Neural network approach for characterizing structural transformations by X-ray absorption fine structure

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

Timoshenko, Janis; Frenkel, Anatoly I.; Cintins, Arturs

The knowledge of coordination environment around various atomic species in many functional materials provides a key for explaining their properties and working mechanisms. Many structural motifs and their transformations are difficult to detect and quantify in the process of work (operando conditions), due to their local nature, small changes, low dimensionality of the material, and/or extreme conditions. Here we use artificial neural network approach to extract the information on the local structure and its in-situ changes directly from the X-ray absorption fine structure spectra. We illustrate this capability by extracting the radial distribution function (RDF) of atoms in ferritic andmore » austenitic phases of bulk iron across the temperature-induced transition. Integration of RDFs allows us to quantify the changes in the iron coordination and material density, and to observe the transition from body-centered to face-centered cubic arrangement of iron atoms. Furthermore, this method is attractive for a broad range of materials and experimental conditions« less

Neural network approach for characterizing structural transformations by X-ray absorption fine structure

DOE PAGES

Timoshenko, Janis; Frenkel, Anatoly I.; Cintins, Arturs; ...

2018-05-25

The knowledge of coordination environment around various atomic species in many functional materials provides a key for explaining their properties and working mechanisms. Many structural motifs and their transformations are difficult to detect and quantify in the process of work (operando conditions), due to their local nature, small changes, low dimensionality of the material, and/or extreme conditions. Here we use artificial neural network approach to extract the information on the local structure and its in-situ changes directly from the X-ray absorption fine structure spectra. We illustrate this capability by extracting the radial distribution function (RDF) of atoms in ferritic andmore » austenitic phases of bulk iron across the temperature-induced transition. Integration of RDFs allows us to quantify the changes in the iron coordination and material density, and to observe the transition from body-centered to face-centered cubic arrangement of iron atoms. Furthermore, this method is attractive for a broad range of materials and experimental conditions« less

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

Interference between extrinsic and intrinsic losses in x-ray absorption fine structure

NASA Astrophysics Data System (ADS)

Campbell, L.; Hedin, L.; Rehr, J. J.; Bardyszewski, W.

2002-02-01

The interference between extrinsic and intrinsic losses in x-ray absorption fine structure (XAFS) is treated within a Green's-function formalism, without explicit reference to final states. The approach makes use of a quasiboson representation of excitations and perturbation theory in the interaction potential between electrons and quasibosons. These losses lead to an asymmetric broadening of the main quasiparticle peak plus an energy-dependent satellite in the spectral function. The x-ray absorption spectra (XAS) is then given by a convolution of an effective spectral function over a one-electron cross section. It is shown that extrinsic and intrinsic losses tend to cancel near excitation thresholds, and correspondingly, the strength in the main peak increases. At high energies, the theory crosses over to the sudden approximation. These results thus explain the observed weakness of multielectron excitations in XAS. The approach is applied to estimate the many-body corrections to XAFS, beyond the usual mean-free path, using a phasor summation over the spectral function. The asymmetry of the spectral function gives rise to an additional many-body phase shift in the XAFS formula.

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

Neural Network Approach for Characterizing Structural Transformations by X-Ray Absorption Fine Structure Spectroscopy

NASA Astrophysics Data System (ADS)

Timoshenko, Janis; Anspoks, Andris; Cintins, Arturs; Kuzmin, Alexei; Purans, Juris; Frenkel, Anatoly I.

2018-06-01

The knowledge of the coordination environment around various atomic species in many functional materials provides a key for explaining their properties and working mechanisms. Many structural motifs and their transformations are difficult to detect and quantify in the process of work (operando conditions), due to their local nature, small changes, low dimensionality of the material, and/or extreme conditions. Here we use an artificial neural network approach to extract the information on the local structure and its in situ changes directly from the x-ray absorption fine structure spectra. We illustrate this capability by extracting the radial distribution function (RDF) of atoms in ferritic and austenitic phases of bulk iron across the temperature-induced transition. Integration of RDFs allows us to quantify the changes in the iron coordination and material density, and to observe the transition from a body-centered to a face-centered cubic arrangement of iron atoms. This method is attractive for a broad range of materials and experimental conditions.

X-ray absorption fine structure (XAFS) analysis of titanium-implanted soft tissue.

PubMed

Uo, Motohiro; Asakura, Kiyotaka; Yokoyama, Atsuro; Ishikawa, Makoto; Tamura, Kazuchika; Totsuka, Yasunori; Akasaka, Tsukasa; Watari, Fumio

2007-03-01

Tissues contacting Ti dental implants were subjected to X-ray absorption fine structure (XAFS) analysis to examine the chemical state of Ti transferred from the placed implant into the surrounding tissue. Nine tissues that contacted pure Ti cover screws for several months were excised in a second surgery whereby healing abutments were set. Six tissues that surrounded implants retrieved due to their failure were also excised. Ti distributions in the excised specimens were confirmed by X-ray scanning analytical microscopy (XSAM), and the specimens were subjected to fluorescence XAFS analysis to determine the chemical states of the low concentrations of Ti in the tissues surrounding Ti dental implants. Ti mostly existed in the metallic state and was considered to be debris derived from the abrasion of implant pieces during implant surgery. Oxidized forms of Ti, such as anatase and rutile, were also detected in a few specimens-and existed in either a pure state or mixed state with metallic Ti. It was concluded that the existence of Ti in the tissue did not cause implant failure. Moreover, the usefulness of XAFS for analysis of the chemical states of rarely contained elements in biological tissue was demonstrated.

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

Fluorescence x-ray absorption fine structure studies of Fe-Ni-S and Fe-Ni-Si melts to 1600 K

NASA Astrophysics Data System (ADS)

Manghnani, M. H.; Hong, X.; Balogh, J.; Amulele, G.; Sekar, M.; Newville, M.

2008-04-01

We report NiK -edge fluorescence x-ray absorption fine structure spectra (XAFS) for Fe0.75Ni0.05S0.20 and Fe0.75Ni0.05Si0.20 ternary alloys from room temperature up to 1600 K. A high-temperature furnace designed for these studies incorporates two x-ray transparent windows and enables both a vertical orientation of the molten sample and a wide opening angle, so that XAFS can be measured in the fluorescence mode with a detector at 90° with respect to the incident x-ray beam. An analysis of the Ni XAFS data for these two alloys indicates different local structural environments for Ni in Fe0.75Ni0.05S0.20 and Fe0.75Ni0.05Si0.20 melts, with more Ni-Si coordination than Ni-S coordination persisting from room temperature through melting. These results suggest that light elements such as S and Si may impact the structural and chemical properties of Fe-Ni alloys with a composition similar to the earth’s core.

Extended X-ray Absorption Fine Structure (EXAFS) Analysis of Vitreous Rare Earth Sodium Phosphates

NASA Astrophysics Data System (ADS)

Yoo, Changhyeon; Marasinghe, Kanishka; Segre, Carlo; Shibata, Tomohiro

2015-03-01

The local structure around rare-earth ions (RE3+) in rare-earth ultraphosphate (REUP) glasses has been studied using RE LIII edge (RE = Nd, Er, Dy, and Eu) and K edge (RE = Nd, Pr, Dy, and Eu) extended X-ray absorption fine structure (EXAFS) spectroscopy. (RE2O3)x (Na2O)y(P2O5) 1 - x - y glasses in the compositional range 0 <= x <= 0.14 and x + y = 0.3 and 0.4 were studied. RE-oxygen (RE-O) coordination number decreases from ~ 10 to ~ 7.5 with increasing RE-content for Nd, Pr, Eu, and Dy. For Er, RE-O coordination number increases from ~ 8.7 to ~ 10 with increasing RE-content. For the first oxygen shell, the RE-O distance ranges between 2.41-2.43 Å, 2.44-2.46 Å, 2.24-2.26 Å, 2.28-2.32 Å, and 2.32-2.36 Å for Nd, Pr, Er, Dy, and EU glasses, respectively. Second shell around RE ions consists of phosphorus atoms, with RE-P distance about 3.0-3.5 Å and coordination number ranging from 1 to 3. The third shell primarily contains oxygen and is at a distance about 4.0-4.1 Å from RE ions.

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.

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.

Dynamical Study of Femtosecond-Laser-Ablated Liquid-Aluminum Nanoparticles Using Spatiotemporally Resolved X-Ray-Absorption Fine-Structure Spectroscopy

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

Oguri, Katsuya; Okano, Yasuaki; Nishikawa, Tadashi

2007-10-19

We study the temperature evolution of aluminum nanoparticles generated by femtosecond laser ablation with spatiotemporally resolved x-ray-absorption fine-structure spectroscopy. We successfully identify the nanoparticles based on the L-edge absorption fine structure of the ablation plume in combination with the dependence of the edge structure on the irradiation intensity and the expansion velocity of the plume. In particular, we show that the lattice temperature of the nanoparticles is estimated from the L-edge slope, and that its spatial dependence reflects the cooling of the nanoparticles during plume expansion. The results reveal that the emitted nanoparticles travel in a vacuum as a condensedmore » liquid phase with a lattice temperature of about 2500 to 4200 K in the early stage of plume expansion.« less

Composition analysis of a polymer electrolyte membrane fuel cell microporous layer using scanning transmission X-ray microscopy and near edge X-ray absorption fine structure analysis

NASA Astrophysics Data System (ADS)

George, Michael G.; Wang, Jian; Banerjee, Rupak; Bazylak, Aimy

2016-03-01

The novel application of scanning transmission X-ray microscopy (STXM) to the microporous layer (MPL) of a polymer electrolyte membrane fuel cell is investigated. A spatially resolved chemical component distribution map is obtained for the MPL of a commercially available SGL 25 BC sample. This is achieved with near edge X-ray absorption fine structure spectroscopic analysis. Prior to analysis the sample is embedded in non-reactive epoxy and ultra-microtomed to a thickness of 100 nm. Polytetrafluoroethylene (PTFE), carbon particle agglomerates, and supporting epoxy resin distributions are identified and reconstructed for a scanning area of 6 μm × 6 μm. It is observed that the spatial distribution of PTFE is strongly correlated to the carbon particle agglomerations. Additionally, agglomerate structures of PTFE are identified, possibly indicating the presence of a unique mesostructure in the MPL. STXM analysis is presented as a useful technique for the investigation of chemical species distributions in the MPL.

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

Structure of Co-Doped Alq3 thin films investigated by grazing incidence X-ray absorption fine structure and Fourier transform infrared spectroscopy.

PubMed

Lin, Liang; Pang, Zhiyong; Fang, Shaojie; Wang, Fenggong; Song, Shumei; Huang, Yuying; Wei, Xiangjun; Yu, Haisheng; Han, Shenghao

2011-02-10

The structural properties of Co-doped tris(8-hydroxyquinoline)aluminum (Alq(3)) have been studied by grazing incidence X-ray absorption fine structure (GIXAFS) and Fourier transform infrared spectroscopy (FTIR). GIXAFS analysis suggests that there are multivalent Co-Alq(3) complexes and the doped Co atoms tend to locate at the attraction center with respect to N and O atoms and bond with them. The FTIR spectra indicate that the Co atoms interact with the meridional (mer) isomer of Alq(3) rather than forming inorganic compounds.

