reducing the differences between the (quasi-)relativistic and the non-relativistic result by one order of magnitude. In order to further determine the experimental significance of the results, the magnitude of the relativistic effects is compared to the changes of the model structure factor data when charge transfer and chemical bonding is taken into account by a multipolar expansion of {F}({{r}}*).

  3. Molecular structure of hybrid imino-chalcone in the solid state: X-ray diffraction, spectroscopy study and third-order nonlinear optical properties

    NASA Astrophysics Data System (ADS)

    Custodio, J. M. F.; Santos, F. G.; Vaz, W. F.; Cunha, C. E. P.; Silveira, R. G.; Anjos, M. M.; Campos, C. E. M.; Oliveira, G. R.; Martins, F. T.; da Silva, C. C.; Valverde, C.; Baseia, B.; Napolitano, H. B.

    2018-04-01

    A comprehensive structural study of the compound (2E)-1-((E)-4-(4-methoxybenzylideneamino)phenyl)-3-(4-methoxyphenyl)prop-2-en-1-one was carried out in this work. Single crystal X-ray diffraction (SCXRD), X-ray powder diffraction (XRPD), NMR, Raman and Infrared spectroscopies, and DFT calculations were performed for characterization of this iminochalcone hybrid. Intermolecular interactions were described by Hirshfeld surface analysis derived from crystal structure. Reactivity and intramolecular charge transfer were investigated using the frontier molecular orbitals and molecular electrostatic potential. In addition, we have calculated the Nonlinear Optical Properties at the CAM-B3LYP/6-311+g(d) level of theory in the presence of different solvents (gas-phase, acetone, chloroform, dichloromethane, dimethyl sulfoxide, ethanol, methanol, and water), being found meaningful NLO parameters for our compound. At last, there is a good agreement between calculated and experimental IR spectrum, allowing the assignment of some of normal vibrational modes of the iminochalcone hybrid.

  4. Solvation structure of the halides from x-ray absorption spectroscopy

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Antalek, Matthew; Hedman, Britt; Sarangi, Ritimukta, E-mail: ritis@slac.stanford.edu

    2016-07-28

    Three-dimensional models for the aqueous solvation structures of chloride, bromide, and iodide are reported. K-edge extended X-ray absorption fine structure (EXAFS) and Minuit X-ray absorption near edge (MXAN) analyses found well-defined single shell solvation spheres for bromide and iodide. However, dissolved chloride proved structurally distinct, with two solvation shells needed to explain its strikingly different X-ray absorption near edge structure (XANES) spectrum. Final solvation models were as follows: iodide, 8 water molecules at 3.60 ± 0.13 Å and bromide, 8 water molecules at 3.40 ± 0.14 Å, while chloride solvation included 7 water molecules at 3.15 ± 0.10 Å, andmore » a second shell of 7 water molecules at 4.14 ± 0.30 Å. Each of the three derived solvation shells is approximately uniformly disposed about the halides, with no global asymmetry. Time-dependent density functional theory calculations simulating the chloride XANES spectra following from alternative solvation spheres revealed surprising sensitivity of the electronic state to 6-, 7-, or 8-coordination, implying a strongly bounded phase space for the correct structure during an MXAN fit. MXAN analysis further showed that the asymmetric solvation predicted from molecular dynamics simulations using halide polarization can play no significant part in bulk solvation. Classical molecular dynamics used to explore chloride solvation found a 7-water solvation shell at 3.12 (−0.04/+0.3) Å, supporting the experimental result. These experiments provide the first fully three-dimensional structures presenting to atomic resolution the aqueous solvation spheres of the larger halide ions.« less

  5. Molecular modeling, theoretical calculations and property evaluation of three muscarinic agonists. X-ray structures of LU 25-109 and WAL 2014

    NASA Astrophysics Data System (ADS)

    Dolmella, A.; Bandoli, G.; Cavallin, M.

    2000-08-01

    LU 25-109 ( II) and WAL 2014 (talsaclidine, III) are two M1 muscarinic agonists chemically related to the natural substance arecoline ( I). All these compounds have beneficial effects on memory and cognition in animals and humans, and they have been proposed in the treatment of Alzheimer's disease, but only III will likely find a place in therapy. In this work we have investigated the solid state structures of II and III, and the X-ray structures of the two molecules and of the parent compound I have been used to input a series of computational chemistry efforts. In particular, the X-ray geometries have been manipulated to model 20 molecular structures ( 1- 20) which have been submitted to ab initio, semiempirical quantum mechanics and molecular mechanics calculations. The conformational space accessible to the 20 structures has been assessed by means of potential energy maps. The reactivities of 1- 20 have been estimated by examining at the graphics terminal the composition and the extension of the frontier orbitals (HOMOs and LUMOs) and of the molecular electrostatic potential. The information obtained has been interpreted to explain the different degrees of activity shown by I- III. Our data indicate that III has better in vivo activity for its intermediate size, less polar surface, conformational rigidity and orientation of reactive domains.

  6. Roadmap of ultrafast x-ray atomic and molecular physics

    NASA Astrophysics Data System (ADS)

    Young, Linda; Ueda, Kiyoshi; Gühr, Markus; Bucksbaum, Philip H.; Simon, Marc; Mukamel, Shaul; Rohringer, Nina; Prince, Kevin C.; Masciovecchio, Claudio; Meyer, Michael; Rudenko, Artem; Rolles, Daniel; Bostedt, Christoph; Fuchs, Matthias; Reis, David A.; Santra, Robin; Kapteyn, Henry; Murnane, Margaret; Ibrahim, Heide; Légaré, François; Vrakking, Marc; Isinger, Marcus; Kroon, David; Gisselbrecht, Mathieu; L'Huillier, Anne; Wörner, Hans Jakob; Leone, Stephen R.

    2018-02-01

    X-ray free-electron lasers (XFELs) and table-top sources of x-rays based upon high harmonic generation (HHG) have revolutionized the field of ultrafast x-ray atomic and molecular physics, largely due to an explosive growth in capabilities in the past decade. XFELs now provide unprecedented intensity (1020 W cm-2) of x-rays at wavelengths down to ˜1 Ångstrom, and HHG provides unprecedented time resolution (˜50 attoseconds) and a correspondingly large coherent bandwidth at longer wavelengths. For context, timescales can be referenced to the Bohr orbital period in hydrogen atom of 150 attoseconds and the hydrogen-molecule vibrational period of 8 femtoseconds; wavelength scales can be referenced to the chemically significant carbon K-edge at a photon energy of ˜280 eV (44 Ångstroms) and the bond length in methane of ˜1 Ångstrom. With these modern x-ray sources one now has the ability to focus on individual atoms, even when embedded in a complex molecule, and view electronic and nuclear motion on their intrinsic scales (attoseconds and Ångstroms). These sources have enabled coherent diffractive imaging, where one can image non-crystalline objects in three dimensions on ultrafast timescales, potentially with atomic resolution. The unprecedented intensity available with XFELs has opened new fields of multiphoton and nonlinear x-ray physics where behavior of matter under extreme conditions can be explored. The unprecedented time resolution and pulse synchronization provided by HHG sources has kindled fundamental investigations of time delays in photoionization, charge migration in molecules, and dynamics near conical intersections that are foundational to AMO physics and chemistry. This roadmap coincides with the year when three new XFEL facilities, operating at Ångstrom wavelengths, opened for users (European XFEL, Swiss-FEL and PAL-FEL in Korea) almost doubling the present worldwide number of XFELs, and documents the remarkable progress in HHG capabilities since

  7. Roadmap of ultrafast x-ray atomic and molecular physics

    DOE PAGES

    Young, Linda; Ueda, Kiyoshi; Gühr, Markus; ...

    2018-01-09

    X-ray free-electron lasers (XFELs) and table-top sources of x-rays based upon high harmonic generation (HHG) have revolutionized the field of ultrafast x-ray atomic and molecular physics, largely due to an explosive growth in capabilities in the past decade. XFELs now provide unprecedented intensity (10 20 W cm -2) of x-rays at wavelengths down to ~1 Ångstrom, and HHG provides unprecedented time resolution (~50 attoseconds) and a correspondingly large coherent bandwidth at longer wavelengths. For context, timescales can be referenced to the Bohr orbital period in hydrogen atom of 150 attoseconds and the hydrogen-molecule vibrational period of 8 femtoseconds; wavelength scalesmore » can be referenced to the chemically significant carbon K-edge at a photon energy of ~280 eV (44 Ångstroms) and the bond length in methane of ~1 Ångstrom. With these modern x-ray sources one now has the ability to focus on individual atoms, even when embedded in a complex molecule, and view electronic and nuclear motion on their intrinsic scales (attoseconds and Ångstroms). These sources have enabled coherent diffractive imaging, where one can image non-crystalline objects in three dimensions on ultrafast timescales, potentially with atomic resolution. The unprecedented intensity available with XFELs has opened new fields of multiphoton and nonlinear x-ray physics where behavior of matter under extreme conditions can be explored. The unprecedented time resolution and pulse synchronization provided by HHG sources has kindled fundamental investigations of time delays in photoionization, charge migration in molecules, and dynamics near conical intersections that are foundational to AMO physics and chemistry. This roadmap coincides with the year when three new XFEL facilities, operating at Ångstrom wavelengths, opened for users (European XFEL, Swiss-FEL and PAL-FEL in Korea) almost doubling the present worldwide number of XFELs, and documents the remarkable progress in HHG capabilities

  8. Roadmap of ultrafast x-ray atomic and molecular physics

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Young, Linda; Ueda, Kiyoshi; Gühr, Markus

    X-ray free-electron lasers (XFELs) and table-top sources of x-rays based upon high harmonic generation (HHG) have revolutionized the field of ultrafast x-ray atomic and molecular physics, largely due to an explosive growth in capabilities in the past decade. XFELs now provide unprecedented intensity (10 20 W cm -2) of x-rays at wavelengths down to ~1 Ångstrom, and HHG provides unprecedented time resolution (~50 attoseconds) and a correspondingly large coherent bandwidth at longer wavelengths. For context, timescales can be referenced to the Bohr orbital period in hydrogen atom of 150 attoseconds and the hydrogen-molecule vibrational period of 8 femtoseconds; wavelength scalesmore » can be referenced to the chemically significant carbon K-edge at a photon energy of ~280 eV (44 Ångstroms) and the bond length in methane of ~1 Ångstrom. With these modern x-ray sources one now has the ability to focus on individual atoms, even when embedded in a complex molecule, and view electronic and nuclear motion on their intrinsic scales (attoseconds and Ångstroms). These sources have enabled coherent diffractive imaging, where one can image non-crystalline objects in three dimensions on ultrafast timescales, potentially with atomic resolution. The unprecedented intensity available with XFELs has opened new fields of multiphoton and nonlinear x-ray physics where behavior of matter under extreme conditions can be explored. The unprecedented time resolution and pulse synchronization provided by HHG sources has kindled fundamental investigations of time delays in photoionization, charge migration in molecules, and dynamics near conical intersections that are foundational to AMO physics and chemistry. This roadmap coincides with the year when three new XFEL facilities, operating at Ångstrom wavelengths, opened for users (European XFEL, Swiss-FEL and PAL-FEL in Korea) almost doubling the present worldwide number of XFELs, and documents the remarkable progress in HHG capabilities

  9. Insights into photosystem II from isomorphous difference Fourier maps of femtosecond X-ray diffraction data and quantum mechanics/molecular mechanics structural models

    DOE PAGES

    Wang, Jimin; Askerka, Mikhail; Brudvig, Gary W.; ...

    2017-01-12

    Understanding structure–function relations in photosystem II (PSII) is important for the development of biomimetic photocatalytic systems. X-ray crystallography, computational modeling, and spectroscopy have played central roles in elucidating the structure and function of PSII. Recent breakthroughs in femtosecond X-ray crystallography offer the possibility of collecting diffraction data from the X-ray free electron laser (XFEL) before radiation damage of the sample, thereby overcoming the main challenge of conventional X-ray diffraction methods. However, the interpretation of XFEL data from PSII intermediates is challenging because of the issues regarding data-processing, uncertainty on the precise positions of light oxygen atoms next to heavy metalmore » centers, and different kinetics of the S-state transition in microcrystals compared to solution. Lastly, we summarize recent advances and outstanding challenges in PSII structure–function determination with emphasis on the implementation of quantum mechanics/molecular mechanics techniques combined with isomorphous difference Fourier maps, direct methods, and high-resolution spectroscopy.« less

  10. Insights into photosystem II from isomorphous difference Fourier maps of femtosecond X-ray diffraction data and quantum mechanics/molecular mechanics structural models

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wang, Jimin; Askerka, Mikhail; Brudvig, Gary W.

    Understanding structure–function relations in photosystem II (PSII) is important for the development of biomimetic photocatalytic systems. X-ray crystallography, computational modeling, and spectroscopy have played central roles in elucidating the structure and function of PSII. Recent breakthroughs in femtosecond X-ray crystallography offer the possibility of collecting diffraction data from the X-ray free electron laser (XFEL) before radiation damage of the sample, thereby overcoming the main challenge of conventional X-ray diffraction methods. However, the interpretation of XFEL data from PSII intermediates is challenging because of the issues regarding data-processing, uncertainty on the precise positions of light oxygen atoms next to heavy metalmore » centers, and different kinetics of the S-state transition in microcrystals compared to solution. Lastly, we summarize recent advances and outstanding challenges in PSII structure–function determination with emphasis on the implementation of quantum mechanics/molecular mechanics techniques combined with isomorphous difference Fourier maps, direct methods, and high-resolution spectroscopy.« less

  11. The molecular and crystal structure of dextrans: a combined electron and X-ray diffraction study. II. A low temperature, hydrated polymorph.

    PubMed

    Guizard, C; Chanzy, H; Sarko, A

    1985-06-05

    The crystal and molecular structure of a dextran hydrate has been determined through combined electron and X-ray diffraction analysis, aided by stereochemical model refinement. A total of 65 hk0 electron diffraction intensities were measured on frozen single crystals held at the temperature of liquid nitrogen, to a resolution limit of 1.6 A. The X-ray intensities were measured from powder patterns recorded from collections of the single crystals. The structure crystallizes in a monoclinic unit cell with parameters a = 25.71 A, b = 10.21 A, c (chain axis) = 7.76 A and beta = 91.3 degrees. The space group is P2(1) with b axis unique. The unit cell contains six chains and eight water molecules, with three chains of the same polarity and four water molecules constituting the asymmetric unit. Along the chain direction the asymmetric unit is a dimer residue; however, the individual glucopyranose residues are very nearly related by a molecular 2-fold screw axis. The conformation of the chain is very similar to that in the anhydrous structure, but the chain packing differs in the two structures in that the rotational positions of the chains about the helix axes (the chain setting angles) are considerably different. The chains still pack in the form of sheets that are separated by water molecules. The difference in the chain setting angles between the anhydrous and hydrate structures corresponds to the angle between like unit cell axes observed in the diffraction diagrams recorded from hybrid crystals containing both polymorphs. Despite some beam damage effects, the structure was determined to a satisfactory degree of agreement, with the residuals R''(electron diffraction) = 0.258 and R(X-ray) = 0.127.

  12. Structural investigation of porcine stomach mucin by X-ray fiber diffraction and homology modeling

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Veluraja, K., E-mail: veluraja@msuniv.ac.in; Vennila, K.N.; Umamakeshvari, K.

    Research highlights: {yields} Techniques to get oriented mucin fibre. {yields} X-ray fibre diffraction pattern for mucin. {yields} Molecular modeling of mucin based on X-ray fibre diffraction pattern. -- Abstract: The basic understanding of the three dimensional structure of mucin is essential to understand its physiological function. Technology has been developed to achieve orientated porcine stomach mucin molecules. X-ray fiber diffraction of partially orientated porcine stomach mucin molecules show d-spacing signals at 2.99, 4.06, 4.22, 4.7, 5.37 and 6.5 A. The high intense d-spacing signal at 4.22 A is attributed to the antiparallel {beta}-sheet structure identified in the fraction of themore » homology modeled mucin molecule (amino acid residues 800-980) using Nidogen-Laminin complex structure as a template. The X-ray fiber diffraction signal at 6.5 A reveals partial organization of oligosaccharides in porcine stomach mucin. This partial structure of mucin will be helpful in establishing a three dimensional structure for the whole mucin molecule.« less

  13. First-Principles Predictions of Near-Edge X-ray Absorption Fine Structure Spectra of Semiconducting Polymers

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Su, Gregory M.; Patel, Shrayesh N.; Pemmaraju, C. D.

    The electronic structure and molecular orientation of semiconducting polymers in thin films determine their ability to transport charge. Methods based on near-edge X-ray absorption fine structure (NEXAFS) spectroscopy can be used to probe both the electronic structure and microstructure of semiconducting polymers in both crystalline and amorphous films. However, it can be challenging to interpret NEXAFS spectra on the basis of experimental data alone, and accurate, predictive calculations are needed to complement experiments. Here, we show that first-principles density functional theory (DFT) can be used to model NEXAFS spectra of semiconducting polymers and to identify the nature of transitions inmore » complicated NEXAFS spectra. Core-level X-ray absorption spectra of a set of semiconducting polymers were calculated using the excited electron and core-hole (XCH) approach based on constrained-occupancy DFT. A comparison of calculations on model oligomers and periodic structures with experimental data revealed the requirements for accurate prediction of NEXAFS spectra of both conjugated homopolymers and donor–acceptor polymers. The NEXAFS spectra predicted by the XCH approach were applied to study molecular orientation in donor–acceptor polymers using experimental spectra and revealed the complexity of using carbon edge spectra in systems with large monomeric units. The XCH approach has sufficient accuracy in predicting experimental NEXAFS spectra of polymers that it should be considered for design and analysis of measurements using soft X-ray techniques, such as resonant soft X-ray scattering and scanning transmission X-ray microscopy.« less

  14. Structural and Molecular Modeling Features of P2X Receptors

    PubMed Central

    Alves, Luiz Anastacio; da Silva, João Herminio Martins; Ferreira, Dinarte Neto Moreira; Fidalgo-Neto, Antonio Augusto; Teixeira, Pedro Celso Nogueira; de Souza, Cristina Alves Magalhães; Caffarena, Ernesto Raúl; de Freitas, Mônica Santos

    2014-01-01

    Currently, adenosine 5′-triphosphate (ATP) is recognized as the extracellular messenger that acts through P2 receptors. P2 receptors are divided into two subtypes: P2Y metabotropic receptors and P2X ionotropic receptors, both of which are found in virtually all mammalian cell types studied. Due to the difficulty in studying membrane protein structures by X-ray crystallography or NMR techniques, there is little information about these structures available in the literature. Two structures of the P2X4 receptor in truncated form have been solved by crystallography. Molecular modeling has proven to be an excellent tool for studying ionotropic receptors. Recently, modeling studies carried out on P2X receptors have advanced our knowledge of the P2X receptor structure-function relationships. This review presents a brief history of ion channel structural studies and shows how modeling approaches can be used to address relevant questions about P2X receptors. PMID:24637936

  15. A glimpse of structural biology through X-ray crystallography.

    PubMed

    Shi, Yigong

    2014-11-20

    Since determination of the myoglobin structure in 1957, X-ray crystallography, as the anchoring tool of structural biology, has played an instrumental role in deciphering the secrets of life. Knowledge gained through X-ray crystallography has fundamentally advanced our views on cellular processes and greatly facilitated development of modern medicine. In this brief narrative, I describe my personal understanding of the evolution of structural biology through X-ray crystallography-using as examples mechanistic understanding of protein kinases and integral membrane proteins-and comment on the impact of technological development and outlook of X-ray crystallography.

  16. The structure of molten CuCl: Reverse Monte Carlo modeling with high-energy X-ray diffraction data and molecular dynamics of a polarizable ion model

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Alcaraz, Olga; Trullàs, Joaquim, E-mail: quim.trullas@upc.edu; Tahara, Shuta

    2016-09-07

    The results of the structural properties of molten copper chloride are reported from high-energy X-ray diffraction measurements, reverse Monte Carlo modeling method, and molecular dynamics simulations using a polarizable ion model. The simulated X-ray structure factor reproduces all trends observed experimentally, in particular the shoulder at around 1 Å{sup −1} related to intermediate range ordering, as well as the partial copper-copper correlations from the reverse Monte Carlo modeling, which cannot be reproduced by using a simple rigid ion model. It is shown that the shoulder comes from intermediate range copper-copper correlations caused by the polarized chlorides.

  17. X-Ray Dust Tomography: Mapping the Galaxy one X-ray Transient at a Time

    NASA Astrophysics Data System (ADS)

    Heinz, Sebastian; Corrales, Lia

    2018-01-01

    Tomography using X-ray light echoes from dust scattering by interstellar clouds is an accurate tool to study the line-of-sight distribution of dust. It can be used to measure distances to molecular clouds and X-ray sources, it can map Galactic structure in dust, and it can be used for precision measurements of dust composition and grain size distribution. Necessary conditions for observing echoes include a suitable X-ray lightcurve and sufficient dust column density to the source. I will discuss a tool set for studying dust echoes and show results obtained for some of the brightest echoes detected to date.

  18. Conformational analysis of an acyclic tetrapeptide: ab-initio structure determination from X-ray powder diffraction, Hirshfeld surface analysis and electronic structure.

    PubMed

    Das, Uday; Naskar, Jishu; Mukherjee, Alok Kumar

    2015-12-01

    A terminally protected acyclic tetrapeptide has been synthesized, and the crystal structure of its hydrated form, Boc-Tyr-Aib-Tyr-Ile-OMe·2H2O (1), has been determined directly from powder X-ray diffraction data. The backbone conformation of tetrapeptide (1) exhibiting two consecutive β-turns is stabilized by two 4 → 1 intramolecular N-H · · · O hydrogen bonds. In the crystalline state, the tetrapeptide molecules are assembled through water-mediated O-H · · · O hydrogen bonds to form two-dimensional molecular sheets, which are further linked by intermolecular C-H · · · O hydrogen bonds into a three-dimensional supramolecular framework. The molecular electrostatic potential (MEP) surface of (1) has been used to supplement the crystallographic observations. The nature of intermolecular interactions in (1) has been analyzed quantitatively through the Hirshfeld surface and two-dimensional fingerprint plot. The DFT optimized molecular geometry of (1) agrees closely with that obtained from the X-ray structure analysis. The present structure analysis of Boc-Tyr-Aib-Tyr-Ile-OMe·2H2 O (1) represents a case where ab-initio crystal structure of an acyclic tetrapeptide with considerable molecular flexibility has been accomplished from laboratory X-ray powder diffraction data. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.

  19. Probing Photoinduced Structural Phase Transitions by Fast or Ultra-Fast Time-Resolved X-Ray Diffraction

    NASA Astrophysics Data System (ADS)

    Cailleau, Hervé Collet, Eric; Buron-Le Cointe, Marylise; Lemée-Cailleau, Marie-Hélène Koshihara, Shin-Ya

    A new frontier in the field of structural science is the emergence of the fast and ultra-fast X-ray science. Recent developments in time-resolved X-ray diffraction promise direct access to the dynamics of electronic, atomic and molecular motions in condensed matter triggered by a pulsed laser irradiation, i.e. to record "molecular movies" during the transformation of matter initiated by light pulse. These laser pump and X-ray probe techniques now provide an outstanding opportunity for the direct observation of a photoinduced structural phase transition as it takes place. The use of X-ray short-pulse of about 100ps around third-generation synchrotron sources allows structural investigations of fast photoinduced processes. Other new X-ray sources, such as laser-produced plasma ones, generate ultra-short pulses down to 100 fs. This opens the way to femtosecond X-ray crystallography, but with rather low X-ray intensities and more limited experimental possibilities at present. However this new ultra-fast science rapidly progresses around these sources and new large-scale projects exist. It is the aim of this contribution to overview the state of art and the perspectives of fast and ultra-fast X-ray scattering techniques to study photoinduced phase transitions (here, the word ultra-fast is used for sub-picosecond time resolution). In particular we would like to largely present the contribution of crystallographic methods in comparison with optical methods, such as pump-probe reflectivity measurements, the reader being not necessary familiar with X-ray scattering. Thus we want to present which type of physical information can be obtained from the positions of the Bragg peaks, their intensity and their shape, as well as from the diffuse scattering beyond Bragg peaks. An important physical feature is to take into consideration the difference in nature between a photoinduced phase transition and conventional homogeneous photoinduced chemical or biochemical processes where

  20. Molecular Packing of Amphiphilic Nanosheets Resolved by X-ray Scattering

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Harutyunyan, Boris; Dannenhoffer, Adam; Kewalramani, Sumit

    2016-12-29

    Molecular packing in light harvesting 2D assemblies of photocatalytic materials is a critical factor for solar-to-fuel conversion efficiency. However, structure–function correlations have yet to be fully established. This is partly due to the difficulties in extracting the molecular arrangements from the complex 3D powder averaged diffraction patterns of 2D lattices, obtained via in situ wide-angle X-ray scattering. Here, we develop a scattering theory formalism and couple it with a simple geometrical model for the molecular shape of chromophore 9-methoxy-N-(sodium hexanoate)perylene-3,4-dicarboximide (MeO-PMI) used in our study. This generally applicable method fully reproduces the measured diffraction pattern including the asymmetric line shapesmore » for the Bragg reflections and yields the molecular packing arrangement within a 2D crystal structure with a remarkable degree of detail. We find an approximate edge-centered herringbone structure for the PMI fused aromatic rings and ordering of the carboxypentyl chains above and below the nanosheets. Such a packing arrangement differs from the more symmetric face-to-face orientation of the unsubstituted PMI rings. This structural difference is correlated to our measurement of the reduced catalytic performance of MeO-PMI nanosheets as compared to the mesoscopically similar unsubstituted PMI assemblies.« less

  1. Radio and X-ray structure of Centaurus A

    NASA Technical Reports Server (NTRS)

    Feigelson, E. D.

    1982-01-01

    Recent studies of the nearby radio galaxy Centaurus A with the Very Large Array and the Einstein X-Ray Observatory reveal complex radio and X-ray structures. A prominent one-sided jet comprised of resolved knots located 0.2-6 kpc from the nucleus is seen in both radio and X-rays. The X-ray emission is probably synchrotron, requiring in situ reacceleration up to about ten million. Inverse Compton emission is not a likely explanation though a thermal model in which the nucleus ejects dense 100,000 solar mass clouds cannot be excluded. An elongated X-ray region is also found near the 'middle' radio lobe and optical HII regions about 30 kpc NE of the nucleus. Conditions around the active nucleus, the absence of X-rays from the inner radio lobes, and X-ray evidence for a hot interstellar medium are briefly discussed

  2. X-ray diffraction and X-ray standing-wave study of the lead stearate film structure

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Blagov, A. E.; Dyakova, Yu. A.; Kovalchuk, M. V.

    2016-05-15

    A new approach to the study of the structural quality of crystals is proposed. It is based on the use of X-ray standing-wave method without measuring secondary processes and considers the multiwave interaction of diffraction reflections corresponding to different harmonics of the same crystallographic reflection. A theory of multiwave X-ray diffraction is developed to calculate the rocking curves in the X-ray diffraction scheme under consideration for a long-period quasi-one-dimensional crystal. This phase-sensitive method is used to study the structure of a multilayer lead stearate film on a silicon substrate. Some specific structural features are revealed for the surface layer ofmore » the thin film, which are most likely due to the tilt of the upper layer molecules with respect to the external normal to the film surface.« less

  3. Resonant soft X-ray scattering for polymer materials

    DOE PAGES

    Liu, Feng; Brady, Michael A.; Wang, Cheng

    2016-04-16

    Resonant Soft X-ray Scattering (RSoXS) was developed within the last few years, and the first dedicated resonant soft X-ray scattering beamline for soft materials was constructed at the Advanced Light Source, LBNL. RSoXS combines soft X-ray spectroscopy with X-ray scattering and thus offers statistical information for 3D chemical morphology over a large length scale range from nanometers to micrometers. Using RSoXS to characterize multi-length scale soft materials with heterogeneous chemical structures, we have demonstrated that soft X-ray scattering is a unique complementary technique to conventional hard X-ray and neutron scattering. Its unique chemical sensitivity, large accessible size scale, molecular bondmore » orientation sensitivity with polarized X-rays, and high coherence have shown great potential for chemically specific structural characterization for many classes of materials.« less

  4. Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Van Benschoten, Andrew H.; Afonine, Pavel V.; Terwilliger, Thomas C.

    2015-07-28

    A method of simulating X-ray diffuse scattering from multi-model PDB files is presented. Despite similar agreement with Bragg data, different translation–libration–screw refinement strategies produce unique diffuse intensity patterns. Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling andmore » validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier’s equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls-as-xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. These methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis.« less

  5. Structure of Hydrated Poly(d,l-lactic acid) Studied with X-ray Diffraction and Molecular Simulation Methods

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Li, Xianfeng; Murthy, N. Sanjeeva; Latour, Robert A.

    2012-10-10

    The effect of hydration on the molecular structure of amorphous poly(D,L-lactic acid) (PDLLA) with 50:50 L-to-D ratio has been studied by combining experiments with molecular simulations. X-ray diffraction measurements revealed significant changes upon hydration in the structure functions of the copolymer. Large changes in the structure functions at 10 days of incubation coincided with the large increase in the water uptake from {approx} 1 to {approx} 40% and the formation of voids in the film. Computer modeling based on the recently developed TIGER2/TIGER3 mixed sampling scheme was used to interpret these changes by efficiently equilibrating both dry and hydrated modelsmore » of PDLLA. Realistic models of bulk amorphous PDLLA structure were generated as demonstrated by close agreement between the calculated and the experimental structure functions. These molecular simulations were used to identify the interactions between water and the polymer at the atomic level including the change of positional order between atoms in the polymer due to hydration. Changes in the partial O-O structure functions, about 95% of which were due to water-polymer interactions, were apparent in the radial distribution functions. These changes, and somewhat smaller changes in the C-C and C-O partial structure functions, clearly demonstrated the ability of the model to capture the hydrogen-bonding interactions between water and the polymer, with the probability of water forming hydrogen bonds with the carbonyl oxygen of the ester group being about 4 times higher than with its ether oxygen.« less

  6. The O2-Evolving Complex of Photosystem II: Recent Insights from Quantum Mechanics/Molecular Mechanics (QM/MM), Extended X-ray Absorption Fine Structure (EXAFS), and Femtosecond X-ray Crystallography Data.

    PubMed

    Askerka, Mikhail; Brudvig, Gary W; Batista, Victor S

    2017-01-17

    Efficient photoelectrochemical water oxidation may open a way to produce energy from renewable solar power. In biology, generation of fuel due to water oxidation happens efficiently on an immense scale during the light reactions of photosynthesis. To oxidize water, photosynthetic organisms have evolved a highly conserved protein complex, Photosystem II. Within that complex, water oxidation happens at the CaMn 4 O 5 inorganic catalytic cluster, the so-called oxygen-evolving complex (OEC), which cycles through storage "S" states as it accumulates oxidizing equivalents and produces molecular oxygen. In recent years, there has been significant progress in understanding the OEC as it evolves through the catalytic cycle. Studies have combined conventional and femtosecond X-ray crystallography with extended X-ray absorption fine structure (EXAFS) and quantum mechanics/molecular mechanics (QM/MM) methods and have addressed changes in protonation states of μ-oxo bridges and the coordination of substrate water through the analysis of ammonia binding as a chemical analog of water. These advances are thought to be critical to understanding the catalytic cycle since protonation states regulate the relative stability of different redox states and the geometry of the OEC. Therefore, establishing the mechanism for substrate water binding and the nature of protonation/redox state transitions in the OEC is essential for understanding the catalytic cycle of O 2 evolution. The structure of the dark-stable S 1 state has been a target for X-ray crystallography for the past 15 years. However, traditional X-ray crystallography has been hampered by radiation-induced reduction of the OEC. Very recently, a revolutionary X-ray free electron laser (XFEL) technique was applied to PSII to reveal atomic positions at 1.95 Å without radiation damage, which brought us closer than ever to establishing the ultimate structure of the OEC in the S 1 state. However, the atom positions in this crystal

  7. X-Ray Structure determination of the Glycine Cleavage System Protein H of Mycobacterium tuberculosis Using An Inverse Compton Synchrotron X-Ray Source

    PubMed Central

    Abendroth, Jan; McCormick, Michael S.; Edwards, Thomas E.; Staker, Bart; Loewen, Roderick; Gifford, Martin; Rifkin, Jeff; Mayer, Chad; Guo, Wenjin; Zhang, Yang; Myler, Peter; Kelley, Angela; Analau, Erwin; Hewitt, Stephen Nakazawa; Napuli, Alberto J.; Kuhn, Peter; Ruth, Ronald D.; Stewart, Lance J.

    2010-01-01

    Structural genomics discovery projects require ready access to both X-ray and NMR instrumentation which support the collection of experimental data needed to solve large numbers of novel protein structures. The most productive X-ray crystal structure determination laboratories make extensive frequent use of tunable synchrotron X-ray light to solve novel structures by anomalous diffraction methods. This requires that frozen cryo-protected crystals be shipped to large government-run synchrotron facilities for data collection. In an effort to eliminate the need to ship crystals for data collection, we have developed the first laboratory-scale synchrotron light source capable of performing many of the state-of-the-art synchrotron applications in X-ray science. This Compact Light Source is a first-in-class device that uses inverse Compton scattering to generate X-rays of sufficient flux, tunable wavelength and beam size to allow high-resolution X-ray diffraction data collection from protein crystals. We report on benchmarking tests of X-ray diffraction data collection with hen egg white lysozyme, and the successful high-resolution X-ray structure determination of the Glycine cleavage system protein H from Mycobacterium tuberculosis using diffraction data collected with the Compact Light Source X-ray beam. PMID:20364333

  8. Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

    PubMed Central

    Van Benschoten, Andrew H.; Afonine, Pavel V.; Terwilliger, Thomas C.; Wall, Michael E.; Jackson, Colin J.; Sauter, Nicholas K.; Adams, Paul D.; Urzhumtsev, Alexandre; Fraser, James S.

    2015-01-01

    Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier’s equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls_as_xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophos­phodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. These methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis. PMID:26249347

  9. Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

    DOE PAGES

    Van Benschoten, Andrew H.; Afonine, Pavel V.; Terwilliger, Thomas C.; ...

    2015-07-28

    Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier'smore » equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls_as_xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. In addition, these methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis.« less

  10. X-ray absorption fine structure and X-ray excited optical luminescence studies of II-VI semiconducting nanostructures

    NASA Astrophysics Data System (ADS)

    Murphy, Michael Wayne

    2010-06-01

    Various II-VI semiconducting nanomaterials such as ZnO-ZnS nanoribbons (NRs), CdSxSe1-x nanostructures, ZnS:Mn NRs, ZnS:Mn,Eu nanoprsims (NPs), ZnO:Mn nanopowders, and ZnO:Co nanopowders were synthesized for study. These materials were characterized by techniques such as scanning electron microscopy, transmission electron microscopy, element dispersive X-ray spectroscopy, selected area electron diffraction, and X-ray diffraction. The electronic and optical properties of these nanomaterials were studied by X-ray absorption fine structure (XAFS) spectroscopy and X-ray excited optical luminescence (XEOL) techniques, using tuneable soft X-rays from a synchrotron light source. The complementary nature ofthe XAFS and XEOL techniques give site, element and chemical specific measurements which allow a better understanding of the interplay and role of each element in the system. Chemical vapour deposition (CVD) of ZnS powder in a limited oxygen environment resulted in side-by-side biaxial ZnO-ZnS NR heterostructures. The resulting NRs contained distinct wurtzite ZnS and wurtzite ZnO components with widths of 10--100 nm and 20 --500 nm, respectively and a uniform interface region of 5-15 nm. XAFS and XEOL measurements revealed the luminescence of ZnO-ZnS NRs is from the ZnO component. The luminescence of CdSxSe1-x nanostructures is shown to be dependent on the S to Se ratio, with the band-gap emission being tunable between that of pure CdS and CdSe. Excitation of the CdSxSe 1-x nanostructures by X-ray in XEOL has revealed new de-excitation channels which show a defect emission band not seen by laser excitation. CVD of Mn2+ doped ZnS results in nanostructures with luminescence dominated by the yellow Mn2+ emission due to energy transfer from the ZnS host to the Mn dopant sites. The addition of EuCl3 to the reactants in the CVD process results in a change in morphology from NR to NP. Zn1-xMnxO and Zn1-xCOxO nanopowders were prepared by sol-gel methods at dopant concentrations

  11. Electronic structure and optical properties of CdSxSe1-x solid solution nanostructures from X-ray absorption near edge structure, X-ray excited optical luminescence, and density functional theory investigations

    NASA Astrophysics Data System (ADS)

    Murphy, M. W.; Yiu, Y. M.; Ward, M. J.; Liu, L.; Hu, Y.; Zapien, J. A.; Liu, Yingkai; Sham, T. K.

    2014-11-01

    The electronic structure and optical properties of a series of iso-electronic and iso-structural CdSxSe1-x solid solution nanostructures have been investigated using X-ray absorption near edge structure, extended X-ray absorption fine structure, and X-ray excited optical luminescence at various absorption edges of Cd, S, and Se. It is found that the system exhibits compositions, with variable local structure in-between that of CdS and CdSe accompanied by tunable optical band gap between that of CdS and CdSe. Theoretical calculation using density functional theory has been carried out to elucidate the observations. It is also found that luminescence induced by X-ray excitation shows new optical channels not observed previously with laser excitation. The implications of these observations are discussed.

  12. Molecular Level Understanding of Interfaces and Excited State Electronic Structure in Organic Solar Cells Using Soft X-ray Techniques

    NASA Astrophysics Data System (ADS)

    Gliboff, Matthew

    Transparent conductive oxides like indium tin oxide (ITO) are common substrates for optoelectronic devices, including organic light emitting diodes and organic solar cells. Tailoring the interface between the oxide and the active layer by adjusting the work function or wettability of the oxide can improve the performance of these devices in both emissive and photovoltaic applications. Molecular design of self-assembled monolayers (SAMs) allows for a range of surface properties using the same oxide material. The molecular ordering and conformation adopted by the SAMs determine properties such as work function and wettability at these critical interfaces. I use angle-dependent near edge x-ray absorption fine structure (NEXAFS) spectroscopy, to determine the molecular orientations of a variety of dipolar phosphonic acid surface modifiers. For a model system, phenylphosphonic acid on indium zinc oxide, the SAMs prove to be surprisingly well-oriented, with the phenyl ring adopting a well-defined tilt angle of 12-16° from the surface normal. The NEXAFS results agree with polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS) results and orientations calculated from density functional theory (DFT). These results not only provide a detailed picture of the molecular structure of a technologically important class of SAMs, but they also resolve a long-standing ambiguity regarding the vibrational-mode assignments for phosphonic acids on oxide surfaces, thus improving the utility of PM-IRRAS for future studies. The effect of fluorination on the orientation of these phosponic-acid SAMs is non-trivial, due to the combined effects of the fluorination on binding mode and steric packing. The latter effects are found to be more dominant in aliphatic SAMs, leading to a more upright orientation in the fluorinated SAM. In the aromatic case, the fluorinated SAM adopted a less upright orientation which I attribute to changes in binding mode. The relationship

  13. Synchrotron Radiation X-ray Diffraction Techniques Applied to Insect Flight Muscle.

    PubMed

    Iwamoto, Hiroyuki

    2018-06-13

    X-ray fiber diffraction is a powerful tool used for investigating the molecular structure of muscle and its dynamics during contraction. This technique has been successfully applied not only to skeletal and cardiac muscles of vertebrates but also to insect flight muscle. Generally, insect flight muscle has a highly ordered structure and is often capable of high-frequency oscillations. The X-ray diffraction studies on muscle have been accelerated by the advent of 3rd-generation synchrotron radiation facilities, which can generate brilliant and highly oriented X-ray beams. This review focuses on some of the novel experiments done on insect flight muscle by using synchrotron radiation X-rays. These include diffraction recordings from single myofibrils within a flight muscle fiber by using X-ray microbeams and high-speed diffraction recordings from the flight muscle during the wing-beat of live insects. These experiments have provided information about the molecular structure and dynamic function of flight muscle in unprecedented detail. Future directions of X-ray diffraction studies on muscle are also discussed.

  14. The atomic scale structure of CXV carbon: wide-angle x-ray scattering and modeling studies.

    PubMed

    Hawelek, L; Brodka, A; Dore, J C; Honkimaki, V; Burian, A

    2013-11-13

    The disordered structure of commercially available CXV activated carbon produced from finely powdered wood-based carbon has been studied using the wide-angle x-ray scattering technique, molecular dynamics and density functional theory simulations. The x-ray scattering data has been converted to the real space representation in the form of the pair correlation function via the Fourier transform. Geometry optimizations using classical molecular dynamics based on the reactive empirical bond order potential and density functional theory at the B3LYP/6-31g* level have been performed to generate nanoscale models of CXV carbon consistent with the experimental data. The final model of the structure comprises four chain-like and buckled graphitic layers containing a small percentage of four-fold coordinated atoms (sp(3) defects) in each layer. The presence of non-hexagonal rings in the atomic arrangement has been also considered.

  15. Transport Measurements and Synchrotron-Based X-Ray Absorption Spectroscopy of Iron Silicon Germanide Grown by Molecular Beam Epitaxy

    NASA Astrophysics Data System (ADS)

    Elmarhoumi, Nader; Cottier, Ryan; Merchan, Greg; Roy, Amitava; Lohn, Chris; Geisler, Heike; Ventrice, Carl, Jr.; Golding, Terry

    2009-03-01

    Some of the iron-based metal silicide and germanide phases have been predicted to be direct band gap semiconductors. Therefore, they show promise for use as optoelectronic materials. We have used synchrotron-based x-ray absorption spectroscopy to study the structure of iron silicon germanide films grown by molecular beam epitaxy. A series of Fe(Si1-xGex)2 thin films (2000 -- 8000å) with a nominal Ge concentration of up to x = 0.04 have been grown. X-ray absorption near edge structure (XANES) and extended x-ray absorption fine structure (EXAFS) measurements have been performed on the films. The nearest neighbor co-ordination corresponding to the β-FeSi2 phase of iron silicide provides the best fit with the EXAFS data. Temperature dependent (20 < T < 350 K) magneto transport measurements were done on the Fe(Si1-xGex)2 thin films via Van Der Paw (VDP) Hall configuration using a 0.5-1T magnetic field and a current of 10-200 μA through indium ohmic contacts, the Hall coefficient was calculated. Results suggest semiconducting behavior of the films which is consistent with the EXAFS results.

  16. Review of the applications of x-ray refraction and the x-ray waveguide phenomenon to estimation of film structures.

    PubMed

    Hayashi, Kouichi

    2010-12-01

    Based on our previous work, I review the applications of x-ray refraction and the x-ray waveguide phenomenon to organic and inorganic thin films in the present paper. Under grazing incidence conditions, observations of refracted x-rays and guided x-rays due to the x-ray waveguide phenomenon provide information about thin film structures, and thus have potential as alternative methods to x-ray reflectivity. To date, we have measured the spectra of the refracted x-rays and guided x-rays from end faces of thin films using white incident x-ray beams, and utilized them for the determination of film density and thickness. Some of this work is summarized in the present paper. At the end of this paper, I describe our recent achievement in this field, namely the in situ measurement of guided x-rays during the film degradation process due to strong synchrotron radiation damage. Moreover, I discuss the perspective of the present technique from the viewpoint of micro-characterization and real-time estimation of thin films.

  17. Synchrotron X-ray scattering characterization of the molecular structures of star polystyrenes with varying numbers of arms.

    PubMed

    Jin, Sangwoo; Higashihara, Tomoya; Jin, Kyeong Sik; Yoon, Jinhwan; Rho, Yecheol; Ahn, Byungcheol; Kim, Jehan; Hirao, Akira; Ree, Moonhor

    2010-05-20

    We have synthesized well-defined multiarmed star polystyrenes, with 6, 9, 17, 33, and 57 arms, and studied their molecular shapes and structural characteristics in a good solvent (tetrahydrofuran at 25 degrees C) and in a theta (Theta) solvent (cyclohexane at 35 degrees C) by small-angle X-ray scattering (SAXS) using a synchrotron radiation source. Analysis of the SAXS data provided a detailed characterization of the molecular shapes, including the contributions of the blob morphology of the arms, the radius of gyration, the paired distance distribution, the radial electron density distribution, and the Zimm-Stockmayer and Roovers g-factor, for the multiarmed star polystyrenes. In particular, the molecular shapes of the star polystyrenes were found to change from a fuzzy ellipsoid, for the 6-armed polystyrene, to a fuzzy sphere, for the 57-armed polystyrene, with an increasing number of arms. The ellipsoidal character of the star polystyrenes with fewer arms may originate from the extended anisotropically branched architecture at the center of the molecule. The arms of the star polystyrenes were found to be more extended than those of the linear polystyrenes. Furthermore, the degree of chain extension in the arms increased with the number of arms.

  18. X-ray beamsplitter

    DOEpatents

    Ceglio, Natale M.; Stearns, Daniel S.; Hawryluk, Andrew M.; Barbee, Jr., Troy W.

    1989-01-01

    An x-ray beamsplitter which splits an x-ray beam into two coherent parts by reflecting and transmitting some fraction of an incident beam has applications for x-ray interferometry, x-ray holography, x-ray beam manipulation, and x-ray laser cavity output couplers. The beamsplitter is formed of a wavelength selective multilayer thin film supported by a very thin x-ray transparent membrane. The beamsplitter resonantly transmits and reflects x-rays through thin film interference effects. A thin film is formed of 5-50 pairs of alternate Mo/Si layers with a period of 20-250 A. The support membrane is 10-200 nm of silicon nitride or boron nitride. The multilayer/support membrane structure is formed across a window in a substrate by first forming the structure on a solid substrate and then forming a window in the substrate to leave a free-standing structure over the window.

  19. Non Destructive 3D X-Ray Imaging of Nano Structures & Composites at Sub-30 NM Resolution, With a Novel Lab Based X-Ray Microscope

    DTIC Science & Technology

    2006-11-01

    NON DESTRUCTIVE 3D X-RAY IMAGING OF NANO STRUCTURES & COMPOSITES AT SUB-30 NM RESOLUTION, WITH A NOVEL LAB BASED X- RAY MICROSCOPE S H Lau...article we describe a 3D x-ray microscope based on a laboratory x-ray source operating at 2.7, 5.4 or 8.0 keV hard x-ray energies. X-ray computed...tomography (XCT) is used to obtain detailed 3D structural information inside optically opaque materials with sub-30 nm resolution. Applications include

  20. NAD+ administration significantly attenuates synchrotron radiation X-ray-induced DNA damage and structural alterations of rodent testes

    PubMed Central

    Sheng, Caibin; Chen, Heyu; Wang, Ban; Liu, Tengyuan; Hong, Yunyi; Shao, Jiaxiang; He, Xin; Ma, Yingxin; Nie, Hui; Liu, Na; Xia, Weiliang; Ying, Weihai

    2012-01-01

    Synchrotron radiation (SR) X-ray has great potential for its applications in medical imaging and cancer treatment. In order to apply SR X-ray in clinical settings, it is necessary to elucidate the mechanisms underlying the damaging effects of SR X-ray on normal tissues, and to search for the strategies to reduce the detrimental effects of SR X-ray on normal tissues. However, so far there has been little information on these topics. In this study we used the testes of rats as a model to characterize SR X-ray-induced tissue damage, and to test our hypothesis that NAD+ administration can prevent SR X-ray-induced injury of the testes. We first determined the effects of SR X-ray at the doses of 0, 0.5, 1.3, 4 and 40 Gy on the biochemical and structural properties of the testes one day after SR X-ray exposures. We found that 40 Gy of SR X-ray induced a massive increase in double-strand DNA damage, as assessed by both immunostaining and Western blot of phosphorylated H2AX levels, which was significantly decreased by intraperitoneally (i.p.) administered NAD+ at doses of 125 and 625 mg/kg. Forty Gy of SR X-ray can also induce marked increases in abnormal cell nuclei as well as significant decreases in the cell layers of the seminiferous tubules one day after SR X-ray exposures, which were also ameliorated by the NAD+ administration. In summary, our study has shown that SR X-ray can produce both molecular and structural alterations of the testes, which can be significantly attenuated by NAD+ administration. These results have provided not only the first evidence that SR X-ray-induced tissue damage can be ameliorated by certain approaches, but also a valuable basis for elucidating the mechanisms underlying SR X-ray-induced tissue injury. PMID:22518270

  1. The development of structural x-ray crystallography

    NASA Astrophysics Data System (ADS)

    Woolfson, M. M.

    2018-03-01

    From its birth in 1912, when only the simplest structures could be solved, x-ray structural crystallography is now able to solve macromolecular structures containing many thousands of independent non-hydrogen atoms. This progress has depended on, and been driven by, great technical advances in the development of powerful synchrotron x-ray sources, advanced automated equipment for the collection and storage of large data sets and powerful computers to deal with everything from data processing to running programmes employing complex algorithms for the automatic solution of structures. The sheer number of developments in the subject over the past century makes it impossible for this review to be exhaustive, but it will describe some major developments that will enable the reader to understand how the subject has grown from its humble beginnings to what it is today.

  2. X-ray beamsplitter

    DOEpatents

    Ceglio, N.M.; Stearns, D.G.; Hawryluk, A.M.; Barbee, T.W. Jr.

    1987-08-07

    An x-ray beamsplitter which splits an x-ray beam into two coherent parts by reflecting and transmitting some fraction of an incident beam has applications for x-ray interferometry, x-ray holography, x-ray beam manipulation, and x-ray laser cavity output couplers. The beamsplitter is formed of a wavelength selective multilayer thin film supported by a very thin x-ray transparent membrane. The beamsplitter resonantly transmits and reflects x-rays through thin film interference effects. A thin film is formed of 5--50 pairs of alternate Mo/Si layers with a period of 20--250 A. The support membrane is 10--200 nm of silicon nitride or boron nitride. The multilayer/support membrane structure is formed across a window in a substrate by first forming the structure on a solid substrate and then forming a window in the substrate to leave a free-standing structure over the window. 6 figs.

  3. First-principles calculations of K-shell X-ray absorption spectra for warm dense nitrogen

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Li, Zi; Zhang, Shen; Kang, Wei

    2016-05-15

    X-ray absorption spectrum is a powerful tool for atomic structure detection on warm dense matter. Here, we perform first-principles molecular dynamics and X-ray absorption spectrum calculations on warm dense nitrogen along a Hugoniot curve. From the molecular dynamics trajectory, the detailed atomic structures are examined for each thermodynamical condition. The K-shell X-ray absorption spectrum is calculated, and its changes with temperature and pressure along the Hugoniot curve are discussed. The warm dense nitrogen systems may contain isolated nitrogen atoms, N{sub 2} molecules, and nitrogen clusters, which show quite different contributions to the total X-ray spectrum due to their different electronmore » density of states. The changes of X-ray spectrum along the Hugoniot curve are caused by the different nitrogen structures induced by the temperature and the pressure. Some clear signatures on X-ray spectrum for different thermodynamical conditions are pointed out, which may provide useful data for future X-ray experiments.« less

  4. The O 2 -Evolving Complex of Photosystem II: Recent Insights from Quantum Mechanics/Molecular Mechanics (QM/MM), Extended X-ray Absorption Fine Structure (EXAFS), and Femtosecond X-ray Crystallography Data

    DOE PAGES

    Askerka, Mikhail; Brudvig, Gary W.; Batista, Victor S.

    2016-12-21

    Efficient photoelectrochemical water oxidation may open a way to produce energy from renewable solar power. In biology, generation of fuel due to water oxidation happens efficiently on an immense scale during the light reactions of photosynthesis. To oxidize water, photosynthetic organisms have evolved a highly conserved protein complex, Photosystem II. Within that complex, water oxidation happens at the CaMn 4O 5 inorganic catalytic cluster, the so-called oxygen-evolving complex (OEC), which cycles through storage “S” states as it accumulates oxidizing equivalents and produces molecular oxygen. In recent years, there has been significant progress in understanding the OEC as it evolves throughmore » the catalytic cycle. Studies have combined conventional and femtosecond X-ray crystallography with extended X-ray absorption fine structure (EXAFS) and quantum mechanics/molecular mechanics (QM/ MM) methods and have addressed changes in protonation states of μ-oxo bridges and the coordination of substrate water through the analysis of ammonia binding as a chemical analog of water. These advances are thought to be critical to understanding the catalytic cycle since protonation states regulate the relative stability of different redox states and the geometry of the OEC. Therefore, establishing the mechanism for substrate water binding and the nature of protonation/redox state transitions in the OEC is essential for understanding the catalytic cycle of O 2 evolution. The structure of the dark-stable S1 state has been a target for X-ray crystallography for the past 15 years. However, traditional Xray crystallography has been hampered by radiation-induced reduction of the OEC. Very recently, a revolutionary X-ray free electron laser (XFEL) technique was applied to PSII to reveal atomic positions at 1.95 Å without radiation damage, which brought us closer than ever to establishing the ultimate structure of the OEC in the S 1 state. However, the atom positions in this

  5. The O 2 -Evolving Complex of Photosystem II: Recent Insights from Quantum Mechanics/Molecular Mechanics (QM/MM), Extended X-ray Absorption Fine Structure (EXAFS), and Femtosecond X-ray Crystallography Data

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Askerka, Mikhail; Brudvig, Gary W.; Batista, Victor S.

    Efficient photoelectrochemical water oxidation may open a way to produce energy from renewable solar power. In biology, generation of fuel due to water oxidation happens efficiently on an immense scale during the light reactions of photosynthesis. To oxidize water, photosynthetic organisms have evolved a highly conserved protein complex, Photosystem II. Within that complex, water oxidation happens at the CaMn 4O 5 inorganic catalytic cluster, the so-called oxygen-evolving complex (OEC), which cycles through storage “S” states as it accumulates oxidizing equivalents and produces molecular oxygen. In recent years, there has been significant progress in understanding the OEC as it evolves throughmore » the catalytic cycle. Studies have combined conventional and femtosecond X-ray crystallography with extended X-ray absorption fine structure (EXAFS) and quantum mechanics/molecular mechanics (QM/ MM) methods and have addressed changes in protonation states of μ-oxo bridges and the coordination of substrate water through the analysis of ammonia binding as a chemical analog of water. These advances are thought to be critical to understanding the catalytic cycle since protonation states regulate the relative stability of different redox states and the geometry of the OEC. Therefore, establishing the mechanism for substrate water binding and the nature of protonation/redox state transitions in the OEC is essential for understanding the catalytic cycle of O 2 evolution. The structure of the dark-stable S1 state has been a target for X-ray crystallography for the past 15 years. However, traditional Xray crystallography has been hampered by radiation-induced reduction of the OEC. Very recently, a revolutionary X-ray free electron laser (XFEL) technique was applied to PSII to reveal atomic positions at 1.95 Å without radiation damage, which brought us closer than ever to establishing the ultimate structure of the OEC in the S 1 state. However, the atom positions in this

  6. Structure and photoinduced structural changes in nonstoichiometric a -As sub x S sub 1 minus x : A study by x-ray-absorption fine structure

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhou, W.; Paesler, M.A.; Sayers, D.E.

    1992-08-15

    X-ray-absorption fine-structure data show that chemical ordering plays an important role in nonstoichiometric amorphous ({ital a}-)As{sub {ital x}}S{sub 1{minus}{ital x}} films at 0.4{le}{ital x}{lt}=0.5. The mixture of different chemical bonding behaviors of As-S and As-As in an {ital a}-As{sub 2}S{sub 3} random covalent network and an {ital a}-As{sub 4}S{sub 4} disordered molecular solid lead the structure to a more disordered state for 0.4{lt}{ital x}{lt}0.5. In particular, the structure at a composition around {ital x}=0.43 in {ital a}-As{sub {ital x}}S{sub 1{minus}{ital x}} represents a maximum of flexibility. Photoillumination results in (1) a more disordered state as indicated by an increase inmore » the static Debye-Waller factors (which are related to the creation of As-As homopolar bonds) and (2) modifications in the network structure, such as the increase of the As-As radial distances in the second shells. In nonstoichiometric material, the presence of As{sub 4}S{sub 4} molecules in the As{sub 2}S{sub 3} network tends to break up this network into small segments. This decoupling of pieces of the As{sub 2}S{sub 3} network (composed of S-bridged AsS{sub 3} pyramids and As-As wrong bonds) may lead to increased steric freedom that is related to a more disordered state that appears to be associated with photoinduced structural changes in amorphous arsenic sulfide.« less

  7. Complementary uses of small angle X-ray scattering and X-ray crystallography.

    PubMed

    Pillon, Monica C; Guarné, Alba

    2017-11-01

    Most proteins function within networks and, therefore, protein interactions are central to protein function. Although stable macromolecular machines have been extensively studied, dynamic protein interactions remain poorly understood. Small-angle X-ray scattering probes the size, shape and dynamics of proteins in solution at low resolution and can be used to study samples in a large range of molecular weights. Therefore, it has emerged as a powerful technique to study the structure and dynamics of biomolecular systems and bridge fragmented information obtained using high-resolution techniques. Here we review how small-angle X-ray scattering can be combined with other structural biology techniques to study protein dynamics. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Structure of a monolayer of molecular rotors on aqueous subphase from grazing-incidence X-ray diffraction.

    PubMed

    Kaleta, Jiří; Wen, Jin; Magnera, Thomas F; Dron, Paul I; Zhu, Chenhui; Michl, Josef

    2018-03-23

    In situ grazing-incidence X-ray scattering shows that a monolayer of artificial rod-shaped dipolar molecular rotors produced on the surface of an aqueous subphase in a Langmuir trough has a structure conducive to a 2D ferroelectric phase. The axes of the rotors stand an average of 0.83 nm apart in a triangular grid, perpendicular to the surface within experimental error. They carry 2,3-dichlorophenylene rotators near rod centers, between two decks of interlocked triptycenes installed axially on the rotor axle. The analysis is based first on simultaneous fitting of observed Bragg rods and second on fitting the reflectivity curve with only three adjustable parameters and the calculated rotor electron density, which also revealed the presence of about seven molecules of water near each rotator. Dependent on preparation conditions, a minor and variable amount of a different crystal phase may also be present in the monolayer.

  9. X-ray Diffraction from Membrane Protein Nanocrystals

    PubMed Central

    Hunter, M.S.; DePonte, D.P.; Shapiro, D.A.; Kirian, R.A.; Wang, X.; Starodub, D.; Marchesini, S.; Weierstall, U.; Doak, R.B.; Spence, J.C.H.; Fromme, P.

    2011-01-01

    Membrane proteins constitute >30% of the proteins in an average cell, and yet the number of currently known structures of unique membrane proteins is <300. To develop new concepts for membrane protein structure determination, we have explored the serial nanocrystallography method, in which fully hydrated protein nanocrystals are delivered to an x-ray beam within a liquid jet at room temperature. As a model system, we have collected x-ray powder diffraction data from the integral membrane protein Photosystem I, which consists of 36 subunits and 381 cofactors. Data were collected from crystals ranging in size from 100 nm to 2 μm. The results demonstrate that there are membrane protein crystals that contain <100 unit cells (200 total molecules) and that 3D crystals of membrane proteins, which contain <200 molecules, may be suitable for structural investigation. Serial nanocrystallography overcomes the problem of x-ray damage, which is currently one of the major limitations for x-ray structure determination of small crystals. By combining serial nanocrystallography with x-ray free-electron laser sources in the future, it may be possible to produce molecular-resolution electron-density maps using membrane protein crystals that contain only a few hundred or thousand unit cells. PMID:21190672

  10. Structural and mechanical properties of cardiolipin lipid bilayers determined using neutron spin echo, small angle neutron and X-ray scattering, and molecular dynamics simulations

    DOE PAGES

    Pan, Jianjun; Cheng, Xiaolin; Sharp, Melissa; ...

    2014-10-29

    We report that the detailed structural and mechanical properties of a tetraoleoyl cardiolipin (TOCL) bilayer were determined using neutron spin echo (NSE) spectroscopy, small angle neutron and X-ray scattering (SANS and SAXS, respectively), and molecular dynamics (MD) simulations. We used MD simulations to develop a scattering density profile (SDP) model, which was then utilized to jointly refine SANS and SAXS data. In addition to commonly reported lipid bilayer structural parameters, component distributions were obtained, including the volume probability, electron density and neutron scattering length density.

  11. Depth profiling of marker layers using x-ray waveguide structures

    NASA Astrophysics Data System (ADS)

    Gupta, Ajay; Rajput, Parasmani; Saraiya, Amit; Reddy, V. R.; Gupta, Mukul; Bernstorff, Sigrid; Amenitsch, H.

    2005-08-01

    It is demonstrated that x-ray waveguide structures can be used for depth profiling of a marker layer inside the guiding layer with an accuracy of better than 0.2 nm. A combination of x-ray fluorescence and x-ray reflectivity measurements can provide detailed information about the structure of the guiding layer. The position and thickness of the marker layer affect different aspects of the angle-dependent x-ray fluorescence pattern, thus making it possible to determine the structure of the marker layer in an unambiguous manner. As an example, effects of swift heavy ion irradiation on a Si/M/Si trilayer ( M=Fe , W), forming the cavity of the waveguide structure, have been studied. It is found that in accordance with the prediction of thermal spike model, Fe is much more sensitive to swift heavy ion induced modifications as compared to W, even in thin film form. However, a clear evidence of movement of the Fe marker layer towards the surface is observed after irradiation, which cannot be understood in terms of the thermal spike model alone.

  12. Towards simultaneous measurements of electronic and structural properties in ultra-fast x-ray free electron laser absorption spectroscopy experiments

    NASA Astrophysics Data System (ADS)

    Gaudin, J.; Fourment, C.; Cho, B. I.; Engelhorn, K.; Galtier, E.; Harmand, M.; Leguay, P. M.; Lee, H. J.; Nagler, B.; Nakatsutsumi, M.; Ozkan, C.; Störmer, M.; Toleikis, S.; Tschentscher, Th; Heimann, P. A.; Dorchies, F.

    2014-04-01

    The rapidly growing ultrafast science with X-ray lasers unveils atomic scale processes with unprecedented time resolution bringing the so called ``molecular movie'' within reach. X-ray absorption spectroscopy is one of the most powerful x-ray techniques providing both local atomic order and electronic structure when coupled with ad-hoc theory. Collecting absorption spectra within few x-ray pulses is possible only in a dispersive setup. We demonstrate ultrafast time-resolved measurements of the LIII-edge x-ray absorption near-edge spectra of irreversibly laser excited Molybdenum using an average of only few x-ray pulses with a signal to noise ratio limited only by the saturation level of the detector. The simplicity of the experimental set-up makes this technique versatile and applicable for a wide range of pump-probe experiments, particularly in the case of non-reversible processes.

  13. Three-dimensional structure determination protocol for noncrystalline biomolecules using x-ray free-electron laser diffraction imaging.

    PubMed

    Oroguchi, Tomotaka; Nakasako, Masayoshi

    2013-02-01

    Coherent and intense x-ray pulses generated by x-ray free-electron laser (XFEL) sources are paving the way for structural determination of noncrystalline biomolecules. However, due to the small scattering cross section of electrons for x rays, the available incident x-ray intensity of XFEL sources, which is currently in the range of 10(12)-10(13) photons/μm(2)/pulse, is lower than that necessary to perform single-molecule diffraction experiments for noncrystalline biomolecules even with the molecular masses of megadalton and submicrometer dimensions. Here, we propose an experimental protocol and analysis method for visualizing the structure of those biomolecules by the combined application of coherent x-ray diffraction imaging and three-dimensional reconstruction methods. To compensate the small scattering cross section of biomolecules, in our protocol, a thin vitreous ice plate containing several hundred biomolecules/μm(2) is used as sample, a setup similar to that utilized by single-molecule cryoelectron microscopy. The scattering cross section of such an ice plate is far larger than that of a single particle. The images of biomolecules contained within irradiated areas are then retrieved from each diffraction pattern, and finally provide the three-dimensional electron density model. A realistic atomic simulation using large-scale computations proposed that the three-dimensional structure determination of the 50S ribosomal subunit embedded in a vitreous ice plate is possible at a resolution of 0.8 nm when an x-ray beam of 10(16) photons/500×500 nm(2)/pulse is available.

  14. From the X-rays to a reliable “low cost” computational structure of caffeic acid: DFT, MP2, HF and integrated molecular dynamics-X-ray diffraction approach to condensed phases

    NASA Astrophysics Data System (ADS)

    Lombardo, Giuseppe M.; Portalone, Gustavo; Colapietro, Marcello; Rescifina, Antonio; Punzo, Francesco

    2011-05-01

    The ability of caffeic acid to act as antioxidant against hyperoxo-radicals as well as its recently found therapeutic properties in the treatment of hepatocarcinoma, still make this compound, more than 20 years later the refinement of its crystal structure, object of study. It belongs to the vast family of humic substances, which play a key role in the biodegradation processes and easily form complexes with ions widely diffused in the environment. This class of compounds is therefore interesting for potential environmental chemistry applications concerning the possible complexation of heavy metals. Our study focused on the characterization of caffeic acid as a starting necessary step, which will be followed in the future by the application of our findings on the study of the properties of caffeate anion interaction with heavy metal ions. To reach this goal, we applied a low cost approach - in terms of computational time and resources - aimed at the achievement of a high resolution, robust and trustable structure using the X-ray single crystal data, recollected with a higher resolution, as touchstone for a detailed check. A comparison between the calculations carried out with density functional theory (DFT), Hartree-Fock (HF) method and post SCF second order Møller-Plesset perturbation method (MP2), at the 6-31G ** level of the theory, molecular mechanics (MM) and molecular dynamics (MD) was performed. As a consequence we explained on one hand the possible reasons for the pitfalls of the DFT approach and on the other the benefits of using a good and robust force field developed for condensed phases, as AMBER, with MM and MD. The reliability of the latter, highlighted by the overall agreement extended up to the anisotropic displacement parameters calculated by means of MD and the ones gathered by X-ray measurements, makes it very promising for the above-mentioned goals.

  15. Structural Basis of Pullulanase Membrane Binding and Secretion Revealed by X-Ray Crystallography, Molecular Dynamics and Biochemical Analysis.