An X-ray Absorption Fine Structure study of Au adsorbed onto the non-metabolizing cells of two soil bacterial species

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

Song, Zhen; Kenney, Janice P.L.; Fein, Jeremy B.

2015-02-09

Gram-positive and Gram-negative bacterial cells can remove Au from Au(III)-chloride solutions, and the extent of removal is strongly pH dependent. In order to determine the removal mechanisms, X-ray Absorption Fine Structure (XAFS) spectroscopy experiments were conducted on non-metabolizing biomass of Bacillus subtilis and Pseudomonas putida with fixed Au(III) concentrations over a range of bacterial concentrations and pH values. X-ray Absorption Near Edge Structure (XANES) and Extended X-ray Absorption Fine Structure (EXAFS) data on both bacterial species indicate that more than 90% of the Au atoms on the bacterial cell walls were reduced to Au(I). In contrast to what has beenmore » observed for Au(III) interaction with metabolizing bacterial cells, no Au(0) or Au-Au nearest neighbors were observed in our experimental systems. All of the removed Au was present as adsorbed bacterial surface complexes. For both species, the XAFS data suggest that although Au-chloride-hydroxide aqueous complexes dominate the speciation of Au in solution, Au on the bacterial cell wall is characterized predominantly by binding of Au atoms to sulfhydryl functional groups and amine and/or carboxyl functional groups, and the relative importance of the sulfhydryl groups increases with increasing pH and with decreasing Au loading. The XAFS data for both microorganism species suggest that adsorption is the first step in the formation of Au nanoparticles by bacteria, and the results enhance our ability to account for the behavior of Au in bacteria-bearing geologic systems.« less

An X-ray Absorption Fine Structure study of Au adsorbed onto the non-metabolizing cells of two soil bacterial species

NASA Astrophysics Data System (ADS)

Song, Zhen; Kenney, Janice P. L.; Fein, Jeremy B.; Bunker, Bruce A.

2012-06-01

Gram-positive and Gram-negative bacterial cells can remove Au from Au(III)-chloride solutions, and the extent of removal is strongly pH dependent. In order to determine the removal mechanisms, X-ray Absorption Fine Structure (XAFS) spectroscopy experiments were conducted on non-metabolizing biomass of Bacillus subtilis and Pseudomonas putida with fixed Au(III) concentrations over a range of bacterial concentrations and pH values. X-ray Absorption Near Edge Structure (XANES) and Extended X-ray Absorption Fine Structure (EXAFS) data on both bacterial species indicate that more than 90% of the Au atoms on the bacterial cell walls were reduced to Au(I). In contrast to what has been observed for Au(III) interaction with metabolizing bacterial cells, no Au(0) or Au-Au nearest neighbors were observed in our experimental systems. All of the removed Au was present as adsorbed bacterial surface complexes. For both species, the XAFS data suggest that although Au-chloride-hydroxide aqueous complexes dominate the speciation of Au in solution, Au on the bacterial cell wall is characterized predominantly by binding of Au atoms to sulfhydryl functional groups and amine and/or carboxyl functional groups, and the relative importance of the sulfhydryl groups increases with increasing pH and with decreasing Au loading. The XAFS data for both microorganism species suggest that adsorption is the first step in the formation of Au nanoparticles by bacteria, and the results enhance our ability to account for the behavior of Au in bacteria-bearing geologic systems.

Applications of x ray absorption fine structure to the in situ study of the effect of cobalt in nickel hydrous oxide electrodes for fuel cells and rechargeable batteries

NASA Technical Reports Server (NTRS)

Kim, Sunghyun; Tryk, Donald A.; Scherson, Daniel A.; Antonio, Mark R.

1993-01-01

Electronic and structural aspects of composite nickel-cobalt hydrous oxides have been examined in alkaline solutions using in situ X-ray absorption fine structure (XAFS). The results obtained have indicated that cobalt in this material is present as cobaltic ions regardless of the oxidation state of nickel in the lattice. Furthermore, careful analysis of the Co K-edge Extended X-ray absorption fine structure data reveals that the co-electrodeposition procedure generates a single phase, mixed metal hydrous oxide, in which cobaltic ions occupy nickel sites in the NiO2 sheet-like layers and not two intermixed phases each consisting of a single metal hydrous oxide.

Development of the surface-sensitive soft x-ray absorption fine structure measurement technique for the bulk insulator

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

Yonemura, Takumi, E-mail: yonemura-takumi@sei.co.jp; Iihara, Junji; Uemura, Shigeaki

We have succeeded in measuring X-ray absorption fine structure (TEY-XAFS) spectra of insulating plate samples by total electron yield. The biggest problem is how to suppress the charge-up. We have attempted to deposit a gold stripe electrode on the surface and obtained a TEY-XAFS spectrum. This indicates that the metal stripe electrode is very useful in the TEY-XAFS measurement of the insulating plate samples. In the detailed analysis, we have found that the effective area for suppressing charge-up was approximately 120 μm from the edge of the electrode.

A high pressure La K-edge X-ray absorption fine structure spectroscopy investigation of La1/3NbO3

NASA Astrophysics Data System (ADS)

Marini, C.; Joseph, B.; Noked, O.; Shuker, R.; Kennedy, B. J.; Mathon, O.; Pascarelli, S.; Sterer, E.

2018-01-01

La K-edge X-ray absorption spectroscopy has been used to elucidate the changes in the local electronic and lattice structure that occur in the A-site deficient double perovskite La?NbO? up to 6 GPa. The pressure evolution of the oxygen dodecahedrum around the A-site has been examined. XANES (X-ray absorption near edge structure) data show modifications ascribed to the increase of bands overlapping as a consequence of the bond distance contraction, which has been directly probed by EXAFS (extended x-ray absorption fine structure) spectra. The La-O Debye Waller factors (DWFs) tend to increase whereas the La-Nb bond DWFs show only a tendency to decrease indicating the robustness of the crystal lattice structure, even in presence of the oxygen disordering. This permits the system to reverse back to its original conditions in this pressure range as evident from the measurements upon pressure release. The present results have been interpreted in the light of charge transfer related to the two-step reduction mechanism acting at the Nb site (with niobium ions passing from Nb? to Nb?) which also results in the elongation of the Nb-O bond distances in the octahedra, in agreement with the Nb K-edge results reported earlier.

Bond-length relaxation in crystalline Si1-xGex alloys: An extended x-ray-absorption fine-structure study

NASA Astrophysics Data System (ADS)

Kajiyama, Hiroshi; Muramatsu, Shin-Ichi; Shimada, Toshikazu; Nishino, Yoichi

1992-06-01

Extended x-ray-absorption fine-structure spectra for crystalline Si1-xGex alloys, measured at the K edge of Ge at room temperature, are analyzed with a curve-fitting method based on the spherical-wave approximation. The Ge-Ge and Ge-Si bond lengths, coordination numbers of Ge and Si atoms around a Ge atom, and Debye-Waller factors of Ge and Si atoms are obtained. It is shown that Ge-Ge and Ge-Si bonds relax completely, for all Ge concentrations of their study, while the lattice constant varies monotonically, following Vegard's law. As noted by Bragg and later by Pauling and Huggins, the Ge-Ge and Ge-Si bond lengths are close to the sum of their constituent-element atomic radii: nearly 2.45 Å for Ge-Ge bonds and 2.40 Å for Ge-Si bonds. A study on the coordination around a Ge atom in the alloys revealed that Ge and Si atoms mix randomly throughout the compositional range studied.

X-Ray Absorption Near Edge Structure And Extended X-Ray Absorption Fine Structure Analysis of Standards And Biological Samples Containing Mixed Oxidation States of Chromium(III) And Chromium(VI)

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

Parsons, J.G.; Dokken, K.; Peralta-Videa, J.R.

For the first time a method has been developed for the extended X-ray absorption fine structure (EXAFS) data analyses of biological samples containing multiple oxidation states of chromium. In this study, the first shell coordination and interatomic distances based on the data analysis of known standards of potassium chromate (Cr(VI)) and chromium nitrate hexahydrate (Cr(III)) were investigated. The standards examined were mixtures of the following molar ratios of Cr(VI):Cr(III), 0:1, 0.25:0.75, 0.5:0.5, 0.75:0.25, and 1:0. It was determined from the calibration data that the fitting error associated with linear combination X-ray absorption near edge structure (LC-XANES) fittings was approximately {+-}10%more » of the total fitting. The peak height of the Cr(VI) pre-edge feature after normalization of the X-ray absorption (XAS) spectra was used to prepare a calibration curve. The EXAFS fittings of the standards were also investigated and fittings to lechuguilla biomass samples laden with different ratios of Cr(III) and Cr(VI) were performed as well. An excellent agreement between the XANES data and the data presented in the EXAFS spectra was observed. The EXFAS data also presented mean coordination numbers directly related to the ratios of the different chromium oxidation states in the sample. The chromium oxygen interactions had two different bond lengths at approximately 1.68 and 1.98 {angstrom} for the Cr(VI) and Cr(III) in the sample, respectively.« less

Non-patchy strategy for inter-atomic distances from Extended X-ray Absorption Fine Structure

PubMed Central

Xu, Gu; Li, Guifang; LI, Xianya; Liang, Yi; Feng, Zhechuan

2017-01-01

Extended X-ray Absorption Fine Structure (EXAFS) has been one of the few structural probes available for crystalline, non-crystalline and even highly disordered specimens. However, the data analysis involves a patchy and tinkering process, including back-and-forth fitting and filtering, leading to ambiguous answers sometimes. Here we try to resolve this long standing problem, to extract the inter-atomic distances from the experimental data by a single step minimization, in order to replace the tedious and tinkering process. The new strategy is built firmly by the mathematical logic, and made straightforward and undeniable. The finding demonstrates that it is possible to break off from the traditional patchy model fitting, and to remove the logical confusion of a priori prediction of the structure to be matched with experimental data, making it a much more powerful technique than the existing methods. The new method is expected to benefit EXAFS users covering all disciplines. Also, it is anticipated that the current work to be the motivation and inspiration to the further efforts. PMID:28181529

Many-particle-effects in the theory of the extended X-ray absorption fine structure

NASA Astrophysics Data System (ADS)

Tran Thoai, D. B.; Ekardt, W.

1981-10-01

The Lee-Beni-procedure for the calculation of the extended X-ray absorption fine structure (EXAFS) is extended so as to include the effects of the electronic charge density outside the localized muffin-tin potentials. In our scheme EXAFS is caused by back-scattering of an elementary excitation of a homogeneous electron gas by localized energy dependent many-particle muffin-tin potentials. The difference between the two schemes is negligible at large k's, as expected from physical grounds. However, at small and intermediate k-values the difference is quite large. The effect of the outer electrons as compared to the Lee-Beni-model is twofold. First, they renormalize the scattered electron in the usual way. Second, they are missing within the scattering muffin-tins. Hence, we avoid to count some of the electrons twice. Results are presented for Cu as an example.

The coefficient of bond thermal expansion measured by extended x-ray absorption fine structure.

PubMed

Fornasini, P; Grisenti, R

2014-10-28

The bond thermal expansion is in principle different from the lattice expansion and can be measured by correlation sensitive probes such as extended x-ray absorption fine structure (EXAFS) and diffuse scattering. The temperature dependence of the coefficient α(bond)(T) of bond thermal expansion has been obtained from EXAFS for CdTe and for Cu. A coefficient α(tens)(T) of negative expansion due to tension effects has been calculated from the comparison of bond and lattice expansions. Negative lattice expansion is present in temperature intervals where α(bond) prevails over α(tens); this real-space approach is complementary but not equivalent to the Grüneisen theory. The relevance of taking into account the asymmetry of the nearest-neighbours distribution of distances in order to get reliable bond expansion values and the physical meaning of the third cumulant are thoroughly discussed.

Depressurization-induced fines migration in hydrate-bearing clayey sands: X-ray CT imaging and quantification

NASA Astrophysics Data System (ADS)

Han, G.; Kwon, T. H.; Lee, J. Y.

2016-12-01

As gas and water flows induced by depressurization of hydrate-bearing sediments exert seepage forces on fines in sediments, such as clay particles, depressurization is reported to accompany the transport of fine particles through sediment pores, i.e., fines migration. Because such fines migration can cause pore clogging, the fines migration is considered as one of the critical phenomena contributing to the transport of fluids among various pore-scale processes associated with depressurization. However, quantification of fines migration during depressurization still remains poorly understood. This study thus investigated fines migration caused by depressurization using X-ray computerized tomography(X-ray CT) imaging. A host sediment was prepared by mixing fine sand with kaolinite clay minerals to achieve 10% mass fraction of fines (less than 75 um). Then, methane hydrate was synthesized in the host clayey sand, and thereafter water was injected to saturate the hydrate-bearing sediment sample. Step-wise depressurization was applied while the produced gas was collected through an outlet fluid port. X-ray CT imaging was conducted on the sediment sample over the courses of the experiment to monitor the sample preparation, hydrate formation, depressurization, and fines migration. Based on the calibration tests, the amount and locations of methane hydrate formed in the sample was estimated, and the gas migration path was also identified. Finally, the spatial distribution of fines after completion of depressurization was first assessed using the obtained X-ray images and then compared with the post-mortem mine-back results.Notably, we found that the middle part of the sample was clogged possibly by fines or by re-formed hydrate, leading to a big pressure difference between the inlet and outlet fluid port of the sample by 3 MPa. Owing to this clogging and the lost in pressure communication, hydrate dissociation first occurred at the bottom half and the hydrate dissociation

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.

Sulfur K-edge extended X-ray absorption fine structure spectroscopy of homoleptic thiolato complexes with Zn(II) and Cd(II).

PubMed

Matsunaga, Yuki; Fujisawa, Kiyoshi; Ibi, Naoko; Fujita, Mitsuharu; Ohashi, Tetuya; Amir, Nagina; Miyashita, Yoshitaro; Aika, Ken-Ichi; Izumi, Yasuo; Okamoto, Ken-Ichi

2006-02-01

The sulfur K-edge extended X-ray absorption fine structure (EXAFS) spectroscopy is applied to homoleptic thiolato complexes with Zn(II) and Cd(II), (Et(4)N)[Zn(SAd)(3)] (1), (Et(4)N)(2)[{Zn(ScHex)(2)}(2)(mu-ScHex)(2)] (2), (Et(4)N)(2)[{Cd(ScHex)(2)}(2)(mu-ScHex)(2)] (3), (Et(4)N)(2)[{Cd(ScHex)}(4)(mu-ScHex)(6)] (4), [Zn(mu-SAd)(2)](n) (5), and [Cd(mu-SAd)(2)](n) (6) (HSAd=1-adamantanethiol, HScHex=cyclohexanethiol). The EXAFS results are consistent with the X-ray crystal data of 1-4. The structures of 5 and 6, which have not been determined by X-ray crystallography, are proposed to be polynuclear structures on the basis of the sulfur K-edge EXAFS, far-IR spectra, and elemental analysis. Clear evidences of the S...S interactions (between bridging atoms or neighboring sulfur atoms) and the S...C(far) interactions (in which C(far) atom is next to carbon atom directly bonded to sulfur atom) were observed in the EXAFS data for all complexes and thus lead to the reliable determination of the structures of 5 and 6 in combination with conventional zinc K-edge EXAFS analysis for 5. This new methodology, sulfur K-edge EXAFS, could be applied for the structural determination of in vivo metalloproteins as well as inorganic compounds.

X-ray Absorption Fine Structure (XAFS) Studies of Oxide Glasses—A 45-Year Overview

PubMed Central

Zanotto, Edgar Dutra

2018-01-01

X-ray Absorption Fine Structure (XAFS) spectroscopy has been widely used to characterize the short-range order of glassy materials since the theoretical basis was established 45 years ago. Soon after the technique became accessible, mainly due to the existence of Synchrotron laboratories, a wide range of glassy materials was characterized. Silicate glasses have been the most studied because they are easy to prepare, they have commercial value and are similar to natural glasses, but borate, germanate, phosphate, tellurite and other less frequent oxide glasses have also been studied. In this manuscript, we review reported advances in the structural characterization of oxide-based glasses using this technique. A focus is on structural characterization of transition metal ions, especially Ti, Fe, and Ni, and their role in different properties of synthetic oxide-based glasses, as well as their important function in the formation of natural glasses and magmas, and in nucleation and crystallization. We also give some examples of XAFS applications for structural characterization of glasses submitted to high pressure, glasses used to store radioactive waste and medieval glasses. This updated, comprehensive review will likely serve as a useful guide to clarify the details of the short-range structure of oxide glasses. PMID:29382102

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.

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.

Insight into the biological effects of acupuncture points by X-ray absorption fine structure.

PubMed

Liu, Chenglin; Liu, Qinghua; Zhang, Dongming; Liu, Wei; Yan, Xiaohui; Zhang, Xinyi; Oyanagi, Hiroyuki; Pan, Zhiyun; Hu, Fengchun; Wei, Shiqiang

2018-06-02

Exploration of the biological effects of transition metal ions in acupuncture points is essential to clarify the functional mechanism of acupuncture treatment. Here we show that in the SP6 acupuncture point (Sanyinjiao) the Fe ions are in a high-spin state of approximately t 2g 4.5 e g 1.5 in an Fe-N(O) octahedral crystal field. The Fe K-edge synchrotron radiation X-ray absorption fine structure results reveal that the Fe-N and Fe-O bond lengths in the SP6 acupuncture point are 2.05 and 2.13 Å, respectively, and are 0.05-0.10 Å longer than those in the surrounding tissue. The distorted atomic structure reduces the octahedral symmetry and weakens the crystal field around the Fe ions by approximately 0.3 eV, leading to the high-spin configuration of the Fe ions, which is favorable for strengthening the magnetotransport and oxygen transportation properties in the acupuncture point by the enhanced spin coherence. This finding might provide some insight into the microscopic effect of the atomic and electronic interactions of transition metal ions in the acupuncture point. Graphical Abstract ᅟ.

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

Portable ultrahigh-vacuum sample storage system for polarization-dependent total-reflection fluorescence x-ray absorption fine structure spectroscopy

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

Watanabe, Yoshihide, E-mail: e0827@mosk.tytlabs.co.jp; Nishimura, Yusaku F.; Suzuki, Ryo

A portable ultrahigh-vacuum sample storage system was designed and built to investigate the detailed geometric structures of mass-selected metal clusters on oxide substrates by polarization-dependent total-reflection fluorescence x-ray absorption fine structure spectroscopy (PTRF-XAFS). This ultrahigh-vacuum (UHV) sample storage system provides the handover of samples between two different sample manipulating systems. The sample storage system is adaptable for public transportation, facilitating experiments using air-sensitive samples in synchrotron radiation or other quantum beam facilities. The samples were transferred by the developed portable UHV transfer system via a public transportation at a distance over 400 km. The performance of the transfer system was demonstratedmore » by a successful PTRF-XAFS study of Pt{sub 4} clusters deposited on a TiO{sub 2}(110) surface.« less

Structure formation in organic thin films observed in real time by energy dispersive near-edge x-ray absorption fine-structure spectroscopy

NASA Astrophysics Data System (ADS)

Scholz, M.; Sauer, C.; Wiessner, M.; Nguyen, N.; Schöll, A.; Reinert, F.

2013-08-01

We study the structure formation of 1,4,5,8-naphthalene-tetracarboxylicacid-dianhydride (NTCDA) multilayer films on Ag(111) surfaces by energy dispersive near-edge x-ray absorption fine-structure spectroscopy (NEXAFS) and photoelectron spectroscopy. The time resolution of seconds of the method allows us to identify several sub-processes, which occur during the post-growth three-dimensional structural ordering, as well as their characteristic time scales. After deposition at low temperature the NTCDA molecules are preferentially flat lying and the films exhibit no long-range order. Upon annealing the molecules flip into an upright orientation followed by an aggregation in a transient phase which exists for several minutes. Finally, three-dimensional islands are established with bulk-crystalline structure involving substantial mass transport on the surface and morphological roughening. By applying the Kolmogorov-Johnson-Mehl-Avrami model the activation energies of the temperature-driven sub-processes can be derived from the time evolution of the NEXAFS signal.

X ray absorption fine structure of systems in the anharmonic limit

NASA Astrophysics Data System (ADS)

Mustredeleon, J.; Conradson, S. D.; Batistic, I.; Bishop, A. R.; Raistrick, I.; Jackson, W. E.; Brown, G. E.

A new approach to the analysis of x-ray absorption fine structure (XAFS) data is presented. It is based on the use of radial distribution functions directly calculated from a single-particle ion Hamiltonian containing model potentials. The starting point of this approach is the statistical average of the XAFS for an atomic pair. This average can be computed using a radial distribution function (RDF), which can be expressed in terms of the eigenvalues and wavefunctions associated with the model potential. The pair potential describing the ionic motion is then expressed in terms of parameters that are determined by fitting this statistical average to the experimental XAFS spectrum. This approach allows the use of XAFS as a tool for mapping near-neighbor interatomic potentials, and allows the treatment of systems which exhibit strongly anharmonic potentials which can be treated by perturbative methods. Using this method we have analyzed the high temperature behavior of the oxygen contributions to the Fe K-edge XAFS in the ferrosilicate minerals andradite (Ca3Fe2Si3O12) and magnesiowustite (Mg(0.9)Fe(0.1)O). Using a temperature dependent anharmonic correction derived from these model compounds, we have found evidence for a local structural change in the Fe-O coordination environment upon melting of the geologically important mineral fayalite (Fe2SiO4). We have also employed this method to the study of the axial oxygen contributions to the polarized Cu K-edge XAFS on oriented samples of YBa2Cu3O7 and related compounds. From this study we find evidence for an axial oxygen-centered lattice distortion accompanying the superconducting phase transition and a correlation between this distortion and Tc. The relation of the observed lattice distortion to mechanisms of superconductivity is discussed.