    PubMed

    East, Alexandra; Mechaly, Ariel E; Huysmans, Gerard H M; Bernarde, Cédric; Tello-Manigne, Diana; Nadeau, Nathalie; Pugsley, Anthony P; Buschiazzo, Alejandro; Alzari, Pedro M; Bond, Peter J; Francetic, Olivera

    2016-01-05

    The Klebsiella lipoprotein pullulanase (PulA) is exported to the periplasm, triacylated, and anchored via lipids in the inner membrane (IM) prior to its transport to the bacterial surface through a type II secretion system (T2SS). X-Ray crystallography and atomistic molecular dynamics (MD) simulations of PulA in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) model membrane provided an unprecedented molecular view of an N-terminal unstructured tether and the IM lipoprotein retention signal, and revealed novel interactions with the IM via N-terminal immunoglobulin-like domains in PulA. An efficiently secreted nonacylated variant (PulANA) showed similar peripheral membrane association during MD simulations, consistent with the binding of purified PulANA to liposomes. Remarkably, combined X-ray, MD, and functional studies identified a novel subdomain, Ins, inserted in the α-amylase domain, which is required for PulA secretion. Available data support a model in which PulA binding to the IM promotes interactions with the T2SS, possibly via the Ins subdomain. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Novel Drift Structures for Silicon and Compound Semiconductor X-Ray and Gamma-Ray Detectors

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bradley E. Patt; Jan S. Iwanczyk

    Recently developed silicon- and compound-semiconductor-based drift detector structures have produced excellent performance for charged particles, X rays, and gamma rays and for low-signal visible light detection. The silicon drift detector (SDD) structures that we discuss relate to direct X-ray detectors and scintillation photon detectors coupled with scintillators for gamma rays. Recent designs include several novel features that ensure very low dark current (both bulk silicon dark current and surface dark current) and hence low noise. In addition, application of thin window technology ensures a very high quantum efficiency entrance window on the drift photodetector.

  17. Polarized x-ray excitation for scatter reduction in x-ray fluorescence computed tomography.

    PubMed

    Vernekohl, Don; Tzoumas, Stratis; Zhao, Wei; Xing, Lei

    2018-05-25

    X-ray fluorescence computer tomography (XFCT) is a new molecular imaging modality which uses x-ray excitation to stimulate the emission of fluorescent photons in high atomic number contrast agents. Scatter contamination is one of the main challenges in XFCT imaging which limits the molecular sensitivity. When polarized x rays are used, it is possible to reduce the scatter contamination significantly by placing detectors perpendicular to the polarization direction. This study quantifies scatter contamination for polarized and unpolarized x-ray excitation and determines the advantages of scatter reduction. The amount of scatter in preclinical XFCT is quantified in Monte Carlo simulations. The fluorescent x rays are emitted isotropically, while scattered x rays propagate in polarization direction. The magnitude of scatter contamination is studied in XFCT simulations of a mouse phantom. In this study, the contrast agent gold is examined as an example, but a scatter reduction from polarized excitation is also expected for other elements. The scatter reduction capability is examined for different polarization intensities with a monoenergetic x-ray excitation energy of 82 keV. The study evaluates two different geometrical shapes of CZT detectors which are modeled with an energy resolution of 1 keV FWHM at an x-ray energy of 80 keV. Benefits of a detector placement perpendicular to the polarization direction are shown in iterative and analytic image reconstruction including scatter correction. The contrast to noise ratio (CNR) and the normalized mean square error (NMSE) are analyzed and compared for the reconstructed images. A substantial scatter reduction for common detector sizes was achieved for 100% and 80% linear polarization while lower polarization intensities provide a decreased scatter reduction. By placing the detector perpendicular to the polarization direction, a scatter reduction by factor up to 5.5 can be achieved for common detector sizes. The image

  18. From lows to highs: using low-resolution models to phase X-ray data

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Stuart, David I.; Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot; Abrescia, Nicola G. A., E-mail: nabrescia@cicbiogune.es

    2013-11-01

    An unusual example of how virus structure determination pushes the limits of the molecular replacement method is presented. The study of virus structures has contributed to methodological advances in structural biology that are generally applicable (molecular replacement and noncrystallographic symmetry are just two of the best known examples). Moreover, structural virology has been instrumental in forging the more general concept of exploiting phase information derived from multiple structural techniques. This hybridization of structural methods, primarily electron microscopy (EM) and X-ray crystallography, but also small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy, is central to integrative structural biology. Here,more » the interplay of X-ray crystallography and EM is illustrated through the example of the structural determination of the marine lipid-containing bacteriophage PM2. Molecular replacement starting from an ∼13 Å cryo-EM reconstruction, followed by cycling density averaging, phase extension and solvent flattening, gave the X-ray structure of the intact virus at 7 Å resolution This in turn served as a bridge to phase, to 2.5 Å resolution, data from twinned crystals of the major coat protein (P2), ultimately yielding a quasi-atomic model of the particle, which provided significant insights into virus evolution and viral membrane biogenesis.« less

  19. Towards simultaneous measurements of electronic and structural properties in ultra-fast x-ray free electron laser absorption spectroscopy experiments

    PubMed Central

    Gaudin, J.; Fourment, C.; Cho, B. I.; Engelhorn, K.; Galtier, E.; Harmand, M.; Leguay, P. M.; Lee, H. J.; Nagler, B.; Nakatsutsumi, M.; Ozkan, C.; Störmer, M.; Toleikis, S.; Tschentscher, Th; Heimann, P. A.; Dorchies, F.

    2014-01-01

    The rapidly growing ultrafast science with X-ray lasers unveils atomic scale processes with unprecedented time resolution bringing the so called “molecular movie” within reach. X-ray absorption spectroscopy is one of the most powerful x-ray techniques providing both local atomic order and electronic structure when coupled with ad-hoc theory. Collecting absorption spectra within few x-ray pulses is possible only in a dispersive setup. We demonstrate ultrafast time-resolved measurements of the LIII-edge x-ray absorption near-edge spectra of irreversibly laser excited Molybdenum using an average of only few x-ray pulses with a signal to noise ratio limited only by the saturation level of the detector. The simplicity of the experimental set-up makes this technique versatile and applicable for a wide range of pump-probe experiments, particularly in the case of non-reversible processes. PMID:24740172

  20. Towards simultaneous measurements of electronic and structural properties in ultra-fast x-ray free electron laser absorption spectroscopy experiments

    DOE PAGES

    Gaudin, J.; Fourment, C.; Cho, B. I.; ...

    2014-04-17

    The rapidly growing ultrafast science with X-ray lasers unveils atomic scale processes with unprecedented time resolution bringing the so called “molecular movie” within reach. X-ray absorption spectroscopy is one of the most powerful x-ray techniques providing both local atomic order and electronic structure when coupled with ad-hoc theory. Collecting absorption spectra within few x-ray pulses is possible only in a dispersive setup. We demonstrate ultrafast time-resolved measurements of the LIII-edge x-ray absorption near-edge spectra of irreversibly laser excited Molybdenum using an average of only few x-ray pulses with a signal to noise ratio limited only by the saturation level ofmore » the detector. The simplicity of the experimental set-up makes this technique versatile and applicable for a wide range of pump-probe experiments, particularly in the case of non-reversible processes.« less

  1. Mesoscale imaging with cryo-light and X-rays: Larger than molecular machines, smaller than a cell: Mesoscale imaging with cryo-light and X-rays

    DOE PAGES

    Ekman, Axel A.; Chen, Jian-Hua; Guo, Jessica; ...

    2016-11-14

    In the context of cell biology, the term mesoscale describes length scales ranging from that of an individual cell, down to the size of the molecular machines. In this spatial regime, small building blocks self-organise to form large, functional structures. A comprehensive set of rules governing mesoscale self-organisation has not been established, making the prediction of many cell behaviours difficult, if not impossible. Our knowledge of mesoscale biology comes from experimental data, in particular, imaging. Here, we explore the application of soft X-ray tomography (SXT) to imaging the mesoscale, and describe the structural insights this technology can generate. We alsomore » discuss how SXT imaging is complemented by the addition of correlative fluorescence data measured from the same cell. This combination of two discrete imaging modalities produces a 3D view of the cell that blends high-resolution structural information with precise molecular localisation data.« less

  2. On the large scale structure of X-ray background sources

    NASA Technical Reports Server (NTRS)

    Bi, H. G.; Meszaros, A.; Meszaros, P.

    1991-01-01

    The large scale clustering of the sources responsible for the X-ray background is discussed, under the assumption of a discrete origin. The formalism necessary for calculating the X-ray spatial fluctuations in the most general case where the source density contrast in structures varies with redshift is developed. A comparison of this with observational limits is useful for obtaining information concerning various galaxy formation scenarios. The calculations presented show that a varying density contrast has a small impact on the expected X-ray fluctuations. This strengthens and extends previous conclusions concerning the size and comoving density of large scale structures at redshifts 0.5 between 4.0.

  3. Photoelectron diffraction from single oriented molecules: Towards ultrafast structure determination of molecules using x-ray free-electron lasers

    NASA Astrophysics Data System (ADS)

    Kazama, Misato; Fujikawa, Takashi; Kishimoto, Naoki; Mizuno, Tomoya; Adachi, Jun-ichi; Yagishita, Akira

    2013-06-01

    We provide a molecular structure determination method, based on multiple-scattering x-ray photoelectron diffraction (XPD) calculations. This method is applied to our XPD data on several molecules having different equilibrium geometries. Then it is confirmed that, by our method, bond lengths and bond angles can be determined with a resolution of less than 0.1 Å and 10∘, respectively. Differently from any other scenario of ultrafast structure determination, we measure the two- or three-dimensional XPD of aligned or oriented molecules in the energy range from 100 to 200 eV with a 4π detection velocity map imaging spectrometer. Thanks to the intense and ultrashort pulse properties of x-ray free-electron lasers, our approach exhibits the most probable method for obtaining ultrafast real-time structural information on small to medium-sized molecules consisting of light elements, i.e., a “molecular movie.”

  4. Novel drift structures for silicon and compound semiconductor X-ray and gamma-ray detectors

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Patt, B.E.; Iwanczyk, J.S.

    Recently developed silicon- and compound-semiconductor-based drift detector structures have produced excellent performance for charged particles, X-rays, and gamma rays and for low-signal visible light detection. The silicon drift detector (SDD) structures that the authors discuss relate to direct X-ray detectors and scintillation photon detectors coupled with scintillators for gamma rays. Recent designs include several novel features that ensure very low dark current and hence low noise. In addition, application of thin window technology ensures a very high quantum efficiency entrance window on the drift photodetector. The main features of the silicon drift structures for X rays and light detection aremore » very small anode capacitance independent of the overall detector size, low noise, and high throughput. To take advantage of the small detector capacitance, the first stage of the electronics needs to be integrated into the detector anode. In the gamma-ray application, factors other than electronic noise dominate, and there is no need to integrate the electronics into the anode. Thus, a different drift structure is needed in conjunction with a high-Z material. The main features in this case are large active detector volume and electron-only induced signal.« less

  5. Hydration structure of the barite (001)–water interface: Comparison of x-ray reflectivity with molecular dynamics simulations

    DOE PAGES

    Bracco, Jacquelyn N.; Lee, Sang Soo; Stubbs, Joanne E.; ...

    2017-05-11

    The three-dimensional structure of the barite (001)-water interface was studied using in situ specular and non-specular X-ray reflectivity (XR). Displacements of the barium and sulfate ions in the surface of a barite crystal and the interfacial water structure were defined in the analyses. The largest relaxations (0.13 Å lateral and 0.08 Å vertical) were observed for the barium and sulfate ions in the topmost unit cell layer, which diminished rapidly with depth. The best fit structure identified four distinct adsorbed species, which in comparison with molecular dynamics (MD) simulations, reveals that they are associated with positions of adsorbed water, eachmore » of which coordinates one or two surface ions (either barium, sulfate, or both). These water molecules also adsorb in positions consistent with those of bariums and sulfates in the bulk crystal lattice. These results demonstrate the importance of combining high resolution XR with MD simulations to fully describe the atomic structure of the hydrated mineral surface. As a result, the agreement between the results indicates both the uniqueness of the structural model obtained from the XR analysis and the accuracy of the force field used in the simulations.« less

  6. Hydration structure of the barite (001)–water interface: Comparison of x-ray reflectivity with molecular dynamics simulations

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bracco, Jacquelyn N.; Lee, Sang Soo; Stubbs, Joanne E.

    The three-dimensional structure of the barite (001)-water interface was studied using in situ specular and non-specular X-ray reflectivity (XR). Displacements of the barium and sulfate ions in the surface of a barite crystal and the interfacial water structure were defined in the analyses. The largest relaxations (0.13 Å lateral and 0.08 Å vertical) were observed for the barium and sulfate ions in the topmost unit cell layer, which diminished rapidly with depth. The best fit structure identified four distinct adsorbed species, which in comparison with molecular dynamics (MD) simulations, reveals that they are associated with positions of adsorbed water, eachmore » of which coordinates one or two surface ions (either barium, sulfate, or both). These water molecules also adsorb in positions consistent with those of bariums and sulfates in the bulk crystal lattice. These results demonstrate the importance of combining high resolution XR with MD simulations to fully describe the atomic structure of the hydrated mineral surface. As a result, the agreement between the results indicates both the uniqueness of the structural model obtained from the XR analysis and the accuracy of the force field used in the simulations.« less

  7. Synthesis, spectroscopic investigations (X-ray, NMR and TD-DFT), antimicrobial activity and molecular docking of 2,6-bis(hydroxy(phenyl)methyl)cyclohexanone.

    PubMed

    Barakat, Assem; Ghabbour, Hazem A; Al-Majid, Abdullah Mohammed; Soliman, Saied M; Ali, M; Mabkhot, Yahia Nasser; Shaik, Mohammed Rafi; Fun, Hoong-Kun

    2015-07-21

    The synthesis of 2,6-bis(hydroxy(phenyl)methyl)cyclohexanone 1 is described. The molecular structure of the title compound 1 was confirmed by NMR, FT-IR, MS, CHN microanalysis, and X-ray crystallography. The molecular structure was also investigated by a set of computational studies and found to be in good agreement with the experimental data obtained from the various spectrophotometric techniques. The antimicrobial activity and molecular docking of the synthesized compound was investigated.

  8. Development of a hybrid molecular beam epitaxy deposition system for in situ surface x-ray studies

    NASA Astrophysics Data System (ADS)

    Andersen, Tassie K.; Cook, Seyoung; Benda, Erika; Hong, Hawoong; Marks, Laurence D.; Fong, Dillon D.

    2018-03-01

    A portable metalorganic gas delivery system designed and constructed to interface with an existing molecular beam epitaxy chamber at beamline 33-ID-E of the Advanced Photon Source is described. This system offers the ability to perform in situ X-ray measurements of complex oxide growth via hybrid molecular beam epitaxy. The performance of the hybrid molecular beam epitaxy system while delivering metalorganic source materials is described. The high-energy X-ray scattering capabilities of the hybrid molecular beam epitaxy system are demonstrated both on oxide films grown solely from the metalorganic source and ABO3 oxide perovskites containing elements from both the metalorganic source and a traditional effusion cell.

  9. Advances in functional X-ray imaging techniques and contrast agents

    PubMed Central

    Chen, Hongyu; Rogalski, Melissa M.

    2012-01-01

    X-rays have been used for non-invasive high-resolution imaging of thick biological specimens since their discovery in 1895. They are widely used for structural imaging of bone, metal implants, and cavities in soft tissue. Recently, a number of new contrast methodologies have emerged which are expanding X-ray’s biomedical applications to functional as well as structural imaging. These techniques are promising to dramatically improve our ability to study in situ biochemistry and disease pathology. In this review, we discuss how X-ray absorption, X-ray fluorescence, and X-ray excited optical luminescence can be used for physiological, elemental, and molecular imaging of vasculature, tumours, pharmaceutical distribution, and the surface of implants. Imaging of endogenous elements, exogenous labels, and analytes detected with optical indicators will be discussed. PMID:22962667

  10. Testing the limits of sensitivity in a solid-state structural investigation by combined X-ray powder diffraction, solid-state NMR, and molecular modelling.

    PubMed

    Filip, Xenia; Borodi, Gheorghe; Filip, Claudiu

    2011-10-28

    A solid state structural investigation of ethoxzolamide is performed on microcrystalline powder by using a multi-technique approach that combines X-ray powder diffraction (XRPD) data analysis based on direct space methods with information from (13)C((15)N) solid-state Nuclear Magnetic Resonance (SS-NMR) and molecular modeling. Quantum chemical computations of the crystal were employed for geometry optimization and chemical shift calculations based on the Gauge Including Projector Augmented-Wave (GIPAW) method, whereas a systematic search in the conformational space was performed on the isolated molecule using a molecular mechanics (MM) approach. The applied methodology proved useful for: (i) removing ambiguities in the XRPD crystal structure determination process and further refining the derived structure solutions, and (ii) getting important insights into the relationship between the complex network of non-covalent interactions and the induced supra-molecular architectures/crystal packing patterns. It was found that ethoxzolamide provides an ideal case study for testing the accuracy with which this methodology allows to distinguish between various structural features emerging from the analysis of the powder diffraction data. This journal is © the Owner Societies 2011

  11. Low-temperature adsorption of H2S on Ni(001) studied by near-edge- and surface-extended-x-ray-absorption fine structure

    NASA Astrophysics Data System (ADS)

    McGrath, R.; MacDowell, A. A.; Hashizume, T.; Sette, F.; Citrin, P. H.

    1989-11-01

    The adsorption of H2S on Ni(001) has been studied with surface-extended x-ray-absorption fine structure and near-edge x-ray-absorption fine structure (NEXAFS) using the AT&T Bell Laboratories X15B beamline at the National Synchrotron Light Source. At 95 K and full saturation coverage, ~0.45 monolayer (ML) of S atoms in fourfold-hollow sites are produced, characteristic of room-temperature adsorption, accompanied by ~0.05 ML of oriented molecular H2S. Both these atomic and molecular chemisorbed species are buried under ~0.9 ML of disordered physisorbed H2S. No evidence for HS is found. Above 190 K the two molecular H2S phases desorb, leaving only dissociated S. These findings differ from previously reported interpretations of data obtained with high-resolution electron-energy-loss spectroscopy. They also exemplify the utility of NEXAFS for identifying and quantifying atomic and molecular surface species even when their difference involves only H and the two species coexist.

  12. Thin film growth studies using time-resolved x-ray scattering

    NASA Astrophysics Data System (ADS)

    Kowarik, Stefan

    2017-02-01

    Thin-film growth is important for novel functional materials and new generations of devices. The non-equilibrium growth physics involved is very challenging, because the energy landscape for atomic scale processes is determined by many parameters, such as the diffusion and Ehrlich-Schwoebel barriers. We review the in situ real-time techniques of x-ray diffraction (XRD), x-ray growth oscillations and diffuse x-ray scattering (GISAXS) for the determination of structure and morphology on length scales from Å to µm. We give examples of time resolved growth experiments mainly from molecular thin film growth, but also highlight growth of inorganic materials using molecular beam epitaxy (MBE) and electrochemical deposition from liquids. We discuss how scaling parameters of rate equation models and fundamental energy barriers in kinetic Monte Carlo methods can be determined from fits of the real-time x-ray data.

  13. Thin film growth studies using time-resolved x-ray scattering.

    PubMed

    Kowarik, Stefan

    2017-02-01

    Thin-film growth is important for novel functional materials and new generations of devices. The non-equilibrium growth physics involved is very challenging, because the energy landscape for atomic scale processes is determined by many parameters, such as the diffusion and Ehrlich-Schwoebel barriers. We review the in situ real-time techniques of x-ray diffraction (XRD), x-ray growth oscillations and diffuse x-ray scattering (GISAXS) for the determination of structure and morphology on length scales from Å to µm. We give examples of time resolved growth experiments mainly from molecular thin film growth, but also highlight growth of inorganic materials using molecular beam epitaxy (MBE) and electrochemical deposition from liquids. We discuss how scaling parameters of rate equation models and fundamental energy barriers in kinetic Monte Carlo methods can be determined from fits of the real-time x-ray data.

  14. Electronic structure of Cr doped Fe3O4 thin films by X-ray absorption near-edge structure spectroscopy

    NASA Astrophysics Data System (ADS)

    Chen, Chi-Liang; Dong, Chung-Li; Asokan, Kandasami; Chern, G.; Chang, C. L.

    2018-04-01

    Present study reports the electronic structures of Cr doped Fe3O4 (Fe3-xCrxO4 (0 ≤ x ≤ 3) grown on MgO (100) substrates in the form of thin films fabricated by a plasma-oxygen assisted Molecular Beam Epitaxy (MBE). X-ray absorption near-edge structure (XANES) spectra at Cr & Fe L-, and O K-edges were used to understand the electronic structure: changes in the bonding nature, valence states, and site occupancies. Cr doping in Fe3O4 results in the change of charge transfer, crystal structure, and selective occupation of ions in octahedral and tetrahedral sites. Such change modifies the electrical and magnetic properties due to the covalency of Cr ions. The physical and chemical properties of ferrites are strongly dependent on the lattice site, ion size of dopant, and magnetic nature present at different structural symmetry of the spinel structure.

  15. Precision mechanical structure of an ultra-high-resolution spectrometer for inelastic X-ray scattering instrument

    DOEpatents

    Shu, Deming; Shvydko, Yuri; Stoupin, Stanislav A.; Khachatryan, Ruben; Goetze, Kurt A.; Roberts, Timothy

    2015-04-14

    A method and an ultrahigh-resolution spectrometer including a precision mechanical structure for positioning inelastic X-ray scattering optics are provided. The spectrometer includes an X-ray monochromator and an X-ray analyzer, each including X-ray optics of a collimating (C) crystal, a pair of dispersing (D) element crystals, anomalous transmission filter (F) and a wavelength (W) selector crystal. A respective precision mechanical structure is provided with the X-ray monochromator and the X-ray analyzer. The precision mechanical structure includes a base plate, such as an aluminum base plate; positioning stages for D-crystal alignment; positioning stages with an incline sensor for C/F/W-crystal alignment, and the positioning stages including flexure-based high-stiffness structure.

  16. Experimental investigation of a HOPG crystal fan for x-ray fluorescence molecular imaging

    NASA Astrophysics Data System (ADS)

    Rosentreter, Tanja; Müller, Bernhard; Schlattl, Helmut; Hoeschen, Christoph

    2017-03-01

    Imaging x-ray fluorescence generally generates a conflict between the best image quality or highest sensitivity and lowest possible radiation dose. Consequently many experimental studies investigating the feasibility of this molecular imaging method, deal with either monochromatic x-ray sources that are not practical in clinical environment or accept high x-ray doses in order to maintain the advantage of high sensitivity and producing high quality images. In this work we present a x-ray fluorescence imaging setup using a HOPG crystal fan construction consisting of a Bragg reflecting analyzer array together with a scatter reducing radial collimator. This method allows for the use of polychromatic x-ray tubes that are in general easily accessible in contrast to monochromatic x-ray sources such as synchrotron facilities. Moreover this energy-selecting device minimizes the amount of Compton scattered photons while simultaneously increasing the fluorescence signal yield, thus significantly reducing the signal to noise ratio. The aim is to show the feasibility of this approach by measuring the Bragg reflected Kα fluorescence signal of an object containing an iodine solution using a large area detector with moderate energy resolution. Contemplating the anisotropic energy distribution of background scattered x-rays we compare the detection sensitivity, applying two different detector angular configurations. Our results show that even for large area detectors with limited energy resolution, iodine concentrations of 0.12 % can be detected. However, the potentially large scan times and therefore high radiation dose need to be decreased in further investigations.

  17. Synchrotron Powder X-ray Diffraction Study of the Structure and Dehydration Behavior of Sepiolite

    NASA Astrophysics Data System (ADS)

    Post, J. E.; Bish, D. L.; Heaney, P. J.

    2006-05-01

    Sepiolite is a hydrous Mg-silicate clay mineral with fibrous morphology that typically occurs as fine-grained, poorly crystalline masses. It occurs in a wide variety of geological environments and has been mined for centuries because of its many uses, e.g. in the pharmaceutical, fertilizer, and pesticide industries. Its versatile functionality derives from the large surface area and microporosity that are characteristic of the material. In recent years, sepiolite has received considerable attention with regard to the adsorption of organics, for use as a support for catalysts, as a molecular sieve, and as an inorganic membrane for ultrafiltration. Because of its fine-grained and poorly crystalline nature, it has not been possible to study sepiolite's crystal structure using single-crystal X-ray diffraction methods, and consequently many details of the structure are still not well known. In this study, Rietveld refinements using synchrotron powder X-ray diffraction data were used to investigate the crystal structure and dehydration behavior of sepiolite from Durango, Mexico. The room- temperature (RT) sepiolite structure in air compares well with previous models but reveals an additional zeolitic water site. The RT structure under vacuum retained only ~1/8 of the zeolitic water and the volume decreased 1.3%. Real-time, temperature-resolved synchrotron powder X-ray diffraction data and Rietveld refinements were used to investigate the behavior of the sepiolite structure from 300 to 925 K. Rietveld refinements revealed that most of the zeolitic water is lost by ~390 K, accompanied by a decrease in the a and c unit-cell parameters. Above ~600 K the sepiolite structure folds as one-half of the crystallographically bound water is lost. Rietveld refinements of the "anhydrous" sepiolite structure reveal that, in general, unit-cell parameters a, b, â and volume steadily decrease with increasing temperature; there is an obvious change in slope at ~820 K suggesting a phase

  18. X-ray crystallography

    NASA Technical Reports Server (NTRS)

    2001-01-01

    X-rays diffracted from a well-ordered protein crystal create sharp patterns of scattered light on film. A computer can use these patterns to generate a model of a protein molecule. To analyze the selected crystal, an X-ray crystallographer shines X-rays through the crystal. Unlike a single dental X-ray, which produces a shadow image of a tooth, these X-rays have to be taken many times from different angles to produce a pattern from the scattered light, a map of the intensity of the X-rays after they diffract through the crystal. The X-rays bounce off the electron clouds that form the outer structure of each atom. A flawed crystal will yield a blurry pattern; a well-ordered protein crystal yields a series of sharp diffraction patterns. From these patterns, researchers build an electron density map. With powerful computers and a lot of calculations, scientists can use the electron density patterns to determine the structure of the protein and make a computer-generated model of the structure. The models let researchers improve their understanding of how the protein functions. They also allow scientists to look for receptor sites and active areas that control a protein's function and role in the progress of diseases. From there, pharmaceutical researchers can design molecules that fit the active site, much like a key and lock, so that the protein is locked without affecting the rest of the body. This is called structure-based drug design.

  19. Development of a hybrid molecular beam epitaxy deposition system for in situ surface x-ray studies

    DOE PAGES

    Andersen, Tassie K.; Cook, Seyoung; Benda, Erika; ...

    2018-03-08

    A portable metalorganic gas delivery system designed and constructed to interface with an existing molecular beam epitaxy chamber at beamline 33-ID-E of the Advanced Photon Source is described. This system offers the ability to perform in situ X-ray measurements of complex oxide growth via hybrid molecular beam epitaxy. The performance of the hybrid molecular beam epitaxy system while delivering metalorganic source materials is described. In conclusion, the high-energy X-ray scattering capabilities of the hybrid molecular beam epitaxy system are demonstrated both on oxide films grown solely from the metalorganic source and ABO 3 oxide perovskites containing elements from both themore » metalorganic source and a traditional effusion cell.« less

  20. Development of a hybrid molecular beam epitaxy deposition system for in situ surface x-ray studies

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Andersen, Tassie K.; Cook, Seyoung; Benda, Erika

    A portable metalorganic gas delivery system designed and constructed to interface with an existing molecular beam epitaxy chamber at beamline 33-ID-E of the Advanced Photon Source is described. This system offers the ability to perform in situ X-ray measurements of complex oxide growth via hybrid molecular beam epitaxy. The performance of the hybrid molecular beam epitaxy system while delivering metalorganic source materials is described. In conclusion, the high-energy X-ray scattering capabilities of the hybrid molecular beam epitaxy system are demonstrated both on oxide films grown solely from the metalorganic source and ABO 3 oxide perovskites containing elements from both themore » metalorganic source and a traditional effusion cell.« less

  1. X-ray Crystallographic Structure of Thermophilic Rhodopsin

    PubMed Central

    Tsukamoto, Takashi; Mizutani, Kenji; Hasegawa, Taisuke; Takahashi, Megumi; Honda, Naoya; Hashimoto, Naoki; Shimono, Kazumi; Yamashita, Keitaro; Yamamoto, Masaki; Miyauchi, Seiji; Takagi, Shin; Hayashi, Shigehiko; Murata, Takeshi; Sudo, Yuki

    2016-01-01

    Thermophilic rhodopsin (TR) is a photoreceptor protein with an extremely high thermal stability and the first characterized light-driven electrogenic proton pump derived from the extreme thermophile Thermus thermophilus JL-18. In this study, we confirmed its high thermal stability compared with other microbial rhodopsins and also report the potential availability of TR for optogenetics as a light-induced neural silencer. The x-ray crystal structure of TR revealed that its overall structure is quite similar to that of xanthorhodopsin, including the presence of a putative binding site for a carotenoid antenna; but several distinct structural characteristics of TR, including a decreased surface charge and a larger number of hydrophobic residues and aromatic-aromatic interactions, were also clarified. Based on the crystal structure, the structural changes of TR upon thermal stimulation were investigated by molecular dynamics simulations. The simulations revealed the presence of a thermally induced structural substate in which an increase of hydrophobic interactions in the extracellular domain, the movement of extracellular domains, the formation of a hydrogen bond, and the tilting of transmembrane helices were observed. From the computational and mutational analysis, we propose that an extracellular LPGG motif between helices F and G plays an important role in the thermal stability, acting as a “thermal sensor.” These findings will be valuable for understanding retinal proteins with regard to high protein stability and high optogenetic performance. PMID:27129243

  2. Ultrafast isomerization initiated by X-ray core ionization

    NASA Astrophysics Data System (ADS)

    Liekhus-Schmaltz, Chelsea E.; Tenney, Ian; Osipov, Timur; Sanchez-Gonzalez, Alvaro; Berrah, Nora; Boll, Rebecca; Bomme, Cedric; Bostedt, Christoph; Bozek, John D.; Carron, Sebastian; Coffee, Ryan; Devin, Julien; Erk, Benjamin; Ferguson, Ken R.; Field, Robert W.; Foucar, Lutz; Frasinski, Leszek J.; Glownia, James M.; Gühr, Markus; Kamalov, Andrei; Krzywinski, Jacek; Li, Heng; Marangos, Jonathan P.; Martinez, Todd J.; McFarland, Brian K.; Miyabe, Shungo; Murphy, Brendan; Natan, Adi; Rolles, Daniel; Rudenko, Artem; Siano, Marco; Simpson, Emma R.; Spector, Limor; Swiggers, Michele; Walke, Daniel; Wang, Song; Weber, Thorsten; Bucksbaum, Philip H.; Petrovic, Vladimir S.

    2015-09-01

    Rapid proton migration is a key process in hydrocarbon photochemistry. Charge migration and subsequent proton motion can mitigate radiation damage when heavier atoms absorb X-rays. If rapid enough, this can improve the fidelity of diffract-before-destroy measurements of biomolecular structure at X-ray-free electron lasers. Here we study X-ray-initiated isomerization of acetylene, a model for proton dynamics in hydrocarbons. Our time-resolved measurements capture the transient motion of protons following X-ray ionization of carbon K-shell electrons. We Coulomb-explode the molecule with a second precisely delayed X-ray pulse and then record all the fragment momenta. These snapshots at different delays are combined into a `molecular movie' of the evolving molecule, which shows substantial proton redistribution within the first 12 fs. We conclude that significant proton motion occurs on a timescale comparable to the Auger relaxation that refills the K-shell vacancy.

  3. Nano-structuring of multi-layer material by single x-ray vortex pulse with femtosecond duration

    NASA Astrophysics Data System (ADS)

    Kohmura, Yoshiki; Zhakhovsky, Vasily; Takei, Dai; Suzuki, Yoshio; Takeuchi, Akihisa; Inoue, Ichiro; Inubushi, Yuichi; Inogamov, Nail; Ishikawa, Tetsuya; Yabashi, Makina

    2018-03-01

    A narrow zero-intensity spot arising from an x-ray vortex has huge potential for future applications such as nanoscopy and nanofabrication. We here present an X-ray Free Electron Laser (XFEL) experiment with a focused vortex wavefront which generated high aspect ratio nanoneedles on a Cr/Au multi-layer (ML) specimen. A sharp needle with a typical width and height of 310 and 600 nm was formed with a high occurrence rate at the center of a 7.71 keV x-ray vortex on this ML specimen, respectively. The observed width exceeds the diffraction limit, and the smallest structures ever reported using an intense-XFEL ablation were fabricated. We found that the elemental composition of the nanoneedles shows a significant difference from that of the unaffected area of Cr/Au ML. All these results are well explained by the molecular dynamics simulations, leading to the elucidation of the needle formation mechanism on an ultra-fast timescale.

  4. X-ray spectra and electron structure of A15 compounds of transition metals

    NASA Astrophysics Data System (ADS)

    Kurmaev, E. Z.; Iarmoshenko, Iu. M.

    1988-01-01

    Results of an X-ray emission spectroscopy study of the electron structure of A15 compounds are reported. In particular, attention is given to the X-ray spectra of A15 compounds of the A3B type with transition and nontransition elements, effect of alloying on the formation of the electron structure of ternary phases, and effect of atomic ordering in the X-ray spectra of A15 compounds with changes in heat treament and concentration. The X-ray spectra of A15 compounds irradiated by fast neutrons are also examined.

  5. X-ray structure investigation of some substituted indoles, and the x-ray crystal of 1,1'-bishomocubane

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Quarles, William G.

    1970-05-01

    The crystal structures of 5-methoxytryptamine, melatonin, and the p-bromobenzoate of 1,1'-bishomocubane have been solved by x-ray diffraction methods. A computer program for the trial and error solution of crystal structures is also described here.

  6. X-ray and IR Surveys of the Orion Molecular Clouds and the Cepheus OB3b Cluster

    NASA Astrophysics Data System (ADS)

    Megeath, S. Thomas; Wolk, Scott J.; Pillitteri, Ignazio; Allen, Tom

    2014-08-01

    X-ray and IR surveys of molecular clouds between 400 and 700 pc provide complementary means to map the spatial distribution of young low mass stars associated with the clouds. We overview an XMM survey of the Orion Molecular Clouds, at a distance of 400 pc. By using the fraction of X-ray sources with disks as a proxy for age, this survey has revealed three older clusters rich in diskless X-ray sources. Two are smaller clusters found at the northern and southern edges of the Orion A molecular cloud. The third cluster surrounds the O-star Iota Ori (the point of Orion's sword) and is in the foreground to the Orion molecular cloud. In addition, we present a Chandra and Spitzer survey of the Cep OB3b cluster at 700 pc. These data show a spatially variable disk fraction indicative of age variations within the cluster. We discuss the implication of these results for understanding the spread of ages in young clusters and the star formation histories of molecular clouds.

  7. A structural study of bone changes in knee osteoarthritis by synchrotron-based X-ray fluorescence and X-ray absorption spectroscopy techniques

    NASA Astrophysics Data System (ADS)

    Sindhupakorn, Bura; Thienpratharn, Suwittaya; Kidkhunthod, Pinit

    2017-10-01

    Osteoarthritis (OA) is characterized by degeneration of articular cartilage and thickening of subchondral bone. The present study investigated the changing of biochemical components of cartilage and bone compared between normal and OA people. Using Synchrotron-based X-ray fluorescence (SR-XRF) and X-ray absorption spectroscopy (XAS) techniquesincluding X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) were employed for the bone changes in kneeosteoarthritisstudies. The bone samples were collected from various osteoarthritis patients with both male and female in the ages range between 20 and 74 years old. SR-XRF results excited at 4240 eV for Ca elements show a majority three main groups, based on their XRF intensities, 20-36 years, 40-60 years and over 70 years, respectively. By employing XAS techniques, XANES features can be used to clearly explain in term of electronic transitions occurring in bone samples which are affected from osteoarthritis symptoms. Moreover, a structural change around Ca ions in bone samples is obviously obtained by EXAFS results indicating an increase of Ca-amorphous phase when the ages increase.

  8. Probing interfacial characteristics of rubrene/pentacene and pentacene/rubrene bilayers with soft X-ray spectroscopy.

    PubMed

    Seo, J H; Pedersen, T M; Chang, G S; Moewes, A; Yoo, K-H; Cho, S J; Whang, C N

    2007-08-16

    The electronic structure of rubrene/pentacene and pentacene/rubrene bilayers has been investigated using soft X-ray absorption spectroscopy, resonant X-ray emission spectroscopy, and density-functional theory calculations. X-ray absorption and emission measurements reveal that it has been possible to alter the lowest unoccupied and the highest occupied molecular orbital states of rubrene in rubrene/pentacene bilayer. In the reverse case, one gets p* molecular orbital states originating from the pentacene layer. Resonant X-ray emission spectra suggest a reduction in the hole-transition probabilities for the pentacene/rubrene bilayer in comparison to reference pentacene layer. For the rubrenepentacene structure, the hole-transition probability shows an increase in comparison to the rubrene reference. We also determined the energy level alignment of the pentacene-rubrene interface by using X-ray and ultraviolet photoelectron spectroscopy. From these comparisons, it is found that the electronic structure of the pentacene-rubrene interface has a strong dependence on interface characteristics which depends on the order of the layers used.

  9. Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering.

    PubMed

    Wall, Michael E

    2018-03-01

    Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structure to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.

  10. The structure of aqueous sodium hydroxide solutions: a combined solution x-ray diffraction and simulation study.

    PubMed

    Megyes, Tünde; Bálint, Szabolcs; Grósz, Tamás; Radnai, Tamás; Bakó, Imre; Sipos, Pál

    2008-01-28

    To determine the structure of aqueous sodium hydroxide solutions, results obtained from x-ray diffraction and computer simulation (molecular dynamics and Car-Parrinello) have been compared. The capabilities and limitations of the methods in describing the solution structure are discussed. For the solutions studied, diffraction methods were found to perform very well in describing the hydration spheres of the sodium ion and yield structural information on the anion's hydration structure. Classical molecular dynamics simulations were not able to correctly describe the bulk structure of these solutions. However, Car-Parrinello simulation proved to be a suitable tool in the detailed interpretation of the hydration sphere of ions and bulk structure of solutions. The results of Car-Parrinello simulations were compared with the findings of diffraction experiments.

  11. The continuous and discrete molecular orbital x-ray bands from Xe(q+) (12≤q≤29) +Zn collisions.

    PubMed

    Guo, Yipan; Yang, Zhihu; Hu, Bitao; Wang, Xiangli; Song, Zhangyong; Xu, Qiumei; Zhang, Boli; Chen, Jing; Yang, Bian; Yang, Jie

    2016-07-29

    In this paper, the x-ray emissions are measured by the interaction of 1500-3500 keV Xe(q+) (q = 12, 15, 17, 19, 21, 23, 26 and 29) ions with Zn target. When q < 29, we observe Ll, Lα, Lβ1, Lβ2 and Lγ characteristic x-rays from Xe(q+) ions and a broad M-shell molecular orbital (MO) x-ray band from the transient quasi-molecular levels. It is found that their yields quickly increase with different rates as the incident energy increases. Besides, the widths of the broad MO x-ray bands are about 0.9-1.32 keV over the energy range studied and are proportional to v(1/2) (v = projectile velocity). Most remarkably, when the projectile charge state is 29, the broad x-ray band separates into several narrow discrete spectra, which was never observed before in this field.

  12. Selenium single-wavelength anomalous diffraction de novo phasing using an X-ray-free electron laser

    DOE PAGES

    Hunter, Mark S.; Yoon, Chun Hong; DeMirci, Hasan; ...

    2016-11-04

    Structural information about biological macromolecules near the atomic scale provides important insight into the functions of these molecules. To date, X-ray crystallography has been the predominant method used for macromolecular structure determination. However, challenges exist when solving structures with X-rays, including the phase problem and radiation damage. X-ray-free electron lasers (X-ray FELs) have enabled collection of diffraction information before the onset of radiation damage, yet the majority of structures solved at X-ray FELs have been phased using external information via molecular replacement. De novo phasing at X-ray FELs has proven challenging due in part to per-pulse variations in intensity andmore » wavelength. Here we report the solution of a selenobiotinyl-streptavidin structure using phases obtained by the anomalous diffraction of selenium measured at a single wavelength (Se-SAD) at the Linac Coherent Light Source. Finally, our results demonstrate Se-SAD, routinely employed at synchrotrons for novel structure determination, is now possible at X-ray FELs.« less

  13. Structural Significance of Lipid Diversity as Studied by Small Angle Neutron and X-ray Scattering

    DOE PAGES

    Kučerka, Norbert; Heberle, Frederick A.; Pan, Jianjun; ...

    2015-09-21

    In this paper, we review recent developments in the rapidly growing field of membrane biophysics, with a focus on the structural properties of single lipid bilayers determined by different scattering techniques, namely neutron and X-ray scattering. The need for accurate lipid structural properties is emphasized by the sometimes conflicting results found in the literature, even in the case of the most studied lipid bilayers. Increasingly, accurate and detailed structural models require more experimental data, such as those from contrast varied neutron scattering and X-ray scattering experiments that are jointly refined with molecular dynamics simulations. This experimental and computational approach producesmore » robust bilayer structural parameters that enable insights, for example, into the interplay between collective membrane properties and its components (e.g., hydrocarbon chain length and unsaturation, and lipid headgroup composition). Finally, from model studies such as these, one is better able to appreciate how a real biological membrane can be tuned by balancing the contributions from the lipid’s different moieties (e.g., acyl chains, headgroups, backbones, etc.).« less

  14. Intact Imaging of Human Heart Structure Using X-ray Phase-Contrast Tomography.

    PubMed

    Kaneko, Yukihiro; Shinohara, Gen; Hoshino, Masato; Morishita, Hiroyuki; Morita, Kiyozo; Oshima, Yoshihiro; Takahashi, Masashi; Yagi, Naoto; Okita, Yutaka; Tsukube, Takuro

    2017-02-01

    Structural examination of human heart specimens at the microscopic level is a prerequisite for understanding congenital heart diseases. It is desirable not to destroy or alter the properties of such specimens because of their scarcity. However, many of the currently available imaging techniques either destroy the specimen through sectioning or alter the chemical and mechanical properties of the specimen through staining and contrast agent injection. As a result, subsequent studies may not be possible. X-ray phase-contrast tomography is an imaging modality for biological soft tissues that does not destroy or alter the properties of the specimen. The feasibility of X-ray phase-contrast tomography for the structural examination of heart specimens was tested using infantile and fetal heart specimens without congenital diseases. X-ray phase-contrast tomography was carried out at the SPring-8 synchrotron radiation facility using the Talbot grating interferometer at the bending magnet beamline BL20B2 to visualize the structure of five non-pretreated whole heart specimens obtained by autopsy. High-resolution, three-dimensional images were obtained for all specimens. The images clearly showed the myocardial structure, coronary vessels, and conduction bundle. X-ray phase-contrast tomography allows high-resolution, three-dimensional imaging of human heart specimens. Intact imaging using X-ray phase-contrast tomography can contribute to further structural investigation of heart specimens with congenital heart diseases.

  15. Direct detection of x-rays for protein crystallography employing a thick, large area CCD

    DOEpatents

    Atac, Muzaffer; McKay, Timothy

    1999-01-01

    An apparatus and method for directly determining the crystalline structure of a protein crystal. The crystal is irradiated by a finely collimated x-ray beam. The interaction of the x-ray beam with the crystal produces scattered x-rays. These scattered x-rays are detected by means of a large area, thick CCD which is capable of measuring a significant number of scattered x-rays which impact its surface. The CCD is capable of detecting the position of impact of the scattered x-ray on the surface of the CCD and the quantity of scattered x-rays which impact the same cell or pixel. This data is then processed in real-time and the processed data is outputted to produce a image of the structure of the crystal. If this crystal is a protein the molecular structure of the protein can be determined from the data received.

  16. Design of novel HIV-1 protease inhibitors incorporating isophthalamide-derived P2-P3 ligands: Synthesis, biological evaluation and X-ray structural studies of inhibitor-HIV-1 protease complex

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ghosh, Arun K.; Brindisi, Margherita; Nyalapatla, Prasanth R.

    Based upon molecular insights from the X-ray structures of inhibitor-bound HIV-1 protease complexes, we have designed a series of isophthalamide-derived inhibitors incorporating substituted pyrrolidines, piperidines and thiazolidines as P2-P3 ligands for specific interactions in the S2-S3 extended site. Compound 4b has shown an enzyme Ki of 0.025 nM and antiviral IC50 of 69 nM. An X-ray crystal structure of inhibitor 4b-HIV-1 protease complex was determined at 1.33 Å resolution. We have also determined X-ray structure of 3b-bound HIV-1 protease at 1.27 Å resolution. These structures revealed important molecular insight into the inhibitor–HIV-1 protease interactions in the active site.

  17. X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

    NASA Astrophysics Data System (ADS)

    Zhou, X. Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A.; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W.; Suino-Powell, Kelly M.; Boutet, Sébastien; Williams, Garth J.; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N.; Spence, John C. H.; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C.; Cherezov, Vadim; Melcher, Karsten; Xu, H. Eric

    2016-04-01

    Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.

  18. X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex.

    PubMed

    Zhou, X Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W; Suino-Powell, Kelly M; Boutet, Sébastien; Williams, Garth J; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N; Spence, John C H; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C; Cherezov, Vadim; Melcher, Karsten; Xu, H Eric

    2016-04-12

    Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.

  19. X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

    PubMed Central

    Zhou, X. Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A.; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W.; Suino-Powell, Kelly M.; Boutet, Sébastien; Williams, Garth J.; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N.; Spence, John C.H.; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C.; Cherezov, Vadim; Melcher, Karsten; Xu, H. Eric

    2016-01-01

    Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes. PMID:27070998

  20. Irradiation with X-rays phase-advances the molecular clockwork in liver, adrenal gland and pancreas.

    PubMed

    Müller, Mareike Hildegard; Rödel, Franz; Rüb, Udo; Korf, Horst-Werner

    2015-02-01

    The circadian clock of man and mammals shows a hierarchic organization. The master clock, located in the suprachiasmatic nuclei (SCN), controls peripheral oscillators distributed throughout the body. Rhythm generation depends on molecular clockworks based on transcriptional/translational interaction of clock genes. Numerous studies have shown that the clockwork in peripheral oscillators is capable to maintain circadian rhythms for several cycles in vitro, i.e. in the absence of signals from the SCN. The aim of the present study is to analyze the effects of irradiation with X-rays on the clockwork of liver, adrenal and pancreas. To this end organotypic slice cultures of liver (OLSC) and organotypic explant cultures of adrenal glands (OAEC) and pancreas (OPEC) were prepared from transgenic mPer2(luc) mice which express luciferase under the control of the promoter of an important clock gene, Per2, and allow to study the dynamics of the molecular clockwork by bioluminometry. The preparations were cultured in a membrane-based liquid-air interface culturing system and irradiated with X-rays at doses of 10 Gy and 50 Gy or left untreated. Bioluminometric real-time recordings show a stable oscillation of all OLSC, OAEC and OPEC for up to 12 days in vitro. Oscillations persist after irradiation with X-rays. However, a dose of 50 Gy caused a phase advance in the rhythm of the OLSC by 5 h, in the OPEC by 7 h and in the OAEC by 6 h. Our study shows that X-rays affect the molecular clockwork in liver, pancreas and adrenal leading to phase advances. Our results confirm and extend previous studies showing a phase-advancing effect of X-rays at the level of the whole animal and single cells.

  1. The solvation structure of Mg ions in dichloro complex solutions from first-principles molecular dynamics and simulated X-ray absorption spectra.

    PubMed

    Wan, Liwen F; Prendergast, David

    2014-10-15

    The knowledge of Mg solvation structure in the electrolyte is requisite to understand the transport behavior of Mg ions and their dissolution/deposition mechanism at electrolyte/electrode interfaces. In the first established rechargeable Mg-ion battery system [D. Aurbach et al. Nature 2000, 407, 724], the electrolyte is of the dichloro complex (DCC) solution family, Mg(AlCl2BuEt)2/THF, resulting from the reaction of Bu2Mg and EtAlCl2 with a molar ratio of 1:2. There is disagreement in the literature regarding the exact solvation structure of Mg ions in such solutions, i.e., whether Mg(2+) is tetra- or hexacoordinated by a combination of Cl(-) and THF. In this work, theoretical insight into the solvation complexes present is provided based on first-principles molecular dynamics simulations (FPMD). Both Mg monomer and dimer structures are considered in both neutral and positively charged states. We found that, at room temperature, the Mg(2+) ion tends to be tetracoordinated in the THF solution phase instead of hexacoordinated, which is the predominant solid-phase coordination. Simulating the X-ray absorption spectra (XAS) at the Mg K-edge by sampling our FPMD trajectories, our predicted solvation structure can be readily compared with experimental measurements. It is found that when changing from tetra- to hexacoordination, the onset of X-ray absorption should exhibit at least a 1 eV blue shift. We propose that this energy shift can be used to monitor changes in the Mg solvation sphere as it migrates through the electrolyte to electrolyte/electrode interfaces and to elucidate the mechanism of Mg dissolution/deposition.

  2. Serial femtosecond X-ray diffraction of enveloped virus microcrystals

    DOE PAGES

    Lawrence, Robert M.; Conrad, Chelsie E.; Zatsepin, Nadia A.; ...

    2015-08-20

    Serial femtosecond crystallography (SFX) using X-ray free-electron lasers has produced high-resolution, room temperature, time-resolved protein structures. We report preliminary SFX of Sindbis virus, an enveloped icosahedral RNA virus with ~700 Å diameter. Microcrystals delivered in viscous agarose medium diffracted to ~40 Å resolution. Small-angle diffuse X-ray scattering overlaid Bragg peaks and analysis suggests this results from molecular transforms of individual particles. Viral proteins undergo structural changes during entry and infection, which could, in principle, be studied with SFX. This is a pertinent step toward determining room temperature structures from virus microcrystals that may enable time-resolved studies of enveloped viruses.

  3. Attosecond time-energy structure of X-ray free-electron laser pulses

    NASA Astrophysics Data System (ADS)

    Hartmann, N.; Hartmann, G.; Heider, R.; Wagner, M. S.; Ilchen, M.; Buck, J.; Lindahl, A. O.; Benko, C.; Grünert, J.; Krzywinski, J.; Liu, J.; Lutman, A. A.; Marinelli, A.; Maxwell, T.; Miahnahri, A. A.; Moeller, S. P.; Planas, M.; Robinson, J.; Kazansky, A. K.; Kabachnik, N. M.; Viefhaus, J.; Feurer, T.; Kienberger, R.; Coffee, R. N.; Helml, W.

    2018-04-01

    The time-energy information of ultrashort X-ray free-electron laser pulses generated by the Linac Coherent Light Source is measured with attosecond resolution via angular streaking of neon 1s photoelectrons. The X-ray pulses promote electrons from the neon core level into an ionization continuum, where they are dressed with the electric field of a circularly polarized infrared laser. This induces characteristic modulations of the resulting photoelectron energy and angular distribution. From these modulations we recover the single-shot attosecond intensity structure and chirp of arbitrary X-ray pulses based on self-amplified spontaneous emission, which have eluded direct measurement so far. We characterize individual attosecond pulses, including their instantaneous frequency, and identify double pulses with well-defined delays and spectral properties, thus paving the way for X-ray pump/X-ray probe attosecond free-electron laser science.

  4. X-Ray Crystallography Reagent

    NASA Technical Reports Server (NTRS)

    Morrison, Dennis R. (Inventor); Mosier, Benjamin (Inventor)

    2003-01-01

    Microcapsules prepared by encapsulating an aqueous solution of a protein, drug or other bioactive substance inside a semi-permeable membrane by are disclosed. The microcapsules are formed by interfacial coacervation under conditions where the shear forces are limited to 0-100 dynes per square centimeter at the interface. By placing the microcapsules in a high osmotic dewatering solution. the protein solution is gradually made saturated and then supersaturated. and the controlled nucleation and crystallization of the protein is achieved. The crystal-filled microcapsules prepared by this method can be conveniently harvested and stored while keeping the encapsulated crystals in essentially pristine condition due to the rugged. protective membrane. Because the membrane components themselves are x-ray transparent, large crystal-containing microcapsules can be individually selected, mounted in x-ray capillary tubes and subjected to high energy x-ray diffraction studies to determine the 3-D smucture of the protein molecules. Certain embodiments of the microcapsules of the invention have composite polymeric outer membranes which are somewhat elastic, water insoluble, permeable only to water, salts, and low molecular weight molecules and are structurally stable in fluid shear forces typically encountered in the human vascular system.

  5. Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wall, Michael E.

    Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structuremore » to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.« less

  6. Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering

    DOE PAGES

    Wall, Michael E.

    2018-01-25

    Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structuremore » to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.« less

  7. Effects of phonon broadening on x-ray near-edge spectra in molecular crystals

    NASA Astrophysics Data System (ADS)

    Vinson, John; Jach, Terrence; Elam, Tim; Denlinger, Jonathon

    2014-03-01

    Calculations of near-edge x-ray spectra are often carried out using the average atomic coordinates from x-ray or neutron scattering experiments or from density functional theory (DFT) energy minimization. This neglects disorder from thermal and zero-point vibrations. Here we look at the nitrogen K-edge of ammonium chloride and ammonium nitrate, comparing Bethe-Salpeter calculations of absorption and fluorescence to experiment. We find that intra-molecular vibrational effects lead to significant, non-uniform broadening of the spectra, and that for some features zero-point motion is the primary source of the observed shape.

  8. X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhou, X. Edward; Gao, Xiang; Barty, Anton

    Here, serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solvedmore » with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.« less

  9. X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

    DOE PAGES

    Zhou, X. Edward; Gao, Xiang; Barty, Anton; ...

    2016-04-12

    Here, serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solvedmore » with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.« less

  10. Enhanced Imaging of Corrosion in Aircraft Structures with Reverse Geometry X-ray(registered tm)

    NASA Technical Reports Server (NTRS)

    Winfree, William P.; Cmar-Mascis, Noreen A.; Parker, F. Raymond

    2000-01-01

    The application of Reverse Geometry X-ray to the detection and characterization of corrosion in aircraft structures is presented. Reverse Geometry X-ray is a unique system that utilizes an electronically scanned x-ray source and a discrete detector for real time radiographic imaging of a structure. The scanned source system has several advantages when compared to conventional radiography. First, the discrete x-ray detector can be miniaturized and easily positioned inside a complex structure (such as an aircraft wing) enabling images of each surface of the structure to be obtained separately. Second, using a measurement configuration with multiple detectors enables the simultaneous acquisition of data from several different perspectives without moving the structure or the measurement system. This provides a means for locating the position of flaws and enhances separation of features at the surface from features inside the structure. Data is presented on aircraft specimens with corrosion in the lap joint. Advanced laminographic imaging techniques utilizing data from multiple detectors are demonstrated to be capable of separating surface features from corrosion in the lap joint and locating the corrosion in multilayer structures. Results of this technique are compared to computed tomography cross sections obtained from a microfocus x-ray tomography system. A method is presented for calibration of the detectors of the Reverse Geometry X-ray system to enable quantification of the corrosion to within 2%.

  11. Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation

    PubMed Central

    Nasedkin, Alexandr; Marcellini, Moreno; Religa, Tomasz L.; Freund, Stefan M.; Menzel, Andreas; Fersht, Alan R.; Jemth, Per; van der Spoel, David; Davidsson, Jan

    2015-01-01

    The folding and unfolding of protein domains is an apparently cooperative process, but transient intermediates have been detected in some cases. Such (un)folding intermediates are challenging to investigate structurally as they are typically not long-lived and their role in the (un)folding reaction has often been questioned. One of the most well studied (un)folding pathways is that of Drosophila melanogaster Engrailed homeodomain (EnHD): this 61-residue protein forms a three helix bundle in the native state and folds via a helical intermediate. Here we used molecular dynamics simulations to derive sample conformations of EnHD in the native, intermediate, and unfolded states and selected the relevant structural clusters by comparing to small/wide angle X-ray scattering data at four different temperatures. The results are corroborated using residual dipolar couplings determined by NMR spectroscopy. Our results agree well with the previously proposed (un)folding pathway. However, they also suggest that the fully unfolded state is present at a low fraction throughout the investigated temperature interval, and that the (un)folding intermediate is highly populated at the thermal midpoint in line with the view that this intermediate can be regarded to be the denatured state under physiological conditions. Further, the combination of ensemble structural techniques with MD allows for determination of structures and populations of multiple interconverting structures in solution. PMID:25946337

  12. Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation.

    PubMed

    Nasedkin, Alexandr; Marcellini, Moreno; Religa, Tomasz L; Freund, Stefan M; Menzel, Andreas; Fersht, Alan R; Jemth, Per; van der Spoel, David; Davidsson, Jan

    2015-01-01

    The folding and unfolding of protein domains is an apparently cooperative process, but transient intermediates have been detected in some cases. Such (un)folding intermediates are challenging to investigate structurally as they are typically not long-lived and their role in the (un)folding reaction has often been questioned. One of the most well studied (un)folding pathways is that of Drosophila melanogaster Engrailed homeodomain (EnHD): this 61-residue protein forms a three helix bundle in the native state and folds via a helical intermediate. Here we used molecular dynamics simulations to derive sample conformations of EnHD in the native, intermediate, and unfolded states and selected the relevant structural clusters by comparing to small/wide angle X-ray scattering data at four different temperatures. The results are corroborated using residual dipolar couplings determined by NMR spectroscopy. Our results agree well with the previously proposed (un)folding pathway. However, they also suggest that the fully unfolded state is present at a low fraction throughout the investigated temperature interval, and that the (un)folding intermediate is highly populated at the thermal midpoint in line with the view that this intermediate can be regarded to be the denatured state under physiological conditions. Further, the combination of ensemble structural techniques with MD allows for determination of structures and populations of multiple interconverting structures in solution.

  13. Near Edge X-Ray Absorption and X-Ray Photoelectron Diffraction Studies of the Structural Environment of Ge-Si Systems

    NASA Astrophysics Data System (ADS)

    Castrucci, P.; Gunnella, R.; Pinto, N.; Bernardini, R.; de Crescenzi, M.; Sacchi, M.

    Near edge X-ray absorption spectroscopy (XAS), X-ray photoelectron diffraction (XPD) and Auger electron diffraction (AED) are powerful techniques for the qualitative study of the structural and electronic properties of several systems. The recent development of a multiple scattering approach to simulating experimental spectra opened a friendly way to the study of structural environments of solids and surfaces. This article reviews recent X-ray absorption experiments using synchrotron radiation which were performed at Ge L edges and core level electron diffraction measurements obtained using a traditional X-ray source from Ge core levels for ultrathin Ge films deposited on silicon substrates. Thermodynamics and surface reconstruction have been found to play a crucial role in the first stages of Ge growth on Si(001) and Si(111) surfaces. Both techniques show the occurrence of intermixing processes even for room-temperature-grown Ge/Si(001) samples and give a straightforward measurement of the overlayer tetragonal distortion. The effects of Sb as a surfactant on the Ge/Si(001) interface have also been investigated. In this case, evidence of layer-by-layer growth of the fully strained Ge overlayer with a reduced intermixing is obtained when one monolayer of Sb is predeposited on the surface.

  14. X-ray Radiative Transfer in Protoplanetary Disks with ProDiMo

    NASA Astrophysics Data System (ADS)

    Rab, Christian; Woitke, Peter; Güdel, Manuel; Min, Michiel; Diana Team

    2013-07-01

    X-ray emission is a common property of YSOs. T Tauri stars show X-ray luminosities up to 10^32 erg/s but also Herbig Ae/Be stars can have moderate X-ray emission in the range of 10^28 to 10^31 erg/s. We want to investigate the impact of X-ray radiation on the thermal and chemical structure of protoplanetary discs around these YSOs. Therefore we have added a new X-ray Radiative Transfer module to the radiation thermo-chemical code ProDiMo (Protoplanetary Disc Modeling) extending the existing implementation of X-ray chemistry implemented by Aresu et al. This new module considers gas and dust opacities (including scattering) and a possible X-ray background field. Further we added a new set of FUV - photoreactions to the X-ray chemistry module of ProDiMo as fast electrons created in X-ray ionisation can produce a significant secondary FUV radiation field by exciting atomic or molecular hydrogen. We discuss the importance of these processes on the thermal and chemical structure of the protoplanetary disc, and present them on the basis of a typical T Tauri disc model. This work is performed in the context of the EU FP7-project DIANA (www.diana-project.com).

  15. The X-ray structure of Centaurus A

    NASA Technical Reports Server (NTRS)

    Feigelson, E. D.; Schreier, E. J.; Delvaille, J. P.; Giacconi, R.; Grindlay, J. E.; Lightman, A. P.

    1981-01-01

    The Einstein X-ray observatory imaging detectors have found X-ray emission associated with several components of the nearby radio galaxy Cen A = NGC 5128: (1) the compact nucleus; (2) an X-ray jet pointed toward the NE radio lobes; (3) the middle NE radio lobe; (4) the disk or dust lane; and (5) diffuse emission extending several arcmin around the nucleus. The intensity of the nucleus changed by a factor of seven over six months. The X-ray jet is considered in terms of thermal, inverse Compton, and synchrotron models. The emission of the NE radio lobe is greater than that expected from inverse Compton or synchrotron processes. Two ridges of emission are found along each edge of the dust lane, within several arcmin of the nucleus. The diffuse X-ray component has a luminosity which is too high to be due to bulge population X-ray sources, but which may be produced by main sequence stars under appropriate circumstances.

  16. Solid state structural investigations of the bis(chalcone) compound with single crystal X-ray crystallography, DFT, gamma-ray spectroscopy and chemical spectroscopy methods

    NASA Astrophysics Data System (ADS)

    Yakalı, Gül; Biçer, Abdullah; Eke, Canel; Cin, Günseli Turgut

    2018-04-01

    A bis(chalcone), (2E,6E)-2,6-bis((E)-3phenylallidene)cyclohexanone, was characterized by 1H NMR, 13C NMR, FTIR, UV-Vis spectroscopy, gamma-ray spectroscopy and single crystal X- ray structural analysis. The optimized molecular structure of the compound is calculated using DFT/B3LYP with 6-31G (d,p) level. The calculated geometrical parameters are in good agreement with the experimental data obtained from our reported X-ray structure. The powder and single crystal compounds were gama-irradiated using clinical electron linear accelerator and 60Co gamma-ray source, respectively. Spectral studies (1H NMR, 13C NMR, FTIR and UV-Vis) of powder chalcone compound were also investigated before and after irradiation. Depending on the irradiation notable changes were observed in spectral features powder sample. Single crystal X-ray diffraction investigation shows that both unirradiated and irradiated single crystal samples crystallizes in a orthorhombic crystal system in the centrosymmetric space group Pbcn and exhibits an C-H..O intramolecular and intermolecular hydrogen bonds. The crystal packing is stabilised by strong intermolecular bifurcate C-H..O hydrogen bonds and π…π stacking interactions. The asymmetric unit of the title compound contains one-half of a molecule. The other half of the molecule is generated with (1-x,y,-3/2-z) symmetry operator. The molecule is almost planar due to having π conjugated system of chalcones. However, irradiated single crystal compound showed significant changes lattice parameters, crystal volume and density. According to results of gamma-ray spectroscopy, radioactive elements of powder compound which are 123Sb(n,g),124Sb,57Fe(g,p),56Mn, 55Mn(g,n), and 54Mn were determined using photoactivation analysis. However, the most intensive gamma-ray energy signals are 124Sb.

  17. Molecular Environment and an X-Ray Spectroscopy of Supernova Remnant Kesteven 78

    NASA Astrophysics Data System (ADS)

    Zhou, Ping; Chen, Yang

    2011-12-01

    We investigate the molecular environment of the Galactic supernova remnant (SNR) Kesteven 78 and perform an XMM-Newton X-ray spectroscopic study for the northeastern edge of the remnant. SNR Kes 78 is found to interact with the molecular clouds (MCs) at a systemic local standard of rest velocity of 81 km s-1. At around this velocity, the SNR appears to contact a long molecular strip in the northeast and a large cloud in the east as revealed in the 13CO line, which may be responsible for the radio brightness peak and the OH maser, respectively. The 12CO-line bright region morphologically matches the eastern bright radio shell in general, and the SNR is consistent in extent with a CO cavity. Broadened 12CO-line profiles discerned in the eastern maser region and the western clumpy molecular arc and the elevated 12CO (J = 2-1)/(J = 1-0) ratios along the SNR boundary may be signatures of shock perturbation in the molecular gas. The SNR-MC association places the SNR at a kinematic distance of 4.8 kpc. The X-rays arising from the northeastern radio shell are emitted by underionized hot (~1.5 keV), low-density (~0.1 cm-3) plasma with solar abundance, and the plasma may be of intercloud origin. The age of the remnant is inferred to be about 6 kyr. The size of the molecular cavity in Kes 78 implies an initial mass around 22 M ⊙ for the progenitor.

  18. Solution x-ray scattering and structure formation in protein dynamics

    NASA Astrophysics Data System (ADS)

    Nasedkin, Alexandr; Davidsson, Jan; Niemi, Antti J.; Peng, Xubiao

    2017-12-01

    We propose a computationally effective approach that builds on Landau mean-field theory in combination with modern nonequilibrium statistical mechanics to model and interpret protein dynamics and structure formation in small- to wide-angle x-ray scattering (S/WAXS) experiments. We develop the methodology by analyzing experimental data in the case of Engrailed homeodomain protein as an example. We demonstrate how to interpret S/WAXS data qualitatively with a good precision and over an extended temperature range. We explain experimental observations in terms of protein phase structure, and we make predictions for future experiments and for how to analyze data at different ambient temperature values. We conclude that the approach we propose has the potential to become a highly accurate, computationally effective, and predictive tool for analyzing S/WAXS data. For this, we compare our results with those obtained previously in an all-atom molecular dynamics simulation.

  19. Structure of Poly(dialkylsiloxane) Melts:  Comparisons of Wide-Angle X-ray Scattering, Molecular Dynamics Simulations, and Integral Equation Theory

    DOE PAGES

    Habenschuss, Anton; Tsige, Mesfin; Curro, John G.; ...