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).

Local structure and polarization resistance of Ce doped SrMnO{sub 3} using extended x-ray fine structure analysis

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

Ryu, Jiseung; Lee, Heesoo, E-mail: heesoo@pusan.ac.kr

2014-09-15

Changes to the local structure of Sr and Mn atoms in Sr{sub 1−x}Ce{sub x}MnO{sub 3} (SCM) according to increasing Ce content and the effect of the structural change on the polarization resistance of SCM were investigated. The reduction of manganese was confirmed by the absorption edge shift of the Mn K-edge toward lower energies. The noise of oscillation in extended X-ray absorption fine structure k{sup 3}χ data at Mn K-edge reveals the distortion of the local structure of Mn atoms, and the peak that indicates the bonding length of Mn-O, Sr/Ce, and -Mn decreased with the addition of Ce contentmore » in Fourier transformations of the Mn K-edge. The distortion of the local structure at Mn atoms was affected by the reduced manganese ions having larger ionic radii than Mn{sup 4+}. Meanwhile, few distortions of local atomic structures of Sr atoms occurred, and the average nearest neighboring distances of Sr-O and Sr-Mn are ∼2.13 Å and ∼2.95 Å, respectively. The average bonding lengths of the Ce-O and Ce-Mn increased because the ionic radius of substituted Ce ion with 12 coordination number is smaller than that of Sr ion, which leads the reduction of Mn ions and the distortion of local structure at the substituted A-site. Therefore, we reasoned that the distortion of the local atomic structure at Mn atoms in MnO{sub 6} and Ce atoms in A-site is one of the causes for interrupting oxygen ion transfers as a geometric factor, which results in an increase in the polarization resistance of SCM within the Ce composition range from 10 mol. % to 30 mol. %.« less

Changes in the near edge X-ray absorption fine structure of hybrid organic-inorganic resists upon exposure.

PubMed

Fallica, Roberto; Watts, Benjamin; Roesner, Benedikt; Della Giustina, Gioia; Brigo, Laura; Brusatin, Giovanna; Ekinci, Yasin

2018-06-14

We report on the near edge X-ray absorption fine structure (NEXAFS) spectroscopy of hybrid organic-inorganic resists. These materials are nonchemically amplified systems based on Si, Zr, and Ti oxides, synthesized from organically modified precursors and transition metal alkoxides by a sol-gel route and designed for ultraviolet, extreme ultraviolet and electron beam lithography. The experiments were conducted using a scanning transmission X-ray microscope (STXM) which combines high spatial-resolution microscopy and NEXAFS spectroscopy. The absorption spectra were collected in the proximity of the carbon edge (~ 290 eV) before and after in situ exposure, enabling the measurement of a significant photo-induced degradation of the organic group (phenyl or methyl methacrylate, respectively), the degree of which depends on the configuration of the ligand. Photo-induced degradation was more efficient in the resist synthesized with pendant phenyl substituents than it was in the case of systems based on bridging phenyl groups. The degradation of the methyl methacrylate group was relatively efficient, with about half of the initial ligands dissociated upon exposure. Our data reveal that the such dissociation can produce different outcomes, depending on the structural configuration. While all the organic groups were expected to detach and desorb from the resist in their entirety, a sizeable amount of them remain and form undesired byproducts such as alkene chains. In the framework of the materials synthesis and engineering through specific building blocks, these results provide a deeper insight into the photochemistry of resists, in particular for extreme ultraviolet lithography. © 2018 IOP Publishing Ltd.

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.

Extended X-ray absorption fine structure investigation of Sn local environment in strained and relaxed epitaxial Ge{sub 1−x}Sn{sub x} films

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

Gencarelli, F., E-mail: federica.gencarelli@imec.be; Heyns, M.; Department of Metallurgy and Materials Engineering, KU Leuven, Kasteelpark Arenberg 44, B-3001 Leuven

2015-03-07

We present an extended X-ray absorption fine structure investigation of the local environment of Sn atoms in strained and relaxed Ge{sub 1−x}Sn{sub x} layers with different compositions. We show that the preferred configuration for the incorporation of Sn atoms in these Ge{sub 1−x}Sn{sub x} layers is that of a α-Sn defect, with each Sn atom covalently bonded to four Ge atoms in a classic tetrahedral configuration. Sn interstitials, Sn-split vacancy complexes, or Sn dimers, if present at all, are not expected to involve more than 2.5% of the total Sn atoms. This finding, along with a relative increase of Snmore » atoms in the second atomic shell around a central Sn atom in Ge{sub 1−x}Sn{sub x} layers with increasing Sn concentrations, suggests that the investigated materials are homogeneous random substitutional alloys. Within the accuracy of the measurements, the degree of strain relaxation of the Ge{sub 1−x}Sn{sub x} layers does not have a significant impact on the local atomic surrounding of the Sn atoms. Finally, the calculated topological rigidity parameter a** = 0.69 ± 0.29 indicates that the strain due to alloying in Ge{sub 1−x}Sn{sub x} is accommodated via bond stretching and bond bending, with a slight predominance of the latter, in agreement with ab initio calculations reported in literature.« less

High Electrochemical Sensitivity of TiO2- x Nanosheets and an Electron-Induced Mutual Interference Effect toward Heavy Metal Ions Demonstrated Using X-ray Absorption Fine Structure Spectra.

PubMed

Zhou, Wen-Yi; Li, Shan-Shan; Song, Jie-Yao; Jiang, Min; Jiang, Tian-Jia; Liu, Jin-Yun; Liu, Jin-Huai; Huang, Xing-Jiu

2018-04-03

Mutual interference is a severe issue that occurs during the electrochemical detection of heavy metal ions. This limitation presents a notable drawback for its high sensitivity to specific targets. Here, we present a high electrochemical sensitivity of ∼237.1 μA cm -2 μM -1 toward copper(II) [Cu(II)] based on oxygen-deficient titanium dioxide (TiO 2- x ) nanosheets. We fully demonstrated an atomic-level relationship between electrochemical behaviors and the key factors, including the high-energy (001) facet percentage, oxygen vacancy concentration, surface -OH content, and charge carrier density, is fully demonstrated. These four factors were quantified using Raman, electron spin resonance, X-ray photoelectron spectroscopy spectra, and Mott-Schottky plots. In the mutual interference investigation, we selected cadmium(II) [Cd(II)] as the target ion because of the significant difference in its stripping potential (∼700 mV). The results show that the Cd(II) can enhance the sensitivity of TiO 2- x nanosheets toward Cu(II), exhibiting an electron-induced mutual interference effect, as demonstrated by X-ray absorption fine structure spectra.

Structural analysis of strontium in human teeth treated with surface pre-reacted glass-ionomer filler eluate by using extended X-ray absorption fine structure analysis.

PubMed

Uo, Motohiro; Wada, Takahiro; Asakura, Kiyotaka

2017-03-31

The bioactive effects of strontium released from surface pre-reacted glass-ionomer (S-PRG) fillers may aid in caries prevention. In this study, the local structure of strontium taken up by teeth was estimated by extended X-ray absorption fine structure analysis. Immersing teeth into S-PRG filler eluate increased the strontium content in enamel and dentin by more than 100 times. The local structure of strontium in enamel and dentin stored in distilled water was the same as that in synthetic strontium-containing hydroxyapatite (SrHAP). Moreover, the local structure of strontium in enamel and dentin after immersion in the S-PRG filler eluate was also similar to that of SrHAP. After immersion in the S-PRG filler eluate, strontium was suggested to be incorporated into the hydroxyapatite (HAP) of enamel and dentin at the calcium site in HAP.

Extended x-ray absorption fine structure study of phase transitions in the piezoelectric perovskite K0.5Na0.5NbO3

NASA Astrophysics Data System (ADS)

Kodre, A.; Tellier, J.; Arčon, I.; Malič, B.; Kosec, M.

2009-06-01

Following an x-ray diffraction study of phase transitions of the piezoelectric perovskite K0.5Na0.5NbO3 the structural changes of the material are studied using extended x-ray absorption fine structure analysis, whereby the neighborhood of Nb atom is determined in the temperature range of monoclinic, tetragonal, and cubic phases. Within the entire range Nb atom is displaced from the center of the octahedron of its immediate oxygen neighbors, as witnessed by the splitting of Nb-O distance. The model shows high prevalence of the displacement in the (111) crystallographic direction of the simple perovskite cell. The corresponding splitting of the Nb-Nb distance is negligible. There is no observable disalignment of the linear Nb-O-Nb bonds from the ideal cubic arrangement, judging from the intensity of the focusing of the photoelectron wave on the Nb-Nb scattering path by the interposed oxygen atom. As a general result, the phase transitions are found as an effect of the long-range order, while the placement of the atoms in the immediate vicinity remains largely unaffected.

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.

Local Fine Structural Insight into Mechanism of Electrochemical Passivation of Titanium.

PubMed

Wang, Lu; Yu, Hongying; Wang, Ke; Xu, Haisong; Wang, Shaoyang; Sun, Dongbai

2016-07-20

Electrochemically formed passive film on titanium in 1.0 M H2SO4 solution and its thickness, composition, chemical state, and local fine structure are examined by Auger electron spectroscopy (AES), X-ray photoelectron spectroscopy (XPS), and X-ray absorption fine structure. AES analysis reveals that the thickness and composition of oxide film are proportional to the reciprocal of current density in potentiodynamic polarization. XPS depth profiles of the chemical states of titanium exhibit the coexistence of various valences cations in the surface. Quantitative X-ray absorption near edge structure analysis of the local electronic structure of the topmost surface (∼5.0 nm) shows that the ratio of [TiO2]/[Ti2O3] is consistent with that of passivation/dissolution of electrochemical activity. Theoretical calculation and analysis of extended X-ray absorption fine structure spectra at Ti K-edge indicate that both the structures of passivation and dissolution are distorted caused by the appearance of two different sites of Ti-O and Ti-Ti. And the bound water in the topmost surface plays a vital role in structural disorder confirmed by XPS. Overall, the increase of average Ti-O coordination causes the electrochemical passivation, and the dissolution is due to the decrease of average Ti-Ti coordination. The structural variations of passivation in coordination number and interatomic distance are in good agreement with the prediction of point defect model.

Structural properties of rutile TiO2 nanoparticles accumulated in a model of gastrointestinal epithelium elucidated by micro-beam x-ray absorption fine structure spectroscopy

NASA Astrophysics Data System (ADS)

Veronesi, G.; Brun, E.; Fayard, B.; Cotte, M.; Carrière, M.

2012-05-01

Micro-beam x-ray absorption fine structure spectroscopy was used to investigate rutile TiO2 nanoparticles internalized into gastrointestinal cells during their crossing of a gut model barrier. Nanoparticles diluted in culture medium tend to accumulate in cells after 48 h exposure; however, no spectral differences arise between particles in cellular and in acellular environments, as corroborated by quantitative analysis. This finding establishes that no modification of the lattice properties of the nanoparticles occurs upon interaction with the barrier. These measurements demonstrate the possibility of interrogating nanoparticles in situ within cells, suggesting a way to investigate their fate when incorporated in biological hosts.