    2007-08-21

    Here, wide-angle X-ray scattering, molecular dynamics (MD) simulations, and integral equation theory are used to study the structure of poly(diethylsiloxane) (PDES), poly(ethylmethylsiloxane) (PEMS), and poly(dimethylsiloxane) (PDMS) melts. The structure functions of PDES, PEMS, and PDMS are similar, but systematic trends in the intermolecular packing are observed. The local intramolecular structure is extracted from the experimental structure functions. The bond distances and bond angles obtained, including the large Si-O-Si angle, are in good agreement with the explicit atom (EA) and united atom (UA) potentials used in the simulations and theory and from other sources. Very good agreement is found between themore » MD simulations using the EA potentials and the experimental scattering results. Good agreement is also found between the polymer reference interaction site model (PRISM theory) and the UA MD simulations. The intermolecular structure is examined experimentally using an appropriately weighted radial distribution function and with theory and simulation using intermolecular site/site pair correlation functions. Finally, experiment, simulation, and theory show systematic increases in the chain/chain packing distances in the siloxanes as the number of sites in the pendant side chains is increased.« less

  20. Observation of femtosecond X-ray interactions with matter using an X-ray–X-ray pump–probe scheme

    PubMed Central

    Inoue, Ichiro; Inubushi, Yuichi; Sato, Takahiro; Tono, Kensuke; Katayama, Tetsuo; Kameshima, Takashi; Ogawa, Kanade; Togashi, Tadashi; Owada, Shigeki; Amemiya, Yoshiyuki; Tanaka, Takashi; Hara, Toru

    2016-01-01

    Resolution in the X-ray structure determination of noncrystalline samples has been limited to several tens of nanometers, because deep X-ray irradiation required for enhanced resolution causes radiation damage to samples. However, theoretical studies predict that the femtosecond (fs) durations of X-ray free-electron laser (XFEL) pulses make it possible to record scattering signals before the initiation of X-ray damage processes; thus, an ultraintense X-ray beam can be used beyond the conventional limit of radiation dose. Here, we verify this scenario by directly observing femtosecond X-ray damage processes in diamond irradiated with extraordinarily intense (∼1019 W/cm2) XFEL pulses. An X-ray pump–probe diffraction scheme was developed in this study; tightly focused double–5-fs XFEL pulses with time separations ranging from sub-fs to 80 fs were used to excite (i.e., pump) the diamond and characterize (i.e., probe) the temporal changes of the crystalline structures through Bragg reflection. It was found that the pump and probe diffraction intensities remain almost constant for shorter time separations of the double pulse, whereas the probe diffraction intensities decreased after 20 fs following pump pulse irradiation due to the X-ray–induced atomic displacement. This result indicates that sub-10-fs XFEL pulses enable conductions of damageless structural determinations and supports the validity of the theoretical predictions of ultraintense X-ray–matter interactions. The X-ray pump–probe scheme demonstrated here would be effective for understanding ultraintense X-ray–matter interactions, which will greatly stimulate advanced XFEL applications, such as atomic structure determination of a single molecule and generation of exotic matters with high energy densities. PMID:26811449

  1. Watching proteins function with picosecond X-ray crystallography and molecular dynamics simulations.

    NASA Astrophysics Data System (ADS)

    Anfinrud, Philip

    2006-03-01

    Time-resolved electron density maps of myoglobin, a ligand-binding heme protein, have been stitched together into movies that unveil with < 2-å spatial resolution and 150-ps time-resolution the correlated protein motions that accompany and/or mediate ligand migration within the hydrophobic interior of a protein. A joint analysis of all-atom molecular dynamics (MD) calculations and picosecond time-resolved X-ray structures provides single-molecule insights into mechanisms of protein function. Ensemble-averaged MD simulations of the L29F mutant of myoglobin following ligand dissociation reproduce the direction, amplitude, and timescales of crystallographically-determined structural changes. This close agreement with experiments at comparable resolution in space and time validates the individual MD trajectories, which identify and structurally characterize a conformational switch that directs dissociated ligands to one of two nearby protein cavities. This unique combination of simulation and experiment unveils functional protein motions and illustrates at an atomic level relationships among protein structure, dynamics, and function. In collaboration with Friedrich Schotte and Gerhard Hummer, NIH.

  2. Hydrogen atoms in protein structures: high-resolution X-ray diffraction structure of the DFPase

    PubMed Central

    2013-01-01

    Background Hydrogen atoms represent about half of the total number of atoms in proteins and are often involved in substrate recognition and catalysis. Unfortunately, X-ray protein crystallography at usual resolution fails to access directly their positioning, mainly because light atoms display weak contributions to diffraction. However, sub-Ångstrom diffraction data, careful modeling and a proper refinement strategy can allow the positioning of a significant part of hydrogen atoms. Results A comprehensive study on the X-ray structure of the diisopropyl-fluorophosphatase (DFPase) was performed, and the hydrogen atoms were modeled, including those of solvent molecules. This model was compared to the available neutron structure of DFPase, and differences in the protein and the active site solvation were noticed. Conclusions A further examination of the DFPase X-ray structure provides substantial evidence about the presence of an activated water molecule that may constitute an interesting piece of information as regard to the enzymatic hydrolysis mechanism. PMID:23915572

  3. Probing multi-scale mechanical damage in connective tissues using X-ray diffraction.

    PubMed

    Bianchi, Fabio; Hofmann, Felix; Smith, Andrew J; Thompson, Mark S

    2016-11-01

    The accumulation of microstructural collagen damage following repetitive loading is linked to painful and debilitating tendon injuries. As a hierarchical, semi-crystalline material, collagen mechanics can be studied using X-ray diffraction. The aim of the study was to describe multi-structural changes in tendon collagen following controlled plastic damage (5% permanent strain). We used small angle X-ray scattering (SAXS) to interrogate the spacing of collagen molecules within a fibril, and wide angle X-ray scattering (WAXS) to measure molecular strains under macroscopic loading. Simultaneous recordings of SAXS and WAXS patterns, together with whole-tissue strain in physiologically hydrated rat-tail tendons were made during increments of in situ tensile loading. Results showed that while tissue level modulus was unchanged, fibril modulus decreased significantly, and molecular modulus significantly increased. Further, analysis of higher order SAXS peaks suggested structural changes in the gap and overlap regions, possibly localising the damage to molecular cross-links. Our results provide new insight into the fundamental damage processes at work in collagenous tissues and point to new directions for their mitigation and repair. This article reports the first in situ loading synchrotron studies on mechanical damage in collagenous tissues. We provide new insight into the nano- and micro-structural mechanisms of damage processes. Pre-damaged tendons showed differential alteration of moduli at macro, micro and nano-scales as measured using X-ray scattering techniques. Detailed analysis of higher order diffraction peaks suggested damage is localised to molecular cross-links. The results are consistent with previous X-ray scattering studies of tendons and also with recent thermal stability studies on damaged material. Detailed understanding of damage mechanisms is essential in the development of new therapies promoting tissue repair. Copyright © 2016 Acta Materialia Inc

  4. X-ray (image)

    MedlinePlus

    X-rays are a form of electromagnetic radiation, just like visible light. Structures that are dense (such as bone) will block most of the x-ray particles, and will appear white. Metal and contrast media ( ...

  5. X-ray structure determination and deuteration of nattokinase.

    PubMed

    Yanagisawa, Yasuhide; Chatake, Toshiyuki; Naito, Sawa; Ohsugi, Tadanori; Yatagai, Chieko; Sumi, Hiroyuki; Kawaguchi, Akio; Chiba-Kamosida, Kaori; Ogawa, Megumi; Adachi, Tatsumi; Morimoto, Yukio

    2013-11-01

    Nattokinase (NK) is a strong fibrinolytic enzyme, which is produced in abundance by Bacillus subtilis natto. Although NK is a member of the subtilisin family, it displays different substrate specificity when compared with other subtilisins. The results of molecular simulations predict that hydrogen arrangements around Ser221 at the active site probably account for the substrate specificity of NK. Therefore, neutron crystallographic analysis should provide valuable information that reveals the enzymatic mechanism of NK. In this report, the X-ray structure of the non-hydrogen form of undeuterated NK was determined, and the preparation of deuterated NK was successfully achieved. The non-hydrogen NK structure was determined at 1.74 Å resolution. The three-dimensional structures of NK and subtilisin E from Bacillus subtilis DB104 are near identical. Deuteration of NK was carried out by cultivating Bacillus subtilis natto in deuterated medium. The D2O resistant strain of Bacillus subtilis natto was obtained by successive cultivation rounds, in which the concentration of D2O in the medium was gradually increased. NK was purified from the culture medium and its activity was confirmed by the fibrin plate method. The results lay the framework for neutron protein crystallography analysis.

  6. X-ray structure determination and deuteration of nattokinase

    PubMed Central

    Yanagisawa, Yasuhide; Chatake, Toshiyuki; Naito, Sawa; Ohsugi, Tadanori; Yatagai, Chieko; Sumi, Hiroyuki; Kawaguchi, Akio; Chiba-Kamosida, Kaori; Ogawa, Megumi; Adachi, Tatsumi; Morimoto, Yukio

    2013-01-01

    Nattokinase (NK) is a strong fibrinolytic enzyme, which is produced in abundance by Bacillus subtilis natto. Although NK is a member of the subtilisin family, it displays different substrate specificity when compared with other subtilisins. The results of molecular simulations predict that hydrogen arrangements around Ser221 at the active site probably account for the substrate specificity of NK. Therefore, neutron crystallographic analysis should provide valuable information that reveals the enzymatic mechanism of NK. In this report, the X-ray structure of the non-hydrogen form of undeuterated NK was determined, and the preparation of deuterated NK was successfully achieved. The non-hydrogen NK structure was determined at 1.74 Å resolution. The three-dimensional structures of NK and subtilisin E from Bacillus subtilis DB104 are near identical. Deuteration of NK was carried out by cultivating Bacillus subtilis natto in deuterated medium. The D2O resistant strain of Bacillus subtilis natto was obtained by successive cultivation rounds, in which the concentration of D2O in the medium was gradually increased. NK was purified from the culture medium and its activity was confirmed by the fibrin plate method. The results lay the framework for neutron protein crystallography analysis. PMID:24121331

  7. Discovery of Spatial and Spectral Structure in the X-Ray Emission from the Crab Nebula

    NASA Technical Reports Server (NTRS)

    Weisskopf, Martin C.; Hester, J. Jeff; Tennant, Allyn F.; Elsner, Ronald F.; Schulz, Norbert S.; Marshall, Herman L.; Karovska, Margarita; Nichols, Joy S.; Swartz, Douglas A.; Kolodziejczak, Jeffery J.

    2000-01-01

    The Chandra X-Ray Observatory observed the Crab Nebula and pulsar during orbital calibration. Zeroth-order images with the High-Energy Transmission Grating (HETG) readout by the Advanced Charge Coupled Devices (CCD) Imaging Spectrometer spectroscopy array (ACIS-S) show a striking richness of X-ray structure at a resolution comparable to that of the best ground-based visible-light observations. The HETG-ACIS-S images reveal, for the first time, an X-ray inner ring within the X-ray torus, the suggestion of a hollow-tube structure for the torus, and X-ray knots along the inner ring and (perhaps) along the inward extension of the X-ray jet. Although complicated by instrumental effects and the brightness of the Crab Nebula, the spectrometric analysis shows systematic variations of the X-ray spectrum throughout the nebula.

  8. Discovery of Spatial and Spectral Structure in the X-Ray Emission from the Crab Nebula.

    PubMed

    Weisskopf; Hester; Tennant; Elsner; Schulz; Marshall; Karovska; Nichols; Swartz; Kolodziejczak; O'Dell

    2000-06-20

    The Chandra X-Ray Observatory observed the Crab Nebula and pulsar during orbital calibration. Zeroth-order images with the High-Energy Transmission Grating (HETG) readout by the Advanced CCD Imaging Spectrometer spectroscopy array (ACIS-S) show a striking richness of X-ray structure at a resolution comparable to that of the best ground-based visible-light observations. The HETG-ACIS-S images reveal, for the first time, an X-ray inner ring within the X-ray torus, the suggestion of a hollow-tube structure for the torus, and X-ray knots along the inner ring and (perhaps) along the inward extension of the X-ray jet. Although complicated by instrumental effects and the brightness of the Crab Nebula, the spectrometric analysis shows systematic variations of the X-ray spectrum throughout the nebula.

  9. Hard X-ray irradiation of cosmic silicate analogs: structural evolution and astrophysical implications

    NASA Astrophysics Data System (ADS)

    Gavilan, L.; Jäger, C.; Simionovici, A.; Lemaire, J. L.; Sabri, T.; Foy, E.; Yagoubi, S.; Henning, T.; Salomon, D.; Martinez-Criado, G.

    2016-03-01

    Context. Protoplanetary disks, interstellar clouds, and active galactic nuclei contain X-ray-dominated regions. X-rays interact with the dust and gas present in such environments. While a few laboratory X-ray irradiation experiments have been performed on ices, X-ray irradiation experiments on bare cosmic dust analogs have been scarce up to now. Aims: Our goal is to study the effects of hard X-rays on cosmic dust analogs via in situ X-ray diffraction. By using a hard X-ray synchrotron nanobeam, we seek to simulate cumulative X-ray exposure on dust grains during their lifetime in these astrophysical environments and provide an upper limit on the effect of hard X-rays on dust grain structure. Methods: We prepared enstatite (MgSiO3) nanograins, which are analogs to cosmic silicates, via the melting-quenching technique. These amorphous grains were then annealed to obtain polycrystalline grains. These were characterized via scanning electron microscopy (SEM) and high-resolution transmission electron microscopy (HRTEM) before irradiation. Powder samples were prepared in X-ray transparent substrates and were irradiated with hard X-rays nanobeams (29.4 keV) provided by beamline ID16B of the European Synchrotron Radiation Facility (Grenoble). X-ray diffraction images were recorded in transmission mode, and the ensuing diffractograms were analyzed as a function of the total X-ray exposure time. Results: We detected the amorphization of polycrystalline silicates embedded in an organic matrix after an accumulated X-ray exposure of 6.4 × 1027 eV cm-2. Pure crystalline silicate grains (without resin) do not exhibit amorphization. None of the amorphous silicate samples (pure and embedded in resin) underwent crystallization. We analyze the evolution of the polycrystalline sample embedded in an organic matrix as a function of X-ray exposure. Conclusions: Loss of diffraction peak intensity, peak broadening, and the disappearance of discrete spots and arcs reveal the amorphization

  10. Simulating Picosecond X-ray Diffraction from shocked crystals by Post-processing Molecular Dynamics Calculations

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kimminau, G; Nagler, B; Higginbotham, A

    2008-06-19

    Calculations of the x-ray diffraction patterns from shocked crystals derived from the results of Non-Equilibrium-Molecular-Dynamics (NEMD) simulations are presented. The atomic coordinates predicted by the NEMD simulations combined with atomic form factors are used to generate a discrete distribution of electron density. A Fast-Fourier-Transform (FFT) of this distribution provides an image of the crystal in reciprocal space, which can be further processed to produce quantitative simulated data for direct comparison with experiments that employ picosecond x-ray diffraction from laser-irradiated crystalline targets.

  11. Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses

    NASA Astrophysics Data System (ADS)

    Kurta, Ruslan P.; Donatelli, Jeffrey J.; Yoon, Chun Hong; Berntsen, Peter; Bielecki, Johan; Daurer, Benedikt J.; DeMirci, Hasan; Fromme, Petra; Hantke, Max Felix; Maia, Filipe R. N. C.; Munke, Anna; Nettelblad, Carl; Pande, Kanupriya; Reddy, Hemanth K. N.; Sellberg, Jonas A.; Sierra, Raymond G.; Svenda, Martin; van der Schot, Gijs; Vartanyants, Ivan A.; Williams, Garth J.; Xavier, P. Lourdu; Aquila, Andrew; Zwart, Peter H.; Mancuso, Adrian P.

    2017-10-01

    We use extremely bright and ultrashort pulses from an x-ray free-electron laser (XFEL) to measure correlations in x rays scattered from individual bioparticles. This allows us to go beyond the traditional crystallography and single-particle imaging approaches for structure investigations. We employ angular correlations to recover the three-dimensional (3D) structure of nanoscale viruses from x-ray diffraction data measured at the Linac Coherent Light Source. Correlations provide us with a comprehensive structural fingerprint of a 3D virus, which we use both for model-based and ab initio structure recovery. The analyses reveal a clear indication that the structure of the viruses deviates from the expected perfect icosahedral symmetry. Our results anticipate exciting opportunities for XFEL studies of the structure and dynamics of nanoscale objects by means of angular correlations.

  12. X-ray Scattering Combined with Coordinate-Based Analyses for Applications in Natural and Artificial Photosynthesis

    PubMed Central

    Tiede, David M.; Mardis, Kristy L.; Zuo, Xiaobing

    2009-01-01

    Advances in x-ray light sources and detectors have created opportunities for advancing our understanding of structure and structural dynamics for supramolecular assemblies in solution by combining x-ray scattering measurement with coordinate-based modeling methods. In this review the foundations for x-ray scattering are discussed and illustrated with selected examples demonstrating the ability to correlate solution x-ray scattering measurements to molecular structure, conformation, and dynamics. These approaches are anticipated to have a broad range of applications in natural and artificial photosynthesis by offering possibilities for structure resolution for dynamic supramolecular assemblies in solution that can not be fully addressed with crystallographic techniques, and for resolving fundamental mechanisms for solar energy conversion by mapping out structure in light-excited reaction states. PMID:19636808

  13. X-Ray Diffraction and the Discovery of the Structure of DNA

    ERIC Educational Resources Information Center

    Crouse, David T.

    2007-01-01

    A method is described for teaching the analysis of X-ray diffraction of DNA through a series of steps utilizing the original methods used by James Watson, Francis Crick, Maurice Wilkins and Rosalind Franklin. The X-ray diffraction pattern led to the conclusion of the basic helical structure of DNA and its dimensions while basic chemical principles…

  14. Colliding Stellar Winds Structure and X-ray Emission

    NASA Astrophysics Data System (ADS)

    Pittard, J. M.; Dawson, B.

    2018-04-01

    We investigate the structure and X-ray emission from the colliding stellar winds in massive star binaries. We find that the opening angle of the contact discontinuity (CD) is overestimated by several formulae in the literature at very small values of the wind momentum ratio, η. We find also that the shocks in the primary (dominant) and secondary winds flare by ≈20° compared to the CD, and that the entire secondary wind is shocked when η ≲ 0.02. Analytical expressions for the opening angles of the shocks, and the fraction of each wind that is shocked, are provided. We find that the X-ray luminosity Lx∝η, and that the spectrum softens slightly as η decreases.

  15. Development of x-ray laminography under an x-ray microscopic condition

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hoshino, Masato; Uesugi, Kentaro; Takeuchi, Akihisa

    2011-07-15

    An x-ray laminography system under an x-ray microscopic condition was developed to obtain a three-dimensional structure of laterally-extended planar objects which were difficult to observe by x-ray tomography. An x-ray laminography technique was introduced to an x-ray transmission microscope with zone plate optics. Three prototype sample holders were evaluated for x-ray imaging laminography. Layered copper grid sheets were imaged as a laminated sample. Diatomite powder on a silicon nitride membrane was measured to confirm the applicability of this method to non-planar micro-specimens placed on the membrane. The three-dimensional information of diatom shells on the membrane was obtained at a spatialmore » resolution of sub-micron. Images of biological cells on the membrane were also obtained by using a Zernike phase contrast technique.« less

  16. Characterization of pentavalent and hexavalent americium complexes in nitric acid using X-ray absorption fine structure spectroscopy and first-principles modeling

    DOE PAGES

    Riddle, Catherine; Czerwinski, Kenneth; Kim, Eunja; ...

    2016-01-18

    We studied the speciation of pentavalent and hexavalent americium (Am) complexes in nitric acidicby X-ray absorption fine structure spectroscopy (XAFS), UV-visible spectroscopy, and density functional theory (DFT). Extended x-ray absorption fine structure (EXAFS) and x-ray absorption near edge structure (XANES) results were consistent with the presence of a mixture of AmO 2 + and AmO 2 2+ with only a small amount AmO 2 present. The resulting average bond distances we found were 1.71 Å for Am=O and 2.44 Å for Am-O. All-electron scalar relativistic calculations were also carried out using DFT to predict the equilibrium geometries and properties ofmore » the AmO 2 + and AmO 2 2+ aquo complexes. Calculated bond distances for the Am(VI) complex are in reasonable agreement with EXAFS data and the computed energy gaps between frontier molecular orbitals suggest a slightly higher kinetic stability and chemical hardness of Am(VI) compared to Am(V).« less

  17. Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses

    DOE PAGES

    Kurta, Ruslan P.; Donatelli, Jeffrey J.; Yoon, Chun Hong; ...

    2017-10-12

    We use extremely bright and ultrashort pulses from an x-ray free-electron laser (XFEL) to measure correlations in x rays scattered from individual bioparticles. This allows us to go beyond the traditional crystallography and single-particle imaging approaches for structure investigations. We employ angular correlations to recover the three-dimensional (3D) structure of nanoscale viruses from x-ray diffraction data measured at the Linac Coherent Light Source. Correlations provide us with a comprehensive structural fingerprint of a 3D virus, which we use both for model-based and ab initio structure recovery. The analyses reveal a clear indication that the structure of the viruses deviates frommore » the expected perfect icosahedral symmetry. Lastly, our results anticipate exciting opportunities for XFEL studies of the structure and dynamics of nanoscale objects by means of angular correlations.« less

  18. Small-angle X-ray scattering (SAXS) studies of the structure of mesoporous silicas

    NASA Astrophysics Data System (ADS)

    Zienkiewicz-Strzałka, M.; Skibińska, M.; Pikus, S.

    2017-11-01

    Mesoporous ordered silica nanostructures show strong interaction with X-ray radiation in the range of small-angles. Small-angle X-ray scattering (SAXS) measurements based on the elastically scattered X-rays are important in analysis of condensed matter. In the case of mesoporous silica materials SAXS technique provides information on the distribution of electron density in the mesoporous material, in particular describing their structure and size of the unit cell as well as type of ordered structure and finally their parameters. The characterization of nanopowder materials, nanocomposites and porous materials by Small-Angle X-ray Scattering seems to be valuable and useful. In presented work, the SAXS investigation of structures from the group of mesoporous ordered silicates was performed. This work has an objective to prepare functional materials modified by noble metal ions and nanoparticles and using the small-angle X-ray scattering to illustrate their properties. We report the new procedure for describing mesoporous materials belonging to SBA-15 and MCM-41 family modified by platinum, palladium and silver nanoparticles, based on detailed analysis of characteristic peaks in the small-angle range of X-ray scattering. This procedure allows to obtained the most useful parameters for mesoporous materials characterization and their successfully compare with experimental measurements reducing the time and material consumption with good precision for particles and pores with a size below 10 nm.

  19. NuSTAR Detection of a Hard X-Ray Source in the Supernova Remnant-molecular Cloud Interaction Site of IC 443

    NASA Astrophysics Data System (ADS)

    Zhang, Shuo; Tang, Xiaping; Zhang, Xiao; Sun, Lei; Gotthelf, Eric V.; Zhang, Zhi-Yu; Li, Hui; Cheng, Allen; Pasham, Dheeraj; Baganoff, Frederick K.; Perez, Kerstin; Hailey, Charles J.; Mori, Kaya

    2018-06-01

    We report on a broadband study of a complex X-ray source (1SAX J0618.0+2227) associated with the interaction site of the supernova remnant (SNR) IC 443 and ambient molecular cloud (MC) using NuSTAR, XMM-Newton, and Chandra observations. Its X-ray spectrum is composed of both thermal and nonthermal components. The thermal component can be equally well represented by either a thin plasma model with kT = 0.19 keV or a blackbody model with kT = 0.11 keV. The nonthermal component can be fit with either a power law with Γ ∼ 1.7 or a cutoff power law with Γ ∼ 1.5 and a cutoff energy at E cut ∼ 18 keV. Using the newly obtained NuSTAR data set, we test three possible scenarios for isolated X-ray sources in the SNR–MC interaction site: (1) a pulsar wind nebula (PWN); (2) an SNR ejecta fragment; and (3) a shocked molecular clump. We conclude that this source is most likely composed of an SNR ejecta (or a PWN) and surrounding shocked molecular clumps. The nature of this hard X-ray source in the SNR–MC interaction site of IC 443 may shed light on unidentified X-ray sources with hard X-ray spectra in rich environments for star-forming regions, such as the Galactic center.

  20. Uranium Hydridoborates: Synthesis, Magnetism, and X-ray/Neutron Diffraction Structures.

    PubMed

    Braunschweig, H; Gackstatter, A; Kupfer, T; Radacki, K; Franke, S; Meyer, K; Fucke, K; Lemée-Cailleau, M-H

    2015-08-17

    While uranium hydridoborate complexes containing the [BH4](-) moiety have been well-known in the literature for many years, species with functionalized borate centers remained considerably rare. We were now able to prepare several uranium hydridoborates (1-4) with amino-substituted borate moieties with high selectivity by smooth reaction of [Cp*2UMe2] (Cp* = C5Me5) and [Cp'2UMe2] (Cp' = 1,2,4-tBu3C5H2) with the aminoborane H2BN(SiMe3)2. A combination of nuclear magnetic resonance spectroscopy, deuteration experiments, magnetic SQUID measurements, and X-ray/neutron diffraction studies was used to verify the anticipated molecular structures and oxidation states of 1-4 and helped to establish a linear tridentate coordination mode of the borate anions.

  1. PREFACE: Structure and dynamics determined by neutron and x-ray scattering Structure and dynamics determined by neutron and x-ray scattering

    NASA Astrophysics Data System (ADS)

    Müller-Buschbaum, Peter

    2011-06-01

    Neutron and x-ray scattering have emerged as powerful methods for the determination of structure and dynamics. Driven by emerging new, powerful neutron and synchrotron radiation sources, the continuous development of new instrumentation and novel scattering techniques gives rise to exciting possibilities. For example, in situ observations become possible via a high neutron or x-ray flux at the sample and, as a consequence, morphological transitions with small time constants can be detected. This special issue covers a broad range of different materials from soft to hard condensed matter. Hence, different material classes such as colloids, polymers, alloys, oxides and metals are addressed. The issue is dedicated to the 60th birthday of Professor Winfried Petry, scientific director of the Research Neutron Source Heinz Maier-Leibnitz (FRM-II), Germany, advisor at the physics department for the Bayerische Elite-Akademie, chair person of the Arbeitsgemeinschaft Metall- und Materialphysik of the German Physical Society (DPG) and a member of the professional council of the German Science Foundation (Deutsche Forschungsgemeinschaft, DFG). We would like to acknowledge and thank all contributors for their submissions, which made this special issue possible in the first place. Moreover, we would like to thank the staff at IOP Publishing for helping us with the administrative aspects and for coordinating the refereeing process, and Valeria Lauter for the beautiful cover artwork. Finally, to the readers, we hope that you find this special issue a valuable resource that provides insights into the present possibilities of neutron and x-ray scattering as powerful tools for the investigation of structure and dynamics. Structure and dynamics determined by neutron and x-ray scattering contents In situ studies of mass transport in liquid alloys by means of neutron radiography F Kargl, M Engelhardt, F Yang, H Weis, P Schmakat, B Schillinger, A Griesche and A Meyer Magnetic spin

  2. X-Ray Shadowing Experiments Toward Infrared Dark Clouds

    NASA Technical Reports Server (NTRS)

    Anderson, L. E.; Snowden, S.; Bania, T. M.

    2009-01-01

    We searched for X-ray shadowing toward two infrared dark clouds (IRDCs) using the MOS detectors on XMM-Newton to learn about the Galactic distribution of X-ray emitting plasma. IRDCs make ideal X-ray shadowing targets of 3/4 keY photons due to their high column densities, relatively large angular sizes, and known kinematic distances. Here we focus on two clouds near 30 deg Galactic longitude at distances of 2 and 5 kpc from the Sun. We derive the foreground and background column densities of molecular and atomic gas in the direction of the clouds. We find that the 3/4 ke V emission must be distributed throughout the Galactic disk. It is therefore linked to the structure of the cooler material of the ISM, and to the birth of stars.

  3. Thermal expansion behavior study of Co nanowire array with in situ x-ray diffraction and x-ray absorption fine structure techniques

    NASA Astrophysics Data System (ADS)

    Mo, Guang; Cai, Quan; Jiang, Longsheng; Wang, Wei; Zhang, Kunhao; Cheng, Weidong; Xing, Xueqing; Chen, Zhongjun; Wu, Zhonghua

    2008-10-01

    In situ x-ray diffraction and x-ray absorption fine structure techniques were used to study the structural change of ordered Co nanowire array with temperature. The results show that the Co nanowires are polycrystalline with hexagonal close packed structure without phase change up until 700 °C. A nonlinear thermal expansion behavior has been found and can be well described by a quadratic equation with the first-order thermal expansion coefficient of 4.3×10-6/°C and the second-order thermal expansion coefficient of 5.9×10-9/°C. The mechanism of this nonlinear thermal expansion behavior is discussed.

  4. Investigating the Defect Structures in Transparent Conducting Oxides Using X-ray and Neutron Scattering Techniques

    PubMed Central

    González, Gabriela B.

    2012-01-01

    Transparent conducting oxide (TCO) materials are implemented into a wide variety of commercial devices because they possess a unique combination of high optical transparency and high electrical conductivity. Created during the processing of the TCOs, defects within the atomic-scale structure are responsible for their desirable optical and electrical properties. Therefore, studying the defect structure is essential to a better understanding of the behavior of transparent conductors. X-ray and neutron scattering techniques are powerful tools to investigate the atomic lattice structural defects in these materials. This review paper presents some of the current developments in the study of structural defects in n-type TCOs using x-ray diffraction (XRD), neutron diffraction, extended x-ray absorption fine structure (EXAFS), pair distribution functions (PDFs), and x-ray fluorescence (XRF). PMID:28817010

  5. Identification and analysis of structures in the corona from X-ray photography

    NASA Technical Reports Server (NTRS)

    Vaiana, G. S.; Krieger, A. S.; Timothy, A. F.

    1973-01-01

    This paper summarizes the results of a program of rocket observations of the solar corona with grazing incidence X-ray telescopes. A series of five flights of a Kanigen-surfaced telescope with a few arc seconds resolution, together with the first flight of a newer telescope have resulted in the identification of six classes of coronal structures observable in the X-ray photographs. These are: active regions, active region interconnections, large loop structures associated with unipolar magnetic regions, coronal holes, coronal bright points, and the structures surrounding filament cavities. Two solar flares have been observed. The methods involved in deriving coronal temperature and density information from X-ray photographs are described and the analysis of a bright active region (McMath plage 11035) observed at the west limb on November 24, 1970 is presented as an example of these techniques.

  6. X-ray diffraction from nonuniformly stretched helical molecules

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Prodanovic, Momcilo; Irving, Thomas C.; Mijailovich, Srboljub M.

    2016-04-18

    The fibrous proteins in living cells are exposed to mechanical forces interacting with other subcellular structures. X-ray fiber diffraction is often used to assess deformation and movement of these proteins, but the analysis has been limited to the theory for fibrous molecular systems that exhibit helical symmetry. However, this approach cannot adequately interpret X-ray data from fibrous protein assemblies where the local strain varies along the fiber length owing to interactions of its molecular constituents with their binding partners. To resolve this problem a theoretical formulism has been developed for predicting the diffraction from individual helical molecular structures nonuniformly strainedmore » along their lengths. This represents a critical first step towards modeling complex dynamical systems consisting of multiple helical structures using spatially explicit, multi-scale Monte Carlo simulations where predictions are compared with experimental data in a `forward' process to iteratively generate ever more realistic models. Here the effects of nonuniform strains and the helix length on the resulting magnitude and phase of diffraction patterns are quantitatively assessed. Examples of the predicted diffraction patterns of nonuniformly deformed double-stranded DNA and actin filaments in contracting muscle are presented to demonstrate the feasibly of this theoretical approach.« less

  7. Soft X-ray scanning transmission X-ray microscopy (STXM) of actinide particles.

    PubMed

    Nilsson, Hans J; Tyliszczak, Tolek; Wilson, Richard E; Werme, Lars; Shuh, David K

    2005-09-01

    A descriptive account is given of our most recent research on the actinide dioxides with the Advanced Light Source Molecular Environmental Science (ALS-MES) Beamline 11.0.2 soft X-ray scanning transmission X-ray microscope (STXM) at the Lawrence Berkeley National Laboratory (LBNL). The ALS-MES STXM permits near-edge X-ray absorption fine structure (NEXAFS) and imaging with 30-nm spatial resolution. The first STXM spectromicroscopy NEXAFS spectra at the actinide 4d5/2 edges of the imaged transuranic particles, NpO2 and PuO2, have been obtained. Radiation damage induced by the STXM was observed in the investigation of a mixed oxidation state particle (Np(V,VI)) and was minimized during collection of the actual spectra at the 4d5/2 edge of the Np(V,VI) solid. A plutonium elemental map was obtained from an irregular PuO2 particle with the dimensions of 650 x 650 nm. The Pu 4d5/2 NEXAFS spectra were collected at several different locations from the PuO2 particle and were identical. A representative oxygen K-edge spectrum from UO2 was collected and resembles the oxygen K-edge from the bulk material. The unique and current performance of the ALS-MES STXM at extremely low energies (ca. 100 eV) that may permit the successful measurement of the actinide 5d edge is documented. Finally, the potential of STXM as a tool for actinide investigations is briefly discussed.

  8. Long-Wavelength X-Ray Diffraction and Its Applications in Macromolecular Crystallography.

    PubMed

    Weiss, Manfred S

    2017-01-01

    For many years, diffraction experiments in macromolecular crystallography at X-ray wavelengths longer than that of Cu-K α (1.54 Å) have been largely underappreciated. Effects caused by increased X-ray absorption result in the fact that these experiments are more difficult than the standard diffraction experiments at short wavelengths. However, due to the also increased anomalous scattering of many biologically relevant atoms, important additional structural information can be obtained. This information, in turn, can be used for phase determination, for substructure identification, in molecular replacement approaches, as well as in structure refinement. This chapter reviews the possibilities and the difficulties associated with such experiments, and it provides a short description of two macromolecular crystallography synchrotron beam lines dedicated to long-wavelength X-ray diffraction experiments.

  9. Study of multilayered SiGe semiconductor structures by X-ray diffractometry, grazing-incidence X-ray reflectometry, and secondary-ion mass spectrometry

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yunin, P. A., E-mail: yunin@ipmras.ru; Drozdov, Yu. N.; Drozdov, M. N.

    2013-12-15

    In this publication, we report the results of studying a multilayerd nonperiodic SiGe/Si structure by the methods of X-ray diffractometry, grazing-angle X-ray reflectometry, and secondary-ion mass spectrometry (SIMS). Special attention is paid to the processing of the component distribution profile using the SIMS method and to consideration of the most significant experimental distortions introduced by this method. A method for processing the measured composition distribution profile with subsequent consideration of the influence of matrix effects, variation in the etching rate, and remnants of ion sputtering is suggested. The results of such processing are compared with a structure model obtained uponmore » combined analysis of X-ray diffractometry and grazing-angle reflectometry data. Good agreement between the results is established. It is shown that the combined use of independent techniques makes it possible to improve the methods of secondary-ion mass spectrometry and grazing-incidence reflectometry as applied to an analysis of multilayered heteroepitaxial structures (to increase the accuracy and informativity of these methods)« less

  10. Deformable complex network for refining low-resolution X-ray structures

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhang, Chong; Wang, Qinghua; Ma, Jianpeng, E-mail: jpma@bcm.edu

    2015-10-27

    A new refinement algorithm called the deformable complex network that combines a novel angular network-based restraint with a deformable elastic network model in the target function has been developed to aid in structural refinement in macromolecular X-ray crystallography. In macromolecular X-ray crystallography, building more accurate atomic models based on lower resolution experimental diffraction data remains a great challenge. Previous studies have used a deformable elastic network (DEN) model to aid in low-resolution structural refinement. In this study, the development of a new refinement algorithm called the deformable complex network (DCN) is reported that combines a novel angular network-based restraint withmore » the DEN model in the target function. Testing of DCN on a wide range of low-resolution structures demonstrated that it constantly leads to significantly improved structural models as judged by multiple refinement criteria, thus representing a new effective refinement tool for low-resolution structural determination.« less

  11. Nonlinear X-Ray and Auger Spectroscopy at X-Ray Free-Electron Laser Sources

    NASA Astrophysics Data System (ADS)

    Rohringer, Nina

    2015-05-01

    X-ray free-electron lasers (XFELs) open the pathway to transfer non-linear spectroscopic techniques to the x-ray domain. A promising all x-ray pump probe technique is based on coherent stimulated electronic x-ray Raman scattering, which was recently demonstrated in atomic neon. By tuning the XFEL pulse to core-excited resonances, a few seed photons in the spectral tail of the XFEL pulse drive an avalanche of resonant inelastic x-ray scattering events, resulting in exponential amplification of the scattering signal by of 6-7 orders of magnitude. Analysis of the line profile of the emitted radiation permits to demonstrate the cross over from amplified spontaneous emission to coherent stimulated resonance scattering. In combination with statistical covariance mapping, a high-resolution spectrum of the resonant inelastic scattering process can be obtained, opening the path to coherent stimulated x-ray Raman spectroscopy. An extension of these ideas to molecules and a realistic feasibility study of stimulated electronic x-ray Raman scattering in CO will be presented. Challenges to realizing stimulated electronic x-ray Raman scattering at present-day XFEL sources will be discussed, corroborated by results of a recent experiment at the LCLS XFEL. Due to the small gain cross section in molecular targets, other nonlinear spectroscopic techniques such as nonlinear Auger spectroscopy could become a powerful alternative. Theory predictions of a novel pump probe technique based on resonant nonlinear Auger spectroscopic will be discussed and the method will be compared to stimulated x-ray Raman spectroscopy.

  12. Repetitive flash x-ray generator operated at low-dose rates for a medical x-ray television system

    NASA Astrophysics Data System (ADS)

    Sato, Eiichi; Isobe, Hiroshi; Takahashi, Kei; Tamakawa, Yoshiharu; Yanagisawa, Toru

    1991-04-01

    The fundamental studies for the repetitive flash x-ray generator operated at lowdose rates for a medical x-ray television system are described. This x-ray generator consisted of the following components: a high-voltage power supply, an energy storage condenser of lOOnF, a coaxial cable condenser with a capacity of l000pF, a repetitive impulse switching system, a turbo molecular pump, and an x-ray tube having a cold cathode. The condenser was charged from 40 to 70kV by a power supply, and the electric charges stored in the condenser were discharged repetitively by using a trigger electrode operated by an impulse switching system. The x-ray tube was of the triode-type which was connected to the turbo molecular pump and had a large discharge impedance in order to prevent the damped oscillations of the tube current and voltage. The maximum tube voltage was equivalent to the initial charged voltage, and the peak current was less than 70A. The durations were about 2ps, and the x-ray intensities were less than 1. OpC/kg at 0. 5m per pulse. The repetition frequency was less than 50Hz, and the effective focal spot size was equivalent to the anode diameter of 3. 0mm. For the x-ray television system used in conjunction with this repetitive pulsed x-ray generator, since the electromagnetic noise primarily caused by the high tube current was decreased, noise-free stroboscopic radiography performed by the television system could be realized.

  13. Emerging opportunities in structural biology with X-ray free-electron lasers

    PubMed Central

    Schlichting, Ilme; Miao, Jianwei

    2012-01-01

    X-ray free-electron lasers (X-FELs) produce X-ray pulses with extremely brilliant peak intensity and ultrashort pulse duration. It has been proposed that radiation damage can be “outrun” by using an ultra intense and short X-FEL pulse that passes a biological sample before the onset of significant radiation damage. The concept of “diffraction-before-destruction” has been demonstrated recently at the Linac Coherent Light Source, the first operational hard X-ray FEL, for protein nanocrystals and giant virus particles. The continuous diffraction patterns from single particles allow solving the classical “phase problem” by the oversampling method with iterative algorithms. If enough data are collected from many identical copies of a (biological) particle, its three-dimensional structure can be reconstructed. We review the current status and future prospects of serial femtosecond crystallography (SFX) and single-particle coherent diffraction imaging (CDI) with X-FELs. PMID:22922042

  14. X-ray Crystallography Facility

    NASA Technical Reports Server (NTRS)

    2000-01-01

    Edward Snell, a National Research Council research fellow at NASA's Marshall Space Flight Center (MSFC), prepares a protein crystal for analysis by x-ray crystallography as part of NASA's structural biology program. The small, individual crystals are bombarded with x-rays to produce diffraction patterns, a map of the intensity of the x-rays as they reflect through the crystal.

  15. Phosphor Scanner For Imaging X-Ray Diffraction

    NASA Technical Reports Server (NTRS)

    Carter, Daniel C.; Hecht, Diana L.; Witherow, William K.

    1992-01-01

    Improved optoelectronic scanning apparatus generates digitized image of x-ray image recorded in phosphor. Scanning fiber-optic probe supplies laser light stimulating luminescence in areas of phosphor exposed to x rays. Luminescence passes through probe and fiber to integrating sphere and photomultiplier. Sensitivity and resolution exceed previously available scanners. Intended for use in x-ray crystallography, medical radiography, and molecular biology.

  16. X-ray structural studies of quinone reductase 2 nanomolar range inhibitors

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Pegan, Scott D.; Sturdy, Megan; Ferry, Gilles

    Quinone reductase 2 (QR2) is one of two members comprising the mammalian quinone reductase family of enzymes responsible for performing FAD mediated reductions of quinone substrates. In contrast to quinone reductase 1 (QR1) which uses NAD(P)H as its co-substrate, QR2 utilizes a rare group of hydride donors, N-methyl or N-ribosyl nicotinamide. Several studies have linked QR2 to the generation of quinone free radicals, several neuronal degenerative diseases, and cancer. QR2 has been also identified as the third melatonin receptor (MT3) through in cellulo and in vitro inhibition of QR2 by traditional MT3 ligands, and through recent X-ray structures of humanmore » QR2 (hQR2) in complex with melatonin and 2-iodomelatonin. Several MT3 specific ligands have been developed that exhibit both potent in cellulo inhibition of hQR2 nanomolar, affinity for MT3. The potency of these ligands suggest their use as molecular probes for hQR2. However, no definitive correlation between traditionally obtained MT3 ligand affinity and hQR2 inhibition exists limiting our understanding of how these ligands are accommodated in the hQR2 active site. To obtain a clearer relationship between the structures of developed MT3 ligands and their inhibitory properties, in cellulo and in vitro IC{sub 50} values were determined for a representative set of MT3 ligands (MCA-NAT, 2-I-MCANAT, prazosin, S26695, S32797, and S29434). Furthermore, X-ray structures for each of these ligands in complex with hQR2 were determined allowing for a structural evaluation of the binding modes of these ligands in relation to the potency of MT3 ligands.« less

  17. Analysis of RNA structure using small-angle X-ray scattering

    PubMed Central

    Cantara, William A.; Olson, Erik D.; Musier-Forsyth, Karin

    2016-01-01

    In addition to their role in correctly attaching specific amino acids to cognate tRNAs, aminoacyl-tRNA synthetases (aaRS) have been found to possess many alternative functions and often bind to and act on other nucleic acids. In contrast to the well-defined 3D structure of tRNA, the structures of many of the other RNAs recognized by aaRSs have not been solved. Despite advances in the use of X-ray crystallography (XRC), nuclear magnetic resonance (NMR) spectroscopy and cryo-electron microscopy (cryo-EM) for structural characterization of biomolecules, significant challenges to solving RNA structures still exist. Recently, small-angle X-ray scattering (SAXS) has been increasingly employed to characterize the 3D structures of RNAs and RNA-protein complexes. SAXS is capable of providing low-resolution tertiary structure information under physiological conditions and with less intensive sample preparation and data analysis requirements than XRC, NMR and cryo-EM. In this article, we describe best practices involved in the process of RNA and RNA-protein sample preparation, SAXS data collection, data analysis, and structural model building. PMID:27777026

  18. Surface layering and melting in an ionic liquid studied by resonant soft X-ray reflectivity

    PubMed Central

    Mezger, Markus; Ocko, Benjamin M.; Reichert, Harald; Deutsch, Moshe

    2013-01-01

    The molecular-scale structure of the ionic liquid [C18mim]+[FAP]− near its free surface was studied by complementary methods. X-ray absorption spectroscopy and resonant soft X-ray reflectivity revealed a depth-decaying near-surface layering. Element-specific interfacial profiles were extracted with submolecular resolution from energy-dependent soft X-ray reflectivity data. Temperature-dependent hard X-ray reflectivity, small- and wide-angle X-ray scattering, and infrared spectroscopy uncovered an intriguing melting mechanism for the layered region, where alkyl chain melting drove a negative thermal expansion of the surface layer spacing. PMID:23431181

  19. Calculation of x-ray scattering patterns from nanocrystals at high x-ray intensity

    PubMed Central

    Abdullah, Malik Muhammad; Jurek, Zoltan; Son, Sang-Kil; Santra, Robin

    2016-01-01

    We present a generalized method to describe the x-ray scattering intensity of the Bragg spots in a diffraction pattern from nanocrystals exposed to intense x-ray pulses. Our method involves the subdivision of a crystal into smaller units. In order to calculate the dynamics within every unit, we employ a Monte-Carlo-molecular dynamics-ab-initio hybrid framework using real space periodic boundary conditions. By combining all the units, we simulate the diffraction pattern of a crystal larger than the transverse x-ray beam profile, a situation commonly encountered in femtosecond nanocrystallography experiments with focused x-ray free-electron laser radiation. Radiation damage is not spatially uniform and depends on the fluence associated with each specific region inside the crystal. To investigate the effects of uniform and non-uniform fluence distribution, we have used two different spatial beam profiles, Gaussian and flattop. PMID:27478859

  20. Annealing induced atomic rearrangements on (Ga,In) (N,As) probed by hard X-ray photoelectron spectroscopy and X-ray absorption fine structure.

    PubMed

    Ishikawa, Fumitaro; Higashi, Kotaro; Fuyuno, Satoshi; Morifuji, Masato; Kondow, Masahiko; Trampert, Achim

    2018-04-13

    We study the effects of annealing on (Ga 0.64 ,In 0.36 ) (N 0.045 ,As 0.955 ) using hard X-ray photoelectron spectroscopy and X-ray absorption fine structure measurements. We observed surface oxidation and termination of the N-As bond defects caused by the annealing process. Specifically, we observed a characteristic chemical shift towards lower binding energies in the photoelectron spectra related to In. This phenomenon appears to be caused by the atomic arrangement, which produces increased In-N bond configurations within the matrix, as indicated by the X-ray absorption fine structure measurements. The reduction in the binding energies of group-III In, which occurs concomitantly with the atomic rearrangements of the matrix, causes the differences in the electronic properties of the system before and after annealing.

  1. Large-area soft x-ray projection lithography using multilayer mirrors structured by RIE

    NASA Astrophysics Data System (ADS)

    Rahn, Steffen; Kloidt, Andreas; Kleineberg, Ulf; Schmiedeskamp, Bernt; Kadel, Klaus; Schomburg, Werner K.; Hormes, F. J.; Heinzmann, Ulrich

    1993-01-01

    SXPL (soft X-ray projection lithography) is one of the most promising applications of X-ray reflecting optics using multilayer mirrors. Within our collaboration, such multilayer mirrors were fabricated, characterized, laterally structured and then used as reflection masks in a projecting lithography procedure. Mo/Si-multilayer mirrors were produced by electron beam evaporation in UHV under thermal treatment with an in-situ X-ray controlled thickness in the region of 2d equals 14 nm. The reflectivities measured at normal incidence reached up to 54%. Various surface analysis techniques have been applied in order to characterize and optimize the X-ray mirrors. The multilayers were patterned by reactive ion etching (RIE) with CF(subscript 4), using a photoresist as the etch mask, thus producing X-ray reflection masks. The masks were tested in the synchrotron radiation laboratory of the electron accelerator ELSA at the Physikalisches Institut of Bonn University. A double crystal X-ray monochromator was modified so as to allow about 0.5 cm(superscript 2) of the reflection mask to be illuminated by white synchrotron radiation. The reflected patterns were projected (with an energy of 100 eV) onto the resist (Hoechst AZ PF 514), which was mounted at an average distance of about 7 mm. In the first test-experiments, structure sizes down to 8 micrometers were nicely reproduced over the whole of the exposed area. Smaller structures were distorted by Fresnel-diffraction. The theoretically calculated diffraction images agree very well with the observed images.

  2. Reconstitution of SNARE proteins into solid-supported lipid bilayer stacks and X-ray structure analysis.

    PubMed

    Xu, Yihui; Kuhlmann, Jan; Brennich, Martha; Komorowski, Karlo; Jahn, Reinhard; Steinem, Claudia; Salditt, Tim

    2018-02-01

    SNAREs are known as an important family of proteins mediating vesicle fusion. For various biophysical studies, they have been reconstituted into supported single bilayers via proteoliposome adsorption and rupture. In this study we extended this method to the reconstitution of SNAREs into supported multilamellar lipid membranes, i.e. oriented multibilayer stacks, as an ideal model system for X-ray structure analysis (X-ray reflectivity and diffraction). The reconstitution was implemented through a pathway of proteomicelle, proteoliposome and multibilayer. To monitor the structural evolution in each step, we used small-angle X-ray scattering for the proteomicelles and proteoliposomes, followed by X-ray reflectivity and grazing-incidence small-angle scattering for the multibilayers. Results show that SNAREs can be successfully reconstituted into supported multibilayers, with high enough orientational alignment for the application of surface sensitive X-ray characterizations. Based on this protocol, we then investigated the effect of SNAREs on the structure and phase diagram of the lipid membranes. Beyond this application, this reconstitution protocol could also be useful for X-ray analysis of many further membrane proteins. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Macromolecular structures probed by combining single-shot free-electron laser diffraction with synchrotron coherent X-ray imaging.

    PubMed

    Gallagher-Jones, Marcus; Bessho, Yoshitaka; Kim, Sunam; Park, Jaehyun; Kim, Sangsoo; Nam, Daewoong; Kim, Chan; Kim, Yoonhee; Noh, Do Young; Miyashita, Osamu; Tama, Florence; Joti, Yasumasa; Kameshima, Takashi; Hatsui, Takaki; Tono, Kensuke; Kohmura, Yoshiki; Yabashi, Makina; Hasnain, S Samar; Ishikawa, Tetsuya; Song, Changyong

    2014-05-02

    Nanostructures formed from biological macromolecular complexes utilizing the self-assembly properties of smaller building blocks such as DNA and RNA hold promise for many applications, including sensing and drug delivery. New tools are required for their structural characterization. Intense, femtosecond X-ray pulses from X-ray free-electron lasers enable single-shot imaging allowing for instantaneous views of nanostructures at ambient temperatures. When combined judiciously with synchrotron X-rays of a complimentary nature, suitable for observing steady-state features, it is possible to perform ab initio structural investigation. Here we demonstrate a successful combination of femtosecond X-ray single-shot diffraction with an X-ray free-electron laser and coherent diffraction imaging with synchrotron X-rays to provide an insight into the nanostructure formation of a biological macromolecular complex: RNA interference microsponges. This newly introduced multimodal analysis with coherent X-rays can be applied to unveil nano-scale structural motifs from functional nanomaterials or biological nanocomplexes, without requiring a priori knowledge.

  4. Purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies of great cormorant (Phalacrocorax carbo) haemoglobin

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Jagadeesan, G.; Malathy, P.; Gunasekaran, K.

    2014-10-25

    The great cormorant hemoglobin has been isolated, purified and crystallized and the three dimensional structure is solved using molecular replacement technique. Haemoglobin is the iron-containing oxygen-transport metalloprotein that is present in the red blood cells of all vertebrates. In recent decades, there has been substantial interest in attempting to understand the structural basis and functional diversity of avian haemoglobins. Towards this end, purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies have been carried out on cormorant (Phalacrocorax carbo) haemoglobin. Crystals were grown by the hanging-drop vapour-diffusion method using PEG 3350, NaCl and glycerol as precipitants. The crystals belonged to themore » trigonal system P3{sub 1}21, with unit-cell parameters a = b = 55.64, c = 153.38 Å, β = 120.00°; a complete data set was collected to a resolution of 3.5 Å. Matthews coefficient analysis indicated that the crystals contained a half-tetramer in the asymmetric unit.« less

  5. Single crystal X-ray structure of the artists' pigment zinc yellow

    NASA Astrophysics Data System (ADS)

    Simonsen, Kim Pilkjær; Christiansen, Marie Bitsch; Vinum, Morten Gotthold; Sanyova, Jana; Bendix, Jesper

    2017-08-01

    The artists' pigment zinc yellow is in general described as a complex potassium zinc chromate with the empirical formula 4ZnCrO4·K2O·3H2O. Even though the pigment has been in use since the second half of the 19th century also in large-scale industrial applications, the exact structure had hitherto been unknown. In this work, zinc yellow was synthesised by precipitation from an aqueous solution of zinc nitrate and potassium chromate under both neutral and basic conditions, and the products were compared with the pigment used in industrial paints. Analyses by Raman microscopy (MRS), scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS), attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR), and powder X-ray diffraction (PXRD), showed that the synthesised products and the industrial pigment were identical. Single-crystal X-ray crystallography determined the structure of zinc yellow as KZn2(CrO4)2(H2O)(OH) or as KZn2(CrO4)2(H3O2) emphasizing the μ-H3O2- moiety. Notably, the zinc yellow is isostructural to the recently structurally characterized cadmium analog and both belong to the natrochalcite structure type.

  6. Robust X-ray angular correlations for the study of meso-structures

    DOE PAGES

    Lhermitte, Julien R.; Tian, Cheng; Stein, Aaron; ...

    2017-05-08

    As self-assembling nanomaterials become more sophisticated, it is becoming increasingly important to measure the structural order of finite-sized assemblies of nano-objects. These mesoscale clusters represent an acute challenge to conventional structural probes, owing to the range of implicated size scales (10 nm to several micrometres), the weak scattering signal and the dynamic nature of meso-clusters in native solution environments. The high X-ray flux and coherence of modern synchrotrons present an opportunity to extract structural information from these challenging systems, but conventional ensemble X-ray scattering averages out crucial information about local particle configurations. Conversely, a single meso-cluster scatters too weakly tomore » recover the full diffraction pattern. Using X-ray angular cross-correlation analysis, it is possible to combine multiple noisy measurements to obtain robust structural information. This paper explores the key theoretical limits and experimental challenges that constrain the application of these methods to probing structural order in real nanomaterials. A metric is presented to quantify the signal-to-noise ratio of angular correlations, and it is used to identify several experimental artifacts that arise. In particular, it is found that background scattering, data masking and inter-cluster interference profoundly affect the quality of correlation analyses. A robust workflow is demonstrated for mitigating these effects and extracting reliable angular correlations from realistic experimental data.« less

  7. Discovery of novel inhibitors for DHODH via virtual screening and X-ray crystallographic structures

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    McLean, Larry R.; Zhang, Ying; Degnen, William

    2010-10-28

    Amino-benzoic acid derivatives 1-4 were found to be inhibitors for DHODH by virtual screening, biochemical, and X-ray crystallographic studies. X-ray structures showed that 1 and 2 bind to DHODH as predicted by virtual screening, but 3 and 4 were found to be structurally different from the corresponding compounds initially identified by virtual screening.

  8. Small-angle X-Ray analysis of macromolecular structure: the structure of protein NS2 (NEP) in solution

    NASA Astrophysics Data System (ADS)

    Shtykova, E. V.; Bogacheva, E. N.; Dadinova, L. A.; Jeffries, C. M.; Fedorova, N. V.; Golovko, A. O.; Baratova, L. A.; Batishchev, O. V.

    2017-11-01

    A complex structural analysis of nuclear export protein NS2 (NEP) of influenza virus A has been performed using bioinformatics predictive methods and small-angle X-ray scattering data. The behavior of NEP molecules in a solution (their aggregation, oligomerization, and dissociation, depending on the buffer composition) has been investigated. It was shown that stable associates are formed even in a conventional aqueous salt solution at physiological pH value. For the first time we have managed to get NEP dimers in solution, to analyze their structure, and to compare the models obtained using the method of the molecular tectonics with the spatial protein structure predicted by us using the bioinformatics methods. The results of the study provide a new insight into the structural features of nuclear export protein NS2 (NEP) of the influenza virus A, which is very important for viral infection development.

  9. X-ray absorption fine structure (XAFS) spectroscopy using synchrotron radiation

    NASA Astrophysics Data System (ADS)

    Shrivastava, B. D.

    2012-05-01

    The X-ray absorption fine structure (XAFS) spectra are best recorded when a highly intense beam of X-rays from a synchrotron is used along with a good resolution double crystal or curved crystal spectrometer and detectors like ionization chambers, scintillation counters, solid state detectors etc. Several synchrotrons around the world have X-ray beamlines dedicated specifically to XAFS spectroscopy. Fortunately, the Indian synchrotron (Indus-2) at Raja Ramanna Centre for Advanced Technology (RRCAT) at Indore has started operation. A dispersive type EXAFS beamline called BL-8 has been commissioned at this synchrotron and another beamline having double crystal monochromator (DCM) is going to be commissioned shortly. In Indian context, in order that more research workers use these beamlines, the study of XAFS spectroscopy using synchrotron radiation becomes important. In the present work some of the works done by our group on XAFS spectroscopy using synchrotron radiation have been described.

  10. Substrate specificity of pyrimidine nucleoside phosphorylases of NP-II family probed by X-ray crystallography and molecular modeling

    NASA Astrophysics Data System (ADS)

    Balaev, V. V.; Lashkov, A. A.; Prokofev, I. I.; Gabdulkhakov, A. G.; Seregina, T. A.; Mironov, A. S.; Betzel, C.; Mikhailov, A. M.

    2016-09-01

    Pyrimidine nucleoside phosphorylases, which are widely used in the biotechnological production of nucleosides, have different substrate specificity for pyrimidine nucleosides. An interesting feature of these enzymes is that the three-dimensional structure of thymidine-specific nucleoside phosphorylase is similar to the structure of nonspecific pyrimidine nucleoside phosphorylase. The three-dimensional structures of thymidine phosphorylase from Salmonella typhimurium and nonspecific pyrimidine nucleoside phosphorylase from Bacillus subtilis in complexes with a sulfate anion were determined for the first time by X-ray crystallography. An analysis of the structural differences between these enzymes demonstrated that Lys108, which is involved in the phosphate binding in pyrimidine nucleoside phosphorylase, corresponds to Met111 in thymidine phosphorylases. This difference results in a decrease in the charge on one of the hydroxyl oxygens of the phosphate anion in thymidine phosphorylase and facilitates the catalysis through SN2 nucleophilic substitution. Based on the results of X-ray crystallography, the virtual screening was performed for identifying a potent inhibitor (anticancer agent) of nonspecific pyrimidine nucleoside phosphorylase, which does not bind to thymidine phosphorylase. The molecular dynamics simulation revealed the stable binding of the discovered compound—2-pyrimidin-2-yl-1H-imidazole-4-carboxylic acid—to the active site of pyrimidine nucleoside phosphorylase.

  11. The STAR-X X-Ray Telescope Assembly (XTA)

    NASA Technical Reports Server (NTRS)

    McClelland, Ryan S.; Bautz, Mark W.; Bonafede, Joseph A.; Miller, Eric D.; Saha, Timo T.; Solly, Peter M.; Zhang, William W.

    2017-01-01

    The Survey and Time-domain Astrophysical Research eXplorer (STAR-X) science goals are to discover what powers the most violent explosions in the Universe, understand how black holes grow across cosmic time and mass scale, and measure how structure formation heats the majority of baryons in the Universe. To achieve these goals, STAR-X requires a powerful X-ray telescope with a large field of view, large collecting area, and excellent point spread function. The STAR-X instrument, the X-Ray Telescope Assembly (XTA), meets these requirements using a powerful X-ray mirror technology based on precision-polished single crystal silicon and a mature CCD detector technology. The XTA is composed of three major subsystems: an X-ray Mirror Assembly (MA) of high resolution, lightweight mirror segments fabricated out of single crystal silicon; a Focal Plane Assembly (FPA) made of back-illuminated CCD's capable of detecting X-rays with excellent quantum efficiency; and a composite Telescope Tube that structurally links the MA and FPA. The MA consists of 5,972 silicon mirror segments mounted into five subassemblies called meta-shells. A meta-shell is constructed from an annular central structural shell covered with interlocking layers of mirror segments. This paper describes the requirements, design, and analysis of the XTA subsystems with particular focus on the MA.

  12. The STAR-X X-Ray Telescope Assembly (XTA)

    NASA Astrophysics Data System (ADS)

    McClelland, Ryan S.

    2017-08-01

    The Survey and Time-domain Astrophysical Research eXplorer (STAR-X) science goals are to discover what powers the most violent explosions in the Universe, understand how black holes grow across cosmic time and mass scale, and measure how structure formation heats the majority of baryons in the Universe. To achieve these goals, STAR-X requires a powerful X-ray telescope with a large field of view, large collecting area, and excellent point spread function. The STAR-X instrument, the X-Ray Telescope Assembly (XTA), meets these requirements using a powerful X-ray mirror technology based on precision-polished single crystal silicon and a mature CCD detector technology. The XTA is composed of three major subsystems: an X-ray Mirror Assembly (MA) of high resolution, lightweight mirror segments fabricated out of single crystal silicon; a Focal Plane Assembly (FPA) made of back-illuminated CCDs capable of detecting X-rays with excellent quantum efficiency; and a composite Telescope Tube that structurally links the MA and FPA. The MA consists of 5,972 silicon mirror segments mounted into five subassemblies called metashells. A meta-shell is constructed from an annular central structural shell covered with interlocking layers of mirror segments. This paper describes the requirements, design, and analysis of the XTA subsystems with particular focus on the MA.

  13. Pollen structure visualization using high-resolution laboratory-based hard X-ray tomography.

    PubMed

    Li, Qiong; Gluch, Jürgen; Krüger, Peter; Gall, Martin; Neinhuis, Christoph; Zschech, Ehrenfried

    2016-10-14

    A laboratory-based X-ray microscope is used to investigate the 3D structure of unstained whole pollen grains. For the first time, high-resolution laboratory-based hard X-ray microscopy is applied to study pollen grains. Based on the efficient acquisition of statistically relevant information-rich images using Zernike phase contrast, both surface- and internal structures of pine pollen - including exine, intine and cellular structures - are clearly visualized. The specific volumes of these structures are calculated from the tomographic data. The systematic three-dimensional study of pollen grains provides morphological and structural information about taxonomic characters that are essential in palynology. Such studies have a direct impact on disciplines such as forestry, agriculture, horticulture, plant breeding and biodiversity. Copyright © 2016 Elsevier Inc. All rights reserved.

  14. Dark-field X-ray microscopy for multiscale structural characterization

    NASA Astrophysics Data System (ADS)

    Simons, H.; King, A.; Ludwig, W.; Detlefs, C.; Pantleon, W.; Schmidt, S.; Snigireva, I.; Snigirev, A.; Poulsen, H. F.

    2015-01-01

    Many physical and mechanical properties of crystalline materials depend strongly on their internal structure, which is typically organized into grains and domains on several length scales. Here we present dark-field X-ray microscopy; a non-destructive microscopy technique for the three-dimensional mapping of orientations and stresses on lengths scales from 100 nm to 1 mm within embedded sampling volumes. The technique, which allows ‘zooming’ in and out in both direct and angular space, is demonstrated by an annealing study of plastically deformed aluminium. Facilitating the direct study of the interactions between crystalline elements is a key step towards the formulation and validation of multiscale models that account for the entire heterogeneity of a material. Furthermore, dark-field X-ray microscopy is well suited to applied topics, where the structural evolution of internal nanoscale elements (for example, positioned at interfaces) is crucial to the performance and lifetime of macro-scale devices and components thereof.

  15. X-ray radiative transfer in protoplanetary disks. The role of dust and X-ray background fields

    NASA Astrophysics Data System (ADS)

    Rab, Ch.; Güdel, M.; Woitke, P.; Kamp, I.; Thi, W.-F.; Min, M.; Aresu, G.; Meijerink, R.

    2018-01-01

    Context. The X-ray luminosities of T Tauri stars are about two to four orders of magnitude higher than the luminosity of the contemporary Sun. As these stars are born in clusters, their disks are not only irradiated by their parent star but also by an X-ray background field produced by the cluster members. Aims: We aim to quantify the impact of X-ray background fields produced by young embedded clusters on the chemical structure of disks. Further, we want to investigate the importance of the dust for X-ray radiative transfer in disks. Methods: We present a new X-ray radiative transfer module for the radiation thermo-chemical disk code PRODIMO (PROtoplanetary DIsk MOdel), which includes X-ray scattering and absorption by both the gas and dust component. The X-ray dust opacities can be calculated for various dust compositions and dust-size distributions. For the X-ray radiative transfer we consider irradiation by the star and by X-ray background fields. To study the impact of X-rays on the chemical structure of disks we use the well established disk ionization tracers N2H+ and HCO+. Results: For evolved dust populations (e.g. grain growth), X-ray opacities are mostly dominated by the gas; only for photon energies E ≳ 5-10 keV do dust opacities become relevant. Consequently the local disk X-ray radiation field is only affected in dense regions close to the disk midplane. X-ray background fields can dominate the local X-ray disk ionization rate for disk radii r ≳ 20 au. However, the N2H+ and HCO+ column densities are only significantly affected in cases of low cosmic-ray ionization rates (≲10-19 s-1), or if the background flux is at least a factor of ten higher than the flux level of ≈10-5 erg cm-2 s-1 expected for clusters typical for the solar vicinity. Conclusions: Observable signatures of X-ray background fields in low-mass star-formation regions, like Taurus, are only expected for cluster members experiencing a strong X-ray background field (e.g. due to

  16. Stages in molecular beam epitaxy growth of GaAs nanowires studied by x-ray diffraction.

    PubMed

    Mariager, Simon O; Lauridsen, Søren L; Sørensen, Claus B; Dohn, Asmus; Willmott, Phillip R; Nygård, Jesper; Feidenhans'l, Robert

    2010-03-19

    GaAs nanowires were grown by molecular beam epitaxy and studied by glancing-angle x-ray diffraction during five different stages of the growth process. An entire forest of randomly positioned epitaxial nanowires was sampled simultaneously and a large variation in the Au-Ga catalyst was found. Au, AuGa, AuGa(2) and the hexagonal beta phase were all identified in several orientations and in similar amounts. The nanowires are shown to consist of regular zinc blende crystal, its twin and the hexagonal wurtzite. The evolution of the various Au-Ga catalysts and the development in the twin to the wurtzite abundance ratio indicate that the Au catalyst is saturated upon initiation of growth leading to an increased amount of wurtzite structure in the wires. A specular x-ray scan identifies the various Au-Ga alloys, three Au lattice constants and a rough interface between nanowires and catalyst. Reciprocal space maps were obtained around Au Bragg points and show the development of the Au catalyst from a distribution largely oriented with respect to the lattice to a non-uniform distribution with several well-defined lattice constants.

  17. Imaging performance of a hybrid x-ray computed tomography-fluorescence molecular tomography system using priors.

    PubMed

    Ale, Angelique; Schulz, Ralf B; Sarantopoulos, Athanasios; Ntziachristos, Vasilis

    2010-05-01

    The performance is studied of two newly introduced and previously suggested methods that incorporate priors into inversion schemes associated with data from a recently developed hybrid x-ray computed tomography and fluorescence molecular tomography system, the latter based on CCD camera photon detection. The unique data set studied attains accurately registered data of high spatially sampled photon fields propagating through tissue along 360 degrees projections. Approaches that incorporate structural prior information were included in the inverse problem by adding a penalty term to the minimization function utilized for image reconstructions. Results were compared as to their performance with simulated and experimental data from a lung inflammation animal model and against the inversions achieved when not using priors. The importance of using priors over stand-alone inversions is also showcased with high spatial sampling simulated and experimental data. The approach of optimal performance in resolving fluorescent biodistribution in small animals is also discussed. Inclusion of prior information from x-ray CT data in the reconstruction of the fluorescence biodistribution leads to improved agreement between the reconstruction and validation images for both simulated and experimental data.

  18. Liquid Structure of CO 2 –Reactive Aprotic Heterocyclic Anion Ionic Liquids from X-ray Scattering and Molecular Dynamics

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sheridan, Quintin R.; Oh, Seungmin; Morales-Collazo, Oscar

    2016-11-23

    A combination of X-ray scattering experiments and molecular dynamics simulations were conducted to investigate the structure of ionic liquids (ILs) which chemically bind CO 2. The structure functions were measured and computed for four different ILs consisting of two different phosphonium cations, triethyloctylphosphonium ([P 2228] +) and trihexyltetradecylphosphonium ([P 66614] +), paired with two different aprotic heterocyclic anions which chemically react with CO 2, 2-cyanopyrrolide, and 1,2,4-triazolide. Simulations were able to reproduce the experimental structure functions, and by deconstructing the simulated structure functions, further information on the liquid structure was obtained. All structure functions of the ILs studied had threemore » primary features which have been seen before in other ILs: a prepeak near 0.3–0.4 Å–1 corresponding to polar/nonpolar domain alternation, a charge alternation peak near 0.8 Å–1, and a peak near 1.5 Å–1 due to interactions of adjacent molecules. The liquid structure functions were only mildly sensitive to the specific anion and whether or not they were reacted with CO 2. Upon reacting with CO 2, small changes were observed in the structure functions of the [P 2228] + ILs, whereas virtually no change was observed upon reacting with CO 2 in the corresponding [P 66614] + ILs. When the [P 2228] + cation was replaced with the [P 66614] + cation, there was a significant increase in the intensities of the prepeak and adjacency interaction peak. While many of the liquid structure functions are similar, the actual liquid structures differ as demonstrated by computed spatial distribution functions.« less

  19. X-ray superbubbles

    NASA Technical Reports Server (NTRS)

    Cash, W.

    1983-01-01

    Four regions of the galaxy, the Cygnus Superbubble, the Eta Carina complex, the Orion/Eridanus complex, and the Gum Nebula, are discussed as examples of collective effects in the interstellar medium. All four regions share certain features, indicating a common structure. The selection effects which determine the observable X-ray properties of the superbubbles are discussed, and it is demonstrated that only a very few more in our Galaxy can be detected in X rays. X-ray observation of extragalactic superbubbles is shown to be possible but requires the capabilities of a large, high quality, AXAF class observatory.

  20. Indus-2 X-ray lithography beamline for X-ray optics and material science applications

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Dhamgaye, V. P., E-mail: vishal@rrcat.gov.in; Lodha, G. S., E-mail: vishal@rrcat.gov.in

    2014-04-24

    X-ray lithography is an ideal technique by which high aspect ratio and high spatial resolution micro/nano structures are fabricated using X-rays from synchrotron radiation source. The technique has been used for fabricating optics (X-ray, visible and infrared), sensors and actuators, fluidics and photonics. A beamline for X-ray lithography is operational on Indus-2. The beamline offers wide lithographic window from 1-40keV photon energy and wide beam for producing microstructures in polymers upto size ∼100mm × 100mm. X-ray exposures are possible in air, vacuum and He gas environment. The air based exposures enables the X-ray irradiation of resist for lithography and alsomore » irradiation of biological and liquid samples.« less

  1. Local Structure Determination of Carbon/Nickel Ferrite Composite Nanofibers Probed by X-ray Absorption Spectroscopy.

    PubMed

    Nilmoung, Sukunya; Kidkhunthod, Pinit; Maensiri, Santi

    2015-11-01

    Carbon/NiFe2O4 composite nanofibers have been successfully prepared by electrospinning method using a various concentration solution of Ni and Fe nitrates dispersed into polyacrylonitride (PAN) solution in N,N' dimethylformamide. The phase and mophology of PAN/NiFe2O4 composite samples were characterized and investigated by X-ray diffraction and scanning electron microscopy. The magnetic properties of the prepared samples were measured at ambient temperature by a vibrating sample magnetometer. It is found that all composite samples exhibit ferromagnetism. This could be local-structurally explained by the existed oxidation states of Ni2+ and Fe3+ in the samples. Moreover, local environments around Ni and Fe ions could be revealed by X-ray absorption spectroscopy (XAS) measurement including X-ray absorption near edge structure (XANES) and Extended X-ray absorption fine structure (EXAFS).

  2. Interaction Analysis of FABP4 Inhibitors by X-ray Crystallography and Fragment Molecular Orbital Analysis.

    PubMed

    Tagami, Uno; Takahashi, Kazutoshi; Igarashi, Shunsuke; Ejima, Chieko; Yoshida, Tomomi; Takeshita, Sen; Miyanaga, Wataru; Sugiki, Masayuki; Tokumasu, Munetaka; Hatanaka, Toshihiro; Kashiwagi, Tatsuki; Ishikawa, Kohki; Miyano, Hiroshi; Mizukoshi, Toshimi

    2016-04-14

    X-ray crystal structural determination of FABP4 in complex with four inhibitors revealed the complex binding modes, and the resulting observations led to improvement of the inhibitory potency of FABP4 inhibitors. However, the detailed structure-activity relationship (SAR) could not be explained from these structural observations. For a more detailed understanding of the interactions between FABP4 and inhibitors, fragment molecular orbital analyses were performed. These analyses revealed that the total interfragment interaction energies of FABP4 and each inhibitor correlated with the ranking of the K i value for the four inhibitors. Furthermore, interactions between each inhibitor and amino acid residues in FABP4 were identified. The oxygen atom of Lys58 in FABP4 was found to be very important for strong interactions with FABP4. These results might provide useful information for the development of novel potent FABP4 inhibitors.

  3. Non-destructive X-ray examination of weft knitted wire structures

    NASA Astrophysics Data System (ADS)

    Obermann, M.; Ellouz, M.; Aumann, S.; Martens, Y.; Bartelt, P.; Klöcker, M.; Kordisch, T.; Ehrmann, A.; Weber, M. O.

    2016-07-01

    Conductive yarns or wires are often integrated in smart textiles to enable data or energy transmission. In woven fabrics, these conductive parts are fixed at defined positions and thus protected from external loads. Knitted fabrics, however, have relatively loose structures, resulting in higher impacts of possible mechanical forces on the individual yarns. Hence, metallic wires with smaller diameters in particular are prone to break when integrated in knitted fabrics. In a recent project, wires of various materials including copper, silver and nickel with diameters varying between 0.05 mm and 0.23 mm were knitted in combination with textile yarns. Hand flat knitting machines of appropriate gauges were used to produce different structures. On these samples, non-destructive examinations, using an industrial X-ray system Seifert x|cube (225 kV) equipped with a minifocus X-ray tube, were carried out, directly after knitting as well as after different mechanical treatments (tensile, burst, and washing tests). In this way, structural changes of the stitch geometry could be visualized before failure. In this paper, the loop geometries in the knitted fabrics are depicted depending on knitted structures, wire properties and the applied mechanical load. Consequently, it is shown which metallic wires and yarns are most suitable to be integrated into knitted smart textiles.

  4. Incorporation of Cadmium and Nickel into Ferrite Spinel Solid Solution: X-ray Diffraction and X-ray Absorption Fine Structure Analyses.

    PubMed

    Su, Minhua; Liao, Changzhong; Chan, Tingshan; Shih, Kaimin; Xiao, Tangfu; Chen, Diyun; Kong, Lingjun; Song, Gang

    2018-01-16

    The feasibility of incorporating Cd and Ni in hematite was studied by investigating the interaction mechanism for the formation of Cd x Ni 1-x Fe 2 O 4 solid solutions (CNFs) from CdO, NiO, and α-Fe 2 O 3 . X-ray diffraction results showed that the CNFs crystallized into spinel structures with increasing lattice parameters as the Cd content in the precursors was increased. Cd 2+ ions were found to occupy the tetrahedral sites, as evidenced by Rietveld refinement and extended X-ray absorption fine structure analyses. The incorporation of Cd and Ni into ferrite spinel solid solution strongly relied on the processing parameters. The incorporation of Cd and Ni into the CNFs was greater at high x values (0.7 < x ≤ 1.0) than at low x values (0.0 ≤ x ≤ 0.7). A feasible treatment technique based on the investigated mechanism of CNF formation was developed, involving thermal treatment of waste sludge containing Cd and Ni. Both of these metals in the waste sludge were successfully incorporated into a ferrite spinel solid solution, and the concentrations of leached Cd and Ni from this solid solution were substantially reduced, stabilizing at low levels. This research offers a highly promising approach for treating the Cd and Ni content frequently encountered in electronic waste and its treatment residues.

  5. Insights into the Distinct Lithiation/Sodiation of Porous Cobalt Oxide by in Operando Synchrotron X-ray Techniques and Ab Initio Molecular Dynamics Simulations.

    PubMed

    Xu, Gui-Liang; Sheng, Tian; Chong, Lina; Ma, Tianyuan; Sun, Cheng-Jun; Zuo, Xiaobing; Liu, Di-Jia; Ren, Yang; Zhang, Xiaoyi; Liu, Yuzi; Heald, Steve M; Sun, Shi-Gang; Chen, Zonghai; Amine, Khalil

    2017-02-08

    Sodium-ion batteries (SIBs) have been considered as one of the promising power source candidates for the stationary storage industries owing to the much lower cost of sodium than lithium. It is well-known that the electrode materials largely determine the energy density of the battery systems. However, recent discoveries on the electrode materials showed that most of them present distinct lithium and sodium storage performance, which is not yet well understood. In this work, we performed a comparative understanding on the structural changes of porous cobalt oxide during its electrochemical lithiation and sodiation process by in operando synchrotron small angel X-ray scattering, X-ray diffraction, and X-ray absorption spectroscopy. It was found that compared to the lithiation process, the porous cobalt oxide undergoes less pore structure changes, oxidation state, and local structure changes as well as crystal structure evolution during its sodiation process, which is attributed to the intrinsic low sodiation activity of cobalt oxide as evidenced by ab initio molecular dynamics simulations. Moreover, it was indicated that the sodiation activity of metal sulfides is higher than that of metal oxides, indicating a better candidate for SIBs. Such understanding is crucial for future design and improvement of high-performance electrode materials for SIBs.

  6. X-ray Spectral Formation In High-mass X-ray Binaries: The Case Of Vela X-1

    NASA Astrophysics Data System (ADS)

    Akiyama, Shizuka; Mauche, C. W.; Liedahl, D. A.; Plewa, T.

    2007-05-01

    We are working to develop improved models of radiatively-driven mass flows in the presence of an X-ray source -- such as in X-ray binaries, cataclysmic variables, and active galactic nuclei -- in order to infer the physical properties that determine the X-ray spectra of such systems. The models integrate a three-dimensional time-dependent hydrodynamics capability (FLASH); a comprehensive and uniform set of atomic data, improved calculations of the line force multiplier that account for X-ray photoionization and non-LTE population kinetics, and X-ray emission-line models appropriate to X-ray photoionized plasmas (HULLAC); and a Monte Carlo radiation transport code that simulates Compton scattering and recombination cascades following photoionization. As a test bed, we have simulated a high-mass X-ray binary with parameters appropriate to Vela X-1. While the orbital and stellar parameters of this system are well constrained, the physics of X-ray spectral formation is less well understood because the canonical analytical wind velocity profile of OB stars does not account for the dynamical and radiative feedback effects due to the rotation of the system and to the irradiation of the stellar wind by X-rays from the neutron star. We discuss the dynamical wind structure of Vela X-1 as determined by the FLASH simulation, where in the binary the X-ray emission features originate, and how the spatial and spectral properties of the X-ray emission features are modified by Compton scattering, photoabsorption, and fluorescent emission. This work was performed under the auspices of the U.S. Department of Energy by University of California, Lawrence Livermore National Laboratory under Contract W-7405-Eng-48.

  7. Yes, one can obtain better quality structures from routine X-ray data collection.

    PubMed

    Sanjuan-Szklarz, W Fabiola; Hoser, Anna A; Gutmann, Matthias; Madsen, Anders Østergaard; Woźniak, Krzysztof

    2016-01-01

    Single-crystal X-ray diffraction structural results for benzidine dihydrochloride, hydrated and protonated N,N,N,N-peri(dimethylamino)naphthalene chloride, triptycene, dichlorodimethyltriptycene and decamethylferrocene have been analysed. A critical discussion of the dependence of structural and thermal parameters on resolution for these compounds is presented. Results of refinements against X-ray data, cut off to different resolutions from the high-resolution data files, are compared to structural models derived from neutron diffraction experiments. The Independent Atom Model (IAM) and the Transferable Aspherical Atom Model (TAAM) are tested. The average differences between the X-ray and neutron structural parameters (with the exception of valence angles defined by H atoms) decrease with the increasing 2θmax angle. The scale of differences between X-ray and neutron geometrical parameters can be significantly reduced when data are collected to the higher, than commonly used, 2θmax diffraction angles (for Mo Kα 2θmax > 65°). The final structural and thermal parameters obtained for the studied compounds using TAAM refinement are in better agreement with the neutron values than the IAM results for all resolutions and all compounds. By using TAAM, it is still possible to obtain accurate results even from low-resolution X-ray data. This is particularly important as TAAM is easy to apply and can routinely be used to improve the quality of structural investigations [Dominiak (2015 ▸). LSDB from UBDB. University of Buffalo, USA]. We can recommend that, in order to obtain more adequate (more accurate and precise) structural and displacement parameters during the IAM model refinement, data should be collected up to the larger diffraction angles, at least, for Mo Kα radiation to 2θmax = 65° (sin θmax/λ < 0.75 Å(-1)). The TAAM approach is a very good option to obtain more adequate results even using data collected to the lower 2θmax angles. Also

  8. X-ray emission from high temperature plasmas

    NASA Technical Reports Server (NTRS)

    Harries, W. L.

    1974-01-01

    X-rays from a 25-hJ plasma focus apparatus were observed with pinhole cameras. The cameras consist of 0.4 mm diameter pinholes in 2 cm thick lead housing enclosing an X-ray intensifying screen at the image plane. Pictures recorded through thin aluminum foils or plastic sheets for X-ray energies sub gamma smaller than 15 keV show distributed X-ray emissions from the focussed plasma and from the anode surface. However, when thick absorbers are used, radial filamentary structure in the X-ray emission from the anode surface is revealed. Occasionally larger structures are observed in addition to the filaments. Possible mechanisms for the filamentary structure are discussed.

  9. Restricted active space calculations of L-edge X-ray absorption spectra: from molecular orbitals to multiplet states.

    PubMed

    Pinjari, Rahul V; Delcey, Mickaël G; Guo, Meiyuan; Odelius, Michael; Lundberg, Marcus

    2014-09-28

    The metal L-edge (2p → 3d) X-ray absorption spectra are affected by a number of different interactions: electron-electron repulsion, spin-orbit coupling, and charge transfer between metal and ligands, which makes the simulation of spectra challenging. The core restricted active space (RAS) method is an accurate and flexible approach that can be used to calculate X-ray spectra of a wide range of medium-sized systems without any symmetry constraints. Here, the applicability of the method is tested in detail by simulating three ferric (3d(5)) model systems with well-known electronic structure, viz., atomic Fe(3+), high-spin [FeCl6](3-) with ligand donor bonding, and low-spin [Fe(CN)6](3-) that also has metal backbonding. For these systems, the performance of the core RAS method, which does not require any system-dependent parameters, is comparable to that of the commonly used semi-empirical charge-transfer multiplet model. It handles orbitally degenerate ground states, accurately describes metal-ligand interactions, and includes both single and multiple excitations. The results are sensitive to the choice of orbitals in the active space and this sensitivity can be used to assign spectral features. A method has also been developed to analyze the calculated X-ray spectra using a chemically intuitive molecular orbital picture.

  10. Expression, purification, crystallization and X-ray diffraction studies of the molecular chaperone prefoldin from Homo sapiens.

    PubMed

    Aikawa, Yoshiki; Kida, Hiroshi; Nishitani, Yuichi; Miki, Kunio

    2015-09-01

    Proper protein folding is an essential process for all organisms. Prefoldin (PFD) is a molecular chaperone that assists protein folding by delivering non-native proteins to group II chaperonin. A heterohexamer of eukaryotic PFD has been shown to specifically recognize and deliver non-native actin and tubulin to chaperonin-containing TCP-1 (CCT), but the mechanism of specific recognition is still unclear. To determine its crystal structure, recombinant human PFD was reconstituted, purified and crystallized. X-ray diffraction data were collected to 4.7 Å resolution. The crystals belonged to space group P21212, with unit-cell parameters a = 123.2, b = 152.4, c = 105.9 Å.

  11. Molecular structure of P2X receptors.

    PubMed

    Egan, Terrance M; Cox, Jane A; Voigt, Mark M

    2004-01-01

    P2X receptors are ligand-gated ion channels that transduce many of the physiological effects of extracellular ATP. There has been a dramatic increase in awareness of these receptors over the past 5 or so years, in great part due to their molecular cloning and characterization. The availability of cDNA clones for the various subunits has led to rapid progress in identifying their tissue-specific expression, resulting in new ideas concerning the functional roles these receptors might play in physiological and pathophysiological processes. In addition, molecular approaches have yielded much information regarding the structure and function of the receptor proteins themselves. In this review we seek to review recent findings concerning the molecular determinants of receptor-channel function, with particular focus on ligand binding and gating, ion selectivity, and subunit assembly.

  12. X-ray radiation generated by a beam of relativistic electrons in composite structure

    NASA Astrophysics Data System (ADS)

    Blazhevich, S. V.; Noskov, A. V.

    2018-04-01

    The dynamic theory of coherent X-ray radiation generated by a beam of relativistic electrons in the three-layer structure consisting of an amorphous layer, a vacuum (air) layer and a single crystal has been developed. The phenomenon description is based on two main radiation mechanisms, namely, parametric X-ray radiation (PXR) and diffracted transition radiation (DTR). The possibility to increase the spectral-angular density of DTR under the condition of constructive interference of the transition radiation waves from different boundaries of such a structure has been demonstrated. It is shown that little changes in the layers thicknesses should not cause a considerable change in the interference picture, for example, the transition of constructive interference into destructive one. It means that in the considered process the conditions of constructive interference are enough stable to use them for increasing the intensity of X-ray source that can be created based on the interaction of relativistic electrons with such a structure.

  13. Diffuse X-ray sky in the Galactic center

    NASA Astrophysics Data System (ADS)

    Koyama, Katsuji

    2018-01-01

    The Galactic diffuse X-ray emission (GDXE) in the Milky Way Galaxy is spatially and spectrally decomposed into the Galactic center X-ray emission (GCXE), the Galactic ridge X-ray emission (GRXE), and the Galactic bulge X-ray emission (GBXE). The X-ray spectra of the GDXE are characterized by the strong K-shell lines of the highly ionized atoms, and the brightest lines are the K-shell transition (principal quantum number transition of n = 2 → 1) of neutral iron (Fe I-Kα), He-like iron (Fe XXV-Heα), and He-like sulfur (S XV-Heα). Accordingly, the GDXE is composed of a high-temperature plasma of ˜7 keV (HTP) and a low-temperature plasma of ˜1 keV, which emit the Fe XXV-Heα and S XV-Heα lines, respectively. The Fe I-Kα line is emitted from nearly neutral irons, and hence the third component of the GDXE is a cool gas (CG). The Fe I-Kα distribution in the GCXE region is clumpy (Fe I-Kα clump), associated with giant molecular cloud (MC) complexes (Sagittarius A, B, C, D, and E) in the central molecular zone. The origin of the Fe I-Kα clumps is the fluorescence and Thomson scattering from the MCs irradiated by past big flares of the supermassive black hole Sagittarius A*. The scale heights and equivalent widths of the Fe I-Kα, Fe XXV-Heα, and Fe XXVI-Lyα (n = 2 → 1 transition of H-like iron) lines are different among the GCXE, GBXE, and GRXE. Therefore, their structures and origins are separately examined. This paper gives an overview of the research history and the present understandings of the GDXE, while in particular focusing on the origin of the HTP and CG in the GCXE.

  14. Generation of High Brightness X-rays with the PLEIADES Thomson X-ray Source

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Brown, W J; Anderson, S G; Barty, C P J

    2003-05-28

    The use of short laser pulses to generate high peak intensity, ultra-short x-ray pulses enables exciting new experimental capabilities, such as femtosecond pump-probe experiments used to temporally resolve material structural dynamics on atomic time scales. PLEIADES (Picosecond Laser Electron InterAction for Dynamic Evaluation of Structures) is a next generation Thomson scattering x-ray source being developed at Lawrence Livermore National Laboratory (LLNL). Ultra-fast picosecond x-rays (10-200 keV) are generated by colliding an energetic electron beam (20-100 MeV) with a high intensity, sub-ps, 800 nm laser pulse. The peak brightness of the source is expected to exceed 10{sup 20} photons/s/0.1% bandwidth/mm2/mrad2. Simulationsmore » of the electron beam production, transport, and final focus are presented. Electron beam measurements, including emittance and final focus spot size are also presented and compared to simulation results. Measurements of x-ray production are also reported and compared to theoretical calculations.« less

  15. Two-dimensional imaging detectors for structural biology with X-ray lasers.

    PubMed

    Denes, Peter

    2014-07-17

    Our ability to harness the advances in microelectronics over the past decade(s) for X-ray detection has resulted in significant improvements in the state of the art. Biology with X-ray free-electron lasers present daunting detector challenges: all of the photons arrive at the same time, and individual high peak power pulses must be read out shot-by-shot. Direct X-ray detection in silicon pixel detectors--monolithic or hybrid--are the standard for XFELs today. For structural biology, improvements are needed for today's 10-100 Hz XFELs, and further improvements are required for tomorrow's 10+ kHz XFELs. This article will discuss detector challenges, why they arise and ways to overcome them, along with the current state of the art. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  16. Monitoring X-Ray Emission from X-Ray Bursters

    NASA Technical Reports Server (NTRS)

    Halpern, Jules P.; Kaaret, Philip

    1999-01-01

    The scientific goal of this project was to monitor a selected sample of x-ray bursters using data from the All-Sky Monitor (ASM) on the Rossi X-Ray Timing Explorer together with data from the Burst and Transient Source Experiment (BATSE) on the Compton Gamma-Ray Observatory to study the long-term temporal evolution of these sources in the x-ray and hard x-ray bands. The project was closely related to "Long-Term Hard X-Ray Monitoring of X-Ray Bursters", NASA project NAG5-3891, and and "Hard x-ray emission of x-ray bursters", NASA project NAG5-4633, and shares publications in common with both of these. The project involved preparation of software for use in monitoring and then the actual monitoring itself. These efforts have lead to results directly from the ASM data and also from Target of Opportunity Observations (TOO) made with the Rossi X-Ray Timing Explorer based on detection of transient hard x-ray outbursts with the ASM and BATSE.

  17. X-ray crystallography and its impact on understanding bacterial cell wall remodeling processes.

    PubMed

    Büttner, Felix Michael; Renner-Schneck, Michaela; Stehle, Thilo

    2015-02-01

    The molecular structure of matter defines its properties and function. This is especially true for biological macromolecules such as proteins, which participate in virtually all biochemical processes. A three dimensional structural model of a protein is thus essential for the detailed understanding of its physiological function and the characterization of essential properties such as ligand binding and reaction mechanism. X-ray crystallography is a well-established technique that has been used for many years, but it is still by far the most widely used method for structure determination. A particular strength of this technique is the elucidation of atomic details of molecular interactions, thus providing an invaluable tool for a multitude of scientific projects ranging from the structural classification of macromolecules over the validation of enzymatic mechanisms or the understanding of host-pathogen interactions to structure-guided drug design. In the first part of this review, we describe essential methodological and practical aspects of X-ray crystallography. We provide some pointers that should allow researchers without a background in structural biology to assess the overall quality and reliability of a crystal structure. To highlight its potential, we then survey the impact X-ray crystallography has had on advancing an understanding of a class of enzymes that modify the bacterial cell wall. A substantial number of different bacterial amidase structures have been solved, mostly by X-ray crystallography. Comparison of these structures highlights conserved as well as divergent features. In combination with functional analyses, structural information on these enzymes has therefore proven to be a valuable template not only for understanding their mechanism of catalysis, but also for targeted interference with substrate binding. Copyright © 2015 Elsevier GmbH. All rights reserved.

  18. X-rays from young stars: A summary of highlights from the XMM-Newton Extended Survey of the Taurus Molecular Cloud (XEST)

    NASA Astrophysics Data System (ADS)

    Güdel, M.

    2008-02-01

    The XMM-Newton Extended Survey of the Taurus Molecular Cloud (XEST) is a survey of the nearest large star-forming region, the Taurus Molecular Cloud (TMC), making use of all instruments on board the XMM-Newton X-ray observatory. The survey, presently still growing, has provided unprecedented spectroscopic results from nearly every observed T Tauri star, and from ≈50% of the studied brown dwarfs and protostars. The survey includes the first coherent statistical sample of high-resolution spectra of T Tauri stars, and is accompanied by an U-band/ultraviolet imaging photometric survey of the TMC. XEST led to the discovery of new, systematic X-ray features not possible before with smaller samples, in particular the X-ray soft excess in classical T Tauri stars and the Two-Absorber X-ray (TAX) spectra of jet-driving T Tauri stars. This paper summarizes highlights from XEST and reviews the key role of this large project.

  19. Structure of N-(5-ethyl-[1,3,4]-thiadiazole-2-yl)toluenesulfonamide by combined X-ray powder diffraction, 13C solid-state NMR and molecular modelling.

    PubMed

    Hangan, Adriana; Borodi, Gheorghe; Filip, Xenia; Tripon, Carmen; Morari, Cristian; Oprean, Luminita; Filip, Claudiu

    2010-12-01

    The crystal structure solution of the title compound is determined from microcrystalline powder using a multi-technique approach that combines X-ray powder diffraction (XRPD) data analysis based on direct-space methods with information from (13)C solid-state NMR (SSNMR), and molecular modelling using the GIPAW (gauge including projector augmented-wave) method. The space group is Pbca with one molecule in the asymmetric unit. The proposed methodology proves very useful for unambiguously characterizing the supramolecular arrangement adopted by the N-(5-ethyl-[1,3,4]-thiadiazole-2-yl)toluenesulfonamide molecules in the crystal, which consists of extended double strands held together by C-H···π non-covalent interactions.

  20. X-ray Crystallography Facility

    NASA Technical Reports Server (NTRS)

    1999-01-01

    University of Alabama engineer Lance Weiss briefs NASA astronaut Dr. Bornie Dunbar about the design and capabilities of the X-ray Crystallography Facility under development at the Center for Macromolecular Crystallography of the University of Alabama at Birmingham, AL, April 21, 1999. The X-ray Crystallography Facility is designed to speed the collection of protein structure information from crystals grown aboard the International Space Station. By measuring and mapping the protein crystal structure in space, researchers will avoid exposing the delicate crystals to the rigors of space travel and make important research data available to scientists much faster. The X-ray Crystallography facility is being designed and developed by the Center for Macromolecular Crystallography of the University of Alabama at Birmingham, a NASA Commercial Space Center.

  1. X-ray Crystallography Facility

    NASA Technical Reports Server (NTRS)

    1999-01-01

    University of Alabama engineer Stacey Giles briefs NASA astronaut Dr. Bornie Dunbar about the design and capabilities of the X-ray Crystallography Facility under development at the Center for Macromolecular Crystallography of the University of Alabama at Birmingham, AL, April 21, 1999. The X-ray Crystallography Facility is designed to speed the collection of protein structure information from crystals grown aboard the International Space Station. By measuring and mapping the protein crystal structure in space, researchers will avoid exposing the delicate crystals to the rigors of space travel and make important research data available to scientists much faster. The X-ray Crystallography facility is being designed and developed by the Center for Macromolecular Crystallography of the University of Alabama at Birmingham, a NASA Commercial Space Center.

  2. Protein structural dynamics in solution unveiled via 100-ps time-resolved x-ray scattering.

    PubMed

    Cho, Hyun Sun; Dashdorj, Naranbaatar; Schotte, Friedrich; Graber, Timothy; Henning, Robert; Anfinrud, Philip

    2010-04-20

    We have developed a time-resolved x-ray scattering diffractometer capable of probing structural dynamics of proteins in solution with 100-ps time resolution. This diffractometer, developed on the ID14B BioCARS (Consortium for Advanced Radiation Sources) beamline at the Advanced Photon Source, records x-ray scattering snapshots over a broad range of q spanning 0.02-2.5 A(-1), thereby providing simultaneous coverage of the small-angle x-ray scattering (SAXS) and wide-angle x-ray scattering (WAXS) regions. To demonstrate its capabilities, we have tracked structural changes in myoglobin as it undergoes a photolysis-induced transition from its carbon monoxy form (MbCO) to its deoxy form (Mb). Though the differences between the MbCO and Mb crystal structures are small (rmsd < 0.2 A), time-resolved x-ray scattering differences recorded over 8 decades of time from 100 ps to 10 ms are rich in structure, illustrating the sensitivity of this technique. A strong, negative-going feature in the SAXS region appears promptly and corresponds to a sudden > 22 A(3) volume expansion of the protein. The ensuing conformational relaxation causes the protein to contract to a volume approximately 2 A(3) larger than MbCO within approximately 10 ns. On the timescale for CO escape from the primary docking site, another change in the SAXS/WAXS fingerprint appears, demonstrating sensitivity to the location of the dissociated CO. Global analysis of the SAXS/WAXS patterns recovered time-independent scattering fingerprints for four intermediate states of Mb. These SAXS/WAXS fingerprints provide stringent constraints for putative models of conformational states and structural transitions between them.

  3. Do All X-ray Structures of Protein-Ligand Complexes Represent Functional States? EPOR, a Case Study.

    PubMed

    Corbett, Michael S P; Mark, Alan E; Poger, David

    2017-02-28

    Based on differences between the x-ray crystal structures of ligand-bound and unbound forms, the activation of the erythropoietin receptor (EPOR) was initially proposed to involve a cross-action scissorlike motion. However, the validity of the motions involved in the scissorlike model has been recently challenged. Here, atomistic molecular dynamics simulations are used to examine the structure of the extracellular domain of the EPOR dimer in the presence and absence of erythropoietin and a series of agonistic or antagonistic mimetic peptides free in solution. The simulations suggest that in the absence of crystal packing effects, the EPOR chains in the different dimers adopt very similar conformations with no clear distinction between the agonist and antagonist-bound complexes. This questions whether the available x-ray crystal structures of EPOR truly represent active or inactive conformations. The study demonstrates the difficulty in using such structures to infer a mechanism of action, especially in the case of membrane receptors where just part of the structure has been considered in addition to potential confounding effects that arise from the comparison of structures in a crystal as opposed to a membrane environment. The work highlights the danger of assigning functional significance to small differences between structures of proteins bound to different ligands in a crystal environment without consideration of the effects of the crystal lattice and thermal motion. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  4. Discovery of Spatial and Spectral Structure in the X-Ray Emission from the Crab Nebula

    NASA Technical Reports Server (NTRS)

    Weisskopf, M.; Hester, J. J.; Tennant, A. F.; Elsner, R. F.; Schulz, N. S.; Marshall, H. L.; Karovska, M.; Nichols, J. S.; Swartz, D. A.; Kolodziejczak, J. J.

    2000-01-01

    The Chandra X-ray Observatory observed the Crab Nebula and Pulsar During orbital calibration. Zeroth-order images with the High-Energy Transmission Grating (HETG) read-out by the Advanced CCD Imaging Spectrometer spectroscopy array (ACIS-S) show a striking richness of X-ray structure, at a resolution comparable to that of the best ground-based visible-light observations. The HETG-ACIS-S images reveal, for the first time, an X-ray knots along the inner ring and (perhaps) along the inward extension of the X-ray jet. Although complicated by instrumental effects and the brightness of the Crab Nebula, the spectrometric analysis shows systematic variations of the X-ray spectrum throughout the Nebula.

  5. Structure of rare-earth chalcogenide glasses by neutron and x-ray diffraction

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Drewitt, James W. E.; Salmon, Philip S.; Zeidler, Anita

    The method of neutron diffraction with isomorphic substitution was used to measure the structure of the rare-earth chalcogenide glasses (R 2X 3) 0.07(Ga 2X 3) 0.33(GeX 2) 0.60 with R = La or Ce and X = S or Se. X-ray diffraction was also used to measure the structure of the sulphide glass. The results are consistent with networks that are built from GeX 4 and GaX 4 tetrahedra, and give R-S and R-Se coordination numbers of 8.0(2) and 8.5(4), respectively. The minimum nearest-neighbour R-R distance associated with rare-earth clustering is discussed.

  6. Structure of rare-earth chalcogenide glasses by neutron and x-ray diffraction

    DOE PAGES

    Drewitt, James W. E.; Salmon, Philip S.; Zeidler, Anita; ...

    2017-04-28

    The method of neutron diffraction with isomorphic substitution was used to measure the structure of the rare-earth chalcogenide glasses (R 2X 3) 0.07(Ga 2X 3) 0.33(GeX 2) 0.60 with R = La or Ce and X = S or Se. X-ray diffraction was also used to measure the structure of the sulphide glass. The results are consistent with networks that are built from GeX 4 and GaX 4 tetrahedra, and give R-S and R-Se coordination numbers of 8.0(2) and 8.5(4), respectively. The minimum nearest-neighbour R-R distance associated with rare-earth clustering is discussed.

  7. Effect of Pressure on Valence and Structural Properties of YbFe 2 Ge 2 Heavy Fermion Compound—A Combined Inelastic X-ray Spectroscopy, X-ray Diffraction, and Theoretical Investigation

    DOE PAGES

    Kumar, Ravhi S.; Svane, Axel; Vaitheeswaran, Ganapathy; ...

    2015-10-19

    We measured the crystal structure and the Yb valence of the YbFe 2Ge 2 heavy fermion compound at room temperature and under high pressures using high-pressure powder X-ray diffraction and X-ray absorption spectroscopy via both partial fluorescence yield and resonant inelastic X-ray emission techniques. Moreover, the measurements are complemented by first-principles density functional theoretical calculations using the self-interaction corrected local spin density approximation investigating in particular the magnetic structure and the Yb valence. Finally, while the ThCr 2Si 2-type tetragonal (I4/mmm) structure is stable up to 53 GPa, the X-ray emission results show an increase of the Yb valence frommore » v = 2.72(2) at ambient pressure to v = 2.93(3) at ~9 GPa, where at low temperature a pressure-induced quantum critical state was reported.« less

  8. Solution Structures of Highly Active Molecular Ir Water-Oxidation Catalysts from Density Functional Theory Combined with High-Energy X-ray Scattering and EXAFS Spectroscopy.

    PubMed

    Yang, Ke R; Matula, Adam J; Kwon, Gihan; Hong, Jiyun; Sheehan, Stafford W; Thomsen, Julianne M; Brudvig, Gary W; Crabtree, Robert H; Tiede, David M; Chen, Lin X; Batista, Victor S

    2016-05-04

    The solution structures of highly active Ir water-oxidation catalysts are elucidated by combining density functional theory, high-energy X-ray scattering (HEXS), and extended X-ray absorption fine structure (EXAFS) spectroscopy. We find that the catalysts are Ir dimers with mono-μ-O cores and terminal anionic ligands, generated in situ through partial oxidation of a common catalyst precursor. The proposed structures are supported by (1)H and (17)O NMR, EPR, resonance Raman and UV-vis spectra, electrophoresis, etc. Our findings are particularly valuable to understand the mechanism of water oxidation by highly reactive Ir catalysts. Importantly, our DFT-EXAFS-HEXS methodology provides a new in situ technique for characterization of active species in catalytic systems.

  9. 3D visualization of subcellular structures of Schizosaccharomyces pombe by hard X-ray tomography.

    PubMed

    Yang, Y; Li, W; Liu, G; Zhang, X; Chen, J; Wu, W; Guan, Y; Xiong, Y; Tian, Y; Wu, Z

    2010-10-01

    Cellular structures of the fission yeast, Schizosaccharomyces pombe, were examined by using hard X-ray tomography. Since cells are nearly transparent to hard X-rays, Zernike phase contrast and heavy metal staining were introduced to improve image contrast. Through using such methods, images taken at 8 keV displayed sufficient contrast for observing cellular structures. The cell wall, the intracellular organelles and the entire structural organization of the whole cells were visualized in three-dimensional at a resolution better than 100 nm. Comparison between phase contrast and absorption contrast was also made, indicating the obvious advantage of phase contrast for cellular imaging at this energy. Our results demonstrate that hard X-ray tomography with Zernike phase contrast is suitable for cellular imaging. Its unique abilities make it have potential to become a useful tool for revealing structural information from cells, especially thick eukaryotic cells. © 2010 The Authors Journal compilation © 2010 The Royal Microscopical Society.

  10. Simultaneous small- and wide-angle scattering at high X-ray energies.

    PubMed

    Daniels, J E; Pontoni, D; Hoo, Rui Ping; Honkimäki, V

    2010-07-01

    Combined small- and wide-angle X-ray scattering (SAXS/WAXS) is a powerful technique for the study of materials at length scales ranging from atomic/molecular sizes (a few angstroms) to the mesoscopic regime ( approximately 1 nm to approximately 1 microm). A set-up to apply this technique at high X-ray energies (E > 50 keV) has been developed. Hard X-rays permit the execution of at least three classes of investigations that are significantly more difficult to perform at standard X-ray energies (8-20 keV): (i) in situ strain analysis revealing anisotropic strain behaviour both at the atomic (WAXS) as well as at the mesoscopic (SAXS) length scales, (ii) acquisition of WAXS patterns to very large q (>20 A(-1)) thus allowing atomic pair distribution function analysis (SAXS/PDF) of micro- and nano-structured materials, and (iii) utilization of complex sample environments involving thick X-ray windows and/or samples that can be penetrated only by high-energy X-rays. Using the reported set-up a time resolution of approximately two seconds was demonstrated. It is planned to further improve this time resolution in the near future.

  11. Transmission X-ray scattering as a probe for complex liquid-surface structures

    DOE PAGES

    Fukuto, Masafumi; Yang, Lin; Nykypanchuk, Dmytro; ...

    2016-01-28

    The need for functional materials calls for increasing complexity in self-assembly systems. As a result, the ability to probe both local structure and heterogeneities, such as phase-coexistence and domain morphologies, has become increasingly important to controlling self-assembly processes, including those at liquid surfaces. The traditional X-ray scattering methods for liquid surfaces, such as specular reflectivity and grazing-incidence diffraction, are not well suited to spatially resolving lateral heterogeneities due to large illuminated footprint. A possible alternative approach is to use scanning transmission X-ray scattering to simultaneously probe local intermolecular structures and heterogeneous domain morphologies on liquid surfaces. To test the feasibilitymore » of this approach, transmission small- and wide-angle X-ray scattering (TSAXS/TWAXS) studies of Langmuir films formed on water meniscus against a vertically immersed hydrophilic Si substrate were recently carried out. First-order diffraction rings were observed in TSAXS patterns from a monolayer of hexagonally packed gold nanoparticles and in TWAXS patterns from a monolayer of fluorinated fatty acids, both as a Langmuir monolayer on water meniscus and as a Langmuir–Blodgett monolayer on the substrate. The patterns taken at multiple spots have been analyzed to extract the shape of the meniscus surface and the ordered-monolayer coverage as a function of spot position. These results, together with continual improvement in the brightness and spot size of X-ray beams available at synchrotron facilities, support the possibility of using scanning-probe TSAXS/TWAXS to characterize heterogeneous structures at liquid surfaces.« less

  12. Structure of the manganese complex in photosystem II: insights from X-ray spectroscopy.

    PubMed Central

    Yachandra, Vittal K

    2002-01-01

    We have used Mn K-edge absorption and Kbeta emission spectroscopy to determine the oxidation states of the Mn complex in the various S states. We have started exploring the new technique of resonant inelastic X-ray scattering spectroscopy; this technique can be characterized as a Raman process that uses K-edge energies (1s to 4p, ca. 6550 eV) to obtain L-edge-like spectra (2p to 3d, ca. 650 eV). The relevance of these data to the oxidation states and structure of the Mn complex is presented. We have obtained extended X-ray absorption fine structure data from the S(0) and S(3) states and observed heterogeneity in the Mn-Mn distances leading us to conclude that there may be three rather than two di-mu-oxo-bridged units present per tetranuclear Mn cluster. In addition, we have obtained data using Ca and Sr X-ray spectroscopy that provide evidence for a heteronuclear Mn-Ca cluster. The possibility of three di-mu-oxo-bridged Mn-Mn moieties and the proximity of Ca is incorporated into developing structural models for the Mn cluster. The involvement of bridging and terminal O ligands of Mn in the mechanism of oxygen evolution is discussed in the context of our X-ray spectroscopy results. PMID:12437873

  13. Ab initio studies of ultrafast x-ray scattering of the photodissociation of iodine

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Debnarova, Andrea; Techert, Simone; Schmatz, Stefan

    2010-09-28

    We computationally examine various aspects of the reaction dynamics of the photodissociation and recombination of molecular iodine. We use our recently proposed formalism to calculate time-dependent x-ray scattering signal changes from first principles. Different aspects of the dynamics of this prototypical reaction are studied, such as coherent and noncoherent processes, features of structural relaxation that are periodic in time versus nonperiodic dissociative processes, as well as small electron density changes caused by electronic excitation, all with respect to x-ray scattering. We can demonstrate that wide-angle x-ray scattering offers a possibility to study the changes in electron densities in nonperiodic systems,more » which render it a suitable technique for the investigation of chemical reactions from a structural dynamics point of view.« less

  14. X-ray detectability of accreting isolated black holes in our Galaxy

    NASA Astrophysics Data System (ADS)

    Tsuna, Daichi; Kawanaka, Norita; Totani, Tomonori

    2018-06-01

    Detectability of isolated black holes (IBHs) without a companion star but emitting X-rays by accretion from dense interstellar medium (ISM) or molecular cloud gas is investigated. We calculate orbits of IBHs in the Galaxy to derive a realistic spatial distribution of IBHs for various mean values of kick velocity at their birth υavg. X-ray luminosities of these IBHs are then calculated considering various phases of ISM and molecular clouds for a wide range of the accretion efficiency λ (a ratio of the actual accretion rate to the Bondi rate) that is rather uncertain. It is found that detectable IBHs mostly reside near the Galactic Centre (GC), and hence taking the Galactic structure into account is essential. In the hard X-ray band, where identification of IBHs from other contaminating X-ray sources may be easier, the expected number of IBHs detectable by the past survey by NuSTAR towards GC is at most order unity. However, 30-100 IBHs may be detected by the future survey by FORCE with an optimistic parameter set of υavg = 50 km s-1 and λ = 0.1, implying that it may be possible to detect IBHs or constrain the model parameters.

  15. Interaction Analysis of FABP4 Inhibitors by X-ray Crystallography and Fragment Molecular Orbital Analysis

    PubMed Central

    2016-01-01

    X-ray crystal structural determination of FABP4 in complex with four inhibitors revealed the complex binding modes, and the resulting observations led to improvement of the inhibitory potency of FABP4 inhibitors. However, the detailed structure–activity relationship (SAR) could not be explained from these structural observations. For a more detailed understanding of the interactions between FABP4 and inhibitors, fragment molecular orbital analyses were performed. These analyses revealed that the total interfragment interaction energies of FABP4 and each inhibitor correlated with the ranking of the Ki value for the four inhibitors. Furthermore, interactions between each inhibitor and amino acid residues in FABP4 were identified. The oxygen atom of Lys58 in FABP4 was found to be very important for strong interactions with FABP4. These results might provide useful information for the development of novel potent FABP4 inhibitors. PMID:27096055

  16. Structural Order-Disorder Transformations Monitored by X-Ray Diffraction and Photoluminescence

    ERIC Educational Resources Information Center

    Lima, R. C.; Paris, E. C.; Leite, E. R.; Espinosa, J. W. M.; Souza, A. G.; Longo, E.

    2007-01-01

    A study was conducted to examine the structural order-disorder transformation promoted by controlled heat treatment using X-ray diffraction technique (XRD) and photoluminescence (PL) techniques as tools to monitor the degree of structural order. The experiment was observed to be versatile and easily achieved with low cost which allowed producing…

  17. NuSTAR Hard X-Ray Survey of the Galactic Center Region I: Hard X-Ray Morphology and Spectroscopy of the Diffuse Emission

    NASA Astrophysics Data System (ADS)

    Mori, Kaya; Hailey, Charles J.; Krivonos, Roman; Hong, Jaesub; Ponti, Gabriele; Bauer, Franz; Perez, Kerstin; Nynka, Melania; Zhang, Shuo; Tomsick, John A.; Alexander, David M.; Baganoff, Frederick K.; Barret, Didier; Barrière, Nicolas; Boggs, Steven E.; Canipe, Alicia M.; Christensen, Finn E.; Craig, William W.; Forster, Karl; Giommi, Paolo; Grefenstette, Brian W.; Grindlay, Jonathan E.; Harrison, Fiona A.; Hornstrup, Allan; Kitaguchi, Takao; Koglin, Jason E.; Luu, Vy; Madsen, Kristen K.; Mao, Peter H.; Miyasaka, Hiromasa; Perri, Matteo; Pivovaroff, Michael J.; Puccetti, Simonetta; Rana, Vikram; Stern, Daniel; Westergaard, Niels J.; Zhang, William W.; Zoglauer, Andreas

    2015-12-01

    We present the first sub-arcminute images of the Galactic Center above 10 keV, obtained with NuSTAR. NuSTAR resolves the hard X-ray source IGR J17456-2901 into non-thermal X-ray filaments, molecular clouds, point sources, and a previously unknown central component of hard X-ray emission (CHXE). NuSTAR detects four non-thermal X-ray filaments, extending the detection of their power-law spectra with Γ ˜ 1.3-2.3 up to ˜50 keV. A morphological and spectral study of the filaments suggests that their origin may be heterogeneous, where previous studies suggested a common origin in young pulsar wind nebulae (PWNe). NuSTAR detects non-thermal X-ray continuum emission spatially correlated with the 6.4 keV Fe Kα fluorescence line emission associated with two Sgr A molecular clouds: MC1 and the Bridge. Broadband X-ray spectral analysis with a Monte-Carlo based X-ray reflection model self-consistently determined their intrinsic column density (˜1023 cm-2), primary X-ray spectra (power-laws with Γ ˜ 2) and set a lower limit of the X-ray luminosity of Sgr A* flare illuminating the Sgr A clouds to LX ≳ 1038 erg s-1. Above ˜20 keV, hard X-ray emission in the central 10 pc region around Sgr A* consists of the candidate PWN G359.95-0.04 and the CHXE, possibly resulting from an unresolved population of massive CVs with white dwarf masses MWD ˜ 0.9 M⊙. Spectral energy distribution analysis suggests that G359.95-0.04 is likely the hard X-ray counterpart of the ultra-high gamma-ray source HESS J1745-290, strongly favoring a leptonic origin of the GC TeV emission.

  18. Near- and Extended-Edge X-Ray-Absorption Fine-Structure Spectroscopy Using Ultrafast Coherent High-Order Harmonic Supercontinua

    NASA Astrophysics Data System (ADS)

    Popmintchev, Dimitar; Galloway, Benjamin R.; Chen, Ming-Chang; Dollar, Franklin; Mancuso, Christopher A.; Hankla, Amelia; Miaja-Avila, Luis; O'Neil, Galen; Shaw, Justin M.; Fan, Guangyu; Ališauskas, Skirmantas; Andriukaitis, Giedrius; Balčiunas, Tadas; Mücke, Oliver D.; Pugzlys, Audrius; Baltuška, Andrius; Kapteyn, Henry C.; Popmintchev, Tenio; Murnane, Margaret M.

    2018-03-01

    Recent advances in high-order harmonic generation have made it possible to use a tabletop-scale setup to produce spatially and temporally coherent beams of light with bandwidth spanning 12 octaves, from the ultraviolet up to x-ray photon energies >1.6 keV . Here we demonstrate the use of this light for x-ray-absorption spectroscopy at the K - and L -absorption edges of solids at photon energies near 1 keV. We also report x-ray-absorption spectroscopy in the water window spectral region (284-543 eV) using a high flux high-order harmonic generation x-ray supercontinuum with 109 photons/s in 1% bandwidth, 3 orders of magnitude larger than has previously been possible using tabletop sources. Since this x-ray radiation emerges as a single attosecond-to-femtosecond pulse with peak brightness exceeding 1026 photons/s /mrad2/mm2/1 % bandwidth, these novel coherent x-ray sources are ideal for probing the fastest molecular and materials processes on femtosecond-to-attosecond time scales and picometer length scales.

  19. X-ray-induced photo-chemistry and X-ray absorption spectroscopy of biological samples

    PubMed Central

    George, Graham N.; Pickering, Ingrid J.; Pushie, M. Jake; Nienaber, Kurt; Hackett, Mark J.; Ascone, Isabella; Hedman, Britt; Hodgson, Keith O.; Aitken, Jade B.; Levina, Aviva; Glover, Christopher; Lay, Peter A.

    2012-01-01

    As synchrotron light sources and optics deliver greater photon flux on samples, X-ray-induced photo-chemistry is increasingly encountered in X-ray absorption spectroscopy (XAS) experiments. The resulting problems are particularly pronounced for biological XAS experiments. This is because biological samples are very often quite dilute and therefore require signal averaging to achieve adequate signal-to-noise ratios, with correspondingly greater exposures to the X-ray beam. This paper reviews the origins of photo-reduction and photo-oxidation, the impact that they can have on active site structure, and the methods that can be used to provide relief from X-ray-induced photo-chemical artifacts. PMID:23093745

  20. X-ray scattering signatures of β-thalassemia

    NASA Astrophysics Data System (ADS)

    Desouky, Omar S.; Elshemey, Wael M.; Selim, Nabila S.

    2009-08-01

    X-ray scattering from lyophilized proteins or protein-rich samples is characterized by the presence of two characteristic broad peaks at scattering angles equivalent to momentum transfer values of 0.27 and 0.6 nm -1, respectively. These peaks arise from the interference of coherently scattered photons. Once the conformation of a protein is changed, these two peaks reflect such change with considerable sensitivity. The present work examines the possibility of characterizing the most common cause of hemolytic anaemia in Egypt and many Mediterranean countries; β-thalassemia, from its X-ray scattering profile. This disease emerges from a genetic defect causing reduced rate in the synthesis of one of the globin chains that make up hemoglobin. As a result, structurally abnormal hemoglobin molecules are formed. In order to detect such molecular disorder, hemoglobin samples of β-thalassemia patients are collected, lyophilized and measured using a conventional X-ray diffractometer. Results show significant differences in the X-ray scattering profiles of most of the diseased samples compared to control. The shape of the first scattering peak at 0.27 nm -1, in addition to the relative intensity of the first to the second scattering peaks, provides the most reliable signs of abnormality in diseased samples. The results are interpreted and confirmed with the aid of Fourier Transform Infrared (FTIR) spectroscopy of normal and thalassemia samples.

  1. X-ray structures define human P2X3 receptor gating cycle and antagonist action

    PubMed Central

    Mansoor, Steven E.; Lü, Wei; Oosterheert, Wout; Shekhar, Mrinal; Tajkhorshid, Emad; Gouaux, Eric

    2016-01-01

    Summary P2X receptors are trimeric, non-selective cation channels activated by ATP that play important roles in cardiovascular, neuronal and immune systems. Despite their central function in human physiology and as potential targets of therapeutic agents, there are no structures of human P2X receptors. Mechanisms of receptor desensitization and ion permeation, principles of antagonism, and complete structure of the pore-forming transmembrane domains remain unclear. We report x-ray crystal structures of human P2X3 receptor in apo/resting, agonist-bound/open-pore, agonist-bound/desensitized and antagonist-bound closed states. The open state structure harbors an intracellular motif we term the “cytoplasmic cap”, that stabilizes the open state of the ion channel pore and creates lateral, phospholipid-lined cytoplasmic fenestrations for water and ion egress. Competitive antagonists TNP-ATP and A-317491 stabilize the apo/resting state and reveal the interactions responsible for competitive inhibition. These structures illuminate the conformational rearrangements underpinning P2X receptor gating and provide a foundation for development of new pharmacologic agents. PMID:27626375

  2. Opportunities and challenges for time-resolved studies of protein structural dynamics at X-ray free-electron lasers.

    PubMed

    Neutze, Richard

    2014-07-17

    X-ray free-electron lasers (XFELs) are revolutionary X-ray sources. Their time structure, providing X-ray pulses of a few tens of femtoseconds in duration; and their extreme peak brilliance, delivering approximately 10(12) X-ray photons per pulse and facilitating sub-micrometre focusing, distinguish XFEL sources from synchrotron radiation. In this opinion piece, I argue that these properties of XFEL radiation will facilitate new discoveries in life science. I reason that time-resolved serial femtosecond crystallography and time-resolved wide angle X-ray scattering are promising areas of scientific investigation that will be advanced by XFEL capabilities, allowing new scientific questions to be addressed that are not accessible using established methods at storage ring facilities. These questions include visualizing ultrafast protein structural dynamics on the femtosecond to picosecond time-scale, as well as time-resolved diffraction studies of non-cyclic reactions. I argue that these emerging opportunities will stimulate a renaissance of interest in time-resolved structural biochemistry.

  3. Nanoplasma Formation by High Intensity Hard X-rays

    PubMed Central

    Tachibana, T.; Jurek, Z.; Fukuzawa, H.; Motomura, K.; Nagaya, K.; Wada, S.; Johnsson, P.; Siano, M.; Mondal, S.; Ito, Y.; Kimura, M.; Sakai, T.; Matsunami, K.; Hayashita, H.; Kajikawa, J.; Liu, X.-J.; Robert, E.; Miron, C.; Feifel, R.; Marangos, J. P.; Tono, K.; Inubushi, Y.; Yabashi, M.; Son, S.-K.; Ziaja, B.; Yao, M.; Santra, R.; Ueda, K.

    2015-01-01

    Using electron spectroscopy, we have investigated nanoplasma formation from noble gas clusters exposed to high-intensity hard-x-ray pulses at ~5 keV. Our experiment was carried out at the SPring-8 Angstrom Compact free electron LAser (SACLA) facility in Japan. Dedicated theoretical simulations were performed with the molecular dynamics tool XMDYN. We found that in this unprecedented wavelength regime nanoplasma formation is a highly indirect process. In the argon clusters investigated, nanoplasma is mainly formed through secondary electron cascading initiated by slow Auger electrons. Energy is distributed within the sample entirely through Auger processes and secondary electron cascading following photoabsorption, as in the hard x-ray regime there is no direct energy transfer from the field to the plasma. This plasma formation mechanism is specific to the hard-x-ray regime and may, thus, also be important for XFEL-based molecular imaging studies. In xenon clusters, photo- and Auger electrons contribute more significantly to the nanoplasma formation. Good agreement between experiment and simulations validates our modelling approach. This has wide-ranging implications for our ability to quantitatively predict the behavior of complex molecular systems irradiated by high-intensity hard x-rays. PMID:26077863

  4. Analysis of solar X-ray data

    NASA Technical Reports Server (NTRS)

    Teske, R. G.

    1972-01-01

    Type III solar bursts occurring in the absence of solar flares were observed to be accompanied by weak X-radiation. The energy scale of an OSO-3 soft X-ray ion chamber was assessed using realistic theoretical X-ray spectra. Relationships between soft solar X-rays and solar activity were investigated. These included optical studies, the role of the Type III acceleration mechanism in establishing the soft X-ray source volume, H alpha flare intensity variations, and gross magnetic field structure.

  5. The optical, ultraviolet, and X-ray structure of the quasar HE 0435–1223

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Blackburne, Jeffrey A.; Kochanek, Christopher S.; Chen, Bin

    2014-07-10

    Microlensing has proved an effective probe of the structure of the innermost regions of quasars and an important test of accretion disk models. We present light curves of the lensed quasar HE 0435–1223 in the R band and in the ultraviolet (UV), and consider them together with X-ray light curves in two energy bands that are presented in a companion paper. Using a Bayesian Monte Carlo method, we constrain the size of the accretion disk in the rest-frame near- and far-UV, and constrain for the first time the size of the X-ray emission regions in two X-ray energy bands. Themore » R-band scale size of the accretion disk is about 10{sup 15.23} cm (∼23r{sub g}), slightly smaller than previous estimates, but larger than would be predicted from the quasar flux. In the UV, the source size is weakly constrained, with a strong prior dependence. The UV to R-band size ratio is consistent with the thin disk model prediction, with large error bars. In soft and hard X-rays, the source size is smaller than ∼10{sup 14.8} cm (∼10r{sub g} ) at 95% confidence. We do not find evidence of structure in the X-ray emission region, as the most likely value for the ratio of the hard X-ray size to the soft X-ray size is unity. Finally, we find that the most likely value for the mean mass of stars in the lens galaxy is ∼0.3 M{sub ☉}, consistent with other studies.« less

  6. X-ray filter for x-ray powder diffraction

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sinsheimer, John Jay; Conley, Raymond P.; Bouet, Nathalie C. D.

    Technologies are described for apparatus, methods and systems effective for filtering. The filters may comprise a first plate. The first plate may include an x-ray absorbing material and walls defining first slits. The first slits may include arc shaped openings through the first plate. The walls of the first plate may be configured to absorb at least some of first x-rays when the first x-rays are incident on the x-ray absorbing material, and to output second x-rays. The filters may comprise a second plate spaced from the first plate. The second plate may include the x-ray absorbing material and wallsmore » defining second slits. The second slits may include arc shaped openings through the second plate. The walls of the second plate may be configured to absorb at least some of second x-rays and to output third x-rays.« less

  7. Protein structural dynamics in solution unveiled via 100-ps time-resolved x-ray scattering

    PubMed Central

    Anfinrud, Philip

    2010-01-01

    We have developed a time-resolved x-ray scattering diffractometer capable of probing structural dynamics of proteins in solution with 100-ps time resolution. This diffractometer, developed on the ID14B BioCARS (Consortium for Advanced Radiation Sources) beamline at the Advanced Photon Source, records x-ray scattering snapshots over a broad range of q spanning 0.02–2.5 Å-1, thereby providing simultaneous coverage of the small-angle x-ray scattering (SAXS) and wide-angle x-ray scattering (WAXS) regions. To demonstrate its capabilities, we have tracked structural changes in myoglobin as it undergoes a photolysis-induced transition from its carbon monoxy form (MbCO) to its deoxy form (Mb). Though the differences between the MbCO and Mb crystal structures are small (rmsd < 0.2 Å), time-resolved x-ray scattering differences recorded over 8 decades of time from 100 ps to 10 ms are rich in structure, illustrating the sensitivity of this technique. A strong, negative-going feature in the SAXS region appears promptly and corresponds to a sudden > 22 Å3 volume expansion of the protein. The ensuing conformational relaxation causes the protein to contract to a volume ∼2 Å3 larger than MbCO within ∼10 ns. On the timescale for CO escape from the primary docking site, another change in the SAXS/WAXS fingerprint appears, demonstrating sensitivity to the location of the dissociated CO. Global analysis of the SAXS/WAXS patterns recovered time-independent scattering fingerprints for four intermediate states of Mb. These SAXS/WAXS fingerprints provide stringent constraints for putative models of conformational states and structural transitions between them. PMID:20406909

  8. An Optimized Table-Top Small-Angle X-ray Scattering Set-up for the Nanoscale Structural Analysis of Soft Matter

    NASA Astrophysics Data System (ADS)

    Sibillano, T.; de Caro, L.; Altamura, D.; Siliqi, D.; Ramella, M.; Boccafoschi, F.; Ciasca, G.; Campi, G.; Tirinato, L.; di Fabrizio, E.; Giannini, C.

    2014-11-01

    The paper shows how a table top superbright microfocus laboratory X-ray source and an innovative restoring-data algorithm, used in combination, allow to analyze the super molecular structure of soft matter by means of Small Angle X-ray Scattering ex-situ experiments. The proposed theoretical approach is aimed to restore diffraction features from SAXS profiles collected from low scattering biomaterials or soft tissues, and therefore to deal with extremely noisy diffraction SAXS profiles/maps. As biological test cases we inspected: i) residues of exosomes' drops from healthy epithelial colon cell line and colorectal cancer cells; ii) collagen/human elastin artificial scaffolds developed for vascular tissue engineering applications; iii) apoferritin protein in solution. Our results show how this combination can provide morphological/structural nanoscale information to characterize new artificial biomaterials and/or to get insight into the transition between healthy and pathological tissues during the progression of a disease, or to morphologically characterize nanoscale proteins, based on SAXS data collected in a room-sized laboratory.

  9. Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers

    PubMed Central

    Hattne, Johan; Echols, Nathaniel; Tran, Rosalie; Kern, Jan; Gildea, Richard J.; Brewster, Aaron S.; Alonso-Mori, Roberto; Glöckner, Carina; Hellmich, Julia; Laksmono, Hartawan; Sierra, Raymond G.; Lassalle-Kaiser, Benedikt; Lampe, Alyssa; Han, Guangye; Gul, Sheraz; DiFiore, Dörte; Milathianaki, Despina; Fry, Alan R.; Miahnahri, Alan; White, William E.; Schafer, Donald W.; Seibert, M. Marvin; Koglin, Jason E.; Sokaras, Dimosthenis; Weng, Tsu-Chien; Sellberg, Jonas; Latimer, Matthew J.; Glatzel, Pieter; Zwart, Petrus H.; Grosse-Kunstleve, Ralf W.; Bogan, Michael J.; Messerschmidt, Marc; Williams, Garth J.; Boutet, Sébastien; Messinger, Johannes; Zouni, Athina; Yano, Junko; Bergmann, Uwe; Yachandra, Vittal K.; Adams, Paul D.; Sauter, Nicholas K.

    2014-01-01

    X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and free from radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract statistically significant high-resolution signals from fewer diffraction measurements. PMID:24633409

  10. X-ray absorption fine structure and x-ray diffraction studies of crystallographic grains in nanocrystalline FePd:Cu thin films

    NASA Astrophysics Data System (ADS)

    Krupinski, M.; Perzanowski, M.; Polit, A.; Zabila, Y.; Zarzycki, A.; Dobrowolska, A.; Marszalek, M.

    2011-03-01

    FePd alloys have recently attracted considerable attention as candidates for ultrahigh density magnetic storage media. In this paper we investigate FePd thin alloy film with a copper admixture composed of nanometer-sized grains. [Fe(0.9 nm)/Pd(1.1 nm)/Cu(d nm)]×5 multilayers were prepared by thermal deposition at room temperature in UHV conditions on Si(100) substrates covered by 100 nm SiO2. The thickness of the copper layer has been changed from 0 to 0.4 nm. After deposition, the multilayers were rapidly annealed at 600 °C in a nitrogen atmosphere, which resulted in the creation of the FePd:Cu alloy. The structure of alloy films obtained this way was determined by x-ray diffraction (XRD), glancing angle x-ray diffraction, and x-ray absorption fine structure (EXAFS). The measurements clearly showed that the L10 FePd:Cu nanocrystalline phase has been formed during the annealing process for all investigated copper compositions. This paper concentrates on the crystallographic grain features of FePd:Cu alloys and illustrates that the EXAFS technique, supported by XRD measurements, can help to extend the information about grain size and grain shape of poorly crystallized materials. We show that, using an appropriate model of the FePd:Cu grains, the comparison of EXAFS and XRD results gives a reasonable agreement.

  11. Expression, purification, crystallization and X-ray diffraction studies of the molecular chaperone prefoldin from Homo sapiens

    PubMed Central

    Aikawa, Yoshiki; Kida, Hiroshi; Nishitani, Yuichi; Miki, Kunio

    2015-01-01

    Proper protein folding is an essential process for all organisms. Prefoldin (PFD) is a molecular chaperone that assists protein folding by delivering non-native proteins to group II chaperonin. A heterohexamer of eukaryotic PFD has been shown to specifically recognize and deliver non-native actin and tubulin to chaperonin-containing TCP-1 (CCT), but the mechanism of specific recognition is still unclear. To determine its crystal structure, recombinant human PFD was reconstituted, purified and crystallized. X-ray diffraction data were collected to 4.7 Å resolution. The crystals belonged to space group P21212, with unit-cell parameters a = 123.2, b = 152.4, c = 105.9 Å. PMID:26323306

  12. Experimental and theoretical comparison of the O K-edge nonresonant inelastic X-ray scattering and X-ray absorption spectra of NaReO4.

    PubMed

    Bradley, Joseph A; Yang, Ping; Batista, Enrique R; Boland, Kevin S; Burns, Carol J; Clark, David L; Conradson, Steven D; Kozimor, Stosh A; Martin, Richard L; Seidler, Gerald T; Scott, Brian L; Shuh, David K; Tyliszczak, Tolek; Wilkerson, Marianne P; Wolfsberg, Laura E

    2010-10-06

    Accurate X-ray absorption spectra (XAS) of first row atoms, e.g., O, are notoriously difficult to obtain due to the extreme sensitivity of the measurement to surface contamination, self-absorption, and saturation affects. Herein, we describe a comprehensive approach for determining reliable O K-edge XAS data for ReO(4)(1-) and provide methodology for obtaining trustworthy and quantitative data on nonconducting molecular systems, even in the presence of surface contamination. This involves comparing spectra measured by nonresonant inelastic X-ray scattering (NRIXS), a bulk-sensitive technique that is not prone to X-ray self-absorption and provides exact peak intensities, with XAS spectra obtained by three different detection modes, namely total electron yield (TEY), fluorescence yield (FY), and scanning transmission X-ray microscopy (STXM). For ReO(4)(1-), TEY measurements were heavily influenced by surface contamination, while the FY and STXM data agree well with the bulk NRIXS analysis. These spectra all showed two intense pre-edge features indicative of the covalent interaction between the Re 5d and O 2p orbitals. Density functional theory calculations were used to assign these two peaks as O 1s excitations to the e and t(2) molecular orbitals that result from Re 5d and O 2p covalent mixing in T(d) symmetry. Electronic structure calculations were used to determine the amount of O 2p character (%) in these molecular orbitals. Time dependent-density functional theory (TD-DFT) was also used to calculate the energies and intensities of the pre-edge transitions. Overall, under these experimental conditions, this analysis suggests that NRIXS, STXM, and FY operate cooperatively, providing a sound basis for validation of bulk-like excitation spectra and, in combination with electronic structure calculations, suggest that NaReO(4) may serve as a well-defined O K-edge energy and intensity standard for future O K-edge XAS studies.

  13. Measuring the Dust Grains and Distance to X Persei Via Its X-ray Halo

    NASA Astrophysics Data System (ADS)

    Smith, Randall

    2006-09-01

    We propose to observe the X-ray halo of the high mass X-ray binary pulsar X Per to measure interstellar dust grains along the line of sight (LOS) and to determine the distance to X Per. The X-ray halo is formed by scattering from grains along the LOS, which for X Per appear to be concentrated in one molecular cloud. Unlike many other X-ray halo observations, this low-absorption high-latitude sightline is well-characterized from absorption spectroscopy done with HST, Copernicus, and FUSE. This halo observation will measure the distance to the cloud and the dust size distribution in it. We will also be able to determine the distance to X Per by measuring the time delayed pulses in the X-ray halo.