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.

Complex polarization propagator approach in the restricted open-shell, self-consistent field approximation: the near K-edge X-ray absorption fine structure spectra of allyl and copper phthalocyanine.

PubMed

Linares, Mathieu; Stafström, Sven; Rinkevicius, Zilvinas; Ågren, Hans; Norman, Patrick

2011-05-12

A presentation of the complex polarization propagator in the restricted open-shell self-consistent field approximation is given. It rests on a formulation of a resonant-convergent, first-order polarization propagator approach that makes it possible to directly calculate the X-ray absorption cross section at a particular frequency without explicitly addressing the excited states. The quality of the predicted X-ray spectra relates only to the type of density functional applied without any separate treatment of dynamical relaxation effects. The method is applied to the calculation of the near K-edge X-ray absorption fine structure spectra of allyl and copper phthalocyanine. Comparison is made between the spectra of the radicals and those of the corresponding cations and anions to assess the effect of the increase of electron charge in the frontier orbital. The method offers the possibility for unique assignment of symmetry-independent atoms. The overall excellent spectral agreement motivates the application of the method as a routine precise tool for analyzing X-ray absorption of large systems of technological interest.

Electronic and atomic structures of Ti{sub 1-x}Al{sub x}N thin films related to their damage behavior

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

Tuilier, M.-H.; Pac, M.-J.; Girleanu, M.

2008-04-15

Ti and Al K-edge x-ray absorption spectroscopy is used to investigate the electronic structure of Ti{sub 1-x}Al{sub x}N thin films deposited by reactive magnetron sputtering. The experimental near edge spectra of TiN and AlN are interpreted in the light of unoccupied density of state band structure calculations. The comparison of the structural parameters derived from x-ray absorption fine structure and x-ray diffraction reveals segregation between Al-rich and Ti-rich domains within the Ti{sub 1-x}Al{sub x}N films. Whereas x-ray diffraction probes only the crystallized domains, the structural information derived from extended x-ray absorption fine structure analysis turns on both crystalline and grainmore » boundaries. The results are discussed by considering the damage behavior of the films depending on the composition.« less

Cation distribution in NiZn-ferrite films determined using x-ray absorption fine structure

NASA Astrophysics Data System (ADS)

Harris, V. G.; Koon, N. C.; Williams, C. M.; Zhang, Q.; Abe, M.

1996-04-01

We have applied extended x-ray absorption fine structure (EXAFS) spectroscopy to study the cation distribution in a series of spin-sprayed NiZn-ferrite films, Ni0.15ZnyFe2.85-yO4 (y=0.16, 0.23, 0.40, 0.60). The Ni, Zn, and Fe EXAFS were collected from each sample and analyzed to Fourier transforms. Samples of Ni-ferrite, Zn-ferrite, and magnetite were similarly studied as empirical standards. These standards, together with EXAFS data generated from the theoretical EXAFS FEFF codes, allowed the correlation of features in the Fourier transforms with specific lattice sites in the spinel unit cell. We find that the Ni ions reside mostly on the octahedral (B) sites whereas the Zn ions are predominantly on the tetrahedral (A) sites. The Fe ions reside on both A and B sites in a ratio determined by the ratio of Zn/Fe. The addition of Zn displaces a larger fraction of Fe cations onto the B sites serving to increase the net magnetization. The fraction of A site Ni ions is measured to increase peaking at ≊25% for y=0.6. At higher Zn concentrations (y≥0.5) the lattice experiences local distortions around the Zn sites causing a decrease in the superexchange resulting in a decrease in the net magnetization.

Orientational behavior of thin films of poly(3-methylthiophene) on platinium: A FTIR and near edge x-ray absorption fine structure (NEXAFS) study

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

Yang, X.Q.; Chen, J.; Hale, P.D.

1988-01-01

Near edge x-ray absorption fine structure (NEXAFS) and infrared reflection-absorption spectroscopy (IRRAS) have been used to study the orientational behavior of thin films of poly(3-methylthiophene) electrochemically polymerized on a platinum surface. Clear orientational effects, with the thiophene rings predominantly oriented parallel to the platinum surface, were observed when the thickness of the polymer films were within a few hundred /angstrom/A. It was found that more highly ordered films were produced at lower polymerization potential (1.4V vs SCE) than at higher potential (1.8V vs SCE). 5 refs., 4 figs., 2 tabs.

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

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

Enhanced Adsorption of p-Arsanilic Acid from Water by Amine-Modified UiO-67 as Examined Using Extended X-ray Absorption Fine Structure, X-ray Photoelectron Spectroscopy, and Density Functional Theory Calculations.

PubMed

Tian, Chen; Zhao, Jian; Ou, Xinwen; Wan, Jieting; Cai, Yuepeng; Lin, Zhang; Dang, Zhi; Xing, Baoshan

2018-03-20

p-Arsanilic acid ( p-ASA) is an emerging organoarsenic pollutant comprising both inorganic and organic moieties. For the efficient removal of p-ASA, adsorbents with high adsorption affinity are urgently needed. Herein, amine-modified UiO-67 (UiO-67-NH 2 ) metal-organic frameworks (MOFs) were synthesized, and their adsorption affinities toward p-ASA were 2 times higher than that of the pristine UiO-67. Extended X-ray absorption fine structure (EXAFS), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT) calculation results revealed adsorption through a combination of As-O-Zr coordination, hydrogen bonding, and π-π stacking, among which As-O-Zr coordination was the dominant force. Amine groups played a significant role in enhancing the adsorption affinity through strengthening the As-O-Zr coordination and π-π stacking, as well as forming new adsorption sites via hydrogen bonding. UiO-67-NH 2 s could remove p-ASA at low concentrations (<5 mg L -1 ) in simulated natural and wastewaters to an arsenic level lower than that of the drinking water standard of World Health Organization (WHO) and the surface water standard of China, respectively. This work provided an emerging and promising method to increase the adsorption affinity of MOFs toward pollutants containing both organic and inorganic moieties, via modifying functional groups based on the pollutant structure to achieve synergistic adsorption effect.

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

X-ray absorption fine structure analysis of molybdenum added to BaTiO3-based ceramics used for multilayer ceramic capacitors

NASA Astrophysics Data System (ADS)

Ogata, Yoichiro; Shimura, Tetsuo; Ryu, Minoru; Iwazaki, Yoshiki

2017-04-01

The effect of slight molybdenum doping of perovskite-type BaTiO3-based ceramics on the reliability of a multilayer ceramic capacitor (MLCC) and on the valence state of molybdenum in the BaTiO3-based ceramics has been investigated by highly accelerated lifetime tests and X-ray absorption fine structure analysis. The molybdenum added to the BaTiO3-based ceramics is located at Ti sites and improves the highly accelerated lifetime and lowers the initial dielectric resistivity in MLCCs. Through sintering in a reducing atmosphere, which is an important process in the fabrication of BaTiO3-based MLCCs, the oxidation state of the molybdenum added could be adjusted from +6 to a value close to +4.

Ethanol fixed brain imaging by phase-contrast X-ray technique

NASA Astrophysics Data System (ADS)

Takeda, Tohoru; Thet-Thet-Lwin; Kunii, Takuya; Sirai, Ryota; Ohizumi, Takahito; Maruyama, Hiroko; Hyodo, Kazuyuki; Yoneyama, Akio; Ueda, Kazuhiro

2013-03-01

The two-crystal phase-contrast X-ray imaging technique using an X-ray crystal interferometer can depict the fine structures of rat's brain such as cerebral cortex, white matter, and basal ganglia. Image quality and contrast by ethanol fixed brain showed significantly better than those by usually used formalin fixation at 35 keV X-ray energy. Image contrast of cortex by ethanol fixation was more than 3-times higher than that by formalin fixation. Thus, the technique of ethanol fixation might be better suited to image cerebral structural detail at 35 keV X-ray energy.

Identifying barriers to charge-carriers in the bulk and surface regions of Cu2ZnSnS4 nanocrystal films by x-ray absorption fine structures (XAFSs)

NASA Astrophysics Data System (ADS)

Turnbull, Matthew J.; Vaccarello, Daniel; Yiu, Yun Mui; Sham, Tsun-Kong; Ding, Zhifeng

2016-11-01

Solar cell performance is most affected by the quality of the light absorber layer. For thin-film devices, this becomes a two-fold problem of maintaining a low-cost design with well-ordered nanocrystal (NC) structure. The use of Cu2ZnSnS4 (CZTS) NCs as the light absorber films forms an ideal low-cost design, but the quaternary structure makes it difficult to maintain a well-ordered layer without the use of high-temperature treatments. There is little understanding of how CZTS NC structures affect the photoconversion efficiency, the charge-carriers, and therefore the performance of the device manufactured from it. To examine these relationships, the measured photoresponse from the photo-generation of charge-carrier electron-hole pairs was compared against the crystal structure, as short-range and long-range crystal orders for the films. The photoresponse simplifies the electronic properties into three basic steps that can be associated with changes in energy levels within the band structure. These changes result in the formation of barriers to charge-carrier flow. The extent of these barriers was determined using synchrotron-based X-ray absorbance fine structure to probe the individual metal centers in the film, and comparing these to molecular simulations of the ideal extended x-ray absorbance fine structure scattering. This allowed for the quantification of bond lengths, and thus an interpretation of the distortions in the crystal lattice. The various characteristics of the photoresponse were then correlated to the crystallographic order and used to gain physical insight into barriers to charge-carriers in the bulk and surface regions of CZTS films.

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

Ultrafast time-resolved X-ray absorption spectroscopy of ferrioxalate photolysis with a laser plasma X-ray source and microcalorimeter array

DOE PAGES

O’Neil, Galen C.; Miaja-Avila, Luis; Joe, Young Il; ...

2017-02-17

The detailed pathways of photoactivity on ultrafast time scales are a topic of contemporary interest. Using a tabletop apparatus based on a laser plasma X-ray source and an array of cryogenic microcalorimeter X-ray detectors, we measured a transient X-ray absorption spectrum during the ferrioxalate photoreduction reaction. With these high-efficiency detectors, we observe the Fe K edge move to lower energies and the amplitude of the extended X-ray absorption fine structure reduce, consistent with a photoreduction mechanism in which electron transfer precedes disassociation. We provide quantitative limits on the Fe–O bond length change. Lastly, we review potential improvements to our measurementmore » technique, highlighting the future potential of tabletop X-ray science using microcalorimeter sensors.« less

Ultrafast time-resolved X-ray absorption spectroscopy of ferrioxalate photolysis with a laser plasma X-ray source and microcalorimeter array

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

O’Neil, Galen C.; Miaja-Avila, Luis; Joe, Young Il

The detailed pathways of photoactivity on ultrafast time scales are a topic of contemporary interest. Using a tabletop apparatus based on a laser plasma X-ray source and an array of cryogenic microcalorimeter X-ray detectors, we measured a transient X-ray absorption spectrum during the ferrioxalate photoreduction reaction. With these high-efficiency detectors, we observe the Fe K edge move to lower energies and the amplitude of the extended X-ray absorption fine structure reduce, consistent with a photoreduction mechanism in which electron transfer precedes disassociation. We provide quantitative limits on the Fe–O bond length change. Lastly, we review potential improvements to our measurementmore » technique, highlighting the future potential of tabletop X-ray science using microcalorimeter sensors.« less

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.

Laboratory-size three-dimensional x-ray microscope with Wolter type I mirror optics and an electron-impact water window x-ray source

NASA Astrophysics Data System (ADS)

Ohsuka, Shinji; Ohba, Akira; Onoda, Shinobu; Nakamoto, Katsuhiro; Nakano, Tomoyasu; Miyoshi, Motosuke; Soda, Keita; Hamakubo, Takao

2014-09-01

We constructed a laboratory-size three-dimensional water window x-ray microscope that combines wide-field transmission x-ray microscopy with tomographic reconstruction techniques, and observed bio-medical samples to evaluate its applicability to life science research fields. It consists of a condenser and an objective grazing incidence Wolter type I mirror, an electron-impact type oxygen Kα x-ray source, and a back-illuminated CCD for x-ray imaging. A spatial resolution limit of around 1.0 line pairs per micrometer was obtained for two-dimensional transmission images, and 1-μm scale three-dimensional fine structures were resolved.

Laboratory-size three-dimensional x-ray microscope with Wolter type I mirror optics and an electron-impact water window x-ray source.

PubMed

Ohsuka, Shinji; Ohba, Akira; Onoda, Shinobu; Nakamoto, Katsuhiro; Nakano, Tomoyasu; Miyoshi, Motosuke; Soda, Keita; Hamakubo, Takao

2014-09-01

We constructed a laboratory-size three-dimensional water window x-ray microscope that combines wide-field transmission x-ray microscopy with tomographic reconstruction techniques, and observed bio-medical samples to evaluate its applicability to life science research fields. It consists of a condenser and an objective grazing incidence Wolter type I mirror, an electron-impact type oxygen Kα x-ray source, and a back-illuminated CCD for x-ray imaging. A spatial resolution limit of around 1.0 line pairs per micrometer was obtained for two-dimensional transmission images, and 1-μm scale three-dimensional fine structures were resolved.

Substitution behavior of x(Na0.5K0.5)NbO3-(1 - x)BaTiO3 ceramics for multilayer ceramic capacitors by a near edge x-ray absorption fine structure analysis

NASA Astrophysics Data System (ADS)

Ha, Jooyeon; Ryu, Jiseung; Lee, Heesoo

2014-06-01

The doping effect of (Na0.5K0.5)NbO3 (NKN) as alternatives for rare-earth elements on the electrical properties of BaTiO3 has been investigated, in terms of their substitution behavior. The dielectric constant of a specimen with x = 0.05 was about 79% higher than that of pure BaTiO3, and the temperature coefficient of capacitance was satisfied by the X7R specification. The specimen with x = 0.05 showed the lowest tetragonality among the four compositions and had a fine grain size of <2 μm. Although the addition of NKN decreased the specimen's tetragonality, the electrical properties were enhanced by the formation of defect dipoles and conduction electrons, which resulted from an acceptor and donor substitution behavior. Through O K-edge near edge x-ray absorption fine structure spectroscopy, the practical substitution behavior was defined by the change in Ti 3d orbital states. The energy separation of the Ti 3d orbitals was more apparent with the specimen of x = 0.05, which is related to the donor level from the donor substitution of Nb5+ ion for Ti-sites. Therefore, the simultaneous substitution of Na+/K+ and Nb5+ ions into BaTiO3 can improve dielectric properties, based on the charge-transfer process.

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.

Probing the influence of the center atom coordination structure in iron phthalocyanine multi-walled carbon nanotube-based oxygen reduction reaction catalysts by X-ray absorption fine structure spectroscopy

NASA Astrophysics Data System (ADS)

Peng, Yingxiang; Li, Zhipan; Xia, Dingguo; Zheng, Lirong; Liao, Yi; Li, Kai; Zuo, Xia

2015-09-01

Three different pentacoordinate iron phthalocyanine (FePc) electrocatalysts with an axial ligand (pyridyl group, Py) anchored to multi-walled carbon nanotubes (MWCNTs) are prepared by a microwave method as high performance composite electrocatalysts (FePc-Py/MWCNTs) for the oxygen reduction reaction (ORR). For comparison, tetracoordinate FePc electrocatalysts without an axial ligand anchored to MWCNTs (FePc/MWCNTs) are assembled in the same way. Ultraviolet-visible spectrophotometry (UV-Vis), Raman spectroscopy (RS), and high-resolution transmission electron microscopy (HRTEM) are used to characterize the obtained electrocatalysts. The electrocatalytic activity of the samples is measured by linear sweep voltammetry (LSV), and the onset potential of all of the FePc-Py/MWCNTs electrocatalysts is found to be more positive than that of their FePc/MWCNTs counterparts. X-ray photoelectron spectroscopy (XPS) and X-ray absorption fine structure (XAFS) spectroscopy are employed to elucidate the relationship between molecular structure and electrocatalytic activity. XPS indicates that higher concentrations of Fe3+ and pyridine-type nitrogen play critical roles in determining the electrocatalytic ORR activity of the samples. XAFS spectroscopy reveals that the FePc-Py/MWCNTs electrocatalysts have a coordination geometry around Fe that is closer to the square pyramidal structure, a higher concentration of Fe3+, and a smaller phthalocyanine ring radius compared with those of FePc/MWCNTs.

Interlaced X-ray diffraction computed tomography

PubMed Central

Vamvakeros, Antonios; Jacques, Simon D. M.; Di Michiel, Marco; Senecal, Pierre; Middelkoop, Vesna; Cernik, Robert J.; Beale, Andrew M.

2016-01-01

An X-ray diffraction computed tomography data-collection strategy that allows, post experiment, a choice between temporal and spatial resolution is reported. This strategy enables time-resolved studies on comparatively short timescales, or alternatively allows for improved spatial resolution if the system under study, or components within it, appear to be unchanging. The application of the method for studying an Mn–Na–W/SiO2 fixed-bed reactor in situ is demonstrated. Additionally, the opportunities to improve the data-collection strategy further, enabling post-collection tuning between statistical, temporal and spatial resolutions, are discussed. In principle, the interlaced scanning approach can also be applied to other pencil-beam tomographic techniques, like X-ray fluorescence computed tomography, X-ray absorption fine structure computed tomography, pair distribution function computed tomography and tomographic scanning transmission X-ray microscopy. PMID:27047305

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

Full-potential theoretical investigations of electron inelastic mean free paths and extended x-ray absorption fine structure in molybdenum.

PubMed

Chantler, C T; Bourke, J D

2014-04-09

X-ray absorption fine structure (XAFS) spectroscopy is one of the most robust, adaptable, and widely used structural analysis tools available for a range of material classes from bulk solids to aqueous solutions and active catalytic structures. Recent developments in XAFS theory have enabled high-accuracy calculations of spectra over an extended energy range using full-potential cluster modelling, and have demonstrated particular sensitivity in XAFS to a fundamental electron transport property-the electron inelastic mean free path (IMFP). We develop electron IMFP theory using a unique hybrid model that simultaneously incorporates second-order excitation losses, while precisely accounting for optical transitions dictated by the complex band structure of the solid. These advances are coupled with improved XAFS modelling to determine wide energy-range absorption spectra for molybdenum. This represents a critical test case of the theory, as measurements of molybdenum K-edge XAFS represent the most accurate determinations of XAFS spectra for any material. We find that we are able to reproduce an extended range of oscillatory structure in the absorption spectrum, and demonstrate a first-time theoretical determination of the absorption coefficient of molybdenum over the entire extended XAFS range utilizing a full-potential cluster model.

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.

Structural Analysis of the Mn(IV)/Fe(III) Cofactor of Chlamydia Trachomatis Ribonucleotide Reductase By Extended X-Ray Absorption Fine Structure Spectroscopy And Density Functional Theory Calculations

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

Younker, J.M.; Krest, C.M.; Jiang, W.

2009-05-28

The class Ic ribonucleotide reductase from Chlamydia trachomatis (C{bar A}) uses a stable Mn(lV)/ Fe(lll) cofactor to initiate nucleotide reduction by a free-radical mechanism. Extended X-ray absorption fine structure (EXAFS) spectroscopy and density functional theory (DFT) calculations are used to postulate a structure for this cofactor. Fe and Mn K-edge EXAFS data yield an intermetallic distance of -2.92 {angstrom}. The Mn data also suggest the presence of a short 1.74 {angstrom} Mn-O bond. These metrics are compared to the results of DFT calculations on 12 cofactor models derived from the crystal structure of the inactive Fe2(lll/ III) form of themore » protein. Models are differentiated by the protonation states of their bridging and terminal OH{sub x} ligands as well as the location of the Mn(lV) ion (site 1 or 2). The models that agree best with experimental observation feature a{mu}-1, 3-carboxylate bridge (E120), terminal solvent (H{sub 2}O/OH) to site 1, one {mu}-O bridge, and one {mu}-OH bridge. The site-placement of the metal ions cannot be discerned from the available data.« less

Near-Edge X-ray Absorption Fine Structure Studies of Electrospun Poly(dimethylsiloxane)/Poly (methyl methacrylate)/Multiwall Carbon Nanotube Composites

PubMed Central

Winter, A. Douglas; Larios, Eduardo; Alamgir, Faisal M.; Jaye, Cherno; Fischer, Daniel; Campo, Eva M.