  14. Near-edge x-ray absorption fine structure spectroscopy at atmospheric pressure with a table-top laser-induced soft x-ray source

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kühl, Frank-Christian, E-mail: Frank-christian.kuehl@mail.de; Müller, Matthias, E-mail: matthias.mueller@llg-ev.de; Schellhorn, Meike

    2016-07-15

    The authors present a table-top soft x-ray absorption spectrometer, accomplishing investigations of the near-edge x-ray absorption fine structure (NEXAFS) in a laboratory environment. The system is based on a low debris plasma ignited by a picosecond laser in a pulsed krypton gas jet, emitting soft x-ray radiation in the range from 1 to 5 nm. For absorption spectroscopy in and around the “water window” (2.3–4.4 nm), a compact helium purged sample compartment for experiments at atmospheric pressure has been constructed and tested. NEXAFS measurements on CaCl{sub 2} and KMnO{sub 4} samples were conducted at the calcium and manganese L-edges, as well asmore » at the oxygen K-edge in air, atmospheric helium, and under vacuum, respectively. The results indicate the importance of atmospheric conditions for an investigation of sample hydration processes.« less

  15. Morphological evolution of X-ray flare structures from the rise through the decay phase. [Skylab study of solar flares

    NASA Technical Reports Server (NTRS)

    Kahler, S. W.; Krieger, A. S.; Vaiana, G. S.

    1975-01-01

    The morphological evolution of 12 solar X-ray subflares from onset through the decay phase has been studied using photographic X-ray images obtained from Skylab. The spatial configurations are found to vary widely from flare to flare, but they appear to be composed of two basic kinds of structures. The first, termed 'X-ray kernels', are brightest during the rise phase; the second, looplike structures, appear during the maximum and decay phases of the event. The X-ray kernels are small pointlike structures which may be related to the nonthermal phases of flares.

  16. Protein crystal structure from non-oriented, single-axis sparse X-ray data

    DOE PAGES

    Wierman, Jennifer L.; Lan, Ti-Yen; Tate, Mark W.; ...

    2016-01-01

    X-ray free-electron lasers (XFELs) have inspired the development of serial femtosecond crystallography (SFX) as a method to solve the structure of proteins. SFX datasets are collected from a sequence of protein microcrystals injected across ultrashort X-ray pulses. The idea behind SFX is that diffraction from the intense, ultrashort X-ray pulses leaves the crystal before the crystal is obliterated by the effects of the X-ray pulse. The success of SFX at XFELs has catalyzed interest in analogous experiments at synchrotron-radiation (SR) sources, where data are collected from many small crystals and the ultrashort pulses are replaced by exposure times that aremore » kept short enough to avoid significant crystal damage. The diffraction signal from each short exposure is so `sparse' in recorded photons that the process of recording the crystal intensity is itself a reconstruction problem. Using theEMCalgorithm, a successful reconstruction is demonstrated here in a sparsity regime where there are no Bragg peaks that conventionally would serve to determine the orientation of the crystal in each exposure. In this proof-of-principle experiment, a hen egg-white lysozyme (HEWL) crystal rotating about a single axis was illuminated by an X-ray beam from an X-ray generator to simulate the diffraction patterns of microcrystals from synchrotron radiation. Millions of these sparse frames, typically containing only ~200 photons per frame, were recorded using a fast-framing detector. It is shown that reconstruction of three-dimensional diffraction intensity is possible using theEMCalgorithm, even with these extremely sparse frames and without knowledge of the rotation angle. Further, the reconstructed intensity can be phased and refined to solve the protein structure using traditional crystallographic software. In conclusion, this suggests that synchrotron-based serial crystallography of micrometre-sized crystals can be practical with the aid of theEMCalgorithm even in cases

  17. Protein crystal structure from non-oriented, single-axis sparse X-ray data

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wierman, Jennifer L.; Lan, Ti-Yen; Tate, Mark W.

    X-ray free-electron lasers (XFELs) have inspired the development of serial femtosecond crystallography (SFX) as a method to solve the structure of proteins. SFX datasets are collected from a sequence of protein microcrystals injected across ultrashort X-ray pulses. The idea behind SFX is that diffraction from the intense, ultrashort X-ray pulses leaves the crystal before the crystal is obliterated by the effects of the X-ray pulse. The success of SFX at XFELs has catalyzed interest in analogous experiments at synchrotron-radiation (SR) sources, where data are collected from many small crystals and the ultrashort pulses are replaced by exposure times that aremore » kept short enough to avoid significant crystal damage. The diffraction signal from each short exposure is so `sparse' in recorded photons that the process of recording the crystal intensity is itself a reconstruction problem. Using theEMCalgorithm, a successful reconstruction is demonstrated here in a sparsity regime where there are no Bragg peaks that conventionally would serve to determine the orientation of the crystal in each exposure. In this proof-of-principle experiment, a hen egg-white lysozyme (HEWL) crystal rotating about a single axis was illuminated by an X-ray beam from an X-ray generator to simulate the diffraction patterns of microcrystals from synchrotron radiation. Millions of these sparse frames, typically containing only ~200 photons per frame, were recorded using a fast-framing detector. It is shown that reconstruction of three-dimensional diffraction intensity is possible using theEMCalgorithm, even with these extremely sparse frames and without knowledge of the rotation angle. Further, the reconstructed intensity can be phased and refined to solve the protein structure using traditional crystallographic software. In conclusion, this suggests that synchrotron-based serial crystallography of micrometre-sized crystals can be practical with the aid of theEMCalgorithm even in cases

  18. AXSIS: Exploring the frontiers in attosecond X-ray science, imaging and spectroscopy.

    PubMed

    Kärtner, F X; Ahr, F; Calendron, A-L; Çankaya, H; Carbajo, S; Chang, G; Cirmi, G; Dörner, K; Dorda, U; Fallahi, A; Hartin, A; Hemmer, M; Hobbs, R; Hua, Y; Huang, W R; Letrun, R; Matlis, N; Mazalova, V; Mücke, O D; Nanni, E; Putnam, W; Ravi, K; Reichert, F; Sarrou, I; Wu, X; Yahaghi, A; Ye, H; Zapata, L; Zhang, D; Zhou, C; Miller, R J D; Berggren, K K; Graafsma, H; Meents, A; Assmann, R W; Chapman, H N; Fromme, P

    2016-09-01

    X-ray crystallography is one of the main methods to determine atomic-resolution 3D images of the whole spectrum of molecules ranging from small inorganic clusters to large protein complexes consisting of hundred-thousands of atoms that constitute the macromolecular machinery of life. Life is not static, and unravelling the structure and dynamics of the most important reactions in chemistry and biology is essential to uncover their mechanism. Many of these reactions, including photosynthesis which drives our biosphere, are light induced and occur on ultrafast timescales. These have been studied with high time resolution primarily by optical spectroscopy, enabled by ultrafast laser technology, but they reduce the vast complexity of the process to a few reaction coordinates. In the AXSIS project at CFEL in Hamburg, funded by the European Research Council, we develop the new method of attosecond serial X-ray crystallography and spectroscopy, to give a full description of ultrafast processes atomically resolved in real space and on the electronic energy landscape, from co-measurement of X-ray and optical spectra, and X-ray diffraction. This technique will revolutionize our understanding of structure and function at the atomic and molecular level and thereby unravel fundamental processes in chemistry and biology like energy conversion processes. For that purpose, we develop a compact, fully coherent, THz-driven atto-second X-ray source based on coherent inverse Compton scattering off a free-electron crystal, to outrun radiation damage effects due to the necessary high X-ray irradiance required to acquire diffraction signals. This highly synergistic project starts from a completely clean slate rather than conforming to the specifications of a large free-electron laser (FEL) user facility, to optimize the entire instrumentation towards fundamental measurements of the mechanism of light absorption and excitation energy transfer. A multidisciplinary team formed by laser

  19. X-rays in the Cryo-EM Era: Structural Biology’s Dynamic Future

    PubMed Central

    Shoemaker, Susannah C.; Ando, Nozomi

    2018-01-01

    Over the past several years, single-particle cryo-electron microscopy (cryo-EM) has emerged as a leading method for elucidating macromolecular structures at near-atomic resolution, rivaling even the established technique of X-ray crystallography. Cryo-EM is now able to probe proteins as small as hemoglobin (64 kDa), while avoiding the crystallization bottleneck entirely. The remarkable success of cryo-EM has called into question the continuing relevance of X-ray methods, particularly crystallography. To say that the future of structural biology is either cryo-EM or crystallography, however, would be misguided. Crystallography remains better suited to yield precise atomic coordinates of macromolecules under a few hundred kDa in size, while the ability to probe larger, potentially more disordered assemblies is a distinct advantage of cryo-EM. Likewise, crystallography is better equipped to provide high-resolution dynamic information as a function of time, temperature, pressure, and other perturbations, whereas cryo-EM offers increasing insight into conformational and energy landscapes, particularly as algorithms to deconvolute conformational heterogeneity become more advanced. Ultimately, the future of both techniques depends on how their individual strengths are utilized to tackle questions on the frontiers of structural biology. Structure determination is just one piece of a much larger puzzle: a central challenge of modern structural biology is to relate structural information to biological function. In this perspective, we share insight from several leaders in the field and examine the unique and complementary ways in which X-ray methods and cryo-EM can shape the future of structural biology. PMID:29227642

  20. Jet-ISM Interaction in the Radio Galaxy 3C 293: Jet-driven Shocks Heat ISM to Power X-Ray and Molecular H2 Emission

    NASA Astrophysics Data System (ADS)

    Lanz, L.; Ogle, P. M.; Evans, D.; Appleton, P. N.; Guillard, P.; Emonts, B.

    2015-03-01

    We present a 70 ks Chandra observation of the radio galaxy 3C 293. This galaxy belongs to the class of molecular hydrogen emission galaxies (MOHEGs) that have very luminous emission from warm molecular hydrogen. In radio galaxies, the molecular gas appears to be heated by jet-driven shocks, but exactly how this mechanism works is still poorly understood. With Chandra, we observe X-ray emission from the jets within the host galaxy and along the 100 kpc radio jets. We model the X-ray spectra of the nucleus, the inner jets, and the X-ray features along the extended radio jets. Both the nucleus and the inner jets show evidence of 107 K shock-heated gas. The kinetic power of the jets is more than sufficient to heat the X-ray emitting gas within the host galaxy. The thermal X-ray and warm H2 luminosities of 3C 293 are similar, indicating similar masses of X-ray hot gas and warm molecular gas. This is consistent with a picture where both derive from a multiphase, shocked interstellar medium (ISM). We find that radio-loud MOHEGs that are not brightest cluster galaxies (BCGs), like 3C 293, typically have LH2/LX˜ 1 and MH2/MX˜ 1, whereas MOHEGs that are BCGs have LH2/LX˜ 0.01 and MH2/MX˜ 0.01. The more massive, virialized, hot atmosphere in BCGs overwhelms any direct X-ray emission from current jet-ISM interaction. On the other hand, LH2/LX˜ 1 in the Spiderweb BCG at z = 2, which resides in an unvirialized protocluster and hosts a powerful radio source. Over time, jet-ISM interaction may contribute to the establishment of a hot atmosphere in BCGs and other massive elliptical galaxies.

  1. Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser

    PubMed Central

    Kang, Yanyong; Zhou, X. Edward; Gao, Xiang; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; Barty, Anton; White, Thomas A.; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W.; Ke, Jiyuan; Eileen Tan, M. H.; Zhang, Chenghai; Moeller, Arne; West, Graham M.; Pascal, Bruce; Van Eps, Ned; Caro, Lydia N.; Vishnivetskiy, Sergey A.; Lee, Regina J.; Suino-Powell, Kelly M.; Gu, Xin; Pal, Kuntal; Ma, Jinming; Zhi, Xiaoyong; Boutet, Sébastien; Williams, Garth J.; Messerschmidt, Marc; Gati, Cornelius; Zatsepin, Nadia A.; Wang, Dingjie; James, Daniel; Basu, Shibom; Roy-Chowdhury, Shatabdi; Conrad, Chelsie; Coe, Jesse; Liu, Haiguang; Lisova, Stella; Kupitz, Christopher; Grotjohann, Ingo; Fromme, Raimund; Jiang, Yi; Tan, Minjia; Yang, Huaiyu; Li, Jun; Wang, Meitian; Zheng, Zhong; Li, Dianfan; Howe, Nicole; Zhao, Yingming; Standfuss, Jörg; Diederichs, Kay; Dong, Yuhui; Potter, Clinton S; Carragher, Bridget; Caffrey, Martin; Jiang, Hualiang; Chapman, Henry N.; Spence, John C. H.; Fromme, Petra; Weierstall, Uwe; Ernst, Oliver P.; Katritch, Vsevolod; Gurevich, Vsevolod V.; Griffin, Patrick R.; Hubbell, Wayne L.; Stevens, Raymond C.; Cherezov, Vadim; Melcher, Karsten; Xu, H. Eric

    2015-01-01

    G protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signaling to numerous G protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly, in which rhodopsin uses distinct structural elements, including TM7 and Helix 8 to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a ~20° rotation between the N- and C- domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. This structure provides a basis for understanding GPCR-mediated arrestin-biased signaling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biology. PMID:26200343

  2. Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser.

    PubMed

    Kang, Yanyong; Zhou, X Edward; Gao, Xiang; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; Barty, Anton; White, Thomas A; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W; Ke, Jiyuan; Tan, M H Eileen; Zhang, Chenghai; Moeller, Arne; West, Graham M; Pascal, Bruce D; Van Eps, Ned; Caro, Lydia N; Vishnivetskiy, Sergey A; Lee, Regina J; Suino-Powell, Kelly M; Gu, Xin; Pal, Kuntal; Ma, Jinming; Zhi, Xiaoyong; Boutet, Sébastien; Williams, Garth J; Messerschmidt, Marc; Gati, Cornelius; Zatsepin, Nadia A; Wang, Dingjie; James, Daniel; Basu, Shibom; Roy-Chowdhury, Shatabdi; Conrad, Chelsie E; Coe, Jesse; Liu, Haiguang; Lisova, Stella; Kupitz, Christopher; Grotjohann, Ingo; Fromme, Raimund; Jiang, Yi; Tan, Minjia; Yang, Huaiyu; Li, Jun; Wang, Meitian; Zheng, Zhong; Li, Dianfan; Howe, Nicole; Zhao, Yingming; Standfuss, Jörg; Diederichs, Kay; Dong, Yuhui; Potter, Clinton S; Carragher, Bridget; Caffrey, Martin; Jiang, Hualiang; Chapman, Henry N; Spence, John C H; Fromme, Petra; Weierstall, Uwe; Ernst, Oliver P; Katritch, Vsevolod; Gurevich, Vsevolod V; Griffin, Patrick R; Hubbell, Wayne L; Stevens, Raymond C; Cherezov, Vadim; Melcher, Karsten; Xu, H Eric

    2015-07-30

    G-protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signalling to numerous G-protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly in which rhodopsin uses distinct structural elements, including transmembrane helix 7 and helix 8, to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a ∼20° rotation between the amino and carboxy domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. This structure provides a basis for understanding GPCR-mediated arrestin-biased signalling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biology.

  3. Ultrafast Independent N-H and N-C Bond Deformation Investigated with Resonant Inelastic X-Ray Scattering

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Eckert, Sebastian; Norell, Jesper; Miedema, Piter S.

    Here, the femtosecond excited-state dynamics following resonant photoexcitation enable the selective deformation of N-H and N-C chemical bonds in 2-thiopyridone in aqueous solution with optical or X-ray pulses. In combination with multiconfigurational quantum-chemical calculations, the orbital-specific electronic structure and its ultrafast dynamics accessed with resonant inelastic X-ray scattering at the N 1s level using synchrotron radiation and the soft X-ray free-electron laser LCLS provide direct evidence for this controlled photoinduced molecular deformation and its ultrashort timescale.

  4. Ultrafast Independent N-H and N-C Bond Deformation Investigated with Resonant Inelastic X-Ray Scattering

    DOE PAGES

    Eckert, Sebastian; Norell, Jesper; Miedema, Piter S.; ...

    2017-04-04

    Here, the femtosecond excited-state dynamics following resonant photoexcitation enable the selective deformation of N-H and N-C chemical bonds in 2-thiopyridone in aqueous solution with optical or X-ray pulses. In combination with multiconfigurational quantum-chemical calculations, the orbital-specific electronic structure and its ultrafast dynamics accessed with resonant inelastic X-ray scattering at the N 1s level using synchrotron radiation and the soft X-ray free-electron laser LCLS provide direct evidence for this controlled photoinduced molecular deformation and its ultrashort timescale.

  5. OSO-8 X-ray spectra of clusters of galaxies. 2: Discussion. [hot intracluster gas structures

    NASA Technical Reports Server (NTRS)

    Smith, B. W.; Mushotzky, R. F.; Serlemitsos, P. J.

    1978-01-01

    X-ray spectral parameters obtained from 2 to 20 keV OSO-8 data on X-ray clusters and optical cluster properties were examined to obtain information for restricting models for hot intracluster gas structures. Topics discussed include the radius of the X-ray core in relation to the galaxy core radius, the viral mass of hotter clusters, and galaxy density and optical central cluster properties. A population of cool, dim X-ray clusters which have not been observed is predicted. The iron abundance determinations recently quoted for intracluster gas are uncertain by 50 to greater than 100 percent from this nonstatistical cause alone.

  6. Coherent x-ray diffraction

    NASA Astrophysics Data System (ADS)

    Pitney, John Allen

    Conventional x-ray diffraction has historically been done under conditions such that the measured signal consists of an incoherent addition of scattering which is coherent only on a length scale determined by the properties of the beam. The result of the incoherent summation is a statistical averaging over the whole illuminated volume of the sample, which yields certain kinds of information with a high degree of precision and has been key to the success of x-ray diffraction in a variety of applications. Coherent x-ray scattering techniques, such as coherent x-ray diffraction (CXD) and x-ray intensity fluctuation spectroscopy (XIFS), attempt to reduce or eliminate any incoherent averaging so that specific, local structures couple to the measurement without being averaged out. In the case of XIFS, the result is analogous to dynamical light scattering, but with sensitivity to length scales less than 200 nm and time scales from 10-3 s to 103 s. When combined with phase retrieval, CXD represents an imaging technique with the penetration, in situ capabilities, and contrast mechanisms associated with x-rays and with a spatial resolution ultimately limited by the x-ray wavelength. In practice, however, the spatial resolution of CXD imaging is limited by exposure to about 100 A. This thesis describes CXD measurements of the binary alloy Cu3Au and the adaptation of phase retrieval methods for the reconstruction of real-space images of Cu3Au antiphase domains. The theoretical foundations of CXD are described in Chapter 1 as derived from the kinematical formulation for x-ray diffraction and from the temporal and spatial coherence of radiation. The antiphase domain structure of Cu 3Au is described, along with the associated reciprocal-space structure which is measured by CXD. CXD measurements place relatively stringent requirements on the coherence properties of the beam and on the detection mechanism of the experiment; these requirements and the means by which they have been

  7. X-ray transmission microscope development

    NASA Technical Reports Server (NTRS)

    Kaukler, William F.; Rosenberger, Franz E.

    1995-01-01

    We are developing a hard x-ray microscope for direct observation of solidification dynamics in metal alloys and metal matrix composites. The Fein-Focus Inc. x-ray source was delivered in September and found to perform better than expected. Confirmed resolution of better than 2 micrometers was obtained and magnifications up to 800X were measured. Nickel beads of 30 micrometer diameter were easily detected through 6mm of aluminum. X-ray metallography was performed on several specimens showing high resolution and clear definition of 3-dimensional structures. Prototype furnace installed and tested.

  8. X-ray grid-detector apparatus

    DOEpatents

    Boone, John M.; Lane, Stephen M.

    1998-01-27

    A hybrid grid-detector apparatus for x-ray systems wherein a microchannel plate structure has an air-interspaced grid portion and a phosphor/optical fluid-filled grid portion. The grids are defined by multiple adjacent channels separated by lead-glass septa. X-rays entering the air-interspaced grid portion at an angle of impingement upon the septa are attenuated, while non-impinging x-rays pass through to the phosphor/fluid filled portion. X-ray energy is converted to luminescent energy in the phosphor/fluid filled portion and the resultant beams of light are directed out of the phosphor/optical fluid filled portion to an imaging device.

  9. Stellar X-Ray Polarimetry

    NASA Technical Reports Server (NTRS)

    Swank, J.

    2011-01-01

    Most of the stellar end-state black holes, pulsars, and white dwarfs that are X-ray sources should have polarized X-ray fluxes. The degree will depend on the relative contributions of the unresolved structures. Fluxes from accretion disks and accretion disk corona may be polarized by scattering. Beams and jets may have contributions of polarized emission in strong magnetic fields. The Gravity and Extreme Magnetism Small Explorer (GEMS) will study the effects on polarization of strong gravity of black holes and strong magnetism of neutron stars. Some part of the flux from compact stars accreting from companion stars has been reflected from the companion, its wind, or accretion streams. Polarization of this component is a potential tool for studying the structure of the gas in these binary systems. Polarization due to scattering can also be present in X-ray emission from white dwarf binaries and binary normal stars such as RS CVn stars and colliding wind sources like Eta Car. Normal late type stars may have polarized flux from coronal flares. But X-ray polarization sensitivity is not at the level needed for single early type stars.

  10. NuSTAR HARD X-RAY SURVEY OF THE GALACTIC CENTER REGION. I. HARD X-RAY MORPHOLOGY AND SPECTROSCOPY OF THE DIFFUSE EMISSION

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Mori, Kaya; Hailey, Charles J.; Perez, Kerstin

    2015-12-01

    We present the first sub-arcminute images of the Galactic Center above 10 keV, obtained with NuSTAR. NuSTAR resolves the hard X-ray source IGR J17456–2901 into non-thermal X-ray filaments, molecular clouds, point sources, and a previously unknown central component of hard X-ray emission (CHXE). NuSTAR detects four non-thermal X-ray filaments, extending the detection of their power-law spectra with Γ ∼ 1.3–2.3 up to ∼50 keV. A morphological and spectral study of the filaments suggests that their origin may be heterogeneous, where previous studies suggested a common origin in young pulsar wind nebulae (PWNe). NuSTAR detects non-thermal X-ray continuum emission spatially correlated with the 6.4more » keV Fe Kα fluorescence line emission associated with two Sgr A molecular clouds: MC1 and the Bridge. Broadband X-ray spectral analysis with a Monte-Carlo based X-ray reflection model self-consistently determined their intrinsic column density (∼10{sup 23} cm{sup −2}), primary X-ray spectra (power-laws with Γ ∼ 2) and set a lower limit of the X-ray luminosity of Sgr A* flare illuminating the Sgr A clouds to L{sub X} ≳ 10{sup 38} erg s{sup −1}. Above ∼20 keV, hard X-ray emission in the central 10 pc region around Sgr A* consists of the candidate PWN G359.95–0.04 and the CHXE, possibly resulting from an unresolved population of massive CVs with white dwarf masses M{sub WD} ∼ 0.9 M{sub ⊙}. Spectral energy distribution analysis suggests that G359.95–0.04 is likely the hard X-ray counterpart of the ultra-high gamma-ray source HESS J1745–290, strongly favoring a leptonic origin of the GC TeV emission.« less

  11. X-ray Fluorescence Holography: Principles, Apparatus, and Applications

    NASA Astrophysics Data System (ADS)

    Hayashi, Kouichi; Korecki, Pawel

    2018-06-01

    X-ray fluorescence holography (XFH) is an atomic structure determination technique that combines the capabilities of X-ray diffraction and X-ray fluorescence spectroscopy. It provides a unique means of gaining fully three-dimensional information about the local atomic structure and lattice site positions of selected elements inside compound samples. In this work, we discuss experimental and theoretical aspects that are essential for the efficient recording and analysis of X-ray fluorescence holograms and review the most recent advances in XFH. We describe experiments performed with brilliant synchrotron radiation as well as with tabletop setups that employ conventional X-ray tubes.

  12. Non-Invasive Early Detection and Molecular Analysis of Low X-ray Dose Effects in the Lens

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Goldstein, Lee

    This is the Final Progress Report for DOE-funded research project DE-PS02-08ER08-01 titled “Non-Invasive Early Detection and Molecular Analysis of Low X-ray Dose Effects in the Lens”. The project focuses on the effects of low-linear energy transfer (LET) radiation on the ocular lens. The lens is an exquisitely radiosensitive tissue with a highly-ordered molecular structure that is amenable to non-invasive optical study from the periphery. These merits point to the lens as an ideal target for laser-based molecular biodosimetry (MBD). Following exposure to different types of ionizing radiations, the lens demonstrates molecular changes (e.g., oxidation, racemization, crosslinkage, truncation, aggregation, etc.) thatmore » impact the structure and function of the long-lived proteins in the cytosol of lens fiber cells. The vast majority of proteins in the lens comprise the highly-ordered crystallins. These highly conserved lens proteins are amongst the most concentrated and stable in the body. Once synthesized, the crystallins are retained in the fiber cell cytoplasm for life. Taken together, these properties point to the lens as an ideal system for quantitative in vivo MBD assessment using quasi-elastic light scattering (QLS) analysis. In this project, we deploy a purpose-designed non-invasive infrared laser QLS instrument as a quantitative tool for longitudinal assessment of pre-cataractous molecular changes in the lenses of living mice exposed to low-dose low-LET radiation compared to non-irradiated sham controls. We hypothesize that radiation exposure will induce dose-dependent changes in the molecular structure of matrix proteins in the lens. Mechanistic assays to ascertain radiation-induced molecular changes in the lens focus on protein aggregation and gene/protein expression patterns. We anticipate that this study will contribute to our understanding of early molecular changes associated with radiation-induced tissue pathology. This study also affords

  13. X-ray structures define human P2X(3) receptor gating cycle and antagonist action.

    PubMed

    Mansoor, Steven E; Lü, Wei; Oosterheert, Wout; Shekhar, Mrinal; Tajkhorshid, Emad; Gouaux, Eric

    2016-10-06

    P2X receptors are trimeric, non-selective cation channels activated by ATP that have important roles in the cardiovascular, neuronal and immune systems. Despite their central function in human physiology and although they are potential targets of therapeutic agents, there are no structures of human P2X receptors. The mechanisms of receptor desensitization and ion permeation, principles of antagonism, and complete structures of the pore-forming transmembrane domains of these receptors remain unclear. Here we report X-ray crystal structures of the human P2X 3 receptor in apo/resting, agonist-bound/open-pore, agonist-bound/closed-pore/desensitized and antagonist-bound/closed states. The open state structure harbours an intracellular motif we term the 'cytoplasmic cap', which stabilizes the open state of the ion channel pore and creates lateral, phospholipid-lined cytoplasmic fenestrations for water and ion egress. The competitive antagonists TNP-ATP and A-317491 stabilize the apo/resting state and reveal the interactions responsible for competitive inhibition. These structures illuminate the conformational rearrangements that underlie P2X receptor gating and provide a foundation for the development of new pharmacological agents.

  14. Combined X-ray CT and mass spectrometry for biomedical imaging applications

    NASA Astrophysics Data System (ADS)

    Schioppa, E., Jr.; Ellis, S.; Bruinen, A. L.; Visser, J.; Heeren, R. M. A.; Uher, J.; Koffeman, E.

    2014-04-01

    Imaging technologies play a key role in many branches of science, especially in biology and medicine. They provide an invaluable insight into both internal structure and processes within a broad range of samples. There are many techniques that allow one to obtain images of an object. Different techniques are based on the analysis of a particular sample property by means of a dedicated imaging system, and as such, each imaging modality provides the researcher with different information. The use of multimodal imaging (imaging with several different techniques) can provide additional and complementary information that is not possible when employing a single imaging technique alone. In this study, we present for the first time a multi-modal imaging technique where X-ray computerized tomography (CT) is combined with mass spectrometry imaging (MSI). While X-ray CT provides 3-dimensional information regarding the internal structure of the sample based on X-ray absorption coefficients, MSI of thin sections acquired from the same sample allows the spatial distribution of many elements/molecules, each distinguished by its unique mass-to-charge ratio (m/z), to be determined within a single measurement and with a spatial resolution as low as 1 μm or even less. The aim of the work is to demonstrate how molecular information from MSI can be spatially correlated with 3D structural information acquired from X-ray CT. In these experiments, frozen samples are imaged in an X-ray CT setup using Medipix based detectors equipped with a CO2 cooled sample holder. Single projections are pre-processed before tomographic reconstruction using a signal-to-thickness calibration. In the second step, the object is sliced into thin sections (circa 20 μm) that are then imaged using both matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and secondary ion (SIMS) mass spectrometry, where the spatial distribution of specific molecules within the sample is determined. The

  15. Structural characterization of sol-gel derived oxide nanostuctures using synchrotron x-ray techniques

    NASA Astrophysics Data System (ADS)

    Sun, Tao

    Ceramic oxides possess extraordinarily rich functionalities. With the advent of nanofabrication techniques, it is now possible to grow nanostructured oxides with precise control of composition, morphology, and microstructure, which has re-vitalized the research in the field of traditional ceramics. The unexpected behavior and enhanced properties of oxide nanostructures have been extensively reported. However, knowledge about the underlying mechanisms as well as structural implications is still quite limited. Therefore, it is imperative to develop and employ sophisticated characterization tools for unraveling the structure-property relationships for oxide nanostructures. The present thesis work aims at addressing the critical issues associated with fabrication, and more importantly, structural characterization of functional oxide nanostructures. The dissertation starts with introducing the strategy for synthesizing phase-pure and highly controlled oxide nanostructures using sol-gel deposition and an innovative approach called "soft" electron beam lithography. Some specific oxides are chosen for the present study, such as BiFeO3, CoFe2O4, and SnO2, because of their scientific and technological significance. Subsequent to fabrication of tailored oxide nanostructures, advanced synchrotron x-ray scattering techniques have been applied for structural characterization. The nucleation and growth behavior of BiFeO3 thin film was investigated using in situ grazing-incidence small-angle x-ray scattering (GISAXS) technique. The results reveal that the kinetics for early-stage nuclei growth are governed by the oriented-attachment model. Moreover, the porous structures of undoped and Pd-doped semiconducting SnOx thin films were quantitatively characterized using GISAXS. By correlating the structural parameters with H2 sensitivity of SnOx films, it is found out that the microstructure of doped film is favorable for gas sensing, but it is not the major reason for the overall

  16. Ultra-short wavelength x-ray system

    DOEpatents

    Umstadter, Donald [Ann Arbor, MI; He, Fei [Ann Arbor, MI; Lau, Yue-Ying [Potomac, MD

    2008-01-22

    A method and apparatus to generate a beam of coherent light including x-rays or XUV by colliding a high-intensity laser pulse with an electron beam that is accelerated by a synchronized laser pulse. Applications include x-ray and EUV lithography, protein structural analysis, plasma diagnostics, x-ray diffraction, crack analysis, non-destructive testing, surface science and ultrafast science.

  17. 1.55 Å resolution X-ray crystal structure of Rv3902c from Mycobacterium tuberculosis

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Reddy, Bharat G.; Moates, Derek B.; Kim, Heung-Bok

    The 1.55 Å resolution X-ray crystal structure of Rv3902c from M. tuberculosis reveals a novel fold. The crystallographic structure of the Mycobacterium tuberculosis (TB) protein Rv3902c (176 residues; molecular mass of 19.8 kDa) was determined at 1.55 Å resolution. The function of Rv3902c is unknown, although several TB genes involved in bacterial pathogenesis are expressed from the operon containing the Rv3902c gene. The unique structural fold of Rv3902c contains two domains, each consisting of antiparallel β-sheets and α-helices, creating a hand-like binding motif with a small binding pocket in the palm. Structural homology searches reveal that Rv3902c has an overallmore » structure similar to that of the Salmonella virulence-factor chaperone InvB, with an r.m.s.d. for main-chain atoms of 2.3 Å along an aligned domain.« less

  18. High-resolution X-ray crystal structure of bovine H-protein using the high-pressure cryocooling method.

    PubMed

    Higashiura, Akifumi; Ohta, Kazunori; Masaki, Mika; Sato, Masaru; Inaka, Koji; Tanaka, Hiroaki; Nakagawa, Atsushi

    2013-11-01

    Recently, many technical improvements in macromolecular X-ray crystallography have increased the number of structures deposited in the Protein Data Bank and improved the resolution limit of protein structures. Almost all high-resolution structures have been determined using a synchrotron radiation source in conjunction with cryocooling techniques, which are required in order to minimize radiation damage. However, optimization of cryoprotectant conditions is a time-consuming and difficult step. To overcome this problem, the high-pressure cryocooling method was developed (Kim et al., 2005) and successfully applied to many protein-structure analyses. In this report, using the high-pressure cryocooling method, the X-ray crystal structure of bovine H-protein was determined at 0.86 Å resolution. Structural comparisons between high- and ambient-pressure cryocooled crystals at ultra-high resolution illustrate the versatility of this technique. This is the first ultra-high-resolution X-ray structure obtained using the high-pressure cryocooling method.

  19. Far-Zone Resonant Energy Transfer in X-ray Photoemission as a Structure Determination Tool.

    PubMed

    Céolin, Denis; Rueff, Jean-Pascal; Zimin, Andrey; Morin, Paul; Kimberg, Victor; Polyutov, Sergey; Ågren, Hans; Gel'mukhanov, Faris

    2017-06-15

    Near-zone Förster resonant energy transfer is the main effect responsible for excitation energy flow in the optical region and is frequently used to obtain structural information. In the hard X-ray region, the Förster law is inadequate because the wavelength is generally shorter than the distance between donors and acceptors; hence, far-zone resonant energy transfer (FZRET) becomes dominant. We demonstrate the characteristics of X-ray FZRET and its fundamental differences with the ordinary near-zone resonant energy-transfer process in the optical region by recording and analyzing two qualitatively different systems: high-density CuO polycrystalline powder and SF 6 diluted gas. We suggest a method to estimate geometrical structure using X-ray FZRET employing as a ruler the distance-dependent shift of the acceptor core ionization potential induced by the Coulomb field of the core-ionized donor.

  20. H-bonding in liquid acetamide as studied by x-ray scattering

    NASA Astrophysics Data System (ADS)

    Nasr, Salah; Ghédira, Mounir; Cortès, Robert

    1999-06-01

    A structural investigation of liquid acetamide was performed at 346 K using x-ray scattering. The data are analyzed to yield the molecular structure factor and the distinct pair correlation function. Two H-bonds per molecule are found on average. The mean N⋯O distance is about 3.03 Å. The liquid structure can be described by some structural units similar to the ones existing either in the rhombohedral or in the orthorhombic crystalline form.

  1. Common structural features of toxic intermediates from α-synuclein and GroES fibrillogenesis detected using cryogenic coherent X-ray diffraction imaging.

    PubMed

    Kameda, Hiroshi; Usugi, Sayaka; Kobayashi, Mana; Fukui, Naoya; Lee, Seki; Hongo, Kunihiro; Mizobata, Tomohiro; Sekiguchi, Yuki; Masaki, Yu; Kobayashi, Amane; Oroguchi, Tomotaka; Nakasako, Masayoshi; Takayama, Yuki; Yamamoto, Masaki; Kawata, Yasushi

    2017-01-01

    The aggregation and deposition of α-synuclein (αSyn) in neuronal cells is correlated to pathogenesis of Parkinson's disease. Although the mechanism of αSyn aggregation and fibril formation has been studied extensively, the structural hallmarks that are directly responsible for toxicity toward cells are still under debate. Here, we have compared the structural characteristics of the toxic intermediate molecular species of αSyn and similar toxic species of another protein, GroES, using coherent X-ray diffraction analysis. Using coherent X-ray free electron laser pulses of SACLA, we analysed αSyn and GroES fibril intermediate species and characterized various aggregate structures. Unlike previous studies where an annular oligomeric form of αSyn was identified, particle reconstruction from scattering traces suggested that the specific forms of the toxic particles were varied, with the sizes of the particles falling within a specific range. We did however discover a common structural feature in both αSyn and GroES samples; the edges of the detected particles were nearly parallel and produced a characteristic diffraction pattern in the diffraction experiments. The presence of parallel-edged particles in toxic intermediates of αSyn and GroES fibrillogenesis pointed towards a plausible common molecular interface that leads to the formation of mature fibrils. © The Authors 2016. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

  2. Microanalysis of iron oxidation state in iron oxides using X Ray Absorption Near Edge Structure (XANES)

    NASA Technical Reports Server (NTRS)

    Sutton, S. R.; Delaney, J.; Bajt, S.; Rivers, M. L.; Smith, J. V.

    1993-01-01

    An exploratory application of x ray absorption near edge structure (XANES) analysis using the synchrotron x ray microprobe was undertaken to obtain Fe XANES spectra on individual sub-millimeter grains in conventional polished sections. The experiments concentrated on determinations of Fe valence in a suite of iron oxide minerals for which independent estimates of the iron speciation could be made by electron microprobe analysis and x ray diffraction.

  3. Microstructure of In x Ga1-x N nanorods grown by molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Webster, R. F.; Soundararajah, Q. Y.; Griffiths, I. J.; Cherns, D.; Novikov, S. V.; Foxon, C. T.

    2015-11-01

    Transmission electron microscopy is used to examine the structure and composition of In x Ga1-x N nanorods grown by plasma-assisted molecular beam epitaxy. The results confirm a core-shell structure with an In-rich core and In-poor shell resulting from axial and lateral growth sectors respectively. Atomic resolution mapping by energy-dispersive x-ray microanalysis and high angle annular dark field imaging show that both the core and the shell are decomposed into Ga-rich and In-rich platelets parallel to their respective growth surfaces. It is argued that platelet formation occurs at the surfaces, through the lateral expansion of surface steps. Studies of nanorods with graded composition show that decomposition ceases for x ≥ 0.8 and the ratio of growth rates, shell:core, decreases with increasing In concentration.

  4. Holographic rugate structures for x-ray optics applications

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Jannson, T.; Savant, Gajendra.; Qiao, Yong.

    1988-07-01

    XUV Bragg Holographic Optical Elements (HOEs), based on a single-step volume holographic recording, have been proposed by Physical Optic Corporation (POC), as an entirely new approach to x-ray optics. Their theory, as well as the first experimental proof-of-concept, have been demonstrated in Phase 1 of the DOE program. During the first year (exactly, 8-month duration) of the on-going Phase 2, the high-efficiency XUV Lippmann holographic mirrors have been fabricated and their optical, physical, and material properties have been investigated over the entire XUV region (1--100nm). The XUV Bragg HOEs, based on dichromated gelatin (DCG) and on DCG/polymer grafts, have beenmore » recorded in the visible region (using an Innova Argo laser) and reconstructed using twelve XUV wavelengths. In addition, these phase high-resolution holographic materials have been shown to be suitable to direct x-ray laser holographic recording (using Princeton's x-ray laser). The volume x-ray holographic recording will be realized within the second year of the program effort.« less

  5. X-ray backscatter imaging of nuclear materials

    DOEpatents

    Chapman, Jeffrey Allen; Gunning, John E; Hollenbach, Daniel F; Ott, Larry J; Shedlock, Daniel

    2014-09-30

    The energy of an X-ray beam and critical depth are selected to detect structural discontinuities in a material having an atomic number Z of 57 or greater. The critical depth is selected by adjusting the geometry of a collimator that blocks backscattered radiation so that backscattered X-ray originating from a depth less than the critical depth is not detected. Structures of Lanthanides and Actinides, including nuclear fuel rod materials, can be inspected for structural discontinuities such as gaps, cracks, and chipping employing the backscattered X-ray.

  6. Angular correlations of photons from solution diffraction at a free-electron laser encode molecular structure

    DOE PAGES

    Mendez, Derek; Watkins, Herschel; Qiao, Shenglan; ...

    2016-09-26

    During X-ray exposure of a molecular solution, photons scattered from the same molecule are correlated. If molecular motion is insignificant during exposure, then differences in momentum transfer between correlated photons are direct measurements of the molecular structure. In conventional small- and wide-angle solution scattering, photon correlations are ignored. This report presents advances in a new biomolecular structural analysis technique, correlated X-ray scattering (CXS), which uses angular intensity correlations to recover hidden structural details from molecules in solution. Due to its intense rapid pulses, an X-ray free electron laser (XFEL) is an excellent tool for CXS experiments. A protocol is outlinedmore » for analysis of a CXS data set comprising a total of half a million X-ray exposures of solutions of small gold nanoparticles recorded at the Spring-8 Ångström Compact XFEL facility (SACLA). From the scattered intensities and their correlations, two populations of nanoparticle domains within the solution are distinguished: small twinned, and large probably non-twinned domains. Finally, it is shown analytically how, in a solution measurement, twinning information is only accessible via intensity correlations, demonstrating how CXS reveals atomic-level information from a disordered solution of like molecules.« less

  7. Near-edge X-ray refraction fine structure microscopy

    DOE PAGES

    Farmand, Maryam; Celestre, Richard; Denes, Peter; ...

    2017-02-06

    We demonstrate a method for obtaining increased spatial resolution and specificity in nanoscale chemical composition maps through the use of full refractive reference spectra in soft x-ray spectro-microscopy. Using soft x-ray ptychography, we measure both the absorption and refraction of x-rays through pristine reference materials as a function of photon energy and use these reference spectra as the basis for decomposing spatially resolved spectra from a heterogeneous sample, thereby quantifying the composition at high resolution. While conventional instruments are limited to absorption contrast, our novel refraction based method takes advantage of the strongly energy dependent scattering cross-section and can seemore » nearly five-fold improved spatial resolution on resonance.« less

  8. The 16th International Conference on X-ray Absorption Fine Structure (XAFS16)

    NASA Astrophysics Data System (ADS)

    Grunwaldt, J.-D.; Hagelstein, M.; Rothe, J.

    2016-05-01

    This preface of the proceedings volume of the 16th International Conference on X- ray Absorption Fine Structure (XAFS16) gives a glance on the five days of cutting-edge X-ray science which were held in Karlsruhe, Germany, August 23 - 28, 2015. In addition, several satellite meetings took place in Hamburg, Berlin and Stuttgart, a Sino-German workshop, three data analysis tutorials as well as special symposia on industrial catalysis and XFELs were held at the conference venue.

  9. Structural studies of P-type ATPase–ligand complexes using an X-ray free-electron laser

    DOE PAGES

    Bublitz, Maike; Nass, Karol; Drachmann, Nikolaj D.; ...

    2015-06-11

    Membrane proteins are key players in biological systems, mediating signalling events and the specific transport ofe.g.ions and metabolites. Consequently, membrane proteins are targeted by a large number of currently approved drugs. Understanding their functions and molecular mechanisms is greatly dependent on structural information, not least on complexes with functionally or medically important ligands. Structure determination, however, is hampered by the difficulty of obtaining well diffracting, macroscopic crystals. Here, the feasibility of X-ray free-electron-laser-based serial femtosecond crystallography (SFX) for the structure determination of membrane protein–ligand complexes using microcrystals of various native-source and recombinant P-type ATPase complexes is demonstrated. The data revealmore » the binding sites of a variety of ligands, including lipids and inhibitors such as the hallmark P-type ATPase inhibitor orthovanadate. By analyzing the resolution dependence of ligand densities and overall model qualities, SFX data quality metrics as well as suitable refinement procedures are discussed. Even at relatively low resolution and multiplicity, the identification of ligands can be demonstrated. This makes SFX a useful tool for ligand screening and thus for unravelling the molecular mechanisms of biologically active proteins.« less

  10. Insights into the distinct lithiation/sodiation of porous cobalt oxide by in operando synchrotron x-ray techniques and ab initio molecular dynamics simulations

    DOE PAGES

    Xu, Gui -Liang; Sheng, Tian; Chong, Lina; ...

    2017-01-10

    Sodium-ion batteries (SIBs) have been considered as one of the promising power source candidates for the stationary storage industries owing to the much lower cost of sodium than lithium. It is well-known that the electrode materials largely determine the energy density of the battery systems. However, recent discoveries on the electrode materials showed that most of them present distinct lithium and sodium storage performance, which is not yet well understood. In this work, we performed a comparative understanding on the structural changes of porous cobalt oxide during its electrochemical lithiation and sodiation process by in operando synchrotron small angel X-raymore » scattering, X-ray diffraction, and X-ray absorption spectroscopy. It was found that compared to the lithiation process, the porous cobalt oxide undergoes less pore structure changes, oxidation state, and local structure changes as well as crystal structure evolution during its sodiation process, which is attributed to the intrinsic low sodiation activity of cobalt oxide as evidenced by ab initio molecular dynamics simulations. Moreover, it was indicated that the sodiation activity of metal sulfides is higher than that of metal oxides, indicating a better candidate for SIBs. Furthermore, such understanding is crucial for future design and improvement of high-performance electrode materials for SIBs.« less

  11. History of Chandra X-Ray Observatory

    NASA Image and Video Library

    2000-04-01

    This Chandra X-Ray Observatory (CXO) image is a spectrum of a black hole, which is similar to the colorful spectrum of sunlight produced by a prism. The x-rays of interest are shown here recorded in bright stripes that run rightward and leftward from the center of the image. These x-rays are sorted precisely according to their energy with the highest-energy x-rays near the center of the image and the lower-energy x-rays farther out. The spectrum was obtained by using the Low Energy Transmission Grating (LETG), which intercepts x-rays and changes their direction by the amounts that depend sensitively on the x-ray energy. The assembly holds 540 gold transmission gratings. When in place behind the mirrors, the gratings intercept the x-rays reflected from the telescope. The bright spot at the center is due to a fraction of the x-ray radiation that is not deflected by the LETG. The spokes that intersect the central spot and the faint diagonal rays that flank the spectrum itself are artifacts due to the structure that supports the LETG grating elements. (Photo credit: NASA Cfa/J. McClintock et al)

  12. X-rays from supernova 1987A

    NASA Technical Reports Server (NTRS)

    Xu, Yueming; Sutherland, Peter; Mccray, Richard; Ross, Randy R.

    1988-01-01

    Detailed calculations of the development of the X-ray spectrum of 1987A are presented using more realistic models for the supernova composition and density structure provided by Woosley. It is shown how the emergence of the X-ray spectrum depends on the parameters of the model and the nature of its central energy source. It is shown that the soft X-ray spectrum should be dominated by a 6.4 keV Fe K(alpha) emission line that could be observed by a sensitive X-ray telescope.

  13. Randic and Schultz molecular topological indices and their correlation with some X-ray absorption parameters

    NASA Astrophysics Data System (ADS)

    Khatri, Sunil; Kekre, Pravin A.; Mishra, Ashutosh

    2016-10-01

    The properties of a molecular system are affected by the topology of molecule. Therefore many studies have been made where the various physic-chemical properties are correlated with the topological indices. These studies have shown a very good correlation demonstrating the utility of the graph theoretical approach. It is, therefore, very natural to expect that the various physical properties obtained by the X-ray absorption spectra may also show correlation with the topological indices. Some complexes were used to establish correlation between topological indices and some X-ray absorption parameters like chemical shift. The chemical shift is on the higher energy side of the metal edge in these complexes. The result obtained in these studies shows that the topological indices of organic molecule acting as a legands can be used for estimating edge shift theoretically.

  14. Si K EDGE STRUCTURE AND VARIABILITY IN GALACTIC X-RAY BINARIES

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Schulz, Norbert S.; Corrales, Lia; Canizares, Claude R.

    2016-08-10

    We survey the Si K edge structure in various absorbed Galactic low-mass X-ray binaries (LMXBs) to study states of silicon in the inter- and circum-stellar medium. The bulk of these LMXBs lie toward the Galactic bulge region and all have column densities above 10{sup 22} cm{sup −2}. The observations were performed using the Chandra High Energy Transmission Grating Spectrometer. The Si K edge in all sources appears at an energy value of 1844 ± 0.001 eV. The edge exhibits significant substructure that can be described by a near edge absorption feature at 1849 ± 0.002 eV and a far edgemore » absorption feature at 1865 ± 0.002 eV. Both of these absorption features appear variable with equivalent widths up to several mÅ. We can describe the edge structure using several components: multiple edge functions, near edge absorption excesses from silicates in dust form, signatures from X-ray scattering optical depths, and a variable warm absorber from ionized atomic silicon. The measured optical depths of the edges indicate much higher values than expected from atomic silicon cross sections and interstellar medium abundances, and they appear consistent with predictions from silicate X-ray absorption and scattering. A comparison with models also indicates a preference for larger dust grain sizes. In many cases, we identify Si xiii resonance absorption and determine ionization parameters between log ξ = 1.8 and 2.8 and turbulent velocities between 300 and 1000 km s{sup −1}. This places the warm absorber in close vicinity of the X-ray binaries. In some data, we observe a weak edge at 1.840 keV, potentially from a lesser contribution of neutral atomic silicon.« less

  15. Nanoscale characterization of local structures and defects in photonic crystals using synchrotron-based transmission soft X-ray microscopy

    PubMed Central

    Nho, Hyun Woo; Kalegowda, Yogesh; Shin, Hyun-Joon; Yoon, Tae Hyun

    2016-01-01

    For the structural characterization of the polystyrene (PS)-based photonic crystals (PCs), fast and direct imaging capabilities of full field transmission X-ray microscopy (TXM) were demonstrated at soft X-ray energy. PS-based PCs were prepared on an O2-plasma treated Si3N4 window and their local structures and defects were investigated using this label-free TXM technique with an image acquisition speed of ~10 sec/frame and marginal radiation damage. Micro-domains of face-centered cubic (FCC (111)) and hexagonal close-packed (HCP (0001)) structures were dominantly found in PS-based PCs, while point and line defects, FCC (100), and 12-fold symmetry structures were also identified as minor components. Additionally, in situ observation capability for hydrated samples and 3D tomographic reconstruction of TXM images were also demonstrated. This soft X-ray full field TXM technique with faster image acquisition speed, in situ observation, and 3D tomography capability can be complementally used with the other X-ray microscopic techniques (i.e., scanning transmission X-ray microscopy, STXM) as well as conventional characterization methods (e.g., electron microscopic and optical/fluorescence microscopic techniques) for clearer structure identification of self-assembled PCs and better understanding of the relationship between their structures and resultant optical properties. PMID:27087141

  16. Structure determination of molecules in an alignment laser field by femtosecond photoelectron diffraction using an X-ray free-electron laser

    PubMed Central

    Minemoto, Shinichirou; Teramoto, Takahiro; Akagi, Hiroshi; Fujikawa, Takashi; Majima, Takuya; Nakajima, Kyo; Niki, Kaori; Owada, Shigeki; Sakai, Hirofumi; Togashi, Tadashi; Tono, Kensuke; Tsuru, Shota; Wada, Ken; Yabashi, Makina; Yoshida, Shintaro; Yagishita, Akira

    2016-01-01

    We have successfully determined the internuclear distance of I2 molecules in an alignment laser field by applying our molecular structure determination methodology to an I 2p X-ray photoelectron diffraction profile observed with femtosecond X-ray free electron laser pulses. Using this methodology, we have found that the internuclear distance of the sample I2 molecules in an alignment Nd:YAG laser field of 6 × 1011 W/cm2 is elongated by from 0.18 to 0.30 Å “in average” relatively to the equilibrium internuclear distance of 2.666 Å. Thus, the present experiment constitutes a critical step towards the goal of femtosecond imaging of chemical reactions and opens a new direction for the study of ultrafast chemical reaction in the gas phase. PMID:27934891

  17. Small Angle X-ray Scattering for Nanoparticle Research

    DOE PAGES

    Li, Tao; Senesi, Andrew J.; Lee, Byeongdu

    2016-04-07

    X-ray scattering is a structural characterization tool that has impacted diverse fields of study. It is unique in its ability to examine materials in real time and under realistic sample environments, enabling researchers to understand morphology at nanometer and ångström length scales using complementary small and wide angle X-ray scattering (SAXS, WAXS), respectively. Herein, we focus on the use of SAXS to examine nanoscale particulate systems. We provide a theoretical foundation for X-ray scattering, considering both form factor and structure factor, as well as the use of correlation functions, which may be used to determine a particle’s size, size distribution,more » shape, and organization into hierarchal structures. The theory is expanded upon with contemporary use cases. Both transmission and reflection (grazing incidence) geometries are addressed, as well the combination of SAXS with other X-ray and non-X ray characterization tools. Furthermore, we conclude with an examination of several key areas of research where X-rays scattering has played a pivotal role, including in situ nanoparticle synthesis, nanoparticle assembly, and in operando studies of catalysts and energy storage materials. Throughout this review we highlight the unique capabilities of X-ray scattering for structural characterization of materials in their native environment.« less

  18. Small Angle X-ray Scattering for Nanoparticle Research

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Li, Tao; Senesi, Andrew J.; Lee, Byeongdu

    X-ray scattering is a structural characterization tool that has impacted diverse fields of study. It is unique in its ability to examine materials in real time and under realistic sample environments, enabling researchers to understand morphology at nanometer and ångström length scales using complementary small and wide angle X-ray scattering (SAXS, WAXS), respectively. Herein, we focus on the use of SAXS to examine nanoscale particulate systems. We provide a theoretical foundation for X-ray scattering, considering both form factor and structure factor, as well as the use of correlation functions, which may be used to determine a particle’s size, size distribution,more » shape, and organization into hierarchal structures. The theory is expanded upon with contemporary use cases. Both transmission and reflection (grazing incidence) geometries are addressed, as well the combination of SAXS with other X-ray and non-X ray characterization tools. Furthermore, we conclude with an examination of several key areas of research where X-rays scattering has played a pivotal role, including in situ nanoparticle synthesis, nanoparticle assembly, and in operando studies of catalysts and energy storage materials. Throughout this review we highlight the unique capabilities of X-ray scattering for structural characterization of materials in their native environment.« less

  19. Structural dissection of human metapneumovirus phosphoprotein using small angle x-ray scattering.

    PubMed

    Renner, Max; Paesen, Guido C; Grison, Claire M; Granier, Sébastien; Grimes, Jonathan M; Leyrat, Cédric

    2017-11-01

    The phosphoprotein (P) is the main and essential cofactor of the RNA polymerase (L) of non-segmented, negative-strand RNA viruses. P positions the viral polymerase onto its nucleoprotein-RNA template and acts as a chaperone of the nucleoprotein (N), thereby preventing nonspecific encapsidation of cellular RNAs. The phosphoprotein of human metapneumovirus (HMPV) forms homotetramers composed of a stable oligomerization domain (P core ) flanked by large intrinsically disordered regions (IDRs). Here we combined x-ray crystallography of P core with small angle x-ray scattering (SAXS)-based ensemble modeling of the full-length P protein and several of its fragments to provide a structural description of P that captures its dynamic character, and highlights the presence of varyingly stable structural elements within the IDRs. We discuss the implications of the structural properties of HMPV P for the assembly and functioning of the viral transcription/replication machinery.

  20. Structural biology at the European X-ray free-electron laser facility

    PubMed Central

    Altarelli, Massimo; Mancuso, Adrian P.

    2014-01-01

    The European X-ray free-electron laser (XFEL) facility, under construction in the Hamburg region, will provide high-peak brilliance (greater than 1033 photons s−1 mm−2 mrad−2 per 0.1% BW), ultrashort pulses (approx. 10 fs) of X-rays, with a high repetition rate (up to 27 000 pulses s−1) from 2016 onwards. The main features of this exceptional X-ray source, and the instrumentation developments necessary to exploit them fully, for application to a variety of scientific disciplines, are briefly summarized. In the case of structural biology, that has a central role in the scientific case of this new facility, the instruments and ancillary laboratories that are being planned and built within the baseline programme of the European XFEL and by consortia of users are also discussed. It is expected that the unique features of the source and the advanced features of the instrumentation will allow operation modes with more efficient use of sample materials, faster acquisition times, and conditions better approaching feasibility of single molecule imaging. PMID:24914145

  1. Small Angle X-Ray Scattering from Lipid-Bound Myelin Basic Protein in Solution

    PubMed Central

    Haas, H.; Oliveira, C. L. P.; Torriani, I. L.; Polverini, E.; Fasano, A.; Carlone, G.; Cavatorta, P.; Riccio, P.

    2004-01-01

    The structure of myelin basic protein (MBP), purified from the myelin sheath in both lipid-free (LF-MBP) and lipid-bound (LB-MBP) forms, was investigated in solution by small angle x-ray scattering. The water-soluble LF-MBP, extracted at pH < 3.0 from defatted brain, is the classical preparation of MBP, commonly regarded as an intrinsically unfolded protein. LB-MBP is a lipoprotein-detergent complex extracted from myelin with its native lipidic environment at pH > 7.0. Under all conditions, the scattering from the two protein forms was different, indicating different molecular shapes. For the LB-MBP, well-defined scattering curves were obtained, suggesting that the protein had a unique, compact (but not globular) structure. Furthermore, these data were compatible with earlier results from molecular modeling calculations on the MBP structure which have been refined by us. In contrast, the LF-MBP data were in accordance with the expected open-coil conformation. The results represent the first direct structural information from x-ray scattering measurements on MBP in its native lipidic environment in solution. PMID:14695288

  2. X-ray magnetic circular dichroism and hard X-ray photoelectron spectroscopy of tetragonal Mn72Ge28 epitaxial thin film

    NASA Astrophysics Data System (ADS)

    Kim, Jinhyeok; Mizuguchi, Masaki; Inami, Nobuhito; Ueno, Tetsuro; Ueda, Shigenori; Takanashi, Koki

    2018-04-01

    An epitaxially grown Mn72Ge28 film with a tetragonal crystal structure was fabricated. It was clarified that the film had a perpendicular magnetization and a high perpendicular magnetic anisotropy energy of 14.3 Merg/cm3. The electronic structure was investigated by X-ray magnetic circular dichroism and hard X-ray photoelectron spectroscopy. The obtained X-ray magnetic circular dichroism spectrum revealed that the Mn orbital magnetic moment governed the magnetocrystalline anisotropy of the Mn72Ge28 film. A doublet structure was observed for the Mn 2p3/2 peak of hard X-ray photoelectron spectrum, indicating the spin exchange interaction between the 2p core-hole and 3d valence electrons.

  3. Soft x-ray contact imaging of biological specimens using a laser-produced plasma as an x-ray source

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Cheng, P.C.

    The use of a laser-produced plasma as an x-ray source provides significant advantages over other types of sources for x-ray microradiography of, particularly, living biological specimens. The pulsed nature of the x-rays enables imaging of the specimen in a living state, and the small source size minimizes penumbral blurring. This makes it possible to make an exposure close to the source, thereby increasing the x-ray intensity. In this article, we will demonstrate the applications of x-ray contact microradiography in structural and developmental botany such as the localization of silica deposition and the floral morphologenesis of maize.

  4. Grating-based X-ray tomography of 3D food structures

    NASA Astrophysics Data System (ADS)

    Miklos, Rikke; Nielsen, Mikkel Schou; Einarsdottir, Hildur; Lametsch, René

    2016-10-01

    A novel grating based X-ray phase-contrast tomographic method has been used to study how partly substitution of meat proteins with two different types of soy proteins affect the structure of the formed protein gel in meat emulsions. The measurements were performed at the Swiss synchrotron radiation light source using a grating interferometric set-up.

  5. X-Ray Snapshots Capture the First Cries of Baby Stars

    NASA Astrophysics Data System (ADS)

    2000-11-01

    CXC PR: 00-27 Stars, like babies, make quite a fuss in their first days after birth. Astronomers using the Chandra X-ray Observatory have discovered that protostars--stars in their youngest, "neonatal" stage--are marked by powerful X rays from plasma ten times hotter and 100 to 100,000 times brighter than the flares on our Sun. This is all long before their nuclear furnaces of hydrogen even ignite, the mark of stellar maturity. The X-ray flares have also provided the closest look yet at the youngest stars in the universe, never before detected because they are hidden within dust and molecular clouds that filter all other types of light. Yohko Tsuboi of the Pennsylvania State University (Penn State) presents these findings today in a press conference at the meeting of the High Energy Astrophysics Division of the American Astronomical Society in Honolulu, Hawaii. "We peered at newborn stars deeply embedded in their cradle and found that their crying is much more tumultuous than we expected," said Tsuboi. "With Chandra, we now have a new tool to examine protostars, which have been impossible to gain access to in any other wavelength." Protostars located in the rho-Ophiuchi molecular cloud Protostars located in the rho-Ophiuchi molecular cloud 1 square light years field X-ray image around rho Ophiuchi molecular cloud core. Red colorrepresents less absorbed X rays, while blue represents absorbed X rays. Lightcurves for each sources are also shown. Tsuboi and her collaborators looked at the two youngest types of protostars: Class-0 (zero) protostars, about 10,000 years old; and Class-I protostars, about 100,000 years old. In human terms, these protostars are like one-hour-old and 10-hour-old babies, respectively. The transition from one class to another is marked by changes in the protostar's infrared spectrum as the gas and dust envelope diminishes. The envelope has been well studied by infrared and radio astronomers. Protostars themselves and their most extreme

  6. Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser

    DOE PAGES

    Kang, Yanyong; Zhou, X. Edward; Gao, Xiang; ...

    2015-07-22

    G-protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signalling to numerous G-protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly in which rhodopsin uses distinct structural elements, including transmembrane helix 7 and helix 8, to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a ~20° rotationmore » between the amino and carboxy domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. In conclusion, this structure provides a basis for understanding GPCR-mediated arrestin-biased signalling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biology.« less

  7. Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kang, Yanyong; Zhou, X. Edward; Gao, Xiang

    G-protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signalling to numerous G-protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly in which rhodopsin uses distinct structural elements, including transmembrane helix 7 and helix 8, to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a ~20° rotationmore » between the amino and carboxy domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. In conclusion, this structure provides a basis for understanding GPCR-mediated arrestin-biased signalling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biology.« less

  8. ATM observations - X-ray results. [solar coronal structure from Skylab experiments

    NASA Technical Reports Server (NTRS)

    Vaiana, G. S.; Zombeck, M.; Krieger, A. S.; Timothy, A. F.

    1976-01-01

    Preliminary results of the solar X-ray observations from Skylab are reviewed which indicate a highly structured nature for the corona, with closed magnetic-loop structures over a wide range of size scales. A description of the S-054 experiments is provided, and values are given for the parameters - including size, density, and temperature - describing a variety of typical coronal features. The structure and evolution of active regions, coronal holes, and bright points are discussed.

  9. New Directions in X-Ray Light Sources

    ScienceCinema

    Falcone, Roger

    2017-12-09

    July 15, 2008 Berkeley Lab lecture: Molecular movies of chemical reactions and material phase transformations need a strobe of x-rays, the penetrating light that reveals how atoms and molecules assemble in chemical and biological systems and complex materials. Roger Falcone, Director of the Advanced Light Source,will discuss a new generation of x ray sources that will enable a new science of atomic dynamics on ultrafast timescales.

  10. X-MIME: An Imaging X-ray Spectrometer for Detailed Study of Jupiter's Icy Moons and the Planet's X-ray Aurora

    NASA Technical Reports Server (NTRS)

    Elsner, R. F.; Ramsey, B. D.; Waite, J. H.; Rehak, P.; Johnson, R. E.; Cooper, J. F.; Swartz, D. A.

    2004-01-01

    Remote observations with the Chandra X-ray Observatory and the XMM-Newton Observatory have shown that the Jovian system is a source of x-rays with a rich and complicated structure. The planet's polar auroral zones and its disk are powerful sources of x-ray emission. Chandra observations revealed x-ray emission from the Io Plasma Torus and from the Galilean moons Io, Europa, and possibly Ganymede. The emission from these moons is certainly due to bombardment of their surfaces of highly energetic protons, oxygen and sulfur ions from the region near the Torus exciting atoms in their surfaces and leading to fluorescent x-ray emission lines. Although the x-ray emission from the Galilean moons is faint when observed from Earth orbit, an imaging x-ray spectrometer in orbit around these moons, operating at 200 eV and above with 150 eV energy resolution, would provide a detailed mapping (down to 40 m spatial resolution) of the elemental composition in their surfaces. Such maps would provide important constraints on formation and evolution scenarios for the surfaces of these moons. Here we describe the characteristics of X-MIME, an imaging x-ray spectrometer under going a feasibility study for the JIMO mission, with the ultimate goal of providing unprecedented x-ray studies of the elemental composition of the surfaces of Jupiter's icy moons and Io, as well as of Jupiter's auroral x-ray emission.

  11. 100 Years Later: Celebrating the Contributions of X-ray Crystallography to Allergy and Clinical Immunology

    PubMed Central

    Pomés, Anna; Chruszcz, Maksymilian; Gustchina, Alla; Minor, Wladek; Mueller, Geoffrey A.; Pedersen, Lars C.; Wlodawer, Alexander; Chapman, Martin D.

    2015-01-01

    Current knowledge of molecules involved in immunology and allergic disease results from significant contributions of X-ray crystallography, a discipline that just celebrated its 100th anniversary. The histories of allergens and X-ray crystallography are intimately intertwined. The first enzyme structure to be determined was lysozyme, also known as the chicken food allergen Gal d 4. Crystallography determines the exact three-dimensional positions of atoms in molecules. Structures of molecular complexes in the disciplines of immunology and allergy have revealed the atoms involved in molecular interactions and in mechanisms of disease. These complexes include peptides presented by MHC class II molecules, cytokines bound to their receptors, allergen-antibody complexes, and innate immune receptors with their ligands. The information derived from crystallographic studies provides insights into the function of molecules. Allergen function is one of the determinants of environmental exposure, which is essential for IgE sensitization. Proteolytic activity of allergens or their capacity to bind lipopolysaccharides may also contribute to allergenicity. The atomic positions define the molecular surface that is accessible to antibodies. This surface in turn determines antibody specificity and cross-reactivity that are important factors for the selection of allergen panels used for molecular diagnosis and for the interpretation of clinical symptoms. This review celebrates the contributions of X-ray crystallography to clinical immunology and allergy, focusing on new molecular perspectives that influence the diagnosis and treatment of allergic diseases. PMID:26145985

  12. 100 Years later: Celebrating the contributions of x-ray crystallography to allergy and clinical immunology.