2014-01-01

This work describes the near conduction band edge structure of electrospun mats of MWCNT-PDMS-PMMA by near edge X-Ray absorption fine structure (NEXAFS) spectroscopy. Effects of adding nanofillers of different sizes were addressed. Despite observed morphological variations and inhomogeneous carbon nanotube distribution, spun mats appeared homogeneous under NEXAFS analysis. Spectra revealed differences in emissions from glancing and normal spectra; which may evidence phase separation within the bulk of the micron-size fibers. Further, dichroic ratios show polymer chains did not align, even in the presence of nanofillers. Addition of nanofillers affected emissions in the C-H, C=O and C-C regimes, suggesting their involvement in interfacial matrix-carbon nanotube bonding. Spectral differences at glancing angles between pristine and composite mats suggest that geometric conformational configurations are taking place between polymeric chains and carbon nanotubes. These differences appear to be carbon nanotube-dimension dependent, and are promoted upon room temperature mixing and shear flow during electrospinning. CH-π bonding between polymer chains and graphitic walls, as well as H-bonds between impurities in the as-grown CNTs and polymer pendant groups are proposed bonding mechanisms promoting matrix conformation. PMID:24308286

Studying the local structures of novel materials using the Extended X-ray Absorption Fine Structure technique

NASA Astrophysics Data System (ADS)

Jiang, Yu

2009-12-01

In this dissertation, investigations on the local lattice structures for a variety of novel materials using Extended X-ray Absorption Fine Structure (EXAFS) technique are presented. Different experiment schemes were applied to obtain EXAFS data with high quality, and some interesting results were obtained by careful analysis. The power of the EXAFS technique was once again proved. In Chapter 1, I first briefly introduce the EXAFS theory and experiments, then give readers who are not familiar with this technique a short introduction on data reduction and analysis, and finally discuss some problems that are easily ignored in the interpretation of the experiment results. In Chapter 2, a temperature-dependent EXAFS investigation of La 1-xCaxMnO 3 is presented for the concentration range that spans the ferromagnetic-insulator (FMI) to ferromagnetic-metal (FMM) transition region, x = 0.16, 0.18, 0.20, and 0.22; the titrated hole concentrations are slightly higher y = 0.2, 0.22, 0.24, and 0.25 respectively. In Chapter 3, I report EXAFS studies of n- and p-type Ba8Ga 16Ge30 samples (type I clathrate) at the Ga, Ge, and Ba K-edges, to probe the local structure, particularly around the Ba atoms located inside 20- and 24-atom cages (Ba1 and Ba2 sites respectively) formed of Ga/Ge atoms. In agreement with diffraction analysis we find Ba2 is off-center, with a component in the bc plane (0.15 A) comparable to that found in diffraction; however, under the assumption of a stiff cage we also require a significant a component. This suggests a coupling or attraction between the Ba2 atoms and the hexagonal rings at the top or bottom of the cage that encloses the Ba2 site. In Chapter 4, I report detailed degradation and rejuvenation studies for AC electro-luminescence (EL) devices made using the phosphor ZnS:Cu,CI. We find that the AC EL emission spectra vary considerably with AC driving frequency but all spectra can be fit to a sum of four Gaussians. The combined experiments place

Structural investigation of spherical hollow excipient Mannit Q by X-ray microtomography.

PubMed

Kajihara, Ryusuke; Noguchi, Shuji; Iwao, Yasunori; Yasuda, Yuki; Segawa, Megumi; Itai, Shigeru

2015-11-10

The structure of Mannit Q particles, an excipient made by spray-drying a d-mannitol solution, and Mannit Q tablets were investigated by synchrotron X-ray microtomography. The Mannit Q particles had a spherical shape with a hollow core. The shells of the particles consisted of fine needle-shaped crystals, and columnar crystals were present in the hollows. These structural features suggested the following formation mechanism for the hollow particles:during the spray-drying process, the solvent rapidly evaporated from the droplet surface, resulting in the formation of shells made of fine needle-shaped crystals.Solvent remaining inside the shells then evaporated slowly and larger columnar crystals grew as the hollows formed. Although most of the Mannit Q particles were crushed on tableting, some of the particles retained their hollow structures, probably because the columnar crystals inside the hollows functioned as props. This demonstrated that the tablets with porous void spaces may be readily manufactured using Mannit Q. Copyright © 2015 Elsevier B.V. All rights reserved.

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

High temperature extended x-ray absorption fine structure study of multiferroic BiFeO3

NASA Astrophysics Data System (ADS)

Raghavendra Reddy, V.; Meneghini, Carlo; Kothari, Deepti; Gupta, Ajay; Aquilanti, Giuliana

2012-08-01

Local atomic structure modifications around Fe atoms in polycrystalline multiferroic BiFeO3 are studied by Fe K edge x-ray absorption spectroscopy as a function of temperature across the Néel temperature (TN = 643 K) in order to reveal local structure modifications related to the magnetic transition. This work demonstrates that on crossing TN the local structure around Fe shows peculiar changes: the Fe-O bond lengths get shorter, the ligand symmetry increases and the Fe-O bond length disorder (σ2) deviates from Debye behaviour. These results suggest that the structural transition at the ferroelectric Curie temperature (TC = 1103 K) is anticipated by early local rearrangement of the structure starting already at TN.

Tomographic image reconstruction using x-ray phase information

NASA Astrophysics Data System (ADS)

Momose, Atsushi; Takeda, Tohoru; Itai, Yuji; Hirano, Keiichi

1996-04-01

We have been developing phase-contrast x-ray computed tomography (CT) to make possible the observation of biological soft tissues without contrast enhancement. Phase-contrast x-ray CT requires for its input data the x-ray phase-shift distributions or phase-mapping images caused by an object. These were measured with newly developed fringe-scanning x-ray interferometry. Phase-mapping images at different projection directions were obtained by rotating the object in an x-ray interferometer, and were processed with a standard CT algorithm. A phase-contrast x-ray CT image of a nonstained cancerous tissue was obtained using 17.7 keV synchrotron x rays with 12 micrometer voxel size, although the size of the observation area was at most 5 mm. The cancerous lesions were readily distinguishable from normal tissues. Moreover, fine structures corresponding to cancerous degeneration and fibrous tissues were clearly depicted. It is estimated that the present system is sensitive down to a density deviation of 4 mg/cm3.

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

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

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

Bond length variation in Zn substituted NiO studied from extended X-ray absorption fine structure

NASA Astrophysics Data System (ADS)

Singh, S. D.; Poswal, A. K.; Kamal, C.; Rajput, Parasmani; Chakrabarti, Aparna; Jha, S. N.; Ganguli, Tapas

2017-06-01

Bond length behavior for Zn substituted NiO is determined through extended x-ray absorption fine structure (EXAFS) measurements performed at ambient conditions. We report bond length value of 2.11±0.01 Å for Zn-O of rock salt (RS) symmetry, when Zn is doped in RS NiO. Bond length for Zn substituted NiO RS ternary solid solutions shows relaxed behavior for Zn-O bond, while it shows un-relaxed behavior for Ni-O bond. These observations are further supported by first-principles calculations. It is also inferred that Zn sublattice remains nearly unchanged with increase in lattice parameter. On the other hand, Ni sublattice dilates for Zn compositions up to 20% to accommodate increase in the lattice parameter. However, for Zn compositions more than 20%, it does not further dilate. It has been attributed to the large disorder that is incorporated in the system at and beyond 20% of Zn incorporation in the cubic RS lattice of ternary solid solutions. For these large percentages of Zn incorporation, the Ni and the Zn atoms re-arrange themselves microscopically about the same nominal bond length rather than systematically increase in magnitude to minimize the energy of the system. This results in an increase in the Debye-Waller factor with increase in the Zn concentration rather than a systematic increase in the bond lengths.

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

Identification of B-K near edge x-ray absorption fine structure peaks of boron nitride thin films prepared by sputtering deposition

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

Niibe, Masahito; Miyamoto, Kazuyoshi; Mitamura, Tohru

2010-09-15

Four {pi}{sup *} resonance peaks were observed in the B-K near edge x-ray absorption fine structure spectra of boron nitride thin films prepared by magnetron sputtering. In the past, these peaks have been explained as the K-absorption of boron atoms, which are present in environment containing nitrogen vacancies, the number of which is 1-3 corresponding to the three peaks at higher photon energy. However, the authors found that there was a strong correlation between the intensities of these three peaks and that of O-K absorption after wide range scanning and simultaneous measurement of nitrogen and oxygen K-absorptions of the BNmore » films. Therefore, the authors conclude that these three peaks at the higher energy side correspond to boron atoms bound to one-to-three oxygen atoms instead of three nitrogen atoms surrounding the boron atom in the h-BN structure. The result of the first-principles calculation with a simple cluster model supported the validity of this explanation.« less

Mercury Speciation by X-ray Absorption Fine Structure Spectroscopy and Sequential Chemical Extractions: A Comparison of Speciation Methods

USGS Publications Warehouse

Kim, C.S.; Bloom, N.S.; Rytuba, J.J.; Brown, Gordon E.

2003-01-01

Determining the chemical speciation of mercury in contaminated mining and industrial environments is essential for predicting its solubility, transport behavior, and potential bioavailability as well as for designing effective remediation strategies. In this study, two techniques for determining Hg speciation-X-ray absorption fine structure (XAFS) spectroscopy and sequential chemical extractions (SCE)-are independently applied to a set of samples with Hg concentrations ranging from 132 to 7539 mg/kg to determine if the two techniques provide comparable Hg speciation results. Generally, the proportions of insoluble HgS (cinnabar, metacinnabar) and HgSe identified by XAFS correlate well with the proportion of Hg removed in the aqua regia extraction demonstrated to remove HgS and HgSe. Statistically significant (> 10%) differences are observed however in samples containing more soluble Hg-containing phases (HgCl2, HgO, Hg3S2O 4). Such differences may be related to matrix, particle size, or crystallinity effects, which could affect the apparent solubility of Hg phases present. In more highly concentrated samples, microscopy techniques can help characterize the Hg-bearing species in complex multiphase natural samples.

Dopant activation mechanism of Bi wire-δ-doping into Si crystal, investigated with wavelength dispersive fluorescence x-ray absorption fine structure and density functional theory.

PubMed

Murata, Koichi; Kirkham, Christopher; Shimomura, Masaru; Nitta, Kiyofumi; Uruga, Tomoya; Terada, Yasuko; Nittoh, Koh-Ichi; Bowler, David R; Miki, Kazushi

2017-04-20

We successfully characterized the local structures of Bi atoms in a wire-δ-doped layer (1/8 ML) in a Si crystal, using wavelength dispersive fluorescence x-ray absorption fine structure at the beamline BL37XU, in SPring-8, with the help of density functional theory calculations. It was found that the burial of Bi nanolines on the Si(0 0 1) surface, via growth of Si capping layer at 400 °C by molecular beam epitaxy, reduced the Bi-Si bond length from [Formula: see text] to [Formula: see text] Å. We infer that following epitaxial growth the Bi-Bi dimers of the nanoline are broken, and the Bi atoms are located at substitutional sites within the Si crystal, leading to the shorter Bi-Si bond lengths.

Reduced-temperature crystallization of thin amorphous Fe80B20 films studied via empirical modeling of extended x-ray absorption fine structure

NASA Astrophysics Data System (ADS)

Harris, V. G.; Oliver, S. A.; Ayers, J. D.; Das, B. N.; Koon, N. C.

1996-04-01

The evolution of the local atomic environment around Fe atoms in very thin (15 nm), amorphous, partially crystallized and fully crystallized films of Fe80B20 was studied using extended x-ray absorption fine structure (EXAFS) measurements. The relative atomic fraction of each crystalline phase present in the annealed samples was extracted from the Fe EXAFS data by a least-squares fitting procedure, using data collected from t-Fe3B, t-Fe2B, and α-Fe standards. The type and relative fraction of the crystallization products follows the trends previously measured in Fe80B20 melt-spun ribbons, except for the fact that crystallization temperatures are ≊200 K lower than those measured in bulk equivalents. This greatly reduced crystallization temperature may arise from the dominant role of surface nucleation sites in the crystallization of very thin amorphous films.

Origin of the magnetic transition at 100 K in ɛ-Fe2O3 nanoparticles studied by x-ray absorption fine structure spectroscopy

NASA Astrophysics Data System (ADS)

López-Sánchez, J.; Muñoz-Noval, A.; Castellano, C.; Serrano, A.; del Campo, A.; Cabero, M.; Varela, M.; Abuín, M.; de la Figuera, J.; Marco, J. F.; Castro, G. R.; Rodríguez de la Fuente, O.; Carmona, N.