    PubMed

    Pomés, Anna; Chruszcz, Maksymilian; Gustchina, Alla; Minor, Wladek; Mueller, Geoffrey A; Pedersen, Lars C; Wlodawer, Alexander; Chapman, Martin D

    2015-07-01

    Current knowledge of molecules involved in immunology and allergic disease results from the significant contributions of x-ray crystallography, a discipline that just celebrated its 100th anniversary. The histories of allergens and x-ray crystallography are intimately intertwined. The first enzyme structure to be determined was lysozyme, also known as the chicken food allergen Gal d 4. Crystallography determines the exact 3-dimensional positions of atoms in molecules. Structures of molecular complexes in the disciplines of immunology and allergy have revealed the atoms involved in molecular interactions and mechanisms of disease. These complexes include peptides presented by MHC class II molecules, cytokines bound to their receptors, allergen-antibody complexes, and innate immune receptors with their ligands. The information derived from crystallographic studies provides insights into the function of molecules. Allergen function is one of the determinants of environmental exposure, which is essential for IgE sensitization. Proteolytic activity of allergens or their capacity to bind LPSs can also contribute to allergenicity. The atomic positions define the molecular surface that is accessible to antibodies. In turn, this surface determines antibody specificity and cross-reactivity, which are important factors for the selection of allergen panels used for molecular diagnosis and the interpretation of clinical symptoms. This review celebrates the contributions of x-ray crystallography to clinical immunology and allergy, focusing on new molecular perspectives that influence the diagnosis and treatment of allergic diseases. Copyright © 2015 American Academy of Allergy, Asthma & Immunology. All rights reserved.

  13. X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel.

    PubMed

    Nury, Hugues; Van Renterghem, Catherine; Weng, Yun; Tran, Alphonso; Baaden, Marc; Dufresne, Virginie; Changeux, Jean-Pierre; Sonner, James M; Delarue, Marc; Corringer, Pierre-Jean

    2011-01-20

    General anaesthetics have enjoyed long and widespread use but their molecular mechanism of action remains poorly understood. There is good evidence that their principal targets are pentameric ligand-gated ion channels (pLGICs) such as inhibitory GABA(A) (γ-aminobutyric acid) receptors and excitatory nicotinic acetylcholine receptors, which are respectively potentiated and inhibited by general anaesthetics. The bacterial homologue from Gloeobacter violaceus (GLIC), whose X-ray structure was recently solved, is also sensitive to clinical concentrations of general anaesthetics. Here we describe the crystal structures of the complexes propofol/GLIC and desflurane/GLIC. These reveal a common general-anaesthetic binding site, which pre-exists in the apo-structure in the upper part of the transmembrane domain of each protomer. Both molecules establish van der Waals interactions with the protein; propofol binds at the entrance of the cavity whereas the smaller, more flexible, desflurane binds deeper inside. Mutations of some amino acids lining the binding site profoundly alter the ionic response of GLIC to protons, and affect its general-anaesthetic pharmacology. Molecular dynamics simulations, performed on the wild type (WT) and two GLIC mutants, highlight differences in mobility of propofol in its binding site and help to explain these effects. These data provide a novel structural framework for the design of general anaesthetics and of allosteric modulators of brain pLGICs.

  14. Operation of a separated-type x-ray interferometer for phase-contrast x-ray imaging

    NASA Astrophysics Data System (ADS)

    Yoneyama, Akio; Momose, Atsushi; Seya, Eiichi; Hirano, Keiichi; Takeda, Tohoru; Itai, Yuji

    1999-12-01

    Aiming at large-area phase-contrast x-ray imaging, a separated-type x-ray interferometer system was designed and developed to produce 25×20 mm interference patterns. The skew-symmetric optical system was adopted because of the feasibility of alignment. The rotation between the separated crystal blocks was controlled within a drift of 0.06 nrad using a feedback positioning system. This interferometer generated a 25×15 mm interference pattern with 0.07 nm synchrotron x-rays. A slice of a rabbit's kidney was observed, and its tubular structure could be revealed in a measured phase map.

  15. Extended x-ray absorption fine structure spectroscopy and x-ray absorption near edge spectroscopy study of aliovalent doped ceria to correlate local structural changes with oxygen vacancies clustering

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Shirbhate, S. C.; Acharya, S. A., E-mail: saha275@yahoo.com; Yadav, A. K.

    2016-04-04

    This study provides atomic scale insight to understand the role of aliovalent dopants on oxygen vacancies clustering and dissociation mechanism in ceria system in order to enhance the performance of oxy-ion conductor. Dopants induced microscale changes in ceria are probed by extended X-ray absorption fine structure spectroscopy, X-ray absorption near edge spectra, and Raman spectroscopy. The results are explored to establish a correlation between atomic level structural changes (coordination number, interatomic spacing) → formation of dimer and trimer type cation-oxygen vacancies defect complex (intrinsic and extrinsic) → dissociation of oxygen vacancies from defect cluster → ionic conductivity temperature. It ismore » a strategic approach to understand key physics of ionic conductivity mechanism in order to reduce operating temperature of electrolytes for intermediate temperature (300–450 °C) electrochemical devices for the first time.« less

  16. Energy-dispersive X-ray emission spectroscopy using an X-ray free-electron laser in a shot-by-shot mode

    DOE PAGES

    Alonso-Mori, Roberto; Kern, Jan; Gildea, Richard J.; ...

    2012-11-05

    The ultrabright femtosecond X-ray pulses provided by X-ray free-electron lasers open capabilities for studying the structure and dynamics of a wide variety of systems beyond what is possible with synchrotron sources. Recently, this “probe-before-destroy” approach has been demonstrated for atomic structure determination by serial X-ray diffraction of microcrystals. There has been the question whether a similar approach can be extended to probe the local electronic structure by X-ray spectroscopy. To address this, we have carried out femtosecond X-ray emission spectroscopy (XES) at the Linac Coherent Light Source using redox-active Mn complexes. XES probes the charge and spin states as wellmore » as the ligand environment, critical for understanding the functional role of redox-active metal sites. Kβ 1,3 XES spectra of Mn II and Mn 2 III,IV complexes at room temperature were collected using a wavelength dispersive spectrometer and femtosecond X-ray pulses with an individual dose of up to >100 MGy. The spectra were found in agreement with undamaged spectra collected at low dose using synchrotron radiation. Our results demonstrate that the intact electronic structure of redox active transition metal compounds in different oxidation states can be characterized with this shot-by-shot method. This opens the door for studying the chemical dynamics of metal catalytic sites by following reactions under functional conditions. Furthermore, the technique can be combined with X-ray diffraction to simultaneously obtain the geometric structure of the overall protein and the local chemistry of active metal sites and is expected to prove valuable for understanding the mechanism of important metalloproteins, such as photosystem II.« less

  17. Energy-dispersive X-ray emission spectroscopy using an X-ray free-electron laser in a shot-by-shot mode

    PubMed Central

    Alonso-Mori, Roberto; Kern, Jan; Gildea, Richard J.; Sokaras, Dimosthenis; Weng, Tsu-Chien; Lassalle-Kaiser, Benedikt; Tran, Rosalie; Hattne, Johan; Laksmono, Hartawan; Hellmich, Julia; Glöckner, Carina; Echols, Nathaniel; Sierra, Raymond G.; Schafer, Donald W.; Sellberg, Jonas; Kenney, Christopher; Herbst, Ryan; Pines, Jack; Hart, Philip; Herrmann, Sven; Grosse-Kunstleve, Ralf W.; Latimer, Matthew J.; Fry, Alan R.; Messerschmidt, Marc M.; Miahnahri, Alan; Seibert, M. Marvin; Zwart, Petrus H.; White, William E.; Adams, Paul D.; Bogan, Michael J.; Boutet, Sébastien; Williams, Garth J.; Zouni, Athina; Messinger, Johannes; Glatzel, Pieter; Sauter, Nicholas K.; Yachandra, Vittal K.; Yano, Junko; Bergmann, Uwe

    2012-01-01

    The ultrabright femtosecond X-ray pulses provided by X-ray free-electron lasers open capabilities for studying the structure and dynamics of a wide variety of systems beyond what is possible with synchrotron sources. Recently, this “probe-before-destroy” approach has been demonstrated for atomic structure determination by serial X-ray diffraction of microcrystals. There has been the question whether a similar approach can be extended to probe the local electronic structure by X-ray spectroscopy. To address this, we have carried out femtosecond X-ray emission spectroscopy (XES) at the Linac Coherent Light Source using redox-active Mn complexes. XES probes the charge and spin states as well as the ligand environment, critical for understanding the functional role of redox-active metal sites. Kβ1,3 XES spectra of MnII and Mn2III,IV complexes at room temperature were collected using a wavelength dispersive spectrometer and femtosecond X-ray pulses with an individual dose of up to >100 MGy. The spectra were found in agreement with undamaged spectra collected at low dose using synchrotron radiation. Our results demonstrate that the intact electronic structure of redox active transition metal compounds in different oxidation states can be characterized with this shot-by-shot method. This opens the door for studying the chemical dynamics of metal catalytic sites by following reactions under functional conditions. The technique can be combined with X-ray diffraction to simultaneously obtain the geometric structure of the overall protein and the local chemistry of active metal sites and is expected to prove valuable for understanding the mechanism of important metalloproteins, such as photosystem II. PMID:23129631

  18. Resonant soft X-ray scattering on protein solutions

    NASA Astrophysics Data System (ADS)

    Ye, Dan; Le, Thinh; Wang, Cheng; Zwart, Peter; Gomez, Esther; Gomez, Enrique

    Protein structure is crucial for biological function, such that characterizing protein folding and packing is important for the design of therapeutics and enzymes. We propose resonant soft X-ray scattering (RSOXS) as an approach to study proteins and other biological assemblies in solution. Calculations of the scattering contrast suggest that soft X-ray scattering is more sensitive than hard X-ray scattering, because of contrast generated at the absorption edges of constituent elements such as carbon, nitrogen and oxygen. We have examined the structure of bovine serum albumin (BSA) in solution by RSOXS. We find that by varying incident X-ray energies, we are able to achieve higher scattering contrast near the absorption edge. From our RSOXS scattering result we are able to reconstruct the structure of BSA in 3D. These RSOXS results also agree with hard X-ray experiments, including crystallographic data. Our study demonstrates the potential of RSOXS for studying protein structure in solution.

  19. Stimulated Electronic X-Ray Raman Scattering

    NASA Astrophysics Data System (ADS)

    Weninger, Clemens; Purvis, Michael; Ryan, Duncan; London, Richard A.; Bozek, John D.; Bostedt, Christoph; Graf, Alexander; Brown, Gregory; Rocca, Jorge J.; Rohringer, Nina

    2013-12-01

    We demonstrate strong stimulated inelastic x-ray scattering by resonantly exciting a dense gas target of neon with femtosecond, high-intensity x-ray pulses from an x-ray free-electron laser (XFEL). A small number of lower energy XFEL seed photons drive an avalanche of stimulated resonant inelastic x-ray scattering processes that amplify the Raman scattering signal by several orders of magnitude until it reaches saturation. Despite the large overall spectral width, the internal spiky structure of the XFEL spectrum determines the energy resolution of the scattering process in a statistical sense. This is demonstrated by observing a stochastic line shift of the inelastically scattered x-ray radiation. In conjunction with statistical methods, XFELs can be used for stimulated resonant inelastic x-ray scattering, with spectral resolution smaller than the natural width of the core-excited, intermediate state.

  20. Synthesis and structural characterization by NMR and X-ray of new Morita-Baylis-Hillman adducts derived from 7-chloroquinoline

    NASA Astrophysics Data System (ADS)

    da Silva Caleffi, Guilherme; de Oliveira, João Paulo Gomes; da Paz Silva, Everton; Olegário, Tayná Rodrigues; Mendes, Rhuan Karlos Santos; Lima-Junior, Cláudio Gabriel; Silva, Fábio Pedrosa Lins; Martins, Felipe Terra; Vasconcellos, Mário Luiz Araújo de Almeida

    2017-04-01

    Herein we describe the design, synthesis and structural characterization by NMR and X-ray of new molecular hybrids 4a-4c containing the nitroaromatic MBHA moiety and the 7-chloroquinoline pharmacophores, linked by an aliphatic spacer as a model for antiprotozoal drugs. Firstly, the 4,7-dichloroquinoline (7) reacted with excess of ethylene glycol, through a SNAr promoted by t-BuOK, to prepare the 2-(7-chloroquinolin-4-yloxy)ethanol (6) in 98% isolated yield. Then, the novel 2-(7-chloroquinolin-4-yloxy) ethyl acrylate (5) was synthesized in 78% isolated yield by reacting the alcohol (6) with acryloyl chloride and TEA in CH2Cl2. Finally, this acrylate (5) reacted with o-nitrobenzaldehyde, m-nitrobenzaldehyde and p-nitrobenzaldehyde through Morita-Baylis-Hillman reactions promoted by DABCO at room temperature, using t-BuOH:Water (9:1) as solvent, to afford the new hybrids 4a-4c in 73-76% isolated yields. Three-dimensional structures were characterized in both monomeric and intermolecular packing by X-Ray experiments.

  1. X-ray scanning of overhead aurorae from rockets

    NASA Technical Reports Server (NTRS)

    Barcus, J. R.; Goldberg, R. A.; Gesell, L. H.

    1981-01-01

    Two Nike Tomahawk rocket payloads were launched into energetic auroral events in September, 1976 to investigate the structure of these events, as well as their effects on the atmosphere. X-ray scintillation detectors with energy discrimination in four ranges were used to measure the deposition of bremsstrahlung produced X-rays within the stratosphere and mesosphere. Iterative computer techniques were used to reconstruct X-ray source maps at 100 km, taking atmospheric absorption effects into account. Payload 18.178 was launched on September 21st into an aurora having two distinct azimuthal regions of optical brightness. The X-ray scanner detected the same features, and overlays of the X-ray source maps on all-sky photographs showed spatial coincidence of the X-ray with optical features at the lower energies (below 40 keV). Payload 18.179 was launched September 23rd into an aurora with a more diffuse character. The optical structure did not coincide as well with the measured X-ray structure. There was also an indication of a two-component spectrum for each event, with the hard component originating in the more diffuse, optically faint regions.

  2. Modeling Contamination Migration on the Chandra X-ray Observatory II

    NASA Technical Reports Server (NTRS)

    O'Dell, Steve; Swartz, Doug; Tice, Neil; Plucinsky, Paul; Grant, Catherine; Marshall, Herman; Vikhlinin, Alexey

    2013-01-01

    During its first 14 years of operation, the cold (about -60degC) optical blocking filter of the Advanced CCD Imaging Spectrometer (ACIS), aboard the Chandra X-ray Observatory, has accumulated a growing layer of molecular contamination that attenuates low-energy x rays. Over the past few years, the accumulation rate, spatial distribution, and composition may have changed, perhaps partially related to changes in the operating temperature of the ACIS housing. This evolution of the accumulation of the molecular contamination has motivated further analysis of contamination migration on the Chandra X-ray Observatory, particularly within and near the ACIS cavity. To this end, the current study employs a higher-fidelity geometric model of the ACIS cavity, detailed thermal modeling based upon monitored temperature data, and an accordingly refined model of the molecular transport.

  3. Ultrafast nonthermal heating of water initiated by an X-ray Free-Electron Laser.

    PubMed

    Beyerlein, Kenneth R; Jönsson, H Olof; Alonso-Mori, Roberto; Aquila, Andrew; Bajt, Saša; Barty, Anton; Bean, Richard; Koglin, Jason E; Messerschmidt, Marc; Ragazzon, Davide; Sokaras, Dimosthenis; Williams, Garth J; Hau-Riege, Stefan; Boutet, Sébastien; Chapman, Henry N; Tîmneanu, Nicuşor; Caleman, Carl

    2018-05-29

    The bright ultrafast pulses of X-ray Free-Electron Lasers allow investigation into the structure of matter under extreme conditions. We have used single pulses to ionize and probe water as it undergoes a phase transition from liquid to plasma. We report changes in the structure of liquid water on a femtosecond time scale when irradiated by single 6.86 keV X-ray pulses of more than 10 6 J/cm 2 These observations are supported by simulations based on molecular dynamics and plasma dynamics of a water system that is rapidly ionized and driven out of equilibrium. This exotic ionic and disordered state with the density of a liquid is suggested to be structurally different from a neutral thermally disordered state.

  4. Ultrafast X-Ray Coherent Control

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Reis, David

    2009-05-01

    This main purpose of this grant was to develop the nascent eld of ultrafast x-ray science using accelerator-based sources, and originally developed from an idea that a laser could modulate the di racting properties of a x-ray di racting crystal on a fast enough time scale to switch out in time a shorter slice from the already short x-ray pulses from a synchrotron. The research was carried out primarily at the Advanced Photon Source (APS) sector 7 at Argonne National Laboratory and the Sub-Picosecond Pulse Source (SPPS) at SLAC; in anticipation of the Linac Coherent Light Source (LCLS) x-ray freemore » electron laser that became operational in 2009 at SLAC (all National User Facilities operated by BES). The research centered on the generation, control and measurement of atomic-scale dynamics in atomic, molecular optical and condensed matter systems with temporal and spatial resolution . It helped develop the ultrafast physics, techniques and scienti c case for using the unprecedented characteristics of the LCLS. The project has been very successful with results have been disseminated widely and in top journals, have been well cited in the eld, and have laid the foundation for many experiments being performed on the LCLS, the world's rst hard x-ray free electron laser.« less

  5. Image enhancement for on-site X-ray nondestructive inspection of reinforced concrete structures.

    PubMed

    Pei, Cuixiang; Wu, Wenjing; Ueaska, Mitsuru

    2016-11-22

    The use of portable and high-energy X-ray system can provide a very promising approach for on-site nondestructive inspection of inner steel reinforcement of concrete structures. However, the noise properties and contrast of the radiographic images for thick concrete structures do often not meet the demands. To enhance the images, we present a simple and effective method for noise reduction based on a combined curvelet-wavelet transform and local contrast enhancement based on neighborhood operation. To investigate the performance of this method for our X-ray system, we have performed several experiments with using simulated and experimental data. With comparing to other traditional methods, it shows that the proposed image enhancement method has a better performance and can significantly improve the inspection performance for reinforced concrete structures.

  6. In Situ X-Ray Studies of Crystallization Kinetics and Ordering in Functional Organic and Hybrid Materials

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yang, Bin; Keum, Jong K.; Geohegan, David B.

    In-Situ and time-resolved X-ray scattering and diffraction is dedicated to yielding the change of structural information as the materials are processed or grown in a controlled environment. In this chapter, we introduce the use of in situ and time-resolved X-ray techniques to understand molecular packing, crystal orientation, and phase transformation during the synthesis and processing of functional organic semiconductors, organic nanowires, and hybrid perovskite materials.

  7. Femtosecond X-ray protein nanocrystallography

    PubMed Central

    Chapman, Henry N.; Fromme, Petra; Barty, Anton; White, Thomas A.; Kirian, Richard A.; Aquila, Andrew; Hunter, Mark S.; Schulz, Joachim; DePonte, Daniel P.; Weierstall, Uwe; Doak, R. Bruce; Maia, Filipe R. N. C.; Martin, Andrew V.; Schlichting, Ilme; Lomb, Lukas; Coppola, Nicola; Shoeman, Robert L.; Epp, Sascha W.; Hartmann, Robert; Rolles, Daniel; Rudenko, Artem; Foucar, Lutz; Kimmel, Nils; Weidenspointner, Georg; Holl, Peter; Liang, Mengning; Barthelmess, Miriam; Caleman, Carl; Boutet, Sébastien; Bogan, Michael J.; Krzywinski, Jacek; Bostedt, Christoph; Bajt, Saša; Gumprecht, Lars; Rudek, Benedikt; Erk, Benjamin; Schmidt, Carlo; Hömke, André; Reich, Christian; Pietschner, Daniel; Strüder, Lothar; Hauser, Günter; Gorke, Hubert; Ullrich, Joachim; Herrmann, Sven; Schaller, Gerhard; Schopper, Florian; Soltau, Heike; Kühnel, Kai-Uwe; Messerschmidt, Marc; Bozek, John D.; Hau-Riege, Stefan P.; Frank, Matthias; Hampton, Christina Y.; Sierra, Raymond G.; Starodub, Dmitri; Williams, Garth J.; Hajdu, Janos; Timneanu, Nicusor; Seibert, M. Marvin; Andreasson, Jakob; Rocker, Andrea; Jönsson, Olof; Svenda, Martin; Stern, Stephan; Nass, Karol; Andritschke, Robert; Schröter, Claus-Dieter; Krasniqi, Faton; Bott, Mario; Schmidt, Kevin E.; Wang, Xiaoyu; Grotjohann, Ingo; Holton, James M.; Barends, Thomas R. M.; Neutze, Richard; Marchesini, Stefano; Fromme, Raimund; Schorb, Sebastian; Rupp, Daniela; Adolph, Marcus; Gorkhover, Tais; Andersson, Inger; Hirsemann, Helmut; Potdevin, Guillaume; Graafsma, Heinz; Nilsson, Björn; Spence, John C. H.

    2012-01-01

    X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded1-3. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction ‘snapshots’ are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source4. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes5. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (~200 nm to 2 μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes6. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage. PMID:21293373

  8. Femtosecond X-ray protein nanocrystallography.

    PubMed

    Chapman, Henry N; Fromme, Petra; Barty, Anton; White, Thomas A; Kirian, Richard A; Aquila, Andrew; Hunter, Mark S; Schulz, Joachim; DePonte, Daniel P; Weierstall, Uwe; Doak, R Bruce; Maia, Filipe R N C; Martin, Andrew V; Schlichting, Ilme; Lomb, Lukas; Coppola, Nicola; Shoeman, Robert L; Epp, Sascha W; Hartmann, Robert; Rolles, Daniel; Rudenko, Artem; Foucar, Lutz; Kimmel, Nils; Weidenspointner, Georg; Holl, Peter; Liang, Mengning; Barthelmess, Miriam; Caleman, Carl; Boutet, Sébastien; Bogan, Michael J; Krzywinski, Jacek; Bostedt, Christoph; Bajt, Saša; Gumprecht, Lars; Rudek, Benedikt; Erk, Benjamin; Schmidt, Carlo; Hömke, André; Reich, Christian; Pietschner, Daniel; Strüder, Lothar; Hauser, Günter; Gorke, Hubert; Ullrich, Joachim; Herrmann, Sven; Schaller, Gerhard; Schopper, Florian; Soltau, Heike; Kühnel, Kai-Uwe; Messerschmidt, Marc; Bozek, John D; Hau-Riege, Stefan P; Frank, Matthias; Hampton, Christina Y; Sierra, Raymond G; Starodub, Dmitri; Williams, Garth J; Hajdu, Janos; Timneanu, Nicusor; Seibert, M Marvin; Andreasson, Jakob; Rocker, Andrea; Jönsson, Olof; Svenda, Martin; Stern, Stephan; Nass, Karol; Andritschke, Robert; Schröter, Claus-Dieter; Krasniqi, Faton; Bott, Mario; Schmidt, Kevin E; Wang, Xiaoyu; Grotjohann, Ingo; Holton, James M; Barends, Thomas R M; Neutze, Richard; Marchesini, Stefano; Fromme, Raimund; Schorb, Sebastian; Rupp, Daniela; Adolph, Marcus; Gorkhover, Tais; Andersson, Inger; Hirsemann, Helmut; Potdevin, Guillaume; Graafsma, Heinz; Nilsson, Björn; Spence, John C H

    2011-02-03

    X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction 'snapshots' are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (∼200 nm to 2 μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.

  9. Characterization and analysis of Porous, Brittle solid structures by X-ray micro computed tomography

    NASA Astrophysics Data System (ADS)

    Lin, C. L.; Videla, A. R.; Yu, Q.; Miller, J. D.

    2010-12-01

    The internal structure of porous, brittle solid structures, such as porous rock, foam metal and wallboard, is extremely complex. For example, in the case of wallboard, the air bubble size and the thickness/composition of the wall structure are spatial parameters that vary significantly and influence mechanical, thermal, and acoustical properties. In this regard, the complex geometry and the internal texture of material, such as wallboard, is characterized and analyzed in 3-D using cone beam x-ray micro computed tomography. Geometrical features of the porous brittle structure are quantitatively analyzed based on calibration of the x-ray linear attenuation coefficient, use of a 3-D watershed algorithm, and use of a 3-D skeletonization procedure. Several examples of the 3-D analysis for porous, wallboard structures are presented and the results discussed.

  10. X-ray induced chemical reaction revealed by in-situ X-ray diffraction and scanning X-ray microscopy in 15 nm resolution (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Ge, Mingyuan; Liu, Wenjun; Bock, David; De Andrade, Vincent; Yan, Hanfei; Huang, Xiaojing; Marschilok, Amy; Takeuchi, Esther; Xin, Huolin; Chu, Yong S.

    2016-09-01

    The detection sensitivity of synchrotron-based X-ray techniques has been largely improved due to the ever increasing source brightness, which have significantly advanced ex-situ and in-situ research for energy materials, such as lithium-ion batteries. However, the strong beam-matter interaction arisen from the high beam flux can significantly modify the material structure. The parasitic beam-induced effect inevitably interferes with the intrinsic material property, which brings difficulties in interpreting experimental results, and therefore requires comprehensive evaluation. Here we present a quantitative in-situ study of the beam-effect on one electrode material Ag2VO2PO4 using four different X-ray probes with different radiation dose rate. The material system we reported exhibits interesting and reversible radiation-induced thermal and chemical reactions, which was further evaluated under electron microscopy to illustrate the underlying mechanism. The work we presented here will provide a guideline in using synchrotron X-rays to distinguish the materials' intrinsic behavior from extrinsic structure changed induced by X-rays, especially in the case of in-situ and operando study where the materials are under external field of either temperature or electric field.

  11. X-ray absorption investigation of the electronic structure of the CuI@SWCNT nanocomposite

    NASA Astrophysics Data System (ADS)

    Generalov, A. V.; Brzhezinskaya, M. M.; Vinogradov, A. S.; Püttner, R.; Chernysheva, M. V.; Lukashin, A. V.; Eliseev, A. A.

    2011-03-01

    The Cu 2 p, I 3 d, and C 1 sX-ray absorption spectra of the CuI@SWCNT nanocomposite prepared by filling single-walled carbon nanotubes (SWCNTs) with the CuI melt by the capillary technique have been measured with a high-energy resolution using the equipment of the Russian-German beamline at the BESSY electron storage ring. In order to characterize the electronic structure of the nanocomposite and possible changes in the atomic and electronic structures of CuI and SWCNTs in the CuI@SWCNT nanocomposite, the spectra obtained have been analyzed in the framework of the quasi-molecular approach by comparing with the spectra of the pristine (CuI and SWCNT) and reference (CuO) systems. It has been revealed that the encapsulation of the CuI compound inside SWCNTs is accompanied by changes in the electronic structure of CuI and SWCNTs due to the chemical interaction between the filler and carbon nanotubes and the change in the atomic structure of CuI.

  12. Time-resolved x-ray absorption spectroscopy: Watching atoms dance

    NASA Astrophysics Data System (ADS)

    Milne, Chris J.; Pham, Van-Thai; Gawelda, Wojciech; van der Veen, Renske M.; El Nahhas, Amal; Johnson, Steven L.; Beaud, Paul; Ingold, Gerhard; Lima, Frederico; Vithanage, Dimali A.; Benfatto, Maurizio; Grolimund, Daniel; Borca, Camelia; Kaiser, Maik; Hauser, Andreas; Abela, Rafael; Bressler, Christian; Chergui, Majed

    2009-11-01

    The introduction of pump-probe techniques to the field of x-ray absorption spectroscopy (XAS) has allowed the monitoring of both structural and electronic dynamics of disordered systems in the condensed phase with unprecedented accuracy, both in time and in space. We present results on the electronically excited high-spin state structure of an Fe(II) molecular species, [FeII(bpy)3]2+, in aqueous solution, resolving the Fe-N bond distance elongation as 0.2 Å. In addition an analysis technique using the reduced χ2 goodness of fit between FEFF EXAFS simulations and the experimental transient absorption signal in energy space has been successfully tested as a function of excited state population and chemical shift, demonstrating its applicability in situations where the fractional excited state population cannot be determined through other measurements. Finally by using a novel ultrafast hard x-ray 'slicing' source the question of how the molecule relaxes after optical excitation has been successfully resolved using femtosecond XANES.

  13. Synchrotron x-ray microdiffraction reveals intrinsic structural features of amyloid deposits in situ.

    PubMed

    Briki, Fatma; Vérine, Jérôme; Doucet, Jean; Bénas, Philippe; Fayard, Barbara; Delpech, Marc; Grateau, Gilles; Riès-Kautt, Madeleine

    2011-07-20

    Amyloidoses are increasingly recognized as a major public health concern in Western countries. All amyloidoses share common morphological, structural, and tinctorial properties. These consist of staining by specific dyes, a fibrillar aspect in electron microscopy and a typical cross-β folding in x-ray diffraction patterns. Most studies that aim at deciphering the amyloid structure rely on fibers generated in vitro or extracted from tissues using protocols that may modify their intrinsic structure. Therefore, the fine details of the in situ architecture of the deposits remain unknown. Here, we present to our knowledge the first data obtained on ex vivo human renal tissue sections using x-ray microdiffraction. The typical cross-β features from fixed paraffin-embedded samples are similar to those formed in vitro or extracted from tissues. Moreover, the fiber orientation maps obtained across glomerular sections reveal an intrinsic texture that is correlated with the glomerulus morphology. These results are of the highest importance to understanding the formation of amyloid deposits and are thus expected to trigger new incentives for tissue investigation. Moreover, the access to intrinsic structural parameters such as fiber size and orientation using synchrotron x-ray microdiffraction, could provide valuable information concerning in situ mechanisms and deposit formation with potential benefits for diagnostic and therapeutic purposes. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  14. X-Ray Crystal Structure of Bone Marrow Kinase in the X Chromosome: A Tec Family Kinase

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Muckelbauer, Jodi; Sack, John S.; Ahmed, Nazia

    Bone marrow kinase in the X chromosome, a member of the Tec family of tyrosine kinases, plays a role in both monocyte/macrophage trafficking as well as cytokine secretion. Although the structures of Tec family kinases Bruton's tyrosine kinase and IL-2-inducible T-cell kinase are known, the crystal structures of other Tec family kinases have remained elusive. We report the X-ray crystal structures of bone marrow kinase in the X chromosome in complex with dasatinib at 2.4 {angstrom} resolution and PP2 at 1.9 {angstrom} resolution. The bone marrow kinase in the X chromosome structures reveal a typical kinase protein fold; with well-orderedmore » protein conformation that includes an open/extended activation loop and a stabilized DFG-motif rendering the kinase in an inactive conformation. Dasatinib and PP2 bind to bone marrow kinase in the X chromosome in the ATP binding pocket and display similar binding modes to that observed in other Tec and Src protein kinases. The bone marrow kinase in the X chromosome structures identify conformational elements of the DFG-motif that could potentially be utilized to design potent and/or selective bone marrow kinase in the X chromosome inhibitors.« less

  15. Forming a structure of the CoNiFe alloys by X-ray irradiation

    NASA Astrophysics Data System (ADS)

    Valko, Natalia; Kasperovich, Andrey; Koltunowicz, Tomasz N.

    The experimental data of electrodeposition kinetics researches and structure formation of ternary CoNiFe alloys deposited onto low-carbon steel 08kp in the presence of X-rays are presented. Relations of deposit rate, current efficiencies, element and phase compositions of CoNiFe coatings formed from sulfate baths with respect to cathode current densities (0.5-3A/dm2), electrolyte composition and irradiation were obtained. It is shown that, the CoNiFe coatings deposited by the electrochemical method involving exposure of the X-rays are characterized by more perfect morphology surfaces with less developed surface geometry than reference coatings. The effect of the X-ray irradiation on the electrodeposition of CoNiFe coatings promotes formatting of alloys with increased electropositive component and modified phase composition.

  16. The UHURU X-ray instrument.

    NASA Technical Reports Server (NTRS)

    Jagoda, N.; Austin, G.; Mickiewicz, S.; Goddard, R.

    1972-01-01

    On Dec. 12, 1970, the UHURU X-ray observatory was launched into equatorial orbit with the prime mission of conducting an all-sky survey of astronomical X-ray sources with intensities of 0.00005 Sco-X1 or greater. The X-ray detection system contains 12 gas-filled proportional counters, 6 behind each collimator. The aspect system is discussed together with the structure, the pulse height analyzer, the command system, the calibration system, and the power distribution system. Pulse shape discrimination circuits used on UHURU use the same technique that was used on the system originally developed for large area proportional counters described by Gorenstein and Mickiewicz (1968).

  17. Simulation of Near-Edge X-ray Absorption Fine Structure with Time-Dependent Equation-of-Motion Coupled-Cluster Theory.

    PubMed

    Nascimento, Daniel R; DePrince, A Eugene

    2017-07-06

    An explicitly time-dependent (TD) approach to equation-of-motion (EOM) coupled-cluster theory with single and double excitations (CCSD) is implemented for simulating near-edge X-ray absorption fine structure in molecular systems. The TD-EOM-CCSD absorption line shape function is given by the Fourier transform of the CCSD dipole autocorrelation function. We represent this transform by its Padé approximant, which provides converged spectra in much shorter simulation times than are required by the Fourier form. The result is a powerful framework for the blackbox simulation of broadband absorption spectra. K-edge X-ray absorption spectra for carbon, nitrogen, and oxygen in several small molecules are obtained from the real part of the absorption line shape function and are compared with experiment. The computed and experimentally obtained spectra are in good agreement; the mean unsigned error in the predicted peak positions is only 1.2 eV. We also explore the spectral signatures of protonation in these molecules.

  18. Chemical Modification of Graphene Oxide by Nitrogenation: An X-ray Absorption and Emission Spectroscopy Study

    DOE PAGES

    Chuang, Cheng-Hao; Ray, Sekhar C.; Mazumder, Debarati; ...

    2017-02-10

    Nitrogen-doped graphene oxides (GO:N x) were synthesized by a partial reduction of graphene oxide (GO) using urea [CO(NH 2) 2 ]. Their electronic/bonding structures were investigated using X-ray absorption near-edge structure (XANES), valence-band photoemission spectroscopy (VB-PES), X-ray emission spectroscopy (XES) and resonant inelastic X-ray scattering (RIXS). During GO:N x synthesis, different nitrogen-bonding species, such as pyrrolic/graphitic-nitrogen, were formed by replacing of oxygen-containing functional groups. At lower N-content (2.7 at%), pyrrolic-N, owing to surface and subsurface diffusion of C, N and NH is deduced from various X-ray spectroscopies. In contrast, at higher N-content (5.0 at%) graphitic nitrogen was formed in whichmore » each N-atom trigonally bonds to three distinct sp 2 -hybridized carbons with substitution of the N-atoms for C atoms in the graphite layer. Upon nitrogen substitution, the total density of state close to Fermi level is increased to raise the valence-band maximum, as revealed by VB-PES spectra, indicating an electron donation from nitrogen, molecular bonding C/N/O coordination or/and lattice structure reorganization in GO:N x . The well-ordered chemical environments induced by nitrogen dopant are revealed by XANES and RIXS measurements.« less

  19. Can isolated single black holes produce X-ray novae?

    NASA Astrophysics Data System (ADS)

    Matsumoto, Tatsuya; Teraki, Yuto; Ioka, Kunihito

    2018-03-01

    Almost all black holes (BHs) and BH candidates in our Galaxy have been discovered as soft X-ray transients, so-called X-ray novae. X-ray novae are usually considered to arise from binary systems. Here, we propose that X-ray novae are also caused by isolated single BHs. We calculate the distribution of the accretion rate from interstellar matter to isolated BHs, and find that BHs in molecular clouds satisfy the condition of the hydrogen-ionization disc instability, which results in X-ray novae. The estimated event rate is consistent with the observed one. We also check an X-ray novae catalogue (Corral-Santana et al.) and find that 16/59 ˜ 0.27 of the observed X-ray novae are potentially powered by isolated BHs. The possible candidates include IGR J17454-2919, XTE J1908-094, and SAX J1711.6-3808. Near-infrared photometric and spectroscopic follow-ups can exclude companion stars for a BH census in our Galaxy.

  20. SOLEIL shining on the solution-state structure of biomacromolecules by synchrotron X-ray footprinting at the Metrology beamline.

    PubMed

    Baud, A; Aymé, L; Gonnet, F; Salard, I; Gohon, Y; Jolivet, P; Brodolin, K; Da Silva, P; Giuliani, A; Sclavi, B; Chardot, T; Mercère, P; Roblin, P; Daniel, R

    2017-05-01

    Synchrotron X-ray footprinting complements the techniques commonly used to define the structure of molecules such as crystallography, small-angle X-ray scattering and nuclear magnetic resonance. It is remarkably useful in probing the structure and interactions of proteins with lipids, nucleic acids or with other proteins in solution, often better reflecting the in vivo state dynamics. To date, most X-ray footprinting studies have been carried out at the National Synchrotron Light Source, USA, and at the European Synchrotron Radiation Facility in Grenoble, France. This work presents X-ray footprinting of biomolecules performed for the first time at the X-ray Metrology beamline at the SOLEIL synchrotron radiation source. The installation at this beamline of a stopped-flow apparatus for sample delivery, an irradiation capillary and an automatic sample collector enabled the X-ray footprinting study of the structure of the soluble protein factor H (FH) from the human complement system as well as of the lipid-associated hydrophobic protein S3 oleosin from plant seed. Mass spectrometry analysis showed that the structural integrity of both proteins was not affected by the short exposition to the oxygen radicals produced during the irradiation. Irradiated molecules were subsequently analysed using high-resolution mass spectrometry to identify and locate oxidized amino acids. Moreover, the analyses of FH in its free state and in complex with complement C3b protein have allowed us to create a map of reactive solvent-exposed residues on the surface of FH and to observe the changes in oxidation of FH residues upon C3b binding. Studies of the solvent accessibility of the S3 oleosin show that X-ray footprinting offers also a unique approach to studying the structure of proteins embedded within membranes or lipid bodies. All the biomolecular applications reported herein demonstrate that the Metrology beamline at SOLEIL can be successfully used for synchrotron X-ray footprinting of

  1. X-ray microscopy of human malaria

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Magowan, C.; Brown, J.T.; Mohandas, N.

    Associations between intracellular organisms and host cells are complex and particularly difficult to examine. X-ray microscopy provides transmission images of subcellular structures in intact cells at resolutions superior to available methodologies. The spatial resolution is 50-60nm with a 1 micron depth of focus, superior to anything achievable with light microscopy. Image contrast is generated by differences in photoelectric absorption by the atoms in different areas (i.e. subcellular structures) throughout the full thickness of the sample. Absorption due to carbon dominates among all the elements in the sample at 2.4 nm x-ray wavelength. Thus images show features or structures, in amore » way not usually seen by other types of microscopy. The authors used soft x-ray microscopy to investigate structural development of Plasmodium falciparum malaria parasites in normal and genetically abnormal erythrocytes, and in infected erythrocytes treated with compounds that have anti-malarial effects. X-ray microscopy showed newly elaborated structures in the cytosol of unstained, intact erythrocytes, redistribution of mass (carbon) in infected erythrocytes, and aberrant parasite morphology. Better understanding of the process of intracellular parasite maturation and the interactions between the parasite and its host erythrocyte can help define new approaches to the control of this deadly disease.« less

  2. X-ray study of the structure of phospholipid monolayers on the water surface

    NASA Astrophysics Data System (ADS)

    Asadchikov, V. E.; Tikhonov, A. M.; Volkov, Yu. O.; Roshchin, B. S.; Ermakov, Yu. A.; Rudakova, E. B.; D'yachkova, I. G.; Nuzhdin, A. D.

    2017-10-01

    The possibility of laboratory X-ray reflectometry study of the structure of dimyristoyl phosphatidylserine (DMPS) phospholipid monolayers on the water surface in various phase states has been demonstrated.

  3. Ultra-Small-Angle X-ray Scattering – X-ray Photon Correlation Spectroscopy Studies of Incipient Structural Changes in Amorphous Calcium Phosphate Based Dental Composites

    PubMed Central

    Zhang, F.; Allen, A.J.; Levine, L.E.; Espinal, L.; Antonucci, J.M.; Skrtic, D.; O’Donnell, J.N.R.; Ilavsky, J.

    2012-01-01

    The local structural changes in amorphous calcium phosphate (ACP) based dental composites were studied under isothermal conditions using both static, bulk measurement techniques and a recently developed methodology based on combined ultra-small angle X-ray scattering – X-ray photon correlation spectroscopy (USAXS-XPCS), which permits a dynamic approach. While results from conventional bulk measurements do not show clear signs of structural change, USAXS-XPCS results reveal unambiguous evidence for local structural variations on a similar time scale to that of water loss in the ACP fillers. A thermal-expansion based simulation indicates that thermal behavior alone does not account for the observed dynamics. Together, these results suggest that changes in the water content of ACP affect the composite morphology due to changes in ACP structure that occur without an amorphous-to-crystalline conversion. It is also noted that biomedical materials research could benefit greatly from USAXS-XPCS, a dynamic approach. PMID:22374649

  4. Metalloprotein structures at ambient conditions and in real-time: biological crystallography and spectroscopy using X-ray free electron lasers

    DOE PAGES

    Kern, Jan; Yachandra, Vittal K.; Yano, Junko

    2015-09-02

    We have studied the structure of enzymes and the chemistry at the catalytic sites, intensively and have acquired an understanding of the atomic-scale chemistry which requires a new approach beyond steady state X-ray crystallography and X-ray spectroscopy at cryogenic temperatures. Following the dynamic changes in the geometric and electronic structure of metallo-enzymes at ambient conditions, while overcoming the severe X-ray-induced changes to the redox active catalytic center, is key for deriving reaction mechanisms. Such studies become possible by the intense and ultra-short femtosecond (fs) X-ray pulses from an X-ray free electron laser (XFEL) by acquiring a signal before the samplemore » is destroyed. Our review describes the recent and pioneering uses of XFELs to study the protein structure and dynamics of metallo-enzymes using crystallography and scattering, as well as the chemical structure and dynamics of the catalytic complexes (charge, spin, and covalency) using spectroscopy during the reaction to understand the electron-transfer processes and elucidate the mechanism.« less

  5. Metalloprotein structures at ambient conditions and in real-time: biological crystallography and spectroscopy using X-ray free electron lasers

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kern, Jan; Yachandra, Vittal K.; Yano, Junko

    We have studied the structure of enzymes and the chemistry at the catalytic sites, intensively and have acquired an understanding of the atomic-scale chemistry which requires a new approach beyond steady state X-ray crystallography and X-ray spectroscopy at cryogenic temperatures. Following the dynamic changes in the geometric and electronic structure of metallo-enzymes at ambient conditions, while overcoming the severe X-ray-induced changes to the redox active catalytic center, is key for deriving reaction mechanisms. Such studies become possible by the intense and ultra-short femtosecond (fs) X-ray pulses from an X-ray free electron laser (XFEL) by acquiring a signal before the samplemore » is destroyed. Our review describes the recent and pioneering uses of XFELs to study the protein structure and dynamics of metallo-enzymes using crystallography and scattering, as well as the chemical structure and dynamics of the catalytic complexes (charge, spin, and covalency) using spectroscopy during the reaction to understand the electron-transfer processes and elucidate the mechanism.« less

  6. Radiation-Induced Chemical Dynamics in Ar Clusters Exposed to Strong X-Ray Pulses.

    PubMed

    Kumagai, Yoshiaki; Jurek, Zoltan; Xu, Weiqing; Fukuzawa, Hironobu; Motomura, Koji; Iablonskyi, Denys; Nagaya, Kiyonobu; Wada, Shin-Ichi; Mondal, Subhendu; Tachibana, Tetsuya; Ito, Yuta; Sakai, Tsukasa; Matsunami, Kenji; Nishiyama, Toshiyuki; Umemoto, Takayuki; Nicolas, Christophe; Miron, Catalin; Togashi, Tadashi; Ogawa, Kanade; Owada, Shigeki; Tono, Kensuke; Yabashi, Makina; Son, Sang-Kil; Ziaja, Beata; Santra, Robin; Ueda, Kiyoshi

    2018-06-01

    We show that electron and ion spectroscopy reveals the details of the oligomer formation in Ar clusters exposed to an x-ray free electron laser (XFEL) pulse, i.e., chemical dynamics triggered by x rays. With guidance from a dedicated molecular dynamics simulation tool, we find that van der Waals bonding, the oligomer formation mechanism, and charge transfer among the cluster constituents significantly affect ionization dynamics induced by an XFEL pulse of moderate fluence. Our results clearly demonstrate that XFEL pulses can be used not only to "damage and destroy" molecular assemblies but also to modify and transform their molecular structure. The accuracy of the predictions obtained makes it possible to apply the cluster spectroscopy, in connection with the respective simulations, for estimation of the XFEL pulse fluence in the fluence regime below single-atom multiple-photon absorption, which is hardly accessible with other diagnostic tools.

  7. Radiation-Induced Chemical Dynamics in Ar Clusters Exposed to Strong X-Ray Pulses

    NASA Astrophysics Data System (ADS)

    Kumagai, Yoshiaki; Jurek, Zoltan; Xu, Weiqing; Fukuzawa, Hironobu; Motomura, Koji; Iablonskyi, Denys; Nagaya, Kiyonobu; Wada, Shin-ichi; Mondal, Subhendu; Tachibana, Tetsuya; Ito, Yuta; Sakai, Tsukasa; Matsunami, Kenji; Nishiyama, Toshiyuki; Umemoto, Takayuki; Nicolas, Christophe; Miron, Catalin; Togashi, Tadashi; Ogawa, Kanade; Owada, Shigeki; Tono, Kensuke; Yabashi, Makina; Son, Sang-Kil; Ziaja, Beata; Santra, Robin; Ueda, Kiyoshi

    2018-06-01

    We show that electron and ion spectroscopy reveals the details of the oligomer formation in Ar clusters exposed to an x-ray free electron laser (XFEL) pulse, i.e., chemical dynamics triggered by x rays. With guidance from a dedicated molecular dynamics simulation tool, we find that van der Waals bonding, the oligomer formation mechanism, and charge transfer among the cluster constituents significantly affect ionization dynamics induced by an XFEL pulse of moderate fluence. Our results clearly demonstrate that XFEL pulses can be used not only to "damage and destroy" molecular assemblies but also to modify and transform their molecular structure. The accuracy of the predictions obtained makes it possible to apply the cluster spectroscopy, in connection with the respective simulations, for estimation of the XFEL pulse fluence in the fluence regime below single-atom multiple-photon absorption, which is hardly accessible with other diagnostic tools.

  8. X-Rays

    MedlinePlus

    X-rays are a type of radiation called electromagnetic waves. X-ray imaging creates pictures of the inside of ... different amounts of radiation. Calcium in bones absorbs x-rays the most, so bones look white. Fat ...

  9. History of Chandra X-Ray Observatory

    NASA Image and Video Library

    2000-10-01

    This most distant x-ray cluster of galaxies yet has been found by astronomers using Chandra X-ray Observatory (CXO). Approximately 10 billion light-years from Earth, the cluster 3C294 is 40 percent farther than the next most distant x-ray galaxy cluster. The existence of such a faraway cluster is important for understanding how the universe evolved. CXO's image reveals an hourglass-shaped region of x-ray emissions centered on the previously known central radio source (seen in this image as the blue central object) that extends outward for 60,000 light- years. The vast clouds of hot gas that surround such galaxies in clusters are thought to be heated by collapse toward the center of the cluster. Until CXO, x-ray telescopes have not had the needed sensitivity to identify such distant clusters of galaxies. Galaxy clusters are the largest gravitationally bound structures in the universe. The intensity of the x-rays in this CXO image of 3C294 is shown as red for low energy x-rays, green for intermediate, and blue for the most energetic x-rays. (Photo credit: NASA/loA/A. Fabian et al)

  10. Accessing protein conformational ensembles using room-temperature X-ray crystallography

    PubMed Central

    Fraser, James S.; van den Bedem, Henry; Samelson, Avi J.; Lang, P. Therese; Holton, James M.; Echols, Nathaniel; Alber, Tom

    2011-01-01

    Modern protein crystal structures are based nearly exclusively on X-ray data collected at cryogenic temperatures (generally 100 K). The cooling process is thought to introduce little bias in the functional interpretation of structural results, because cryogenic temperatures minimally perturb the overall protein backbone fold. In contrast, here we show that flash cooling biases previously hidden structural ensembles in protein crystals. By analyzing available data for 30 different proteins using new computational tools for electron-density sampling, model refinement, and molecular packing analysis, we found that crystal cryocooling remodels the conformational distributions of more than 35% of side chains and eliminates packing defects necessary for functional motions. In the signaling switch protein, H-Ras, an allosteric network consistent with fluctuations detected in solution by NMR was uncovered in the room-temperature, but not the cryogenic, electron-density maps. These results expose a bias in structural databases toward smaller, overpacked, and unrealistically unique models. Monitoring room-temperature conformational ensembles by X-ray crystallography can reveal motions crucial for catalysis, ligand binding, and allosteric regulation. PMID:21918110

  11. Application of a magnetograph and X-ray telescope to the study of coronal structure variations

    NASA Technical Reports Server (NTRS)

    Rust, D. M.

    1980-01-01

    The application of magnetographs and X-ray imaging techniques to determine the magnitude, structure, origin, and evolution of the solar coronal magnetic field is examined. The spatial and temporal resolution of the X-ray telescope is discussed and a comparison of ground based magnetogram sequences versus a magnetograph in space is presented. Skylab photographs of the evolution of transient coronal holes are provided.

  12. Investigation of the Structural Stability of Ion-Implanted Gd 2Ti 2-xSn xO 7 Pyrochlore-Type Oxides by Glancing Angle X-ray Absorption Spectroscopy

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Aluri, Esther Rani; Hayes, John R.; Walker, James D.S.

    2016-03-24

    Rare-earth titanate and stannate pyrochlore-type oxides have been investigated in the past for the sequestration of nuclear waste elements because of their resistance to radiation-induced structural damage. In order to enhance this property, it is necessary to understand the effect of radioactive decay of the incorporated actinide elements on the local chemical environment. In this study, Gd 2Ti 2–xSn xO 7 materials have been implanted with Au– ions to simulate radiation-induced structural damage. Glancing angle X-ray absorption near-edge spectroscopy (GA-XANES), glancing angle X-ray absorption fine structure (GA-EXAFS) analysis, and powder X-ray diffraction have been used to investigate changes in themore » local coordination environment of the metal atoms in the damaged surface layer. Examination of GA-XANES/EXAFS spectra from the implanted Gd 2Ti 2–xSn xO 7 materials collected at various glancing angles allowed for an investigation of how the local coordination environment around the absorbing atoms changed at different depths in the damaged surface layer. This study has shown the usefulness of GA-XANES to the examination of ion-implanted materials and has suggested that Gd 2Ti 2–xSn xO 7 becomes more susceptible to ion-beam-induced structural damage with increasing Sn concentration.« less

  13. Ultrasonic acoustic levitation for fast frame rate X-ray protein crystallography at room temperature.

    PubMed

    Tsujino, Soichiro; Tomizaki, Takashi

    2016-05-06

    Increasing the data acquisition rate of X-ray diffraction images for macromolecular crystals at room temperature at synchrotrons has the potential to significantly accelerate both structural analysis of biomolecules and structure-based drug developments. Using lysozyme model crystals, we demonstrated the rapid acquisition of X-ray diffraction datasets by combining a high frame rate pixel array detector with ultrasonic acoustic levitation of protein crystals in liquid droplets. The rapid spinning of the crystal within a levitating droplet ensured an efficient sampling of the reciprocal space. The datasets were processed with a program suite developed for serial femtosecond crystallography (SFX). The structure, which was solved by molecular replacement, was found to be identical to the structure obtained by the conventional oscillation method for up to a 1.8-Å resolution limit. In particular, the absence of protein crystal damage resulting from the acoustic levitation was carefully established. These results represent a key step towards a fully automated sample handling and measurement pipeline, which has promising prospects for a high acquisition rate and high sample efficiency for room temperature X-ray crystallography.

  14. Ultrasonic acoustic levitation for fast frame rate X-ray protein crystallography at room temperature

    NASA Astrophysics Data System (ADS)

    Tsujino, Soichiro; Tomizaki, Takashi

    2016-05-01

    Increasing the data acquisition rate of X-ray diffraction images for macromolecular crystals at room temperature at synchrotrons has the potential to significantly accelerate both structural analysis of biomolecules and structure-based drug developments. Using lysozyme model crystals, we demonstrated the rapid acquisition of X-ray diffraction datasets by combining a high frame rate pixel array detector with ultrasonic acoustic levitation of protein crystals in liquid droplets. The rapid spinning of the crystal within a levitating droplet ensured an efficient sampling of the reciprocal space. The datasets were processed with a program suite developed for serial femtosecond crystallography (SFX). The structure, which was solved by molecular replacement, was found to be identical to the structure obtained by the conventional oscillation method for up to a 1.8-Å resolution limit. In particular, the absence of protein crystal damage resulting from the acoustic levitation was carefully established. These results represent a key step towards a fully automated sample handling and measurement pipeline, which has promising prospects for a high acquisition rate and high sample efficiency for room temperature X-ray crystallography.

  15. Ultrasonic acoustic levitation for fast frame rate X-ray protein crystallography at room temperature

    PubMed Central

    Tsujino, Soichiro; Tomizaki, Takashi

    2016-01-01

    Increasing the data acquisition rate of X-ray diffraction images for macromolecular crystals at room temperature at synchrotrons has the potential to significantly accelerate both structural analysis of biomolecules and structure-based drug developments. Using lysozyme model crystals, we demonstrated the rapid acquisition of X-ray diffraction datasets by combining a high frame rate pixel array detector with ultrasonic acoustic levitation of protein crystals in liquid droplets. The rapid spinning of the crystal within a levitating droplet ensured an efficient sampling of the reciprocal space. The datasets were processed with a program suite developed for serial femtosecond crystallography (SFX). The structure, which was solved by molecular replacement, was found to be identical to the structure obtained by the conventional oscillation method for up to a 1.8-Å resolution limit. In particular, the absence of protein crystal damage resulting from the acoustic levitation was carefully established. These results represent a key step towards a fully automated sample handling and measurement pipeline, which has promising prospects for a high acquisition rate and high sample efficiency for room temperature X-ray crystallography. PMID:27150272

  16. Structural biology at the European X-ray free-electron laser facility.

    PubMed

    Altarelli, Massimo; Mancuso, Adrian P

    2014-07-17

    The European X-ray free-electron laser (XFEL) facility, under construction in the Hamburg region, will provide high-peak brilliance (greater than 10(33) photons s(-1) mm(-2) mrad(-2) per 0.1% BW), ultrashort pulses (approx. 10 fs) of X-rays, with a high repetition rate (up to 27 000 pulses s(-1)) from 2016 onwards. The main features of this exceptional X-ray source, and the instrumentation developments necessary to exploit them fully, for application to a variety of scientific disciplines, are briefly summarized. In the case of structural biology, that has a central role in the scientific case of this new facility, the instruments and ancillary laboratories that are being planned and built within the baseline programme of the European XFEL and by consortia of users are also discussed. It is expected that the unique features of the source and the advanced features of the instrumentation will allow operation modes with more efficient use of sample materials, faster acquisition times, and conditions better approaching feasibility of single molecule imaging. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  17. The sequence and X-ray structure of the trypsin from Fusarium oxysporum.

    PubMed

    Rypniewski, W R; Hastrup, S; Betzel, C; Dauter, M; Dauter, Z; Papendorf, G; Branner, S; Wilson, K S

    1993-06-01

    The trypsin from Fusarium oxysporum is equally homologous to trypsins from Streptomyces griseus, Streptomyces erythraeus and to bovine trypsin. A DFP (diisopropylfluorophosphate) inhibited form of the enzyme has been crystallized from 1.4 M Na2SO4, buffered with citrate at pH 5.0-5.5. The crystals belong to space group P2(1) with cell parameters a = 33.43 A, b = 67.65 A, c = 39.85 A and beta = 107.6 degrees. There is one protein molecule in the asymmetric unit. X-ray diffraction data to a resolution of 1.8 A were collected on film using synchrotron radiation. The structure was solved by molecular replacement using models of bovine and S. griseus trypsins and refined to an R-factor of 0.141. The overall fold is similar to other trypsins, with some insertions and deletions. There is no evidence of the divalent cation binding sites seen in other trypsins. The covalently bound inhibitor molecule is clearly visible.

  18. An X-ray look at the first head-trail nebula in an X-ray binary

    NASA Astrophysics Data System (ADS)

    Soleri, Paolo

    2011-09-01

    Head-tail trails are a common feature in active galactic nuclei and pulsar bow-shocks. Heinz et al. (2008) suggested that also X-ray binaries, being jet sources moving with high velocities in dense media, can leave trails of highly ionized plasma that should be detectable at radio frequencies. During bservations of faint-persistent X-ray binaries, we discovered an optical nebula around the X-ray binary SAX J1712.6-3739, consisting of a bow-shock ring-like nebula in front of the binary and two trails originating close to it. This is the first detection of such structure in a X-ray binary and it opens a new sub-field in the study of these objects. Observations with XMM-Newton and Chandra are now needed to investigate the properties of the surrounding nebula.

  19. An X-ray look at the first head-trail nebula in an X-ray binary

    NASA Astrophysics Data System (ADS)

    Soleri, Paolo

    2010-10-01

    Head-tail trails are a common feature in active galactic nuclei and pulsar bow-shocks. Heinz et al. (2008) suggested that also X-ray binaries, being jet sources moving with high velocities in dense media, can leave trails of highly ionized plasma that should be detectable at radio frequencies. During observations of faint-persistent X-ray binaries, we discovered an optical nebula around the X-ray binary SAX J1712.6-3739, consisting of a bow-shock ring-like nebula ``in front'' of the binary and two trails originating close to it. This is the first detection of such structure in a X-ray binary and it opens a new sub-field in the study of these objects. Observations with XMM-Newton and Chandra are now needed to investigate the properties of the surrounding nebula.

  20. Spectral structure of a polycapillary lens shaped X-ray beam

    NASA Astrophysics Data System (ADS)

    Gogolev, A. S.; Filatov, N. A.; Uglov, S. R.; Hampai, D.; Dabagov, S. B.

    2018-04-01

    Polycapillary X-ray optics is widely used in X-ray analysis techniques to create a small secondary source, for instance, or to deliver X-rays to the point of interest with minimum intensity losses [1]. The main characteristics of the analytical devices on its base are the size and divergence of the focused or translated beam. In this work, we used the photon-counting pixel detector ModuPIX to study the parameters for polycapillary focused X-ray tube radiation as well as the energy and spatial dependences of radiation at the focus. We have characterized the high-speed spectral camera ModuPIX, which is a single Timepix device with a fast parallel readout allowing up to 850 frames per second with 256 × 256 pixels and a 55 μm pitch defined by the frame frequency. By means of the silicon monochromator the energy response function is measured in clustering mode by the energy scan over total X-ray tube spectrum.

  1. Automatic protein structure solution from weak X-ray data

    NASA Astrophysics Data System (ADS)

    Skubák, Pavol; Pannu, Navraj S.

    2013-11-01

    Determining new protein structures from X-ray diffraction data at low resolution or with a weak anomalous signal is a difficult and often an impossible task. Here we propose a multivariate algorithm that simultaneously combines the structure determination steps. In tests on over 140 real data sets from the protein data bank, we show that this combined approach can automatically build models where current algorithms fail, including an anisotropically diffracting 3.88 Å RNA polymerase II data set. The method seamlessly automates the process, is ideal for non-specialists and provides a mathematical framework for successfully combining various sources of information in image processing.

  2. An X-ray Observation of the L1251 Dark Cloud

    NASA Technical Reports Server (NTRS)

    Simon, Theodore

    2006-01-01

    An X-ray image of the L1251 dark cloud in Cepheus was obtained with the XMM-Newton telescope. More than three dozen sources were detected above a 3 delta limit in X-ray luminosity of L(sub X = 10(exp 29) ergs/s. Among the detections are eight optically visible T Tauri stars, which had been identified in earlier work from their emission at H(alpha). The two strongest X-ray sources have steady luminosities of L(sub X) approx. 10(exp 31) ergs/s and are at the saturation limit for X-ray activity in late-type stars, L(sub X)/L(sub bol) approx. 10(exp -3). X-ray emission was also observed from two CO emission cores in L1251, core C (L1251A) and core E (L1251B). Both regions contain high-velocity molecular gas, bright IRAS sources (Class I protostars), thermal radio sources, and Herbig-Haro (HH) jets. In L1251A strong X-ray emission was discovered in close proximity to the near-inbred and radio source IRSA/VLA 7 and to IRAS 22343+7501. IRSA/VLA 7 thus appears to be the most likely source of the molecular and HH outflows in L1251A. In L1251B X-ray emission was observed from a visible T Tauri star, KP2-44, which is thought to be the driving source for HH 189. Also reported is the tentative detection of X-ray emission from VLA 3, a thermal radio continuum source in L1251B that is closely associated with the extreme Class I protostar IRAS 22376+7455.

  3. Difficult macromolecular structures determined using X-ray diffraction techniques.

    PubMed

    Hernández-Santoyo, Alejandra

    2012-07-01

    Macromolecular crystallography has been, for the last few decades, the main source of structural information of biological macromolecular systems and it is one of the most powerful techniques for the analysis of enzyme mechanisms and macromolecular interactions at the atomic level. In addition, it is also an extremely powerful tool for drug design. Recent technological and methodological developments in macromolecular X-ray crystallography have allowed solving structures that until recently were considered difficult or even impossible, such as structures at atomic or subatomic resolution or large macromolecular complexes and assemblies at low resolution. These developments have also helped to solve the 3D-structure of macromolecules from twin crystals. Recently, this technique complemented with cryo-electron microscopy and neutron crystallography has provided the structure of large macromolecular machines with great precision allowing understanding of the mechanisms of their function.

  4. Structure of cyano-anion ionic liquids: X-ray scattering and simulations.

    PubMed

    Dhungana, Kamal B; Faria, Luiz F O; Wu, Boning; Liang, Min; Ribeiro, Mauro C C; Margulis, Claudio J; Castner, Edward W

    2016-07-14

    Ionic liquids with cyano anions have long been used because of their unique combination of low-melting temperatures, reduced viscosities, and increased conductivities. Recently we have shown that cyano anions in ionic liquids are particularly interesting for their potential use as electron donors to excited state photo-acceptors [B. Wu et al., J. Phys. Chem. B 119, 14790-14799 (2015)]. Here we report on bulk structural and quantum mechanical results for a series of ionic liquids based on the 1-ethyl-3-methylimidazolium cation, paired with the following five cyano anions: SeCN(-), SCN(-), N(CN)2 (-), C(CN)3 (-), and B(CN)4 (-). By combining molecular dynamics simulations, high-energy X-ray scattering measurements, and periodic boundary condition DFT calculations, we are able to obtain a comprehensive description of the liquid landscape as well as the nature of the HOMO-LUMO states for these ionic liquids in the condensed phase. Features in the structure functions for these ionic liquids are somewhat different than the commonly observed adjacency, charge-charge, and polarity peaks, especially for the bulkiest B(CN)4 (-) anion. While the other four cyano-anion ionic liquids present an anionic HOMO, the one for Im2,1 (+)/B(CN)4 (-) is cationic.

  5. History of Chandra X-Ray Observatory

    NASA Image and Video Library

    1998-01-01

    This is a computer rendering of the fully developed Chandra X-Ray Observatory (CXO), formerly Advanced X-Ray Astrophysics Facility (AXAF). In 1999, the AXAF was renamed the CXO in honor of the late Indian-American Novel Laureate Subrahmanyan Chandrasekhar. The CXO is the most sophisticated and the world's most powerful x-ray telescope ever built. It is designed to observe x-rays from high energy regions of the Universe, such as hot gas in the renmants of exploded stars. It produces picture-like images of x-ray emissions analogous to those made in visible light, as well as gathers data on the chemical composition of x-ray radiating objects. The CXO helps astronomers world-wide better understand the structure and evolution of the universe by studying powerful sources of x-ray such as exploding stars, matter falling into black holes, and other exotic celestial objects. The Observatory has three major parts: (1) the x-ray telescope, whose mirrors will focus x-rays from celestial objects; (2) the science instruments that record the x-rays so that x-ray images can be produced and analyzed; and (3) the spacecraft, which provides the environment necessary for the telescope and the instruments to work. TRW, Inc. was the prime contractor for the development of the CXO and NASA's Marshall Space Flight Center was responsible for its project management. The Smithsonian Astrophysical Observatory controls science and flight operations of the CXO for NASA from Cambridge, Massachusetts. The Observatory was launched July 22, 1999 aboard the Space Shuttle Columbia, STS-93 mission. (Image courtesy of TRW).

  6. Soft X-ray radiation damage in EM-CCDs used for Resonant Inelastic X-ray Scattering

    NASA Astrophysics Data System (ADS)

    Gopinath, D.; Soman, M.; Holland, A.; Keelan, J.; Hall, D.; Holland, K.; Colebrook, D.

    2018-02-01

    Advancement in synchrotron and free electron laser facilities means that X-ray beams with higher intensity than ever before are being created. The high brilliance of the X-ray beam, as well as the ability to use a range of X-ray energies, means that they can be used in a wide range of applications. One such application is Resonant Inelastic X-ray Scattering (RIXS). RIXS uses the intense and tuneable X-ray beams in order to investigate the electronic structure of materials. The photons are focused onto a sample material and the scattered X-ray beam is diffracted off a high resolution grating to disperse the X-ray energies onto a position sensitive detector. Whilst several factors affect the total system energy resolution, the performance of RIXS experiments can be limited by the spatial resolution of the detector used. Electron-Multiplying CCDs (EM-CCDs) at high gain in combination with centroiding of the photon charge cloud across several detector pixels can lead to sub-pixel spatial resolution of 2-3 μm. X-ray radiation can cause damage to CCDs through ionisation damage resulting in increases in dark current and/or a shift in flat band voltage. Understanding the effect of radiation damage on EM-CCDs is important in order to predict lifetime as well as the change in performance over time. Two CCD-97s were taken to PTB at BESSY II and irradiated with large doses of soft X-rays in order to probe the front and back surfaces of the device. The dark current was shown to decay over time with two different exponential components to it. This paper will discuss the use of EM-CCDs for readout of RIXS spectrometers, and limitations on spatial resolution, together with any limitations on instrument use which may arise from X-ray-induced radiation damage.

  7. Nondestructive Imaging of Internal Structures of Frog (Xenopus laevis) Embryos by Shadow-Projection X-Ray Microtomography

    NASA Astrophysics Data System (ADS)

    Aoki, Sadao; Yoneda, Ikuo; Nagai, Takeharu; Ueno, Naoto; Murakami, Kazuo

    1994-04-01

    Nondestructive high-resolution imaging of frog ( Xenopus laevis) embryos has been developed by X-ray microtomography. Shadow-projection X-ray microtomography with a brilliant fine focus laboratory X-ray source could image fine structures of Xenopus embryos which were embedded in paraffin wax. The imaging system enabled us to not only distinguish endoderm from ectoderm at the gastrula stage, but also to obtain a cross-section view of the tail bud embryo showing muscle, notochord and neural tube without staining. Furthermore, the distribution of myosin was also imaged in combination with whole-mount immunohistochemistry.

  8. X-ray diffraction study of the molecular propolis films deposited from an alcohol solution onto the cleavage surfaces of layered V2VI3 compounds

    NASA Astrophysics Data System (ADS)

    Drapak, S. I.; Gavrylyuk, S. V.; Kaminskii, V. M.; Kovalyuk, Z. D.

    2008-09-01

    The structures of the molecular propolis films deposited from an alcohol solution on the (0001) cleavage surface of layered bismuth selenide and telluride are studied by X-ray diffraction. Despite the chemical interaction between the semiconductor substrates and the organic-substance components, the molecular structural ordering of the propolis films is shown to be identical to that in the films of this substance on the surface of amorphous glass substrates. The chemical and deformation interaction between the organic substance and the layered V2VI3 compounds is found to result in the formation of an organic-inorganic sandwich nanostructure at a distance of ˜0.3 μm from the layered crystal-propolis film interface.

  9. Effects of rare-earth co-doping on the local structure of rare-earth phosphate glasses using high and low energy X-ray diffraction.

    PubMed

    Cramer, Alisha J; Cole, Jacqueline M; FitzGerald, Vicky; Honkimaki, Veijo; Roberts, Mark A; Brennan, Tessa; Martin, Richard A; Saunders, George A; Newport, Robert J

    2013-06-14

    Rare-earth co-doping in inorganic materials has a long-held tradition of facilitating highly desirable optoelectronic properties for their application to the laser industry. This study concentrates specifically on rare-earth phosphate glasses, (R2O3)x(R'2O3)y(P2O5)(1-(x+y)), where (R, R') denotes (Ce, Er) or (La, Nd) co-doping and the total rare-earth composition corresponds to a range between metaphosphate, RP3O9, and ultraphosphate, RP5O14. Thereupon, the effects of rare-earth co-doping on the local structure are assessed at the atomic level. Pair-distribution function analysis of high-energy X-ray diffraction data (Q(max) = 28 Å(-1)) is employed to make this assessment. Results reveal a stark structural invariance to rare-earth co-doping which bears testament to the open-framework and rigid nature of these glasses. A range of desirable attributes of these glasses unfold from this finding; in particular, a structural simplicity that will enable facile molecular engineering of rare-earth phosphate glasses with 'dial-up' lasing properties. When considered together with other factors, this finding also demonstrates additional prospects for these co-doped rare-earth phosphate glasses in nuclear waste storage applications. This study also reveals, for the first time, the ability to distinguish between P-O and P[double bond, length as m-dash]O bonding in these rare-earth phosphate glasses from X-ray diffraction data in a fully quantitative manner. Complementary analysis of high-energy X-ray diffraction data on single rare-earth phosphate glasses of similar rare-earth composition to the co-doped materials is also presented in this context. In a technical sense, all high-energy X-ray diffraction data on these glasses are compared with analogous low-energy diffraction data; their salient differences reveal distinct advantages of high-energy X-ray diffraction data for the study of amorphous materials.

  10. Calcium in the Oxygen-Evolving Complex: Structural and Mechanistic Role Determined by X-ray Spectroscopy

    PubMed Central

    Yachandra, Vittal K.; Yano, Junko

    2011-01-01

    This review describes the results from X-ray absorption spectroscopy studies that have contributed to an understanding of the role of Ca in the photosynthetic water oxidation reaction. The results include the first Mn, Ca and Sr X-ray spectroscopy studies using Ca or Sr-substituted PS II samples that established the presence of a MnCa heteronuclear structure and its orientation, and the most recent Sr X-ray spectroscopy study using biosynthetically prepared Sr-containing PS II in the various S-states that provide important insights into the requirement for Ca in the mechanism of the Mn4Ca catalytic center. PMID:21524917

  11. X-Ray Diffractive Optics

    NASA Technical Reports Server (NTRS)

    Dennis, Brian; Li, Mary; Skinner, Gerald

    2013-01-01

    X-ray optics were fabricated with the capability of imaging solar x-ray sources with better than 0.1 arcsecond angular resolution, over an order of magnitude finer than is currently possible. Such images would provide a new window into the little-understood energy release and particle acceleration regions in solar flares. They constitute one of the most promising ways to probe these regions in the solar atmosphere with the sensitivity and angular resolution needed to better understand the physical processes involved. A circular slit structure with widths as fine as 0.85 micron etched in a silicon wafer 8 microns thick forms a phase zone plate version of a Fresnel lens capable of focusing approx. =.6 keV x-rays. The focal length of the 3-cm diameter lenses is 100 microns, and the angular resolution capability is better than 0.1 arcsecond. Such phase zone plates were fabricated in Goddard fs Detector Development Lab. (DDL) and tested at the Goddard 600-microns x-ray test facility. The test data verified that the desired angular resolution and throughput efficiency were achieved.

  12. X-ray Reflection

    NASA Astrophysics Data System (ADS)

    Fabian, A. C.; Ross, R. R.

    2010-12-01

    Material irradiated by X-rays produces backscattered radiation which is commonly known as the Reflection Spectrum. It consists of a structured continuum, due at high energies to the competition between photoelectric absorption and electron scattering enhanced at low energies by emission from the material itself, together with a complex line spectrum. We briefly review the history of X-ray reflection in astronomy and discuss various methods for computing the reflection spectrum from cold and ionized gas, illustrated with results from our own work reflionx. We discuss how the reflection spectrum can be used to obtain the geometry of the accretion flow, particularly the inner regions around black holes and neutron stars.

  13. Simulations of X-ray diffraction of shock-compressed single-crystal tantalum with synchrotron undulator sources.

    PubMed

    Tang, M X; Zhang, Y Y; E, J C; Luo, S N

    2018-05-01

    Polychromatic synchrotron undulator X-ray sources are useful for ultrafast single-crystal diffraction under shock compression. Here, simulations of X-ray diffraction of shock-compressed single-crystal tantalum with realistic undulator sources are reported, based on large-scale molecular dynamics simulations. Purely elastic deformation, elastic-plastic two-wave structure, and severe plastic deformation under different impact velocities are explored, as well as an edge release case. Transmission-mode diffraction simulations consider crystallographic orientation, loading direction, incident beam direction, X-ray spectrum bandwidth and realistic detector size. Diffraction patterns and reciprocal space nodes are obtained from atomic configurations for different loading (elastic and plastic) and detection conditions, and interpretation of the diffraction patterns is discussed.

  14. X-ray Crystallographic Structure of Thermophilic Rhodopsin: IMPLICATIONS FOR HIGH THERMAL STABILITY AND OPTOGENETIC FUNCTION.

    PubMed

    Tsukamoto, Takashi; Mizutani, Kenji; Hasegawa, Taisuke; Takahashi, Megumi; Honda, Naoya; Hashimoto, Naoki; Shimono, Kazumi; Yamashita, Keitaro; Yamamoto, Masaki; Miyauchi, Seiji; Takagi, Shin; Hayashi, Shigehiko; Murata, Takeshi; Sudo, Yuki

    2016-06-03

    Thermophilic rhodopsin (TR) is a photoreceptor protein with an extremely high thermal stability and the first characterized light-driven electrogenic proton pump derived from the extreme thermophile Thermus thermophilus JL-18. In this study, we confirmed its high thermal stability compared with other microbial rhodopsins and also report the potential availability of TR for optogenetics as a light-induced neural silencer. The x-ray crystal structure of TR revealed that its overall structure is quite similar to that of xanthorhodopsin, including the presence of a putative binding site for a carotenoid antenna; but several distinct structural characteristics of TR, including a decreased surface charge and a larger number of hydrophobic residues and aromatic-aromatic interactions, were also clarified. Based on the crystal structure, the structural changes of TR upon thermal stimulation were investigated by molecular dynamics simulations. The simulations revealed the presence of a thermally induced structural substate in which an increase of hydrophobic interactions in the extracellular domain, the movement of extracellular domains, the formation of a hydrogen bond, and the tilting of transmembrane helices were observed. From the computational and mutational analysis, we propose that an extracellular LPGG motif between helices F and G plays an important role in the thermal stability, acting as a "thermal sensor." These findings will be valuable for understanding retinal proteins with regard to high protein stability and high optogenetic performance. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  15. Silicon trench photodiodes on a wafer for efficient X-ray-to-current signal conversion using side-X-ray-irradiation mode

    NASA Astrophysics Data System (ADS)

    Ariyoshi, Tetsuya; Takane, Yuta; Iwasa, Jumpei; Sakamoto, Kenji; Baba, Akiyoshi; Arima, Yutaka

    2018-04-01

    In this paper, we report a direct-conversion-type X-ray sensor composed of trench-structured silicon photodiodes, which achieves a high X-ray-to-current conversion efficiency under side X-ray irradiation. The silicon X-ray sensor with a length of 22.6 mm and a trench depth of 300 µm was fabricated using a single-poly single-metal 0.35 µm process. X-rays with a tube voltage of 80 kV were irradiated along the trench photodiode from the side of the test chip. The theoretical limit of X-ray-to-current conversion efficiency of 83.8% was achieved at a low reverse bias voltage of 25 V. The X-ray-to-electrical signal conversion efficiency of conventional indirect-conversion-type X-ray sensors is about 10%. Therefore, the developed sensor has a conversion efficiency that is about eight times higher than that of conventional sensors. It is expected that the developed X-ray sensor will be able to markedly lower the radiation dose required for X-ray diagnoses.

  16. X-ray spectra and atmospheric structures of bursting neutron stars

    NASA Technical Reports Server (NTRS)

    Ebisuzaki, Toshikazu

    1987-01-01

    Atmospheric structures and emitted X-ray spectra of bursting neutron stars are investigated. Theoretical curves are fitted to observational ones on the color temperature vs. luminosity diagram and two relations among mass, radius, and distance of the bursters are obtained. The fit of the theoretical curve to observations is statistically acceptable. Two possible sets of mass, radius, and distance to the X-ray bursts source MXB 1636-536 are derived, taking into account absorption lines at 4.1 keV, theoretical mass-radius relations of neutron star models, and the distance to the Galactic center. If the absorption line is due to Cr XX III, then M = 1.7-2.0 solar masses, R = 11-12 km, and d = 6.3-6.7 kpc, and if it is due to Fe XXV, then M = 1.8-2.1 solar masses, R = 8-10 km, and d = 5.8-6,4 kpc. The distance to the Galactic center is almost the same as that to MXB 1636-536.

  17. New contrasts for x-ray imaging and synergy with optical imaging

    NASA Astrophysics Data System (ADS)

    Wang, Ge

    2017-02-01

    Due to its penetrating power, fine resolution, unique contrast, high-speed, and cost-effectiveness, x-ray imaging is one of the earliest and most popular imaging modalities in biomedical applications. Current x-ray radiographs and CT images are mostly on gray-scale, since they reflect overall energy attenuation. Recent advances in x-ray detection, contrast agent, and image reconstruction technologies have changed our perception and expectation of x-ray imaging capabilities, and generated an increasing interest in imaging biological soft tissues in terms of energy-sensitive material decomposition, phase-contrast, small angle scattering (also referred to as dark-field), x-ray fluorescence and luminescence properties. These are especially relevant to preclinical and mesoscopic studies, and potentially mendable for hybridization with optical molecular tomography. In this article, we review new x-ray imaging techniques as related to optical imaging, suggest some combined x-ray and optical imaging schemes, and discuss our ideas on micro-modulated x-ray luminescence tomography (MXLT) and x-ray modulated opto-genetics (X-Optogenetics).

  18. A comparison of coronal X-ray structures of active regions with magnetic fields computed from photospheric observations

    NASA Technical Reports Server (NTRS)

    Poletto, G.; Vaiana, G. S.; Zombeck, M. V.; Krieger, A. S.; Timothy, A. F.

    1975-01-01

    The appearances of several X-ray active regions observed on March 7, 1970 and June 15, 1973 are compared with the corresponding coronal magnetic-field topology. Coronal fields have been computed from measurements of the longitudinal component of the underlying magnetic fields, based on the current-free hypothesis. An overall correspondence between X-ray structures and calculated field lines is established, and the magnetic counterparts of different X-ray features are also examined. A correspondence between enhanced X-ray emission and the location of compact closed field lines is suggested. Representative magnetic-field values calculated under the assumption of current-free fields are given for heights up to 200 sec.

  19. Polarization and long-term variability of Sgr A* X-ray echo

    NASA Astrophysics Data System (ADS)

    Churazov, E.; Khabibullin, I.; Ponti, G.; Sunyaev, R.

    2017-06-01

    We use a model of the molecular gas distribution within ˜100 pc from the centre of the Milky Way (Kruijssen, Dale & Longmore) to simulate time evolution and polarization properties of the reflected X-ray emission, associated with the past outbursts from Sgr A*. While this model is too simple to describe the complexity of the true gas distribution, it illustrates the importance and power of long-term observations of the reflected emission. We show that the variable part of X-ray emission observed by Chandra and XMM-Newton from prominent molecular clouds is well described by a pure reflection model, providing strong support of the reflection scenario. While the identification of Sgr A* as a primary source for this reflected emission is already a very appealing hypothesis, a decisive test of this model can be provided by future X-ray polarimetric observations, which will allow placing constraints on the location of the primary source. In addition, X-ray polarimeters (like, e.g. XIPE) have sufficient sensitivity to constrain the line-of-sight positions of molecular complexes, removing major uncertainty in the model.

  20. High Resolution X-ray Scattering Studies of Structural Phase Transitions in BaFe2-x Cr x As 2

    NASA Astrophysics Data System (ADS)

    Gaulin, B. D.; Clancy, J. P.; Wagman, J. J.; Sefat, A. S.

    2011-03-01

    While the effects of electron-doping on the parent compounds of the 122 family of Fe-based superconductors have been extremely well-studied in recent years, far less is known about the influence of hole-doping in compounds such as BaFe 2-x Cr x As 2 . In contrast to the electron-doped 122 systems, the hole-doped compounds do not become superconducting. Furthermore, while the hole-doped compounds exhibit similar structural and magnetic phase transitions, they appear to be much less sensitive to dopant concentration. We have performed high resolution x-ray scattering and magnetic susceptibility measurements on single crystal samples of BaFe 2-x Cr x As 2 for Cr concentrations ranging from 0 <= x <= 0.67 . These measurements allow us to determine the magnetic and structural phase transitions for this series and map out the low temperature phase diagram as a function of doping. In particular, we have carried out detailed measurements of the tetragonal (I4/mmm) to orthorhombic (Fmmm) structural phase transition which reveal how the orthorhombicity of the system evolves with increasing Cr concentration and how this correlates with the values of Ts and Tm .

  1. High-pressure studies with x-rays using diamond anvil cells

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Shen, Guoyin; Mao, Ho Kwang

    2016-11-22

    Pressure profoundly alters all states of matter. The symbiotic development of ultrahigh-pressure diamond anvil cells, to compress samples to sustainable multi-megabar pressures; and synchrotron x-ray techniques, to probe materials' properties in situ, has enabled the exploration of rich high-pressure (HP) science. In this article, we first introduce the essential concept of diamond anvil cell technology, together with recent developments and its integration with other extreme environments. We then provide an overview of the latest developments in HP synchrotron techniques, their applications, and current problems, followed by a discussion of HP scientific studies using x-rays in the key multidisciplinary fields. Thesemore » HP studies include: HP x-ray emission spectroscopy, which provides information on the filled electronic states of HP samples; HP x-ray Raman spectroscopy, which probes the HP chemical bonding changes of light elements; HP electronic inelastic x-ray scattering spectroscopy, which accesses high energy electronic phenomena, including electronic band structure, Fermi surface, excitons, plasmons, and their dispersions; HP resonant inelastic x-ray scattering spectroscopy, which probes shallow core excitations, multiplet structures, and spin-resolved electronic structure; HP nuclear resonant x-ray spectroscopy, which provides phonon densities of state and time-resolved Mössbauer information; HP x-ray imaging, which provides information on hierarchical structures, dynamic processes, and internal strains; HP x-ray diffraction, which determines the fundamental structures and densities of single-crystal, polycrystalline, nanocrystalline, and non-crystalline materials; and HP radial x-ray diffraction, which yields deviatoric, elastic and rheological information. Integrating these tools with hydrostatic or uniaxial pressure media, laser and resistive heating, and cryogenic cooling, has enabled investigations of the structural, vibrational, electronic, and

  2. High-pressure studies with x-rays using diamond anvil cells

    NASA Astrophysics Data System (ADS)

    Shen, Guoyin; Mao, Ho Kwang

    2017-01-01

    Pressure profoundly alters all states of matter. The symbiotic development of ultrahigh-pressure diamond anvil cells, to compress samples to sustainable multi-megabar pressures; and synchrotron x-ray techniques, to probe materials’ properties in situ, has enabled the exploration of rich high-pressure (HP) science. In this article, we first introduce the essential concept of diamond anvil cell technology, together with recent developments and its integration with other extreme environments. We then provide an overview of the latest developments in HP synchrotron techniques, their applications, and current problems, followed by a discussion of HP scientific studies using x-rays in the key multidisciplinary fields. These HP studies include: HP x-ray emission spectroscopy, which provides information on the filled electronic states of HP samples; HP x-ray Raman spectroscopy, which probes the HP chemical bonding changes of light elements; HP electronic inelastic x-ray scattering spectroscopy, which accesses high energy electronic phenomena, including electronic band structure, Fermi surface, excitons, plasmons, and their dispersions; HP resonant inelastic x-ray scattering spectroscopy, which probes shallow core excitations, multiplet structures, and spin-resolved electronic structure; HP nuclear resonant x-ray spectroscopy, which provides phonon densities of state and time-resolved Mössbauer information; HP x-ray imaging, which provides information on hierarchical structures, dynamic processes, and internal strains; HP x-ray diffraction, which determines the fundamental structures and densities of single-crystal, polycrystalline, nanocrystalline, and non-crystalline materials; and HP radial x-ray diffraction, which yields deviatoric, elastic and rheological information. Integrating these tools with hydrostatic or uniaxial pressure media, laser and resistive heating, and cryogenic cooling, has enabled investigations of the structural, vibrational, electronic, and

  3. X-ray absorption spectroscopy using a self-seeded soft X-ray free-electron laser

    DOE PAGES

    Kroll, Thomas; Kern, Jan; Kubin, Markus; ...

    2016-09-19

    X-ray free electron lasers (XFELs) enable unprecedented new ways to study the electronic structure and dynamics of transition metal systems. L-edge absorption spectroscopy is a powerful technique for such studies and the feasibility of this method at XFELs for solutions and solids has been demonstrated. But, the required x-ray bandwidth is an order of magnitude narrower than that of self-amplified spontaneous emission (SASE), and additional monochromatization is needed. We compare L-edge x-ray absorption spectroscopy (XAS) of a prototypical transition metal system based on monochromatizing the SASE radiation of the linac coherent light source (LCLS) with a new technique based onmore » self-seeding of LCLS. We demonstrate how L-edge XAS can be performed using the self-seeding scheme without the need of an additional beam line monochromator. Lastly, we show how the spectral shape and pulse energy depend on the undulator setup and how this affects the x-ray spectroscopy measurements.« less

  4. X-ray absorption spectroscopy using a self-seeded soft X-ray free-electron laser

    PubMed Central

    Kroll, Thomas; Kern, Jan; Kubin, Markus; Ratner, Daniel; Gul, Sheraz; Fuller, Franklin D.; Löchel, Heike; Krzywinski, Jacek; Lutman, Alberto; Ding, Yuantao; Dakovski, Georgi L.; Moeller, Stefan; Turner, Joshua J.; Alonso-Mori, Roberto; Nordlund, Dennis L.; Rehanek, Jens; Weniger, Christian; Firsov, Alexander; Brzhezinskaya, Maria; Chatterjee, Ruchira; Lassalle-Kaiser, Benedikt; Sierra, Raymond G.; Laksmono, Hartawan; Hill, Ethan; Borovik, Andrew; Erko, Alexei; Föhlisch, Alexander; Mitzner, Rolf; Yachandra, Vittal K.; Yano, Junko; Wernet, Philippe; Bergmann, Uwe

    2016-01-01

    X-ray free electron lasers (XFELs) enable unprecedented new ways to study the electronic structure and dynamics of transition metal systems. L-edge absorption spectroscopy is a powerful technique for such studies and the feasibility of this method at XFELs for solutions and solids has been demonstrated. However, the required x-ray bandwidth is an order of magnitude narrower than that of self-amplified spontaneous emission (SASE), and additional monochromatization is needed. Here we compare L-edge x-ray absorption spectroscopy (XAS) of a prototypical transition metal system based on monochromatizing the SASE radiation of the linac coherent light source (LCLS) with a new technique based on self-seeding of LCLS. We demonstrate how L-edge XAS can be performed using the self-seeding scheme without the need of an additional beam line monochromator. We show how the spectral shape and pulse energy depend on the undulator setup and how this affects the x-ray spectroscopy measurements. PMID:27828320

  5. In situ synchrotron X-ray diffraction study on epitaxial-growth dynamics of III–V semiconductors

    NASA Astrophysics Data System (ADS)

    Takahasi, Masamitu

    2018-05-01

    The application of in situ synchrotron X-ray diffraction (XRD) to the molecular-beam epitaxial (MBE) growth of III–V semiconductors is overviewed along with backgrounds of the diffraction theory and instrumentation. X-rays are sensitive not only to the surface of growing films but also to buried interfacial structures because of their large penetration depth. Moreover, a spatial coherence length up to µm order makes X-rays widely applicable to the characterization of low-dimensional structures, such as quantum dots and wires. In situ XRD studies during growth were performed using an X-ray diffractometer, which was combined with an MBE chamber. X-ray reciprocal space mapping at a speed matching a typical growth rate was achieved using intense X-rays available from a synchrotron light source and an area detector. The importance of measuring the three-dimensional distribution of XRD intensity in a reciprocal space map is demonstrated for the MBE growth of two-, one-, and zero-dimensional structures. A large amount of information about the growth process of two-dimensional InGaAs/GaAs(001) epitaxial films has been provided by three-dimensional X-ray reciprocal mappings, including the anisotropic strain relaxation, the compositional inhomogeneity, and the evolution of surface and interfacial roughness. For one-dimensional GaAs nanowires grown in a Au-catalyzed vapor-liquid–solid mode, the relationship between the diameter of the nanowires and the formation of polytypes has been suggested on the basis of in situ XRD measurements. In situ three-dimensional X-ray reciprocal space mapping is also shown to be useful for determining the lateral and vertical sizes of self-assembled InAs/GaAs(001) quantum dots as well as their internal strain distributions during growth.

  6. The atmospheric structures of the companion stars of eclipsing binary x ray sources

    NASA Technical Reports Server (NTRS)

    Clark, George W.

    1992-01-01

    This investigation was aimed at determining structural features of the atmospheres of the massive early-type companion stars of eclipse x-ray pulsars by measurement of the attenuation of the x-ray spectrum during eclipse transitions and in deep eclipse. Several extended visits were made to ISAS in Japan by G. Clark and his graduate student, Jonathan Woo to coordinate the Ginga observations and preliminary data reduction, and to work with the Japanese host scientist, Fumiaki Nagase, in the interpretation of the data. At MIT extensive developments were made in software systems for data interpretation. In particular, a Monte Carlo code was developed for a 3-D simulation of the propagation of x-rays from the neutron star through the ionized atmosphere of the companion. With this code it was possible to determine the spectrum of Compton-scattered x-rays in deep eclipse and to subtract that component from the observed spectra, thereby isolating the software component that is attributable in large measure to x-rays that have been scattered by interstellar grains. This research has culminated in the submission of paper to the Astrophysical Journal on the determination of properties of the atmosphere of QV Nor, the BOI companion of 4U 1538-52, and the properties of interstellar dust grains along the line of sight from the source. The latter results were an unanticipated byproduct of the investigation. Data from Ginga observations of the Magellanic binaries SMC X-1 and LMC X-4 are currently under investigation as the PhD thesis project of Jonathan Woo who anticipated completion in the spring of 1993.

  7. Observations of the structure and evolution of solar flares with a soft X-ray telescope

    NASA Technical Reports Server (NTRS)

    Vorpahl, J. A.; Gibson, E. G.; Landecker, P. B.; Mckenzie, D. L.; Underwood, J. M.

    1975-01-01

    Soft X ray flare events were observed with the S-056 X-ray telescope that was part of the ATM complement of instruments aboard SKYLAB. Analyses of these data are reported. The observations are summarized and a detailed discussion of the X-ray flare structures is presented. The data indicated that soft X-ray emitted by a flare come primarily from an intense well-defined core surrounded by a region of fainter, more diffuse emission. An analysis of flare evolution indicates evidence for preliminary heating and energy release prior to the main phase of the flare. Core features are found to be remarkably stable and retain their shape throughout a flare. Most changes in the overall configuration seem to be result of the appearance, disappearance or change in brightness of individual features, rather than the restructuring or reorientation of these features. Brief comparisons with several theories are presented.

  8. Spiral chain structure of high pressure selenium-II{sup '} and sulfur-II from powder x-ray diffraction

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Fujihisa, Hiroshi; Yamawaki, Hiroshi; Sakashita, Mami

    2004-10-01

    The structure of high pressure phases, selenium-II{sup '} (Se-II{sup '}) and sulfur-II (S-II), for {alpha}-Se{sub 8} (monoclinic Se-I) and {alpha}-S{sub 8} (orthorhombic S-I) was studied by powder x-ray diffraction experiments. Se-II{sup '} and S-II were found to be isostructural and to belong to the tetragonal space group I4{sub 1}/acd, which is made up of 16 atoms in the unit cell. The structure consisted of unique spiral chains with both 4{sub 1} and 4{sub 3} screws. The results confirmed that the structure sequence of the pressure-induced phase transitions for the group VIb elements depended on the initial molecular form. The chemicalmore » bonds of the phases are also discussed from the interatomic distances that were obtained.« less

  9. ROSAT X-ray sources embedded in the rho Ophiuchi cloud core

    NASA Astrophysics Data System (ADS)

    Casanova, Sophie; Montmerle, Thierry; Feigelson, Eric D.; Andre, Philippe

    1995-02-01

    We present a deep ROSAT Position Sensitive Proportional Counter (PSPC) image of the central region of the rho Oph star-forming region. The selected area, about 35 x 35 arcmins in size, is rich with dense molecular cores and young stellar objects (YSOs). Fifty-five reliable X-ray sources are detected (and up to 50 more candidates may be present) above approximately 1 keV,, doubling the number of Einstein sources in this area. These sources are cross-identified with an updated list of 88 YSOs associated with the rho Oph cloud core. A third of the reliable X-ray sources do not have optical counterparts on photographic plates. Most can be cross-identified wth Class II and Class III infrared (IR) sources, which are embedded T Tauri stars, but three reliable X-ray sources and up to seven candidate sources are tentatively identified with Class I protostars. Eighteen reliable, and up to 20 candidate, X-ray sources are probably new cloud members. The overall detection rate of the bona fide cloud population is very high (73% for the Class II and Class III objects). The spatial distribution of the X-ray sources closely follows that of the moleclar gas. The visual extinctions Av estimated from near-IR data) of the ROSAT sources can be as high as 50 or more, confirming that most are embedded in the cloud core and are presumably very young. Using bolometric luminosities Lbol estimated from J-magnitudes a tight correlation between Lx and Lbol is found, similar to that seen for older T Tauri stars in the Cha I cloud: Lx approximately 10-4 Lbol. A general relation Lxproportional to LbolLj seems to apply to all T Tauri-like YSOs. The near equality of the extintion in the IR J band and in the keV X-ray rage implies that this relation is valid for the detected fluxes as well as for the dereddened fluxes. The X-ray luminosity function of the embedded sourced in rho Oph spans a range of Lx approximately 1028.5 to approximately equal to or greater than 1031.5 ergs/s and is statistically

  10. History of Chandra X-Ray Observatory

    NASA Image and Video Library

    1995-01-14

    This is an artist's concept of the Chandra X-Ray Observatory (CXO), formerly Advanced X-Ray Astrophysics Facility (AXAF), fully developed in orbit in a star field with Earth. In 1999, the AXAF was renamed the CXO in honor of the late Indian-American Novel Laureate Subrahmanyan Chandrasekhar. The CXO is the most sophisticated and the world's most powerful x-ray telescope ever built. It is designed to observe x-rays from high energy regions of the Universe, such as hot gas in the renmants of exploded stars. It produces picture-like images of x-ray emissions analogous to those made in visible light, as well as gathers data on the chemical composition of x-ray radiating objects. The CXO helps astronomers world-wide better understand the structure and evolution of the universe by studying powerful sources of x-ray such as exploding stars, matter falling into black holes, and other exotic celestial objects. The Observatory has three major parts: (1) the x-ray telescope, whose mirrors will focus x-rays from celestial objects; (2) the science instruments that record the x-rays so that x-ray images can be produced and analyzed; and (3) the spacecraft, which provides the environment necessary for the telescope and the instruments to work. TRW, Inc. was the prime contractor for the development the CXO and NASA's Marshall Space Flight Center was responsible for its project management. The Smithsonian Astrophysical Observatory controls science and flight operations of the CXO for NASA from Cambridge, Massachusetts. The Observatory was launched July 22, 1999 aboard the Space Shuttle Columbia, STS-93 mission. (Image courtesy of TRW).

  11. History of Chandra X-Ray Observatory

    NASA Image and Video Library

    1999-01-01

    This is a computer rendering of the fully developed Chandra X-ray Observatory (CXO), formerly Advanced X-Ray Astrophysics Facility (AXAF), in orbit in a star field. In 1999, the AXAF was renamed the CXO in honor of the late Indian-American Novel Laureate Subrahmanyan Chandrasekhar. The CXO is the most sophisticated and the world's most powerful x-ray telescope ever built. It is designed to observe x-rays from high energy regions of the Universe, such as hot gas in the renmants of exploded stars. It produces picture-like images of x-ray emissions analogous to those made in visible light, as well as gathers data on the chemical composition of x-ray radiating objects. The CXO helps astronomers world-wide better understand the structure and evolution of the universe by studying powerful sources of x-rays such as exploding stars, matter falling into black holes, and other exotic celestial objects. The Observatory has three major parts: (1) the x-ray telescope, whose mirrors will focus x-rays from celestial objects; (2) the science instruments that record the x-rays so that x-ray images can be produced and analyzed; and (3) the spacecraft, which provides the environment necessary for the telescope and the instruments to work. TRW, Inc. was the prime contractor for the development of the CXO and NASA's Marshall Space Flight Center was responsible for its project management. The Smithsonian Astrophysical Observatory controls science and flight operations of the CXO for NASA from Cambridge, Massachusetts. The Observatory was launched July 22, 1999 aboard the Space Shuttle Columbia, STS-93 mission. (Image courtesy of TRW).

  12. Purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies of great cormorant (Phalacrocorax carbo) haemoglobin.

    PubMed

    Jagadeesan, G; Malathy, P; Gunasekaran, K; Harikrishna Etti, S; Aravindhan, S

    2014-11-01

    Haemoglobin is the iron-containing oxygen-transport metalloprotein that is present in the red blood cells of all vertebrates. In recent decades, there has been substantial interest in attempting to understand the structural basis and functional diversity of avian haemoglobins. Towards this end, purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies have been carried out on cormorant (Phalacrocorax carbo) haemoglobin. Crystals were grown by the hanging-drop vapour-diffusion method using PEG 3350, NaCl and glycerol as precipitants. The crystals belonged to the trigonal system P3₁21, with unit-cell parameters a=b=55.64, c=153.38 Å, β=120.00°; a complete data set was collected to a resolution of 3.5 Å. Matthews coefficient analysis indicated that the crystals contained a half-tetramer in the asymmetric unit.

  13. Improving limited-projection-angle fluorescence molecular tomography using a co-registered x-ray computed tomography scan.

    PubMed

    Radrich, Karin; Ale, Angelique; Ermolayev, Vladimir; Ntziachristos, Vasilis

    2012-12-01

    We examine the improvement in imaging performance, such as axial resolution and signal localization, when employing limited-projection-angle fluorescence molecular tomography (FMT) together with x-ray computed tomography (XCT) measurements versus stand-alone FMT. For this purpose, we employed living mice, bearing a spontaneous lung tumor model, and imaged them with FMT and XCT under identical geometrical conditions using fluorescent probes for cancer targeting. The XCT data was employed, herein, as structural prior information to guide the FMT reconstruction. Gold standard images were provided by fluorescence images of mouse cryoslices, providing the ground truth in fluorescence bio-distribution. Upon comparison of FMT images versus images reconstructed using hybrid FMT and XCT data, we demonstrate marked improvements in image accuracy. This work relates to currently disseminated FMT systems, using limited projection scans, and can be employed to enhance their performance.

  14. SphinX Measurements of the 2009 Solar Minimum X-Ray Emission

    NASA Astrophysics Data System (ADS)

    Sylwester, J.; Kowalinski, M.; Gburek, S.; Siarkowski, M.; Kuzin, S.; Farnik, F.; Reale, F.; Phillips, K. J. H.; Bakała, J.; Gryciuk, M.; Podgorski, P.; Sylwester, B.

    2012-06-01

    The SphinX X-ray spectrophotometer on the CORONAS-PHOTON spacecraft measured soft X-ray emission in the 1-15 keV energy range during the deep solar minimum of 2009 with a sensitivity much greater than GOES. Several intervals are identified when the X-ray flux was exceptionally low, and the flux and solar X-ray luminosity are estimated. Spectral fits to the emission at these times give temperatures of 1.7-1.9 MK and emission measures between 4 × 1047 cm-3 and 1.1 × 1048 cm-3. Comparing SphinX emission with that from the Hinode X-ray Telescope, we deduce that most of the emission is from general coronal structures rather than confined features like bright points. For one of 27 intervals of exceptionally low activity identified in the SphinX data, the Sun's X-ray luminosity in an energy range roughly extrapolated to that of ROSAT (0.1-2.4 keV) was less than most nearby K and M dwarfs.

  15. X-ray free electron laser: opportunities for drug discovery.

    PubMed

    Cheng, Robert K Y; Abela, Rafael; Hennig, Michael

    2017-11-08

    Past decades have shown the impact of structural information derived from complexes of drug candidates with their protein targets to facilitate the discovery of safe and effective medicines. Despite recent developments in single particle cryo-electron microscopy, X-ray crystallography has been the main method to derive structural information. The unique properties of X-ray free electron laser (XFEL) with unmet peak brilliance and beam focus allow X-ray diffraction data recording and successful structure determination from smaller and weaker diffracting crystals shortening timelines in crystal optimization. To further capitalize on the XFEL advantage, innovations in crystal sample delivery for the X-ray experiment, data collection and processing methods are required. This development was a key contributor to serial crystallography allowing structure determination at room temperature yielding physiologically more relevant structures. Adding the time resolution provided by the femtosecond X-ray pulse will enable monitoring and capturing of dynamic processes of ligand binding and associated conformational changes with great impact to the design of candidate drug compounds. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

  16. Search for Hard X-Ray Emission from the Soft X-Ray Transient Aquila X-1

    NASA Astrophysics Data System (ADS)

    Harmon, B. A.; Zhang, S. N.; Paciesas, W. S.; Tavani, M.; Kaaret, P.; Ford, E.

    1994-12-01

    We are investigating the possibility of hard x-ray emission from the recurrent soft x-ray transient and x-ray burst source Aquila X-1 (Aql X-1). Outbursts of this source are relatively frequent with a spacing of ~ 4-10 months (Kitamoto, S. et al. 1993, ApJ, 403, 315). The recent detections of hard tails (\\(>\\)20 keV) in low luminosity x-ray bursters (Barret, D. & Vedrenne, G. 1994, ApJ Supp. S. 92, 505) suggest that neutron star transient systems such as Aql X-1 can produce hard x-ray emission which is detectable by BATSE. We are correlating reported optical and soft x-ray observations since 1991 of Aql X-1 with BATSE observations in order to search for hard x-ray emission episodes, and to study their temporal and spectral evolution. We will present preliminary results of this search in the 20-1000 keV band using the Earth occultation technique applied to the large area detectors. If this work is successful, we hope to alert the astronomical community for the next Aql X-1 outburst expected in 1995. Simultaneous x-ray/hard x-ray and optical observations of Aql X-1 during outburst would be of great importance for the modeling of soft x-ray transients and related systems.

  17. Absolute Intra-Molecular Distance Measurements with Ångström-Resolution using Anomalous Small-Angle X-ray Scattering

    DOE PAGES

    Zettl, Thomas; Mathew, Rebecca S.; Seifert, Sönke; ...

    2016-05-31

    Accurate determination of molecular distances is fundamental to understanding the structure, dynamics, and conformational ensembles of biological macromolecules. Here we present a method to determine the full,distance,distribution between small (~7 Å) gold labels attached to macromolecules with very high-precision(≤1 Å) and on an absolute distance scale. Our method uses anomalous small-angle X-ray scattering close to a gold absorption edge to separate the gold-gold interference pattern from other scattering contributions. Results for 10-30 bp DNA constructs achieve excellent signal-to-noise and are in good agreement with previous results obtained by single-energy,SAXS measurements without requiring the preparation and measurement of single labeled andmore » unlabeled samples. Finally, the use of small gold labels in combination with ASAXS read out provides an attractive approach to determining molecular distance distributions that will be applicable to a broad range of macromolecular systems.« less

  18. X-ray phase-contrast imaging

    NASA Astrophysics Data System (ADS)

    Endrizzi, Marco

    2018-01-01

    X-ray imaging is a standard tool for the non-destructive inspection of the internal structure of samples. It finds application in a vast diversity of fields: medicine, biology, many engineering disciplines, palaeontology and earth sciences are just few examples. The fundamental principle underpinning the image formation have remained the same for over a century: the X-rays traversing the sample are subjected to different amount of absorption in different parts of the sample. By means of phase-sensitive techniques it is possible to generate contrast also in relation to the phase shifts imparted by the sample and to extend the capabilities of X-ray imaging to those details that lack enough absorption contrast to be visualised in conventional radiography. A general overview of X-ray phase contrast imaging techniques is presented in this review, along with more recent advances in this fast evolving field and some examples of applications.

  19. 3D X-ray ultra-microscopy of bone tissue.

    PubMed

    Langer, M; Peyrin, F

    2016-02-01

    We review the current X-ray techniques with 3D imaging capability at the nano-scale: transmission X-ray microscopy, ptychography and in-line phase nano-tomography. We further review the different ultra-structural features that have so far been resolved: the lacuno-canalicular network, collagen orientation, nano-scale mineralization and their use as basis for mechanical simulations. X-ray computed tomography at the micro-metric scale is increasingly considered as the reference technique in imaging of bone micro-structure. The trend has been to push towards increasingly higher resolution. Due to the difficulty of realizing optics in the hard X-ray regime, the magnification has mainly been due to the use of visible light optics and indirect detection of the X-rays, which limits the attainable resolution with respect to the wavelength of the visible light used in detection. Recent developments in X-ray optics and instrumentation have allowed to implement several types of methods that achieve imaging that is limited in resolution by the X-ray wavelength, thus enabling computed tomography at the nano-scale. We review here the X-ray techniques with 3D imaging capability at the nano-scale: transmission X-ray microscopy, ptychography and in-line phase nano-tomography. Further, we review the different ultra-structural features that have so far been resolved and the applications that have been reported: imaging of the lacuno-canalicular network, direct analysis of collagen orientation, analysis of mineralization on the nano-scale and use of 3D images at the nano-scale to drive mechanical simulations. Finally, we discuss the issue of going beyond qualitative description to quantification of ultra-structural features.

  20. X-ray Pump–Probe Investigation of Charge and Dissociation Dynamics in Methyl Iodine Molecule

    DOE PAGES

    Fang, Li; Xiong, Hui; Kukk, Edwin; ...

    2017-05-19

    Molecular dynamics is of fundamental interest in natural science research. The capability of investigating molecular dynamics is one of the various motivations for ultrafast optics. Here, we present our investigation of photoionization and nuclear dynamics in methyl iodine (CH 3I) molecule with an X-ray pump X-ray probe scheme. The pump–probe experiment was realized with a two-mirror X-ray split and delay apparatus. Time-of-flight mass spectra at various pump–probe delay times were recorded to obtain the time profile for the creation of high charge states via sequential ionization and for molecular dissociation. We observed high charge states of atomic iodine up tomore » 29+, and visualized the evolution of creating these high atomic ion charge states, including their population suppression and enhancement as the arrival time of the second X-ray pulse was varied. We also show the evolution of the kinetics of the high charge states upon the timing of their creation during the ionization-dissociation coupled dynamics. We demonstrate the implementation of X-ray pump–probe methodology for investigating X-ray induced molecular dynamics with femtosecond temporal resolution. The results indicate the footprints of ionization that lead to high charge states, probing the long-range potential curves of the high charge states.« less

  1. History of Chandra X-Ray Observatory

    NASA Image and Video Library

    1997-05-01

    This photograph shows the Chandra X-Ray Observatory (CXO), formerly Advanced X-Ray Astrophysics Facility (AXAF), High Resolution Mirror Assembly (HRMA) being removed from the test structure in the X-Ray Calibration Facility (XRCF) at the Marshall Space Flight Center (MSFC). The AXAF was renamed CXO in 1999. The CXO is the most sophisticated and the world's most powerful x-ray telescope ever built. It observes x-rays from high-energy regions of the universe, such as hot gas in the remnants of exploded stars. The HRMA, the heart of the telescope system, is contained in the cylindrical "telescope" portion of the observatory. Since high-energy x-rays would penetrate a normal mirror, special cylindrical mirrors were created. The two sets of four nested mirrors resemble tubes within tubes. Incoming x-rays graze off the highly polished mirror surface and are furneled to the instrument section for detection and study. MSFC's XRCF is the world's largest, most advanced laboratory for simulating x-ray emissions from distant celestial objects. It produces a space-like environment in which components related to x-ray telescope imaging are tested and the quality of their performances in space is predicted. TRW, Inc. was the prime contractor for the development of the CXO and NASA's MSFC was responsible for its project management. The Smithsonian Astrophysical Observatory controls science and flight operations of the CXO for NASA from Cambridge, Massachusetts. The CXO was launched July 22, 1999 aboard the Space Shuttle Columbia (STS-93).

  2. History of Chandra X-Ray Observatory

    NASA Image and Video Library

    1997-05-01

    This photograph shows the Chandra X-ray Observatory (CXO), formerly Advanced X-Ray Astrophysics Facility (AXAF), High Resolution Mirror Assembly (HRMA) being removed from the test structure in the X-Ray Calibration Facility (XRCF) at the Marshall Space Flight Center (MSFC). The AXAF was renamed CXO in 1999. The CXO is the most sophisticated and the world's most powerful x-ray telescope ever built. It observes x-rays from high-energy regions of the universe, such as hot gas in the remnants of exploded stars. The HRMA, the heart of the telescope system, is contained in the cylindrical "telescope" portion of the observatory. Since high-energy x-rays would penetrate a normal mirror, special cylindrical mirrors were created. The two sets of four nested mirrors resemble tubes within tubes. Incoming x-rays graze off the highly polished mirror surface and are furneled to the instrument section for detection and study. MSFC's XRCF is the world's largest, most advanced laboratory for simulating x-ray emissions from distant celestial objects. It produces a space-like environment in which components related to x-ray telescope imaging are tested and the quality of their performances in space is predicted. TRW, Inc. was the prime contractor for the development of the CXO and NASA's MSFC was responsible for its project management. The Smithsonian Astrophysical Observatory controls science and flight operations of the CXO for NASA from Cambridge, Massachusetts. The CXO was launched July 22, 1999 aboard the Space Shuttle Columbia (STS-93).

  3. Unveiling the past of the Galactic nucleus with X-ray echoes

    NASA Astrophysics Data System (ADS)

    Chuard, D.; Terrier, R.; Goldwurm, A.; Clavel, M.; Soldi, S.; Morris, M. R.; Ponti, G.; Walls, M.; Chernyakova, M.

    2017-12-01

    Giant molecular clouds populating the central molecular zone have a high enough column density to reflect X-rays coming from strong compact sources in their neighbourhood, including possible powerful outbursts from the Galactic supermassive black hole SgrA. From observations of the molecular complex Sgr C made with the X-ray observatories XMM and Chandra between 2000 and 2014, we confirm this reflection scenario, even though the region hosts several objects (including two PWN candidates) that may be responsible for intense cosmic-ray production. By comparing data to Monte Carlo simulated reflection spectra, we are able to put the best constraints to date on the line-of-sight positions of the main bright clumps of the molecular complex. Ultimately, extending this approach by the inclusion of other molecular complexes allows us to partially reconstruct the past lightcurve of the Galactic supermassive black hole.

  4. Development of a low-cost x-ray mask for high-aspect-ratio MEM smart structures

    NASA Astrophysics Data System (ADS)

    Ajmera, Pratul K.; Stadler, Stefan; Abdollahi, Neda

    1998-07-01

    A cost-effective process with short fabrication time for making x-ray masks for research and development purposes is described here for fabricating high-aspect ratio microelectromechanical structures using synchrotron based x- ray lithography. Microscope cover glass slides as membrane material is described. Slides with an initial thickness of 175 micrometers are etched to a thickness in the range of 10 - 25 micrometers using a diluted HF and buffered hydrofluoric acid solutions. The thinned slides are glued on supportive mask frames and sputtered with a chromium/silver sandwich layer which acts as a plating base layer for the deposition of the gold absorber. The judicial choice of glue and mask frame material are significant parameters in a successful fabrication process. Gold absorber structures are electroplated on the membrane. Calculations are done for contrast and dose ratio obtained in the photoresist after synchrotron radiation as a function of the mask design parameters. Exposure experiments are performed to prove the applicability of the fabricated x-ray mask.

  5. High resolution crystal structure of the methylcobalamin analogues ethylcobalamin and butylcobalamin by X-ray synchrotron diffraction.

    PubMed

    Hannibal, Luciana; Smith, Clyde A; Smith, Jessica A; Axhemi, Armend; Miller, Abby; Wang, Sihe; Brasch, Nicola E; Jacobsen, Donald W

    2009-07-20

    The X-ray crystal structures of the methylcobalamin (MeCbl) analogues ethylcobalamin (EtCbl) and butylcobalamin (BuCbl) are reported. The X-ray crystal structures of EtCbl and BuCbl were obtained with some of the lowest crystallographic residuals ever achieved for cobalamins (R = 0.0468 and 0.0438, respectively). The Co-C bond distances for EtCbl and BuCbl are 2.023(2) and 2.028(4) A, whereas the Co-alpha-5,6-dimethylbenzimidazole (Co-N3B) bond distances were 2.232(1) and 2.244(1) A, respectively. Although EtCbl and BuCbl displayed a longer Co-N3B bond than that observed in the naturally occurring methylcobalamin, the orientation of the alpha-5,6-dimethylbenzimidazole moiety with respect to the corrin ring did not vary substantially among the structures. The lengthening of both Co-C and Co-N3B bonds in EtCbl and BuCbl can be attributed to the "inverse" trans influence exerted by the sigma-donating alkyl groups, typically observed in alkylcobalamins. Analysis of the molecular surface maps showed that the alkyl ligands in EtCbl and BuCbl are directed toward the hydrophobic side of the corrin ring. The corrin fold angles in EtCbl and BuCbl were determined to be 14.7 degrees and 13.1 degrees, respectively. A rough correlation exists between the corrin fold angle and the length of the Co-N3B bond, and both alkylcobalamins follow the same trend.

  6. High Resolution Crystal Structure of the Methylcobalamin Analogs Ethylcobalamin and Butylcobalamin by X-ray Synchrotron Diffraction

    PubMed Central

    Hannibal, Luciana; Smith, Clyde A; Smith, Jessica A.; Axhemi, Armend; Miller, Abby; Wang, Sihe; Brasch, Nicola E.; Jacobsen, Donald W.

    2009-01-01

    The X-ray crystal structures of the methylcobalamin (MeCbl) analogs ethylcobalamin (EtCbl) and butylcobalamin (BuCbl) are reported. The X-ray crystal structures of EtCbl and BuCbl were obtained with some of the lowest crystallographic residuals ever achieved for cobalamins (R = 0.0468 and 0.0438, respectively). The Co-C bond distances for EtCbl and BuCbl are 2.023(2) and 2.028(4) Å, whereas the Co-α-5,6-dimethylbenzimidazole (Co-N3B) bond distances were 2.232(1) and 2.244(1) Å, respectively. Although EtCbl and BuCbl displayed a longer Co-N3B bond than that observed in the naturally occurring methylcobalamin, the orientation of the α-5,6-dimethylbenzimidazole moiety with respect to the corrin ring did not vary substantially amongst the structures. The lengthening of both Co-C and Co-N3B bonds in EtCbl and BuCbl can be attributed to the “inverse” trans influence exerted by the σ-donating alkyl groups, typically observed in alkylcobalamins. Analysis of the molecular surface maps showed that the alkyl ligands in EtCbl and BuCbl are directed towards the hydrophobic side of the corrin ring. The corrin fold angles in EtCbl and BuCbl were determined to be 14.7° and 13.1°, respectively. A rough correlation exists between the corrin fold angle and the length of the Co-N3B bond, and both alkylcobalamins follow the same trend. PMID:19545130

  7. Effect of X-ray flux on polytetrafluoroethylene in X-ray photoelectron spectroscopy

    NASA Technical Reports Server (NTRS)

    Wheeler, D. R.; Pepper, S. V.

    1982-01-01

    The effect of the X-ray flux in X-ray photoelectron spectroscopy (STAT) on the constitution of the polytetrafluoroethylene (PTFE) surface has been examined. The radiation dose rate for our specimen was about 10 to the 7th rad/s. The structure, magnitude and binding energy of the C(1s) and F(1s) features of the XPS spectrum and the mass spectrum of gaseous species evolved during irradiation are observed. The strong time dependence of these signals over a period of several hours indicated that the surface constitution of PTFE is greatly affected by this level of radiation dose. The results are consistent with the development of a heavily cross-linked or branched structure in the PTFE surface region and the evolution of short chain fragments into the gas phase.

  8. Time-resolved structural studies at synchrotrons and X-ray free electron lasers: opportunities and challenges

    PubMed Central

    Neutze, Richard; Moffat, Keith

    2012-01-01

    X-ray free electron lasers (XFELs) are potentially revolutionary X-ray sources because of their very short pulse duration, extreme peak brilliance and high spatial coherence, features that distinguish them from today’s synchrotron sources. We review recent time-resolved Laue diffraction and time-resolved wide angle X-ray scattering (WAXS) studies at synchrotron sources, and initial static studies at XFELs. XFELs have the potential to transform the field of time-resolved structural biology, yet many challenges arise in devising and adapting hardware, experimental design and data analysis strategies to exploit their unusual properties. Despite these challenges, we are confident that XFEL sources are poised to shed new light on ultrafast protein reaction dynamics. PMID:23021004

  9. Resonant inelastic soft x-ray scattering of CdS: a two-dimensional electronic structure map approach

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Weinhardt, L.; Fuchs, O.; Fleszar, A.

    2008-09-24

    Resonant inelastic x-ray scattering (RIXS) with soft x-rays is uniquely suited to study the elec-tronic structure of a variety of materials, but is currently limited by low (fluorescence yield) count rates. This limitation is overcome with a new high-transmission spectrometer that allows to measure soft x-ray RIXS"maps." The S L2,3 RIXS map of CdS is discussed and compared with density functional calculations. The map allows the extraction of decay channel-specific"absorp-tion spectra," giving detailed insight into the wave functions of occupied and unoccupied elec-tronic states.

  10. Pollen structure visualization using high-resolution laboratory-based hard X-ray tomography

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Li, Qiong; Gluch, Jürgen; Krüger, Peter

    A laboratory-based X-ray microscope is used to investigate the 3D structure of unstained whole pollen grains. For the first time, high-resolution laboratory-based hard X-ray microscopy is applied to study pollen grains. Based on the efficient acquisition of statistically relevant information-rich images using Zernike phase contrast, both surface- and internal structures of pine pollen - including exine, intine and cellular structures - are clearly visualized. The specific volumes of these structures are calculated from the tomographic data. The systematic three-dimensional study of pollen grains provides morphological and structural information about taxonomic characters that are essential in palynology. Such studies have amore » direct impact on disciplines such as forestry, agriculture, horticulture, plant breeding and biodiversity. - Highlights: • The unstained whole pine pollen was visualized by high-resolution laboratory-based HXRM for the first time. • The comparison study of pollen grains by LM, SEM and high-resolution laboratory-based HXRM. • Phase contrast imaging provides significantly higher contrast of the raw images compared to absorption contrast imaging. • Surface and internal structure of the pine pollen including exine, intine and cellular structures are clearly visualized. • 3D volume data of unstained whole pollen grains are acquired and the specific volumes of the different layer are calculated.« less

  11. The structure investigations of dehydroacetic acid and 1,8-diaminonaphthalene condensation product by NMR, MS, and X-ray measurements

    NASA Astrophysics Data System (ADS)

    Kołodziej, B.; Morawiak, M.; Kamieński, B.; Schilf, W.

    2016-05-01

    A new unexpected product of condensation reaction of 1,8-diaminonaphthalene (DAN) and carbonyl compound (here: dehydroacetic acid (dha)) was synthesized. Discussion about the molecular structure of possible products of this reaction was done on the base of NMR studies. The structure of the titled product in both DMSO solution and in the solid state was resolved by analysis of its spectral data (X-ray structure analysis, multinuclear NMR in solution and solid state spectra) and MS measurements. The presented studies provided clear evidence that the titled product exists in diluted DMSO solution as the mixture of two kinetic free ionic species whereas in concentrated DMSO solution as well as in the solid state this system forms associated ionic pairs bonded together by hydrogen bonds.

  12. Three-dimensional reciprocal space x-ray coherent scattering tomography of two-dimensional object.

    PubMed

    Zhu, Zheyuan; Pang, Shuo

    2018-04-01

    X-ray coherent scattering tomography is a powerful tool in discriminating biological tissues and bio-compatible materials. Conventional x-ray scattering tomography framework can only resolve isotropic scattering profile under the assumption that the material is amorphous or in powder form, which is not true especially for biological samples with orientation-dependent structure. Previous tomography schemes based on x-ray coherent scattering failed to preserve the scattering pattern from samples with preferred orientations, or required elaborated data acquisition scheme, which could limit its application in practical settings. Here, we demonstrate a simple imaging modality to preserve the anisotropic scattering signal in three-dimensional reciprocal (momentum transfer) space of a two-dimensional sample layer. By incorporating detector movement along the direction of x-ray beam, combined with a tomographic data acquisition scheme, we match the five dimensions of the measurements with the five dimensions (three in momentum transfer domain, and two in spatial domain) of the object. We employed a collimated pencil beam of a table-top copper-anode x-ray tube, along with a panel detector to investigate the feasibility of our method. We have demonstrated x-ray coherent scattering tomographic imaging at a spatial resolution ~2 mm and momentum transfer resolution 0.01 Å -1 for the rotation-invariant scattering direction. For any arbitrary, non-rotation-invariant direction, the same spatial and momentum transfer resolution can be achieved based on the spatial information from the rotation-invariant direction. The reconstructed scattering profile of each pixel from the experiment is consistent with the x-ray diffraction profile of each material. The three-dimensional scattering pattern recovered from the measurement reveals the partially ordered molecular structure of Teflon wrap in our sample. We extend the applicability of conventional x-ray coherent scattering tomography to

  13. Inelastic X-ray Scattering Measurements of Ionization in Warm, Dense Matter

    NASA Astrophysics Data System (ADS)

    Davis, Paul F.

    In this work we demonstrate spectrally resolved x-ray scattering from electron-plasma waves in shock-compressed deuterium and proton-heated matter. Because the spectral signature of inelastic x-ray scattering is strongly dependent on the free electron density of the system, it is used to infer ionization in dynamically heated samples. Using 2-6 ns, 500 J laser pulses from LLNL's Janus laser, we shocked liquid deuterium to pressures approaching 50 GPa, reaching compressions of 4 times liquid density. A second laser produced intense 2 keV x-rays. By collecting and spectrally dispersing forward scattered photons at 45°, the onset of ionization was detected at compressions of about 3 times in the form of plasmon oscillations. Backscattered x-rays bolstered this observation by measuring the free electron distribution through Compton scattering. Comparison with simulations shows very close agreement between the pressure dependence of ionization and molecular dissociation in dynamically compressed deuterium. In a second set of experiments, a 10 ps, 200 J Titan laser pulse was split into two beams. One created a stream of MeV protons to heat samples of boron and boron-nitride and the other pumped 4.5 keV K-alpha radiation in a titanium foil to probe the hot target. We observed scattered x-rays 300 ps after heating, noting a strong difference in average ionization between the two target materials at temperatures of 16 eV and very similar mass densities. Comparison with electron structure calculations suggests that this difference is due to a persistence of long-range ion structure in BN resulting in high-temperature band structure. These results underscore the importance of understanding the complex electron structure of materials even at electron-volt temperatures and gigapascal pressures. Our results provide new data to guide the theoretical modeling of warm, dense matter important to understanding giant planets and inertial fusion targets.

  14. Refractive Optics for Hard X-ray Transmission Microscopy

    NASA Astrophysics Data System (ADS)

    Simon, M.; Ahrens, G.; Last, A.; Mohr, J.; Nazmov, V.; Reznikova, E.; Voigt, A.

    2011-09-01

    For hard x-ray transmission microscopy at photon energies higher than 15 keV we design refractive condenser and imaging elements to be used with synchrotron light sources as well as with x-ray tube sources. The condenser lenses are optimized for low x-ray attenuation—resulting in apertures greater than 1 mm—and homogeneous intensity distribution on the detector plane, whereas the imaging enables high-resolution (<100 nm) full-field imaging. To obtain high image quality at reasonable exposure times, custom-tailored matched pairs of condenser and imaging lenses are being developed. The imaging lenses (compound refractive lenses, CRLs) are made of SU-8 negative resist by deep x-ray lithography. SU-8 shows high radiation stability. The fabrication technique enables high-quality lens structures regarding surface roughness and arrangement precision with arbitrary 2D geometry. To provide point foci, crossed pairs of lenses are used. Condenser lenses have been made utilizing deep x-ray lithographic patterning of thick SU-8 layers, too, whereas in this case, the aperture is limited due to process restrictions. Thus, in terms of large apertures, condenser lenses made of structured and rolled polyimide film are more attractive. Both condenser types, x-ray mosaic lenses and rolled x-ray prism lenses (RXPLs), are considered to be implemented into a microscope setup. The x-ray optical elements mentioned above are characterized with synchrotron radiation and x-ray laboratory sources, respectively.

  15. Ain't no Crab, PWN Got a Brand New Bag: Correlated Radio and X-ray Structures in Pulsar Wind Nebulae

    NASA Astrophysics Data System (ADS)

    Roberts, M. S. E.; Lyutikov, M.; Gaensler, B. M.; Brogan, C. L.; Tam, C. R.; Romani, R. W.

    2005-04-01

    The traditional view of radio pulsar wind nebulae (PWN), encouraged by the Crab nebula's X-ray and radio morphologies, is that they are a result of the integrated history of their pulsars' wind. The radio emission should therefore be largely unaffected by recent pulsar activity, and hence minimally correlated with structures in the X-ray nebulae. Observations of several PWN, both stationary and rapidly moving, now show clear morphological relationships between structures in the radio and X-ray with radio intensity variations on the order of unity. We present high-resolution X-ray and radio images of several PWN of both types and discuss the morphological relationships between the two wavebands.

  16. The origin of luminescence from di[4-(4-diphenylaminophenyl)phenyl]sulfone (DAPSF), a blue light emitter: an X-ray excited optical luminescence (XEOL) and X-ray absorption near edge structure (XANES) study.

    PubMed

    Zhang, Duo; Zhang, Hui; Zhang, Xiaohong; Sham, Tsun-Kong; Hu, Yongfeng; Sun, Xuhui

    2016-03-07

    The electronic structure and optical properties of di[4-(4-diphenylaminophenyl)phenyl]sulfone (denoted as DAPSF), a highly efficient fluorophor, have been investigated using X-ray excited optical luminescence (XEOL) and X-ray absorption near edge structure (XANES) spectroscopy at excitation energies across the C, N, O K-edges and the sulfur K-edge. The results indicate that the blue luminescence is mainly related to the sulfur functional group.

  17. Probing the thermal stability and the decomposition mechanism of a magnesium-fullerene polymer via X-ray Raman spectroscopy, X-ray diffraction and molecular dynamics simulations.

    PubMed

    Aramini, Matteo; Niskanen, Johannes; Cavallari, Chiara; Pontiroli, Daniele; Musazay, Abdurrahman; Krisch, Michael; Hakala, Mikko; Huotari, Simo

    2016-02-21

    We report the microscopic view of the thermal structural stability of the magnesium intercalated fullerene polymer Mg2C60. With the application of X-ray Raman spectroscopy and X-ray diffraction, we study in detail the decomposition pathways of the polymer system upon annealing at temperatures between 300 and 700 °C. We show that there are at least two energy scales involved in the decomposition reaction. Intermolecular carbon bonds, which are responsible for the formation of a 2D fullerene polymer, are broken with a relatively modest thermal energy, while the long-range order of the original polymer remains intact. With an increased thermal energy, the crystal structure in turn is found to undergo a transition to a novel intercalated cubic phase that is stable up to the highest temperature studied here. The local structure surrounding magnesium ions gets severely modified close to, possibly at, the phase transition. We used density functional theory based calculations to study the thermodynamic and kinetic aspects of the collapse of the fullerene network, and to explain the intermediate steps as well as the reaction pathways in the break-up of this peculiar C60 intermolecular bonding architecture.

  18. Measurement of the noise components in the medical x-ray intensity pattern due to overlaying nonrecognizable structures

    NASA Astrophysics Data System (ADS)

    Tischenko, Oleg; Hoeschen, Christoph; Effenberger, Olaf; Reissberg, Steffen; Buhr, Egbert; Doehring, Wilfried

    2003-06-01

    There are many aspects that influence and deteriorate the detection of pathologies in X-ray images. Some of those are due to effects taking place in the stage of forming the X-ray intensity pattern in front of the x-ray detector. These can be described as motion blurring, depth blurring, anatomical background, scatter noise and structural noise. Structural noise results from an overlapping of fine irrelevant anatomical structures. A method for measuring the combined effect of structural noise and scatter noise was developed and will be presented in this paper. This method is based on the consideration that within a pair of projections created after rotation of the object with a small angle (which is within the typical uncertainty in positioning the patient) both images would show the same relevant structures whereas the projection of the fine overlapping structures will appear quite differently in the two images. To demonstrate the method two X-ray radiographs of a lung phantom were produced. The second radiograph was achieved after rotating the lung by an angle of about 3. Dyadic wavelet representations of both images were regarded. For each value of the wavelet scale parameter the corresponding pair of approximations was matched using the cross correlation matching technique. The homologous regions of approximations were extracted. The image containing only those structures that appear in both images simultaneously was then reconstructed from the wavelet coefficients corresponding to the homologous regions. The difference between one of the original images and the noise-reduced image contains the structural noise and the scatter noise.

  19. Defect Chemistry of " BaCuO2" I. Oxygen Non -Stoichiometry, Cation Molecularity and X-ray Diffraction Determinations

    NASA Astrophysics Data System (ADS)

    Spinolo, G.; Anselmi-Tamburini, U.; Arimondi, M.; Ghigna, P.; Flor, G.

    1995-11-01

    "BaCuO2" is the key intermediate in the synthesis of the Ba2YCu3O7-δ superconductor. Its very complex crystal structure is able to accommodate a large change in oxygen content. Oxygen non-stoichiometry of "BaCuO2" materials with 1:1 and 88:90 (Ba :Cu) molecularity has been investigated by polythermal X-ray powder diffraction coupled with isobaric-isothermal gravimetry determinations under different temperature and oxygen partial pressure conditions [300≤ T≤ 820 °C, 1 ≥ P(O2) ≥ 3 • 10-3 atm]. The 1:1 composition does not give well reproducible results, thus suggesting its polyphasic nature, at least in part of the investigated range. The results for the 88:90 ≅ 0.98 (Ba :Cu) composi­ tion are well reproducible and show that the material is single phase. Ba0.98CuO1.98 + δ is oxygen over-stoichiometric in the whole investigated [T, P(O2)] range, with a maximum value δ˜0.21. A Rietveld X-ray profile fitting is in agreement with previous single-crystal data. The trend of δ vs. P(O2) is consistent with the presence of oxygen interstitial defects on (possibly different) crystallographic sites.

  20. Molecular Dynamics Simulations and XAFS (MD-XAFS)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Schenter, Gregory K.; Fulton, John L.

    2017-01-20

    MD-XAFS (Molecular Dynamics X-ray Adsorption Fine Structure) makes the connection between simulation techniques that generate an ensemble of molecular configurations and the direct signal observed from X-ray measurement.

  1. An investigation of coronal active region loop structures using AS&E rocket X-ray images

    NASA Technical Reports Server (NTRS)

    Webb, D. F.

    1983-01-01

    Simultaneous high spatial resolution observations at 6 cm in soft X-rays, in photospheric magnetograms, and in optical filtergrams were used to compare the most intense sources of centimetric emission in two active regions to coronal loops, sunspots, chromospheric structures, and photospheric magnetic fields. Results show that the majority of the bright microwave components are not associated with sunspots or X-ray emission. A nonthermal mechanism appears necessary to explain the brightest microwave components, discrete regions of continuous particle acceleration may be common in active regions. Studies of the plasma parameters of selected loops imply that the radio emission is consistent with gyro-resonance absorption at the third and fourth harmonic, at least from part of each loop. Results are presented for: (1) X-ray and microwave observations of active regions; (2) comparison of coronal holes observed in soft X-rays and Hel 10830 A spectrosheliograms; and (3) the reappearance of polar coronal holes and the evolution of the solar magnetic field.

  2. X-Ray Polarization from High Mass X-Ray Binaries

    NASA Technical Reports Server (NTRS)

    Kallman, T.; Dorodnitsyn, A.; Blondin, J.

    2015-01-01

    X-ray astronomy allows study of objects which may be associated with compact objects, i.e. neutron stars or black holes, and also may contain strong magnetic fields. Such objects are categorically non-spherical, and likely non-circular when projected on the sky. Polarization allows study of such geometric effects, and X-ray polarimetry is likely to become feasible for a significant number of sources in the future. A class of potential targets for future X-ray polarization observations is the high mass X-ray binaries (HMXBs), which consist of a compact object in orbit with an early type star. In this paper we show that X-ray polarization from HMXBs has a distinct signature which depends on the source inclination and orbital phase. The presence of the X-ray source displaced from the star creates linear polarization even if the primary wind is spherically symmetric whenever the system is viewed away from conjunction. Direct X-rays dilute this polarization whenever the X-ray source is not eclipsed; at mid-eclipse the net polarization is expected to be small or zero if the wind is circularly symmetric around the line of centers. Resonance line scattering increases the scattering fraction, often by large factors, over the energy band spanned by resonance lines. Real winds are not expected to be spherically symmetric, or circularly symmetric around the line of centers, owing to the combined effects of the compact object gravity and ionization on the wind hydrodynamics. A sample calculation shows that this creates polarization fractions ranging up to tens of percent at mid-eclipse.

  3. Analysis of X-ray structures of matrix metalloproteinases via chaotic map clustering.

    PubMed

    Giangreco, Ilenia; Nicolotti, Orazio; Carotti, Angelo; De Carlo, Francesco; Gargano, Gianfranco; Bellotti, Roberto

    2010-10-08

    Matrix metalloproteinases (MMPs) are well-known biological targets implicated in tumour progression, homeostatic regulation, innate immunity, impaired delivery of pro-apoptotic ligands, and the release and cleavage of cell-surface receptors. With this in mind, the perception of the intimate relationships among diverse MMPs could be a solid basis for accelerated learning in designing new selective MMP inhibitors. In this regard, decrypting the latent molecular reasons in order to elucidate similarity among MMPs is a key challenge. We describe a pairwise variant of the non-parametric chaotic map clustering (CMC) algorithm and its application to 104 X-ray MMP structures. In this analysis electrostatic potentials are computed and used as input for the CMC algorithm. It was shown that differences between proteins reflect genuine variation of their electrostatic potentials. In addition, the analysis has been also extended to analyze the protein primary structures and the molecular shapes of the MMP co-crystallised ligands. The CMC algorithm was shown to be a valuable tool in knowledge acquisition and transfer from MMP structures. Based on the variation of electrostatic potentials, CMC was successful in analysing the MMP target family landscape and different subsites. The first investigation resulted in rational figure interpretation of both domain organization as well as of substrate specificity classifications. The second made it possible to distinguish the MMP classes, demonstrating the high specificity of the S1' pocket, to detect both the occurrence of punctual mutations of ionisable residues and different side-chain conformations that likely account for induced-fit phenomena. In addition, CMC demonstrated a potential comparable to the most popular UPGMA (Unweighted Pair Group Method with Arithmetic mean) method that, at present, represents a standard clustering bioinformatics approach. Interestingly, CMC and UPGMA resulted in closely comparable outcomes, but often

  4. Structure of nanocrystalline calcium silicate hydrates: insights from X-ray diffraction, synchrotron X-ray absorption and nuclear magnetic resonance.

    PubMed

    Grangeon, Sylvain; Claret, Francis; Roosz, Cédric; Sato, Tsutomu; Gaboreau, Stéphane; Linard, Yannick

    2016-06-01

    The structure of nanocrystalline calcium silicate hydrates (C-S-H) having Ca/Si ratios ranging between 0.57 ± 0.05 and 1.47 ± 0.04 was studied using an electron probe micro-analyser, powder X-ray diffraction, 29 Si magic angle spinning NMR, and Fourier-transform infrared and synchrotron X-ray absorption spectroscopies. All samples can be described as nanocrystalline and defective tobermorite. At low Ca/Si ratio, the Si chains are defect free and the Si Q 3 and Q 2 environments account, respectively, for up to 40.2 ± 1.5% and 55.6 ± 3.0% of the total Si, with part of the Q 3 Si being attributable to remnants of the synthesis reactant. As the Ca/Si ratio increases up to 0.87 ± 0.02, the Si Q 3 environment decreases down to 0 and is preferentially replaced by the Q 2 environment, which reaches 87.9 ± 2.0%. At higher ratios, Q 2 decreases down to 32.0 ± 7.6% for Ca/Si = 1.38 ± 0.03 and is replaced by the Q 1 environment, which peaks at 68.1 ± 3.8%. The combination of X-ray diffraction and NMR allowed capturing the depolymerization of Si chains as well as a two-step variation in the layer-to-layer distance. This latter first increases from ∼11.3 Å (for samples having a Ca/Si ratio <∼0.6) up to 12.25 Å at Ca/Si = 0.87 ± 0.02, probably as a result of a weaker layer-to-layer connectivity, and then decreases down to 11 Å when the Ca/Si ratio reaches 1.38 ± 0.03. The decrease in layer-to-layer distance results from the incorporation of interlayer Ca that may form a Ca(OH) 2 -like structure, nanocrystalline and intermixed with C-S-H layers, at high Ca/Si ratios.

  5. Structure of nanocrystalline calcium silicate hydrates: insights from X-ray diffraction, synchrotron X-ray absorption and nuclear magnetic resonance

    PubMed Central

    Grangeon, Sylvain; Claret, Francis; Roosz, Cédric; Sato, Tsutomu; Gaboreau, Stéphane; Linard, Yannick

    2016-01-01

    The structure of nanocrystalline calcium silicate hydrates (C–S–H) having Ca/Si ratios ranging between 0.57 ± 0.05 and 1.47 ± 0.04 was studied using an electron probe micro-analyser, powder X-ray diffraction, 29Si magic angle spinning NMR, and Fourier-transform infrared and synchrotron X-ray absorption spectroscopies. All samples can be described as nanocrystalline and defective tobermorite. At low Ca/Si ratio, the Si chains are defect free and the Si Q 3 and Q 2 environments account, respectively, for up to 40.2 ± 1.5% and 55.6 ± 3.0% of the total Si, with part of the Q 3 Si being attributable to remnants of the synthesis reactant. As the Ca/Si ratio increases up to 0.87 ± 0.02, the Si Q 3 environment decreases down to 0 and is preferentially replaced by the Q 2 environment, which reaches 87.9 ± 2.0%. At higher ratios, Q 2 decreases down to 32.0 ± 7.6% for Ca/Si = 1.38 ± 0.03 and is replaced by the Q 1 environment, which peaks at 68.1 ± 3.8%. The combination of X-ray diffraction and NMR allowed capturing the depolymerization of Si chains as well as a two-step variation in the layer-to-layer distance. This latter first increases from ∼11.3 Å (for samples having a Ca/Si ratio <∼0.6) up to 12.25 Å at Ca/Si = 0.87 ± 0.02, probably as a result of a weaker layer-to-layer connectivity, and then decreases down to 11 Å when the Ca/Si ratio reaches 1.38 ± 0.03. The decrease in layer-to-layer distance results from the incorporation of interlayer Ca that may form a Ca(OH)2-like structure, nanocrystalline and intermixed with C–S–H layers, at high Ca/Si ratios. PMID:27275135

  6. Synchrotron-based soft X-ray spectroscopic studies of the electronic structure of organic semiconducting molecules

    NASA Astrophysics Data System (ADS)

    Demasi, Alexander

    Organic molecules have been the subject of many scientific studies due to their potential for use in a new generation of optoelectronic and semiconducting devices, such as organic photovoltaics and organic light emitting diodes. These studies are motivated by the fact that organic semiconductor devices have several advantages over traditional inorganic semiconductor devices. Unlike inorganic semiconductors, where the electronic properties are a result of the deliberate introduction of dopants to the material, the properties of organic semiconductors are often intrinsic to the molecules themselves. As a result, organic semiconductor devices are frequently less susceptible to contamination by impurities than their inorganic counterparts, which results in the relatively lower cost of producing such devices. Accurate experimental determination of the bulk and surface electronic structure of organic semiconductors is a prerequisite in developing a comprehensive understanding of such materials. The organic materials studied in this thesis were N,N-Ethylene-bis(1,1,1trifluoropentane-2,4-dioneiminato)-copper(ii) (abbreviated Cu-TFAC), aluminum tris-8hydroxyquinoline (A1g3), lithium quinolate (Liq), tetracyanoquinodimethane (TCNQ), and tetrafluorotetracyanoquinodimethane (F4TCNQ). The electronic structures of these materials were measured with several synchrotron-based x-ray spectroscopies. X-ray photoemission spectroscopy was used to measure the occupied total density of states and the core-level states of the aforementioned materials. X-ray absorption spectroscopy (XAS) was used to probe the element-specific unoccupied partial density of states (PDOS); its angle-resolved variant was used to measure the orientation of the molecules in a film and, in some circumstances, to gauge the extent of an organic film's crystallinity. Most notably, x-ray emission spectroscopy (XES) measures the element- specific occupied PDOS and, when aided by XAS, resonant XES can additionally be

  7. Solar x ray astronomy rocket program

    NASA Technical Reports Server (NTRS)

    1990-01-01

    The dynamics were studied of the solar corona through the imaging of large scale coronal structures with AS&E High Resolution Soft X ray Imaging Solar Sounding Rocket Payload. The proposal for this program outlined a plan of research based on the construction of a high sensitivity X ray telescope from the optical and electronic components of the previous flight of this payload (36.038CS). Specifically, the X ray sensitive CCD camera was to be placed in the prime focus of the grazing incidence X ray mirror. The improved quantum efficiency of the CCD detector (over the film which had previously been used) allows quantitative measurements of temperature and emission measure in regions of low x ray emission such as helmet streamers beyond 1.2 solar radii or coronal holes. Furthermore, the improved sensitivity of the CCD allows short exposures of bright objects to study unexplored temporal regimes of active region loop evolution.

  8. Evidence For Quasi-Periodic X-ray Dips From An Ultraluminous X-ray Source: Implications for the Binary Motion

    NASA Technical Reports Server (NTRS)

    Pasham, Dheeraj R.; Strohmayer, Tod E.

    2013-01-01

    We report results from long-term (approx.1240 days) X-ray (0.3-8.0 keV) monitoring of the ultraluminous X-ray source NGC 5408 X-1 with the Swift/X-Ray Telescope. Here we expand on earlier work by Strohmayer (2009) who used only a part of the present data set. Our primary results are: (1) the discovery of sharp, quasi-periodic, energy-independent dips in the X-ray intensity that recur on average every 243 days, (2) the detection of an energy dependent (variability amplitude decreases with increasing energy), quasi-sinusoidal X-ray modulation with a period of 112.6 +/- 4 days, the amplitude of which weakens during the second half of the light curve, and (3) spectral evidence for an increase in photoelectric absorption during the last continuous segment of the data. We interpret the X-ray modulations within the context of binary motion in analogy to that seen in high-inclination accreting X-ray binaries. If correct, this implies that NGC 5408 X-1 is in a binary with an orbital period of 243 +/- 23 days, in contrast to the 115.5 day quasi-sinusoidal period previously reported by Strohmayer (2009). We discuss the overall X-ray modulation within the framework of accretion via Roche-lobe overflow of the donor star. In addition, if the X-ray modulation is caused by vertically structured obscuring material in the accretion disk, this would imply a high value for the inclination of the orbit. A comparison with estimates from accreting X-ray binaries suggests an inclination > or approx.70deg. We note that, in principle, a precessing accretion disk could also produce the observed X-ray modulations.

  9. Be/X-ray Binary Science for Future X-ray Timing Missions

    NASA Technical Reports Server (NTRS)

    Wilson-Hodge, Colleen A.

    2011-01-01

    For future missions, the Be/X-ray binary community needs to clearly define our science priorities for the future to advocate for their inclusion in future missions. In this talk, I will describe current designs for two potential future missions and Be X-ray binary science enabled by these designs. The Large Observatory For X-ray Timing (LOFT) is an X-ray timing mission selected in February 2011 for the assessment phase from the 2010 ESA M3 call for proposals. The Advanced X-ray Timing ARray (AXTAR) is a NASA explorer concept X-ray timing mission. This talk is intended to initiate discussions of our science priorities for the future.

  10. Radiation damage in polymer films from grazing-incidence X-ray scattering measurements

    DOE PAGES

    Vaselabadi, Saeed Ahmadi; Shakarisaz, David; Ruchhoeft, Paul; ...

    2016-02-16

    Grazing-incidence X-ray scattering (GIXS) is widely used to analyze the crystallinity and nanoscale structure in thin polymer films. However, ionizing radiation will generate free radicals that initiate cross-linking and/or chain scission, and structural damage will impact the ordering kinetics, thermodynamics, and crystallinity in many polymers. We report a simple methodology to screen for beam damage that is based on lithographic principles: films are exposed to patterns of x-ray radiation, and changes in polymer structure are revealed by immersing the film in a solvent that dissolves the shortest chains. The experiments are implemented with high throughput using the standard beam linemore » instrumentation and a typical GIXS configuration. The extent of damage (at a fixed radiation dose) depends on a range of intrinsic material properties and experimental variables, including the polymer chemistry and molecular weight, exposure environment, film thickness, and angle of incidence. The solubility switch for common polymers is detected within 10-60 sec at ambient temperature, and we verified that this first indication of damage corresponds with the onset of network formation in glassy polystyrene and a loss of crystallinity in polyalkylthiophenes. Therefore, grazing-incidence x-ray patterning offers an efficient approach to determine the appropriate data acquisition times for any GIXS experiment.« less

  11. Simulations of X-ray diffraction of shock-compressed single-crystal tantalum with synchrotron undulator sources

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Tang, M. X.; Zhang, Y. Y.; E, J. C.

    Polychromatic synchrotron undulator X-ray sources are useful for ultrafast single-crystal diffraction under shock compression. Here, simulations of X-ray diffraction of shock-compressed single-crystal tantalum with realistic undulator sources are reported, based on large-scale molecular dynamics simulations. Purely elastic deformation, elastic–plastic two-wave structure, and severe plastic deformation under different impact velocities are explored, as well as an edge release case. Transmission-mode diffraction simulations consider crystallographic orientation, loading direction, incident beam direction, X-ray spectrum bandwidth and realistic detector size. Diffraction patterns and reciprocal space nodes are obtained from atomic configurations for different loading (elastic and plastic) and detection conditions, and interpretation of themore » diffraction patterns is discussed.« less

  12. Abdomen X-Ray (Radiography)

    MedlinePlus

    ... News Physician Resources Professions Site Index A-Z X-ray (Radiography) - Abdomen Abdominal x-ray uses a ... of an abdominal x-ray? What is abdominal x-ray? An x-ray (radiograph) is a noninvasive ...

  13. X-Ray Absorption near Edge Structure Spectroscopy of Nanodiamonds from the Allende Meteorite

    NASA Technical Reports Server (NTRS)

    Flynn, G. J.; Keller, L. P.; Hill, H.; Jacobsen, C.; Wirick, S.

    2000-01-01

    Carbon X-ray Absorption Near Edge Structure Spectroscopy shows Allende DM nanodiamonds have two pre-edge peaks, consistent with other small diamonds, but fail to show a diamond exciton which is seen in 3.6 nm diamond thin films.

  14. X-ray crystal structure of divalent metal-activated ß-xyloisdase, RS223BX

    USDA-ARS?s Scientific Manuscript database

    We report the first X-ray structure of a glycoside hydrolase family 43 ß-xylosidase, RS223BX, which is strongly activated by the addition of divalent metal cations. The 2.69 Å structure reveals that the Ca2+ cation is located at the back of the active site pocket. The Ca2+ coordinates to H274 to sta...

  15. Clusters in intense x-ray pulses

    NASA Astrophysics Data System (ADS)

    Bostedt, Christoph

    2012-06-01

    Free-electron lasers can deliver extremely intense, coherent x-ray flashes with femtosecond pulse length, opening the door for imaging single nanoscale objects in a single shot. All matter irradiated by these intense x-ray pulses, however, will be transformed into a highly-excited non-equilibrium plasma within femtoseconds. During the x-ray pulse complex electron dynamics and the onset of atomic disorder will be induced, leading to a time-varying sample. We have performed first experiments about x-ray laser pulse -- cluster interaction with a combined spectroscopy and imaging approach at both, the FLASH free electron laser in Hamburg (Germany) and the LCLS x-ray free-electron laser in Stanford (California). Atomic clusters are ideal for investigating the light - matter interaction because their size can be tuned from the molecular to the bulk regime, thus allowing to distinguish between intra and inter atomic processes. Imaging experiments with xenon clusters show power-density dependent changes in the scattering patterns. Modeling the scattering data indicates that the optical constants of the clusters change during the femtosecond pulse due to the transient creation of high charge states. The results show that ultra fast scattering is a promising approach to study transient states of matter on a femtosecond time scale. Coincident recording of time-of-flight spectra and scattering patterns allows the deconvolution of focal volume and particle size distribution effects. Single-shot single-particle experiments with keV x-rays reveal that for the highest power densities an highly excited and hot cluster plasma is formed for which recombination is suppressed. Time resolved infrared pump -- x-ray probe experiments have started. Here, the clusters are pumped into a nanoplasma state and their time evolution is probed with femtosecond x-ray scattering. The data show strong variations in the scattering patterns stemming from electronic reconfigurations in the cluster

  16. Spectroscopic imaging, diffraction, and holography with x-ray photoemission

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Not Available

    1992-02-01

    X-ray probes are capable of determining the spatial structure of an atom in a specific chemical state, over length scales from about a micron all the way down to atomic resolution. Examples of these probes include photoemission microscopy, energy-dependent photoemission diffraction, photoelectron holography, and X-ray absorption microspectroscopy. Although the method of image formation, chemical-state sensitivity, and length scales can be very different, these X-ray techniques share a common goal of combining a capability for structure determination with chemical-state specificity. This workshop will address recent advances in holographic, diffraction, and direct imaging techniques using X-ray photoemission on both theoretical and experimentalmore » fronts. A particular emphasis will be on novel structure determinations with atomic resolution using photoelectrons.« less

  17. Cell-free protein synthesis for structure determination by X-ray crystallography.

    PubMed

    Watanabe, Miki; Miyazono, Ken-ichi; Tanokura, Masaru; Sawasaki, Tatsuya; Endo, Yaeta; Kobayashi, Ichizo

    2010-01-01

    Structure determination has been difficult for those proteins that are toxic to the cells and cannot be prepared in a large amount in vivo. These proteins, even when biologically very interesting, tend to be left uncharacterized in the structural genomics projects. Their cell-free synthesis can bypass the toxicity problem. Among the various cell-free systems, the wheat-germ-based system is of special interest due to the following points: (1) Because the gene is placed under a plant translational signal, its toxic expression in a bacterial host is reduced. (2) It has only little codon preference and, especially, little discrimination between methionine and selenomethionine (SeMet), which allows easy preparation of selenomethionylated proteins for crystal structure determination by SAD and MAD methods. (3) Translation is uncoupled from transcription, so that the toxicity of the translation product on DNA and its transcription, if any, can be bypassed. We have shown that the wheat-germ-based cell-free protein synthesis is useful for X-ray crystallography of one of the 4-bp cutter restriction enzymes, which are expected to be very toxic to all forms of cells retaining the genome. Our report on its structure represents the first report of structure determination by X-ray crystallography using protein overexpressed with the wheat-germ-based cell-free protein expression system. This will be a method of choice for cytotoxic proteins when its cost is not a problem. Its use will become popular when the crystal structure determination technology has evolved to require only a tiny amount of protein.

  18. A search for X-ray polarization in cosmic X-ray sources. [binary X-ray sources and supernovae remnants

    NASA Technical Reports Server (NTRS)

    Hughes, J. P.; Long, K. S.; Novick, R.

    1983-01-01

    Fifteen strong X-ray sources were observed by the X-ray polarimeters on board the OSO-8 satellite from 1975 to 1978. The final results of this search for X-ray polarization in cosmic sources are presented in the form of upper limits for the ten sources which are discussed elsewhere. These limits in all cases are consistent with a thermal origin for the X-ray emission.

  19. X-Ray Emission from the Soft X-Ray Transient Aquila X-1

    NASA Technical Reports Server (NTRS)

    Tavani, Marco

    1998-01-01

    Aquila X-1 is the most prolific of soft X-ray transients. It is believed to contain a rapidly spinning neutron star sporadically accreting near the Eddington limit from a low-mass companion star. The interest in studying the repeated X-ray outbursts from Aquila X-1 is twofold: (1) studying the relation between optical, soft and hard X-ray emission during the outburst onset, development and decay; (2) relating the spectral component to thermal and non-thermal processes occurring near the magnetosphere and in the boundary layer of a time-variable accretion disk. Our investigation is based on the BATSE monitoring of Aquila X-1 performed by our group. We observed Aquila X-1 in 1997 and re-analyzed archival information obtained in April 1994 during a period of extraordinary outbursting activity of the source in the hard X-ray range. Our results allow, for the first time for this important source, to obtain simultaneous spectral information from 2 keV to 200 keV. A black body (T = 0.8 keV) plus a broken power-law spectrum describe accurately the 1994 spectrum. Substantial hard X-ray emission is evident in the data, confirming that the accretion phase during sub-Eddington limit episodes is capable of producing energetic hard emission near 5 x 10(exp 35) ergs(exp -1). A preliminary paper summarizes our results, and a more comprehensive account is being written. We performed a theoretical analysis of possible emission mechanisms, and confirmed that a non-thermal emission mechanism triggered in a highly sheared magnetosphere at the accretion disk inner boundary can explain the hard X-ray emission. An anticorrelation between soft and hard X-ray emission is indeed prominently observed as predicted by this model.

  20. Development of scanning electron and x-ray microscope

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Matsumura, Tomokazu, E-mail: tomokzau.matsumura@etd.hpk.co.jp; Hirano, Tomohiko, E-mail: tomohiko.hirano@etd.hpk.co.jp; Suyama, Motohiro, E-mail: suyama@etd.hpk.co.jp

    We have developed a new type of microscope possessing a unique feature of observing both scanning electron and X-ray images under one unit. Unlike former X-ray microscopes using SEM [1, 2], this scanning electron and X-ray (SELX) microscope has a sample in vacuum, thus it enables one to observe a surface structure of a sample by SEM mode, to search the region of interest, and to observe an X-ray image which transmits the region. For the X-ray observation, we have been focusing on the soft X-ray region from 280 eV to 3 keV to observe some bio samples and softmore » materials. The resolutions of SEM and X-ray modes are 50 nm and 100 nm, respectively, at the electron energy of 7 keV.« less

  1. Resonant Soft X-ray Scattering as a Powerful Probe of Buried Polymer Interfaces

    NASA Astrophysics Data System (ADS)

    Chen, Wei; Jiang, Zhang; Tirrell, Matthew

    Elucidation of polymer interfacial structures provides insights into interfacial molecular mechanisms for coating protection, adhesion, lubrication, friction, wettability, biocompatibility, and even charge transport properties. Resonant Soft X-ray Scattering (RSoXS) offers a unique element, site and valence specific probe to study spatial modulations of molecular orbital degrees of freedom on the nanoscopic length scale. This unique sensitivity is achieved by merging small angle x-ray scattering and x-ray absorption spectroscopy into a single experiment, where the scattering provides information about spatial modulations and the spectroscopy provides sensitivity to the molecular anisotropy. Here we applied RSoXS to polystyrene (PS) films at solid-solid interfaces and poly(2-methacryloyloxyethyl phosphorylcholine) (PMPC) brushes at solid-liquid interfaces. It is found that the interfacial width of PS thin film is about one order of magnitude large than those observed by traditional scattering techniques. In addition, although the ion-induced changes of PMPC thickness are not apparent in aqueous solutions, their chain conformations like polyzwitterion distribution and correlation varied, dependent on salt types, ionic strengths and ion valences. Consequently, it is evident that RSoXS is a powerful probe of buried polymer interlaces with both spatial and chemical sensitivities. This work was supported by the U.S. Department of Energy, Office of Science, Program in Basic Energy Sciences, Division of Materials Science and Engineering.

  2. Probing solid catalysts under operating conditions: electrons or X-rays?

    PubMed

    Thomas, John Meurig; Hernandez-Garrido, Juan-Carlos

    2009-01-01

    Seeing is believing: In light of recent advances, the pros and cons of using electrons and X-rays for in situ studies of catalysts are analyzed: by using X-rays the structure of bound reactants at steady state are obtained from extended X-ray adsorption fine structure spectroscopy (EXAFS) data (see graph), thereby affording mechanistic insights.

  3. Healing X-ray scattering images

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Liu, Jiliang; Lhermitte, Julien; Tian, Ye

    X-ray scattering images contain numerous gaps and defects arising from detector limitations and experimental configuration. Here, we present a method to heal X-ray scattering images, filling gaps in the data and removing defects in a physically meaningful manner. Unlike generic inpainting methods, this method is closely tuned to the expected structure of reciprocal-space data. In particular, we exploit statistical tests and symmetry analysis to identify the structure of an image; we then copy, average and interpolate measured data into gaps in a way that respects the identified structure and symmetry. Importantly, the underlying analysis methods provide useful characterization of structuresmore » present in the image, including the identification of diffuseversussharp features, anisotropy and symmetry. The presented method leverages known characteristics of reciprocal space, enabling physically reasonable reconstruction even with large image gaps. The method will correspondingly fail for images that violate these underlying assumptions. The method assumes point symmetry and is thus applicable to small-angle X-ray scattering (SAXS) data, but only to a subset of wide-angle data. Our method succeeds in filling gaps and healing defects in experimental images, including extending data beyond the original detector borders.« less

  4. Healing X-ray scattering images

    DOE PAGES

    Liu, Jiliang; Lhermitte, Julien; Tian, Ye; ...

    2017-05-24

    X-ray scattering images contain numerous gaps and defects arising from detector limitations and experimental configuration. Here, we present a method to heal X-ray scattering images, filling gaps in the data and removing defects in a physically meaningful manner. Unlike generic inpainting methods, this method is closely tuned to the expected structure of reciprocal-space data. In particular, we exploit statistical tests and symmetry analysis to identify the structure of an image; we then copy, average and interpolate measured data into gaps in a way that respects the identified structure and symmetry. Importantly, the underlying analysis methods provide useful characterization of structuresmore » present in the image, including the identification of diffuseversussharp features, anisotropy and symmetry. The presented method leverages known characteristics of reciprocal space, enabling physically reasonable reconstruction even with large image gaps. The method will correspondingly fail for images that violate these underlying assumptions. The method assumes point symmetry and is thus applicable to small-angle X-ray scattering (SAXS) data, but only to a subset of wide-angle data. Our method succeeds in filling gaps and healing defects in experimental images, including extending data beyond the original detector borders.« less

  5. "X-Ray Transients in Star-Forming Regions" and "Hard X-Ray Emission from X-Ray Bursters"

    NASA Technical Reports Server (NTRS)

    Halpern, Jules P.; Kaaret, Philip

    1999-01-01

    This grant funded work on the analysis of data obtained with the Burst and Transient Experiment (BATSE) on the Compton Gamma-Ray Observatory. The goal of the work was to search for hard x-ray transients in star forming regions using the all-sky hard x-ray monitoring capability of BATSE. Our initial work lead to the discovery of a hard x-ray transient, GRO J1849-03. Follow-up observations of this source made with the Wide Field Camera on BeppoSAX showed that the source should be identified with the previously known x-ray pulsar GS 1843-02 which itself is identified with the x-ray source X1845-024 originally discovered with the SAS-3 satellite. Our identification of the source and measurement of the outburst recurrence time, lead to the identification of the source as a Be/X-ray binary with a spin period of 94.8 s and an orbital period of 241 days. The funding was used primarily for partial salary and travel support for John Tomsick, then a graduate student at Columbia University. John Tomsick, now Dr. Tomsick, received his Ph.D. from Columbia University in July 1999, based partially on results obtained under this investigation. He is now a postdoctoral research scientist at the University of California, San Diego.

  6. Chemical Modification of Graphene Oxide by Nitrogenation: An X-ray Absorption and Emission Spectroscopy Study

    NASA Astrophysics Data System (ADS)

    Chuang, Cheng-Hao; Ray, Sekhar C.; Mazumder, Debarati; Sharma, Surbhi; Ganguly, Abhijit; Papakonstantinou, Pagona; Chiou, Jau-Wern; Tsai, Huang-Ming; Shiu, Hung-Wei; Chen, Chia-Hao; Lin, Hong-Ji; Guo, Jinghua; Pong, Way-Faung

    2017-02-01

    Nitrogen-doped graphene oxides (GO:Nx) were synthesized by a partial reduction of graphene oxide (GO) using urea [CO(NH2)2]. Their electronic/bonding structures were investigated using X-ray absorption near-edge structure (XANES), valence-band photoemission spectroscopy (VB-PES), X-ray emission spectroscopy (XES) and resonant inelastic X-ray scattering (RIXS). During GO:Nx synthesis, different nitrogen-bonding species, such as pyrrolic/graphitic-nitrogen, were formed by replacing of oxygen-containing functional groups. At lower N-content (2.7 at%), pyrrolic-N, owing to surface and subsurface diffusion of C, N and NH is deduced from various X-ray spectroscopies. In contrast, at higher N-content (5.0 at%) graphitic nitrogen was formed in which each N-atom trigonally bonds to three distinct sp2-hybridized carbons with substitution of the N-atoms for C atoms in the graphite layer. Upon nitrogen substitution, the total density of state close to Fermi level is increased to raise the valence-band maximum, as revealed by VB-PES spectra, indicating an electron donation from nitrogen, molecular bonding C/N/O coordination or/and lattice structure reorganization in GO:Nx. The well-ordered chemical environments induced by nitrogen dopant are revealed by XANES and RIXS measurements.

  7. Structure of the X-ray source in the Virgo cluster of galaxies

    NASA Technical Reports Server (NTRS)

    Gorenstein, P.; Fabricant, D.; Topka, K.; Tucker, W.; Harnden, F. R., Jr.

    1977-01-01

    High-angular-resolution observations in the 0.15-1.5-keV band with an imaging X-ray telescope shows the extended X-ray source in the Virgo cluster of galaxies to be a diffuse halo of about 15 arcmin core radius surrounding M87. The angular structure of the surface brightness is marginally consistent with either of two simple models: (1) an isothermal (or adiabatic or hydrostatic) sphere plus a point source at M87 accounting for 12% of the total 0.5-1.5-keV intensity or (2) a power-law function without a discrete point source. No evidence for a point source is seen in the 0.15-0.28-keV band, which is consistent with self-absorption by about 10 to the 21st power per sq cm of matter having a cosmic abundance. The power-law models are motivated by the idea that radiation losses regulate the accretion of matter onto M87 and can account for the observed difference in the size of the X-ray source as seen in the present measurements and at higher energies.

  8. Rosetta Structure Prediction as a Tool for Solving Difficult Molecular Replacement Problems.

    PubMed

    DiMaio, Frank

    2017-01-01

    Molecular replacement (MR), a method for solving the crystallographic phase problem using phases derived from a model of the target structure, has proven extremely valuable, accounting for the vast majority of structures solved by X-ray crystallography. However, when the resolution of data is low, or the starting model is very dissimilar to the target protein, solving structures via molecular replacement may be very challenging. In recent years, protein structure prediction methodology has emerged as a powerful tool in model building and model refinement for difficult molecular replacement problems. This chapter describes some of the tools available in Rosetta for model building and model refinement specifically geared toward difficult molecular replacement cases.

  9. X-ray insights into star and planet formation

    PubMed Central

    Feigelson, Eric D.

    2010-01-01

    Although stars and planets form in cold environments, X-rays are produced in abundance by young stars. This review examines the implications of stellar X-rays for star and planet formation studies, highlighting the contributions of NASA’s (National Aeronautics and Space Administration) Chandra X-ray Observatory. Seven topics are covered: X-rays from protostellar outflow shocks, X-rays from the youngest protostars, the stellar initial mass function, the structure of young stellar clusters, the fate of massive stellar winds, X-ray irradiation of protoplanetary disks, and X-ray flare effects on ancient meteorites. Chandra observations of star-forming regions often show dramatic star clusters, powerful magnetic reconnection flares, and parsec-scale diffuse plasma. X-ray selected samples of premain sequence stars significantly advance studies of star cluster formation, the stellar initial mass function, triggered star-formation processes, and protoplanetary disk evolution. Although X-rays themselves may not play a critical role in the physics of star formation, they likely have important effects on protoplanetary disks by heating and ionizing disk gases. PMID:20404197

  10. X-ray insights into star and planet formation.

    PubMed

    Feigelson, Eric D

    2010-04-20

    Although stars and planets form in cold environments, X-rays are produced in abundance by young stars. This review examines the implications of stellar X-rays for star and planet formation studies, highlighting the contributions of NASA's (National Aeronautics and Space Administration) Chandra X-ray Observatory. Seven topics are covered: X-rays from protostellar outflow shocks, X-rays from the youngest protostars, the stellar initial mass function, the structure of young stellar clusters, the fate of massive stellar winds, X-ray irradiation of protoplanetary disks, and X-ray flare effects on ancient meteorites. Chandra observations of star-forming regions often show dramatic star clusters, powerful magnetic reconnection flares, and parsec-scale diffuse plasma. X-ray selected samples of premain sequence stars significantly advance studies of star cluster formation, the stellar initial mass function, triggered star-formation processes, and protoplanetary disk evolution. Although X-rays themselves may not play a critical role in the physics of star formation, they likely have important effects on protoplanetary disks by heating and ionizing disk gases.

  11. Chemical order in the glassy As/sub x/S/sub 1-//sub x/ system: An x-ray-absorption spectroscopy study

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yang, C.Y.; Paesler, M.A.; Sayers, D.E.

    1989-05-15

    We have examined chemical ordering in the glassy As/sub x/S/sub 1-//sub x/ system by determining the effect of composition on the local structure of these chalcogenide glasses using x-ray-absorption spectroscopy. Structural changes associated with composition indicate that with increasing S content, the S-rich glasses on the As site have a similar local structure to crystalline As/sub 2/S/sub 3/ (orpiment), but the As-S-As linkages are replaced by As-S-S linkages at higher S concentration. In As-rich glasses a breakdown of the local AsS/sub 3/ configuration is evident and the formation of As-As bonds is observed. Further comparison between As-rich alloys and crystallinemore » As/sub 4/S/sub 4/ (realgar) suggests that a significant fraction of disordered As/sub 4/S/sub 4/ molecular fragments is contained in the As-rich region.« less

  12. Structure of cyano-anion ionic liquids: X-ray scattering and simulations

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Dhungana, Kamal B.; Faria, Luiz F. O.; Wu, Boning

    2016-07-14

    Ionic liquids with cyano anions have long been used because of their unique combination of low-melting temperatures, reduced viscosities, and increased conductivities. Recently we have shown that cyano anions in ionic liquids are particularly interesting for their potential use as electron donors to excited state photo-acceptors [B. Wu et al., J. Phys. Chem. B 119, 14790–14799 (2015)]. Here we report on bulk structural and quantum mechanical results for a series of ionic liquids based on the 1-ethyl-3-methylimidazolium cation, paired with the following five cyano anions: SeCN-, SCN-, N(CN)-2N(CN)2-, C(CN)-3C(CN)3-, and B(CN)-4B(CN)4-. By combining molecular dynamics simulations, high-energy X-ray scattering measurements,more » and periodic boundary condition DFT calculations, we are able to obtain a comprehensive description of the liquid landscape as well as the nature of the HOMO-LUMO states for these ionic liquids in the condensed phase. Features in the structure functions for these ionic liquids are somewhat different than the commonly observed adjacency, charge-charge, and polarity peaks, especially for the bulkiest B(CN)-4B(CN)4- anion. While the other four cyano-anion ionic liquids present an anionic HOMO, the one for Im+2,1Im2,1+/B(CN)-4B(CN)4- is cationic.« less

  13. Large Area X-Ray Spectroscopy Mission

    NASA Technical Reports Server (NTRS)

    Tananbaum, H.

    1997-01-01

    The Large Area X-ray Spectroscopy (LAXS) mission concept study continues to evolve strongly following the merging of the LAXS mission with the Next Generation X-ray Observatory (NGXO, PI: Nick White) into the re-named High Throughput X-ray Spectroscopy (HTXS) Mission. HTXS retains key elements of the LAXS proposal, including the use of multiple satellites for risk-reduction and cost savings. A key achievement of the program has been the recommendation by the Structure and Evolution of the Universe (SEUS) (April 1997) for a new start for the HTXS mission in the 2000-2004 timeframe.

  14. Lumbosacral spine x-ray

    MedlinePlus

    X-ray - lumbosacral spine; X-ray - lower spine ... The test is done in a hospital x-ray department or your health care provider's office by an x-ray technician. You will be asked to lie on the x-ray ...

  15. Femtosecond response of polyatomic molecules to ultra-intense hard X-rays.

    PubMed

    Rudenko, A; Inhester, L; Hanasaki, K; Li, X; Robatjazi, S J; Erk, B; Boll, R; Toyota, K; Hao, Y; Vendrell, O; Bomme, C; Savelyev, E; Rudek, B; Foucar, L; Southworth, S H; Lehmann, C S; Kraessig, B; Marchenko, T; Simon, M; Ueda, K; Ferguson, K R; Bucher, M; Gorkhover, T; Carron, S; Alonso-Mori, R; Koglin, J E; Correa, J; Williams, G J; Boutet, S; Young, L; Bostedt, C; Son, S-K; Santra, R; Rolles, D

    2017-06-01

    X-ray free-electron lasers enable the investigation of the structure and dynamics of diverse systems, including atoms, molecules, nanocrystals and single bioparticles, under extreme conditions. Many imaging applications that target biological systems and complex materials use hard X-ray pulses with extremely high peak intensities (exceeding 10 20 watts per square centimetre). However, fundamental investigations have focused mainly on the individual response of atoms and small molecules using soft X-rays with much lower intensities. Studies with intense X-ray pulses have shown that irradiated atoms reach a very high degree of ionization, owing to multiphoton absorption, which in a heteronuclear molecular system occurs predominantly locally on a heavy atom (provided that the absorption cross-section of the heavy atom is considerably larger than those of its neighbours) and is followed by efficient redistribution of the induced charge. In serial femtosecond crystallography of biological objects-an application of X-ray free-electron lasers that greatly enhances our ability to determine protein structure-the ionization of heavy atoms increases the local radiation damage that is seen in the diffraction patterns of these objects and has been suggested as a way of phasing the diffraction data. On the basis of experiments using either soft or less-intense hard X-rays, it is thought that the induced charge and associated radiation damage of atoms in polyatomic molecules can be inferred from the charge that is induced in an isolated atom under otherwise comparable irradiation conditions. Here we show that the femtosecond response of small polyatomic molecules that contain one heavy atom to ultra-intense (with intensities approaching 10 20 watts per square centimetre), hard (with photon energies of 8.3 kiloelectronvolts) X-ray pulses is qualitatively different: our experimental and modelling results establish that, under these conditions, the ionization of a molecule is

  16. Nonlocal heat transport and improved target design for x-ray heating studies at x-ray free electron lasers

    NASA Astrophysics Data System (ADS)

    Hoidn, Oliver; Seidler, Gerald T.

    2018-01-01

    The extremely high-power densities and short durations of single pulses of x-ray free electron lasers (XFELs) have opened new opportunities in atomic physics, where complex excitation-relaxation chains allow for high ionization states in atomic and molecular systems, and in dense plasma physics, where XFEL heating of solid-density targets can create unique dense states of matter having temperatures on the order of the Fermi energy. We focus here on the latter phenomena, with special emphasis on the problem of optimum target design to achieve high x-ray heating into the warm dense matter (WDM) state. We report fully three-dimensional simulations of the incident x-ray pulse and the resulting multielectron relaxation cascade to model the spatial energy density deposition in multicomponent targets, with particular focus on the effects of nonlocal heat transport due to the motion of high energy photoelectrons and Auger electrons. We find that nanoscale high-Z /low-Z multicomponent targets can give much improved energy density deposition in lower-Z materials, with enhancements reaching a factor of 100. This has three important benefits. First, it greatly enlarges the thermodynamic parameter space in XFEL x-ray heating studies of lower-Z materials. Second, it allows the use of higher probe photon energies, enabling higher-information content x-ray diffraction (XRD) measurements such as in two-color XFEL operations. Third, while this is merely one step toward optimization of x-ray heating target design, the demonstration of the importance of nonlocal heat transport establishes important common ground between XFEL-based x-ray heating studies and more traditional laser plasma methods.

  17. Native structure of photosystem II at 1.95 Å resolution viewed by femtosecond X-ray pulses.

    PubMed

    Suga, Michihiro; Akita, Fusamichi; Hirata, Kunio; Ueno, Go; Murakami, Hironori; Nakajima, Yoshiki; Shimizu, Tetsuya; Yamashita, Keitaro; Yamamoto, Masaki; Ago, Hideo; Shen, Jian-Ren

    2015-01-01

    Photosynthesis converts light energy into biologically useful chemical energy vital to life on Earth. The initial reaction of photosynthesis takes place in photosystem II (PSII), a 700-kilodalton homodimeric membrane protein complex that catalyses photo-oxidation of water into dioxygen through an S-state cycle of the oxygen evolving complex (OEC). The structure of PSII has been solved by X-ray diffraction (XRD) at 1.9 ångström resolution, which revealed that the OEC is a Mn4CaO5-cluster coordinated by a well defined protein environment. However, extended X-ray absorption fine structure (EXAFS) studies showed that the manganese cations in the OEC are easily reduced by X-ray irradiation, and slight differences were found in the Mn-Mn distances determined by XRD, EXAFS and theoretical studies. Here we report a 'radiation-damage-free' structure of PSII from Thermosynechococcus vulcanus in the S1 state at a resolution of 1.95 ångströms using femtosecond X-ray pulses of the SPring-8 ångström compact free-electron laser (SACLA) and hundreds of large, highly isomorphous PSII crystals. Compared with the structure from XRD, the OEC in the X-ray free electron laser structure has Mn-Mn distances that are shorter by 0.1-0.2 ångströms. The valences of each manganese atom were tentatively assigned as Mn1D(III), Mn2C(IV), Mn3B(IV) and Mn4A(III), based on the average Mn-ligand distances and analysis of the Jahn-Teller axis on Mn(III). One of the oxo-bridged oxygens, O5, has significantly longer distances to Mn than do the other oxo-oxygen atoms, suggesting that O5 is a hydroxide ion instead of a normal oxygen dianion and therefore may serve as one of the substrate oxygen atoms. These findings provide a structural basis for the mechanism of oxygen evolution, and we expect that this structure will provide a blueprint for the design of artificial catalysts for water oxidation.

  18. X-ray ptychography

    NASA Astrophysics Data System (ADS)

    Pfeiffer, Franz

    2018-01-01

    X-ray ptychographic microscopy combines the advantages of raster scanning X-ray microscopy with the more recently developed techniques of coherent diffraction imaging. It is limited neither by the fabricational challenges associated with X-ray optics nor by the requirements of isolated specimen preparation, and offers in principle wavelength-limited resolution, as well as stable access and solution to the phase problem. In this Review, we discuss the basic principles of X-ray ptychography and summarize the main milestones in the evolution of X-ray ptychographic microscopy and tomography over the past ten years, since its first demonstration with X-rays. We also highlight the potential for applications in the life and materials sciences, and discuss the latest advanced concepts and probable future developments.

  19. Optics Developments for X-Ray Astronomy

    NASA Technical Reports Server (NTRS)

    Ramsey, Brian

    2014-01-01

    X-ray optics has revolutionized x-ray astronomy. The degree of background suppression that these afford, have led to a tremendous increase in sensitivity. The current Chandra observatory has the same collecting area (approx. 10(exp 3)sq cm) as the non-imaging UHURU observatory, the first x-ray observatory which launched in 1970, but has 5 orders of magnitude more sensitivity due to its focusing optics. In addition, its 0.5 arcsec angular resolution has revealed a wealth of structure in many cosmic x-ray sources. The Chandra observatory achieved its resolution by using relatively thick pieces of Zerodur glass, which were meticulously figured and polished to form the four-shell nested array. The resulting optical assembly weighed around 1600 kg, and cost approximately $0.5B. The challenge for future x-ray astronomy missions is to greatly increase the collecting area (by one or more orders of magnitude) while maintaining high angular resolution, and all within realistic mass and budget constraints. A review of the current status of US optics for x-ray astronomy will be provided along with the challenges for future developments.

  20. Electron and fluorescence spectra of a water molecule irradiated by an x-ray free-electron laser pulse

    NASA Astrophysics Data System (ADS)

    Schäfer, Julia M.; Inhester, Ludger; Son, Sang-Kil; Fink, Reinhold F.; Santra, Robin

    2018-05-01

    With the highly intense x-ray light generated by x-ray free-electron lasers (XFELs), molecular samples can be ionized many times in a single pulse. Here we report on a computational study of molecular spectroscopy at the high x-ray intensity provided by XFELs. Calculated photoelectron, Auger electron, and x-ray fluorescence spectra are presented for a single water molecule that reaches many electronic hole configurations through repeated ionization steps. The rich details shown in the spectra depend on the x-ray pulse parameters in a nonintuitive way. We discuss how the observed trends can be explained by the competition of microscopic electronic transition processes. A detailed comparison between spectra calculated within the independent-atom model and within the molecular-orbital framework highlights the chemical sensitivity of the spectral lines of multiple-hole configurations. Our results demonstrate how x-ray multiphoton ionization-related effects such as charge-rearrangement-enhanced x-ray ionization of molecules and frustrated absorption manifest themselves in the electron and fluorescence spectra.

  1. Evaluating structure in thin block copolymer films with soft x-rays (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Sunday, Daniel; Liman, Christopher; Hannon, Adam F.; Ren, Jiaxing; Chen, Xuanxuan; Suh, Hyo Seon; de Pablo, Juan J.; Nealey, Paul F.; Kline, R. Joseph

    2017-03-01

    The semiconductor industry is evaluating a variety of approaches for the cost efficient production of future processing and memory generations. Amongst the technologies being explored are multiple patterning steps, extreme ultraviolet (EUV) lithography, multiple-beam electron beam lithography and the directed self-assembly (DSA) of block copolymers (BCPs). BCP DSA utilizes a chemical or topographical template to induce long range order in a thin film of BCP which enhances the resolution of the original pattern. The characterization of buried structure within a DSA BCP film is challenging due to the lack of contrast between the organic materials. Critical-dimension small angle x-ray scattering (CDSAXS) measurements were performed on DSA BCP films, using soft X-rays to tune the contrast, in order to understand the relationship between template structure and film morphology.1 The results of these measurements show that as the width of the guiding stripe widens the arrangement of the BCP on the guiding stripe inverts, shifting from the A block being centered on the guiding stripe to the B block being centered on the guiding stripe. The initial results of integration of mean field simulations into the analysis of scattering data will also be discussed. In addition to examining the BCP structure with CDSAXS, soft X-ray reflectivity2 measurements were performed on BCP to better understand the relationship between interface width for systems with alternative architectures (triblocks) and additives (polymers/ionic liquids). The addition of a selectively associating additive increases the interaction parameter between the two blocks, resulting in the reduction of the interface width and access to smaller pitches. The use of soft X-ray reflectivity allows the evaluation of the distribution of the additive. (1) Sunday, D. F.; Hammond, M. R.; Wang, C.; Wu, W.; Delongchamp, D. M.; Tjio, M.; Cheng, J. Y.; Kline, R. J.; Pitera, J. W. Determination of the Internal Morphology of

  2. Note: application of a pixel-array area detector to simultaneous single crystal X-ray diffraction and X-ray absorption spectroscopy measurements.

    PubMed

    Sun, Cheng-Jun; Zhang, Bangmin; Brewe, Dale L; Chen, Jing-Sheng; Chow, G M; Venkatesan, T; Heald, Steve M

    2014-04-01

    X-ray diffraction (XRD) and X-ray absorption spectroscopy (XAS) are two main x-ray techniques in synchrotron radiation facilities. In this Note, we present an experimental setup capable of performing simultaneous XRD and XAS measurements by the application of a pixel-array area detector. For XRD, the momentum transfer in specular diffraction was measured by scanning the X-ray energy with fixed incoming and outgoing x-ray angles. By selecting a small fixed region of the detector to collect the XRD signal, the rest of the area was available for collecting the x-ray fluorescence for XAS measurements. The simultaneous measurement of XRD and X-ray absorption near edge structure for Pr0.67Sr0.33MnO3 film was demonstrated as a proof of principle for future time-resolved pump-probe measurements. A static sample makes it easy to maintain an accurate overlap of the X-ray spot and laser pump beam.

  3. A long-term space astrophysics research program: An x-ray perspective of the components and structure of galaxies

    NASA Technical Reports Server (NTRS)

    Fabbiano, G.

    1995-01-01

    X-ray studies of galaxies by the Smithsonian Astrophysical Observatory (SAO) and MIT are described. Activities at SAO include ROSAT PSPC x-ray data reduction and analysis pipeline; x-ray sources in nearby Sc galaxies; optical, x-ray, and radio study of ongoing galactic merger; a radio, far infrared, optical, and x-ray study of the Sc galaxy NGC247; and a multiparametric analysis of the Einstein sample of early-type galaxies. Activities at MIT included continued analysis of observations with ROSAT and ASCA, and continued development of new approaches to spectral analysis with ASCA and AXAF. Also, a new method for characterizing structure in galactic clusters was developed and applied to ROSAT images of a large sample of clusters. An appendix contains preprints generated by the research.

  4. X-ray structural studies of the fungal laccase from Cerrena maxima.

    PubMed

    Lyashenko, Andrey V; Bento, Isabel; Zaitsev, Viatcheslav N; Zhukhlistova, Nadezhda E; Zhukova, Yuliya N; Gabdoulkhakov, Azat G; Morgunova, Ekaterina Y; Voelter, Wolfgang; Kachalova, Galina S; Stepanova, Elena V; Koroleva, Ol'ga V; Lamzin, Victor S; Tishkov, Vladimir I; Betzel, Christian; Lindley, Peter F; Mikhailov, Al'bert M

    2006-11-01

    Laccases are members of the blue multi-copper oxidase family. These enzymes oxidize substrate molecules by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear centre. Dioxygen binds to the trinuclear centre and following the transfer of four electrons is reduced to two molecules of water. The X-ray structure of a laccase from Cerrena maxima has been elucidated at 1.9 A resolution using synchrotron data and the molecular replacement technique. The final refinement coefficients are Rcryst = 16.8% and Rfree = 23.0%, with root mean square deviations on bond lengths and bond angles of 0.015 A and 1.51 degrees , respectively. The type 1 copper centre has an isoleucine residue at the axial position and the "resting" state of the trinuclear centre comprises a single oxygen (OH) moiety asymmetrically disposed between the two type 3 copper ions and a water molecule attached to the type 2 ion. Several carbohydrate binding sites have been identified and the glycan chains appear to promote the formation of well-ordered crystals. Two tyrosine residues near the protein surface have been found in a nitrated state.

  5. ASCA Observation of an "X-Ray Shadow" in the Galactic Plane

    NASA Technical Reports Server (NTRS)

    Park, Sangwook; Ebisawa, Ken

    2001-01-01

    The diffuse X-ray background (DXB) emission near the Galactic plane (l,b approximately 25.6 degrees, 0.78 degrees) has been observed with ASCA (Advanced Satellite for Cosmology and Astrophysics). The observed region is toward a Galactic molecular cloud which was recently reported to cast a deep X-ray shadow in the 0.5 - 2.0 keV band DXB. The selection of this particular region is intended to provide a constraint on the spatial distribution of the DXB emission along the line of sight: i.e., the molecular cloud is optically thick at <2 keV and so the bulk of the observed soft X-rays must originate in the foreground of the cloud, which is at approximately 3 kpc from the Sun. In the 0.8 - 9.0 keV band, the observed spectrum is primarily from multiple components of thermal plasmas. We here report a detection of soft X-ray (0.5 - 2 keV) emission from an approximately 10(exp 7) K thermal plasma. Comparisons with the ROSAT (Roentgen Satellite) data suggest that this soft X-ray emission is absorbed by N(sub H) = 1 - 3 x 10(exp 21) cm(exp -2), which implies a path-length through the soft X-ray emitting regions of approximately less than 1 kpc from the Sun.

  6. Exploring coherent electron excitation and migration dynamics by electron diffraction with ultrashort X-ray pulses.

    PubMed

    Yuan, Kai-Jun; Bandrauk, André D

    2017-10-04

    Exploring ultrafast charge migration is of great importance in biological and chemical reactions. We present a scheme to monitor attosecond charge migration in molecules by electron diffraction with spatial and temporal resolutions from ab initio numerical simulations. An ultraviolet pulse creates a coherent superposition of electronic states, after which a time-delayed attosecond X-ray pulse is used to ionize the molecule. It is found that diffraction patterns in the X-ray photoelectron spectra show an asymmetric structure, which is dependent on the time delay between the pump-probe pulses, encoding the information of molecular orbital symmetry and chemical bonding. We describe these phenomena by developing an electronic time-dependent ultrafast molecular photoionization model of a coherent superposition state. The periodical distortion of electron diffraction patterns illustrates the evolution of the electronic coherence, providing a tool for attosecond imaging of ultrafast molecular reaction processes.

  7. PINPIN a-Si:H based structures for X-ray image detection using the laser scanning technique

    NASA Astrophysics Data System (ADS)

    Fernandes, M.; Vygranenko, Y.; Vieira, M.

    2015-05-01

    Conventional film based X-ray imaging systems are being replaced by their digital equivalents. Different approaches are being followed by considering direct or indirect conversion, with the later technique dominating. The typical, indirect conversion, X-ray panel detector uses a phosphor for X-ray conversion coupled to a large area array of amorphous silicon based optical sensors and a couple of switching thin film transistors (TFT). The pixel information can then be readout by switching the correspondent line and column transistors, routing the signal to an external amplifier. In this work we follow an alternative approach, where the electrical switching performed by the TFT is replaced by optical scanning using a low power laser beam and a sensing/switching PINPIN structure, thus resulting in a simpler device. The optically active device is a PINPIN array, sharing both front and back electrical contacts, deposited over a glass substrate. During X-ray exposure, each sensing side photodiode collects photons generated by the scintillator screen (560 nm), charging its internal capacitance. Subsequently a laser beam (445 nm) scans the switching diodes (back side) retrieving the stored charge in a sequential way, reconstructing the image. In this paper we present recent work on the optoelectronic characterization of the PINPIN structure to be incorporated in the X-ray image sensor. The results from the optoelectronic characterization of the device and the dependence on scanning beam parameters are presented and discussed. Preliminary results of line scans are also presented.

  8. X-ray structures of the anticoagulants coumatetralyl and chlorophacinone. Theoretical calculations and SAR investigations on thirteen anticoagulant rodenticides

    NASA Astrophysics Data System (ADS)

    Dolmella, A.; Gatto, S.; Girardi, E.; Bandoli, G.

    1999-12-01

    Coumatetralyl and chlorophacinone, two substances related to 4-hydroxycoumarin (HC) and to 1,3-indandione (ID), respectively, show activity as anticoagulant rodenticides. In the present study we have investigated the solid-state structures of coumatetralyl and chlorophacinone by means of X-ray single-crystal and powder diffraction, along with thermal analysis. The crystal structures of the two compounds have been used as input geometries for a series of computational chemistry efforts, involving other anticoagulant derivatives as well. Thus, ab initio, semiempirical molecular orbital, molecular mechanics and molecular dynamics/simulated annealing calculations have been performed on thirteen anticoagulant rodenticides. In particular, the annealing calculations have been made to assess the conformational freedom of the compounds under scrutiny. All the generated conformers have been classified into families. The classification has first been made empirically, and then validated by means of a cluster analysis. A number of structural and physico-chemical parameters derived from the calculations has been used in turn for structure-activity relationships (SARs) investigations. In the latter, we have assessed how the selected parameters affect toxicity. The results seem to be consistent with a three-dimensional biophore model, in which higher toxicity is predicted for the more voluminous rodenticides. We suggest that these compounds better fit the active site of the target enzyme vitamin K 2,3-epoxide reductase (KO-reductase).

  9. Structural and dynamical properties of chlorinated hydrocarbons studied with resonant inelastic x-ray scattering

    NASA Astrophysics Data System (ADS)

    Bohinc, R.; Žitnik, M.; Bučar, K.; Kavčič, M.; Carniato, S.; Journel, L.; Guillemin, R.; Marchenko, T.; Kawerk, E.; Simon, M.; Cao, W.

    2016-04-01

    We present a theoretical and experimental study of resonant inelastic x-ray scattering on a large group of chlorinated hydrocarbons: CH3Cl, CH2Cl2, CHCl3, CCl4, CH3CH2Cl, ClCH2CH2Cl, CH3CHCl2, CH3CCl3, C2H2Cl2-iso, C2H2Cl2-cis, C2H2Cl2-trans, and C6H5Cl. Differences in structural and dynamical properties of the molecules generated by diverse chemical environments are observed in the measured Cl(Kα) spectral maps as well as in the Cl(K) total fluorescence yield spectra. The energy position, relative intensity, and the width of the Franck-Condon distribution of low-lying σ∗ and π∗ resonances are extracted by a fitting procedure taking into account the experimental broadening. The theoretical values obtained with the transition potential and Δ Kohn-Sham methods are in good agreement with the experimental parameters indicating subtle differences due to variations in the molecular structure.

  10. Structural and dynamical properties of chlorinated hydrocarbons studied with resonant inelastic x-ray scattering.

    PubMed

    Bohinc, R; Žitnik, M; Bučar, K; Kavčič, M; Carniato, S; Journel, L; Guillemin, R; Marchenko, T; Kawerk, E; Simon, M; Cao, W

    2016-04-07

    We present a theoretical and experimental study of resonant inelastic x-ray scattering on a large group of chlorinated hydrocarbons: CH3Cl, CH2Cl2, CHCl3, CCl4, CH3CH2Cl, ClCH2CH2Cl, CH3CHCl2, CH3CCl3, C2H2Cl2-iso, C2H2Cl2-cis, C2H2Cl2-trans, and C6H5Cl. Differences in structural and dynamical properties of the molecules generated by diverse chemical environments are observed in the measured Cl(K(α)) spectral maps as well as in the Cl(K) total fluorescence yield spectra. The energy position, relative intensity, and the width of the Franck-Condon distribution of low-lying σ* and π* resonances are extracted by a fitting procedure taking into account the experimental broadening. The theoretical values obtained with the transition potential and Δ Kohn-Sham methods are in good agreement with the experimental parameters indicating subtle differences due to variations in the molecular structure.

  11. Small scale H I structure and the soft X-ray background

    NASA Technical Reports Server (NTRS)

    Jahoda, K.; Mccammon, D.; Lockman, F. J.

    1986-01-01

    The observed anticorrelation between diffuse soft X-ray flux and H I column density has been explained as absorption of soft X-rays produced in a hot galactic halo, assuming that the neutral interstellar material is sufficiently clumped to reduce the soft X-ray absorption cross section by a factor of two to three. A 21 cm emission line study of H I column density variations at intermediate and high galactic latitudes to 10' spatial resolution has been done. The results confirm conclusions from preliminary work at coarser resolution, and in combination with other data appear to rule out the hypothesis that clumping of neutral interstellar matter on any angular scale significantly reduces X-ray absorption cross sections in the 0.13 - 0.28 keV energy range. It is concluded therefore that the observed anticorrelation is not primarily a consequence of absorption of soft X-rays produced in a hot galactic halo.

  12. Investigation of internal structure of fine granules by microtomography using synchrotron X-ray radiation.

    PubMed

    Noguchi, Shuji; Kajihara, Ryusuke; Iwao, Yasunori; Fujinami, Yukari; Suzuki, Yoshio; Terada, Yasuko; Uesugi, Kentaro; Miura, Keiko; Itai, Shigeru

    2013-03-10

    Computed tomography (CT) using synchrotron X-ray radiation was evaluated as a non-destructive structural analysis method for fine granules. Two kinds of granules have been investigated: a bromhexine hydrochloride (BHX)-layered Celphere CP-102 granule coated with pH-sensitive polymer Kollicoat Smartseal 30-D, and a wax-matrix granule constructed from acetaminophen (APAP), dibasic calcium phosphate dehydrate, and aminoalkyl methacrylate copolymer E (AMCE) manufactured by melt granulation. The diameters of both granules were 200-300 μm. CT analysis of CP-102 granule could visualize the laminar structures of BHX and Kollicoat layers, and also visualize the high talc-content regions in the Kollicoat layer that could not be detected by scanning electron microscopy. Moreover, CT analysis using X-ray energies above the absorption edge of Br specifically enhanced the contrast in the BHX layer. As for granules manufactured by melt granulation, CT analysis revealed that they had a small inner void space due to a uniform distribution of APAP and other excipients. The distribution of AMCE revealed by CT analysis was also found to involve in the differences of drug dissolution from the granules as described previously. These observations demonstrate that CT analysis using synchrotron X-ray radiation is a powerful method for the detailed internal structure analysis of fine granules. Copyright © 2013 Elsevier B.V. All rights reserved.

  13. Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source

    PubMed Central

    Reddy, Hemanth K.N.; Yoon, Chun Hong; Aquila, Andrew; Awel, Salah; Ayyer, Kartik; Barty, Anton; Berntsen, Peter; Bielecki, Johan; Bobkov, Sergey; Bucher, Maximilian; Carini, Gabriella A.; Carron, Sebastian; Chapman, Henry; Daurer, Benedikt; DeMirci, Hasan; Ekeberg, Tomas; Fromme, Petra; Hajdu, Janos; Hanke, Max Felix; Hart, Philip; Hogue, Brenda G.; Hosseinizadeh, Ahmad; Kim, Yoonhee; Kirian, Richard A.; Kurta, Ruslan P.; Larsson, Daniel S.D.; Duane Loh, N.; Maia, Filipe R.N.C.; Mancuso, Adrian P.; Mühlig, Kerstin; Munke, Anna; Nam, Daewoong; Nettelblad, Carl; Ourmazd, Abbas; Rose, Max; Schwander, Peter; Seibert, Marvin; Sellberg, Jonas A.; Song, Changyong; Spence, John C.H.; Svenda, Martin; Van der Schot, Gijs; Vartanyants, Ivan A.; Williams, Garth J.; Xavier, P. Lourdu

    2017-01-01

    Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65–70 nm, which is considerably smaller than the previously reported ~600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. The data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency. PMID:28654088

  14. Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source.

    PubMed

    Reddy, Hemanth K N; Yoon, Chun Hong; Aquila, Andrew; Awel, Salah; Ayyer, Kartik; Barty, Anton; Berntsen, Peter; Bielecki, Johan; Bobkov, Sergey; Bucher, Maximilian; Carini, Gabriella A; Carron, Sebastian; Chapman, Henry; Daurer, Benedikt; DeMirci, Hasan; Ekeberg, Tomas; Fromme, Petra; Hajdu, Janos; Hanke, Max Felix; Hart, Philip; Hogue, Brenda G; Hosseinizadeh, Ahmad; Kim, Yoonhee; Kirian, Richard A; Kurta, Ruslan P; Larsson, Daniel S D; Duane Loh, N; Maia, Filipe R N C; Mancuso, Adrian P; Mühlig, Kerstin; Munke, Anna; Nam, Daewoong; Nettelblad, Carl; Ourmazd, Abbas; Rose, Max; Schwander, Peter; Seibert, Marvin; Sellberg, Jonas A; Song, Changyong; Spence, John C H; Svenda, Martin; Van der Schot, Gijs; Vartanyants, Ivan A; Williams, Garth J; Xavier, P Lourdu

    2017-06-27

    Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65-70 nm, which is considerably smaller than the previously reported ~600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. The data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency.

  15. Mode-Locked Multichromatic X-Rays in a Seeded Free-Electron Laser for Single-Shot X-Ray Spectroscopy

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Xiang, Dao; Ding, Yuantao; Raubenheimer, Tor

    2012-05-10

    We present the promise of generating gigawatt mode-locked multichromatic x rays in a seeded free-electron laser (FEL). We show that, by using a laser to imprint periodic modulation in electron beam phase space, a single-frequency coherent seed can be amplified and further translated to a mode-locked multichromatic output in an FEL. With this configuration the FEL output consists of a train of mode-locked ultrashort pulses which span a wide frequency gap with a series of equally spaced sharp lines. These gigawatt multichromatic x rays may potentially allow one to explore the structure and dynamics of a large number of atomicmore » states simultaneously. The feasibility of generating mode-locked x rays ranging from carbon K edge ({approx}284 eV) to copper L{sub 3} edge ({approx}931 eV) is confirmed with numerical simulation using the realistic parameters of the linac coherent light source (LCLS) and LCLS-II. We anticipate that the mode-locked multichromatic x rays in FELs may open up new opportunities in x-ray spectroscopy (i.e. resonant inelastic x-ray scattering, time-resolved scattering and spectroscopy, etc.).« less

  16. Interferometric phase-contrast X-ray CT imaging of VX2 rabbit cancer at 35keV X-ray energy

    NASA Astrophysics Data System (ADS)

    Takeda, Tohoru; Wu, Jin; Tsuchiya, Yoshinori; Yoneyama, Akio; Lwin, Thet-Thet; Hyodo, Kazuyuki; Itai, Yuji

    2004-05-01

    Imaging of large objects at 17.7-keV low x-ray energy causes huge x-ray exposure to the objects even using interferometric phase-contrast x-ray CT (PCCT). Thus, we tried to obtain PCCT images at high x-ray energy of 35keV and examined the image quality using a formalin-fixed VX2 rabbit cancer specimen with 15-mm in diameter. The PCCT system consisted of an asymmetrically cut silicon (220) crystal, a monolithic x-ray interferometer, a phase-shifter, an object cell and an x-ray CCD camera. The PCCT at 35 keV clearly visualized various inner structures of VX2 rabbit cancer such as necrosis, cancer, the surrounding tumor vessels, and normal liver tissue. Besides, image-contrast was not degraded significantly. These results suggest that the PCCT at 35 KeV is sufficient to clearly depict the histopathological morphology of VX2 rabbit cancer specimen.

  17. UNDERSTANDING X-RAY STARS:. The Discovery of Binary X-ray Sources

    NASA Astrophysics Data System (ADS)

    Schreier, E. J.; Tananbaum, H.

    2000-09-01

    The discovery of binary X-ray sources with UHURU introduced many new concepts to astronomy. It provided the canonical model which explained X-ray emission from a large class of galactic X-ray sources: it confirmed the existence of collapsed objects as the source of intense X-ray emission; showed that such collapsed objects existed in binary systems, with mass accretion as the energy source for the X-ray emission; and provided compelling evidence for the existence of black holes. This model also provided the basis for explaining the power source of AGNs and QSOs. The process of discovery and interpretation also established X-ray astronomy as an essential sub-discipline of astronomy, beginning its incorporation into the mainstream of astronomy.

  18. Thoracic spine x-ray

    MedlinePlus

    Vertebral radiography; X-ray - spine; Thoracic x-ray; Spine x-ray; Thoracic spine films; Back films ... The test is done in a hospital radiology department or in the health care provider's office. You will lie on the x-ray table in different positions. If the x-ray ...

  19. Composite structure of helicopter rotor blades studied by neutron- and X-ray radiography

    NASA Astrophysics Data System (ADS)

    Balaskó, M.; Veres, I.; Molnár, Gy.; Balaskó, Zs.; Sváb, E.

    2004-07-01

    In order to inspect the possible defects in the composite structure of helicopter rotor blades combined neutron- and X-ray radiography investigations were performed at the Budapest Research Reactor. Imperfections in the honeycomb structure, resin rich or starved areas at the core-honeycomb surfaces, inhomogeneities at the adhesive filling and water percolation at the sealing interfaces of the honeycomb sections were discovered.

  20. X-ray binaries

    NASA Technical Reports Server (NTRS)

    1976-01-01

    Satellite X-ray experiments and ground-based programs aimed at observation of X-ray binaries are discussed. Experiments aboard OAO-3, OSO-8, Ariel 5, Uhuru, and Skylab are included along with rocket and ground-based observations. Major topics covered are: Her X-1, Cyg X-3, Cen X-3, Cyg X-1, the transient source A0620-00, other possible X-ray binaries, and plans and prospects for future observational programs.