2017-12-01

The current study unveils the structural origin of the magnetic transition of the ɛ-Fe2O3 polymorph from an incommensurate magnetic order to a collinear ferrimagnetic state at low temperature. The high crystallinity of the samples and the absence of other iron oxide polymorphs have allowed us to carry out temperature-dependent x-ray absorption fine structure spectroscopy experiments out. The deformation of the structure is followed by the Debye-Waller factor for each selected Fe-O and Fe-Fe sub-shell. For nanoparticle sizes between 7 and 15 nm, the structural distortions between the Fete and Fe-D1oc sites are localized in a temperature range before the magnetic transition starts. On the contrary, the inherent interaction between the other sub-shells (named Fe-O1,2 and Fe-Fe1) provokes cooperative magneto-structural changes in the same temperature range. This means that the Fete with Fe-D1oc polyhedron interaction seems to be uncoupled with temperature dealing with these nanoparticle sizes wherein the structural distortions are likely moderate due to surface effects.

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

Role of defects in BiFeO₃ multiferroic films and their local electronic structure by x-ray absorption spectroscopy

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

Ravalia, Ashish; Vagadia, Megha; Solanki, P. S.

2014-10-21

Present study reports the role of defects in the electrical transport in BiFeO₃ (BFO) multiferroic films and its local electronic structure investigated by near-edge X-ray absorption fine structure. Defects created by high energy 200 MeV Ag⁺¹⁵ ion irradiation with a fluence of ∼5 × 10¹¹ ions/cm² results in the increase in structural strain and reduction in the mobility of charge carriers and enhancement in resistive (I-V) and polarization (P-E) switching behaviour. At higher fluence of ∼5 × 10¹² ions/cm², there is a release in the structural strain due to local annealing effect, resulting in an increase in the mobility of charge carriers, which are releasedmore » from oxygen vacancies and hence suppression in resistive and polarization switching. Near-edge X-ray absorption fine structure studies at Fe L₃,₂- and O K-edges show a significant change in the spectral features suggesting the modifications in the local electronic structure responsible for changes in the intrinsic magnetic moment and electrical transport properties of BFO.« less

Time dependent density functional theory study of the near-edge x-ray absorption fine structure of benzene in gas phase and on metal surfaces.

PubMed

Asmuruf, Frans A; Besley, Nicholas A

2008-08-14

The near-edge x-ray absorption fine structure of benzene in the gas phase and adsorbed on the Au(111) and Pt(111) surfaces is studied with time dependent density functional theory. Excitation energies computed with hybrid exchange-correlation functionals are too low compared to experiment. However, after applying a constant shift the spectra are in good agreement with experiment. For benzene on the Au(111) surface, two bands arising from excitation to the e(2u)(pi(*)) and b(2g)(pi(*)) orbitals of benzene are observed for photon incidence parallel to the surface. On Pt(111) surface, a broader band arises from excitation to benzene orbitals that are mixed with the surface and have both sigma(*)(Pt-C) and pi(*) characters.

Effects of the environmental factors on the casein micelle structure studied by cryo transmission electron microscopy and small-angle x-ray scattering/ultrasmall-angle x-ray scattering

NASA Astrophysics Data System (ADS)

Marchin, Stéphane; Putaux, Jean-Luc; Pignon, Frédéric; Léonil, Joëlle

2007-01-01

Casein micelles are colloidal protein-calcium-transport complexes whose structure has not been unequivocally elucidated. This study used small-angle x-ray scattering (SAXS) and ultrasmall angle x-ray scattering (USAXS) as well as cryo transmission electron microscopy (cryo-TEM) to provide fine structural details on their structure. Cryo-TEM observations of native casein micelles fractionated by differential centrifugation showed that colloidal calcium phosphate appeared as nanoclusters with a diameter of about 2.5nm. They were uniformly distributed in a homogeneous tangled web of caseins and were primarily responsible for the intensity distribution in the SAXS profiles at the highest q vectors corresponding to the internal structure of the casein micelles. A specific demineralization of casein micelles by decreasing the pH from 6.7 to 5.2 resulted in a reduced granular aspect of the micelles observed by cryo-TEM and the existence of a characteristic point of inflection in SAXS profiles. This supports the hypothesis that the smaller substructures detected by SAXS are colloidal calcium phosphate nanoclusters rather than putative submicelles.

New consistency tests for high-accuracy measurements of X-ray mass attenuation coefficients by the X-ray extended-range technique.

PubMed

Chantler, C T; Islam, M T; Rae, N A; Tran, C Q; Glover, J L; Barnea, Z

2012-03-01

An extension of the X-ray extended-range technique is described for measuring X-ray mass attenuation coefficients by introducing absolute measurement of a number of foils - the multiple independent foil technique. Illustrating the technique with the results of measurements for gold in the 38-50 keV energy range, it is shown that its use enables selection of the most uniform and well defined of available foils, leading to more accurate measurements; it allows one to test the consistency of independently measured absolute values of the mass attenuation coefficient with those obtained by the thickness transfer method; and it tests the linearity of the response of the counter and counting chain throughout the range of X-ray intensities encountered in a given experiment. In light of the results for gold, the strategy to be ideally employed in measuring absolute X-ray mass attenuation coefficients, X-ray absorption fine structure and related quantities is discussed.

Chromium oxide as a metal diffusion barrier layer: An x-ray absorption fine structure spectroscopy study

NASA Astrophysics Data System (ADS)

Ahamad Mohiddon, Md.; Lakshun Naidu, K.; Ghanashyam Krishna, M.; Dalba, G.; Ahmed, S. I.; Rocca, F.

2014-01-01

The interaction at the interface between chromium and amorphous Silicon (a-Si) films in the presence of a sandwich layer of chromium oxide is investigated using X-ray absorption fine structure (XAFS) spectroscopy. The oxidized interface was created, in situ, prior to the deposition of a 400 nm tick a-Si layer over a 50 nm tick Cr layer. The entire stack of substrate/metallic Cr/Cr2O3/a-Si was then annealed at temperatures from 300 up to 700 °C. Analysis of the near edge and extended regions of each XAFS spectrum shows that only a small fraction of Cr is able to diffuse through the oxide layer up to 500 °C, while the remaining fraction is buried under the oxide layer in the form of metallic Cr. At higher temperatures, diffusion through the oxide layer is enhanced and the diffused metallic Cr reacts with a-Si to form CrSi2. At 700 °C, the film contains Cr2O3 and CrSi2 without evidence of unreacted metallic Cr. The activation energy and diffusion coefficient of Cr are quantitatively determined in the two temperature regions, one where the oxide acts as diffusion barrier and another where it is transparent to Cr diffusion. It is thus demonstrated that chromium oxide can be used as a diffusion barrier to prevent metal diffusion into a-Si.

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.

On the Electronic Structure of Cu Chlorophyllin and Its Breakdown Products: A Carbon K-Edge X-ray Absorption Spectroscopy Study.

PubMed

Witte, Katharina; Mantouvalou, Ioanna; Sánchez-de-Armas, Rocío; Lokstein, Heiko; Lebendig-Kuhla, Janina; Jonas, Adrian; Roth, Friedrich; Kanngießer, Birgit; Stiel, Holger

2018-02-15

Using near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, the carbon backbone of sodium copper chlorophyllin (SCC), a widely used chlorophyll derivative, and its breakdown products are analyzed to elucidate their electronic structure and physicochemical properties. Using various sample preparation methods and complementary spectroscopic methods (including UV/Vis, X-ray photoelectron spectroscopy), a comprehensive insight into the SCC breakdown process is presented. The experimental results are supported by density functional theory calculations, allowing a detailed assignment of characteristic NEXAFS features to specific C bonds. SCC can be seen as a model system for the large group of porphyrins; thus, this work provides a novel and detailed description of the electronic structure of the carbon backbone of those molecules and their breakdown products. The achieved results also promise prospective optical pump/X-ray probe investigations of dynamic processes in chlorophyll-containing photosynthetic complexes to be analyzed more precisely.

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.

High-resolution x-ray imaging using a structured scintillator.

PubMed

Hormozan, Yashar; Sychugov, Ilya; Linnros, Jan

2016-02-01

In this study, the authors introduce a new generation of finely structured scintillators with a very high spatial resolution (a few micrometers) compared to conventional scintillators, yet maintaining a thick absorbing layer for improved detectivity. Their concept is based on a 2D array of high aspect ratio pores which are fabricated by ICP etching, with spacings (pitches) of a few micrometers, on silicon and oxidation of the pore walls. The pores were subsequently filled by melting of powdered CsI(Tl), as the scintillating agent. In order to couple the secondary emitted photons of the back of the scintillator array to a CCD device, having a larger pixel size than the pore pitch, an open optical microscope with adjustable magnification was designed and implemented. By imaging a sharp edge, the authors were able to calculate the modulation transfer function (MTF) of this finely structured scintillator. The x-ray images of individually resolved pores suggest that they have been almost uniformly filled, and the MTF measurements show the feasibility of a few microns spatial resolution imaging, as set by the scintillator pore size. Compared to existing techniques utilizing CsI needles as a structured scintillator, their results imply an almost sevenfold improvement in resolution. Finally, high resolution images, taken by their detector, are presented. The presented work successfully shows the functionality of their detector concept for high resolution imaging and further fabrication developments are most likely to result in higher quantum efficiencies.

Large local disorder in superconducting K(0.8)Fe(1.6)Se2 studied by extended x-ray absorption fine structure.

PubMed

Iadecola, A; Joseph, B; Simonelli, L; Puri, A; Mizuguchi, Y; Takeya, H; Takano, Y; Saini, N L

2012-03-21

We have measured the local structure of superconducting K(0.8)Fe(1.6)Se(2) chalcogenide (T(c) = 31.8 K) by temperature dependent polarized extended x-ray absorption fine structure (EXAFS) at the Fe and Se K-edges. We find that the system is characterized by a large local disorder. The Fe-Se and Fe-Fe distances are found to be shorter than the distances measured by diffraction, while the corresponding mean square relative displacements reveal large Fe-site disorder and relatively large c-axis disorder. The local force constant for the Fe-Se bondlength (k ~ 5.8 eV Å(-2)) is similar to the one found in the binary FeSe superconductor, however, the Fe-Fe bondlength appears to be flexible (k ~ 2.1 eV Å(-2)) in comparison to the binary FeSe (k ~ 3.5 eV Å(-2)), an indication of partly relaxed Fe-Fe networks in K(0.8)Fe(1.6)Se(2). The results suggest a glassy nature for the title system, with the superconductivity being similar to that in the granular materials. © 2012 IOP Publishing Ltd

Lead is not off center in PbTe: the importance of r-space phase information in extended x-ray absorption fine structure spectroscopy.

PubMed

Keiber, T; Bridges, F; Sales, B C

2013-08-30

PbTe is a well-known thermoelectric material. Recent x-ray total scattering studies suggest that Pb moves off center along 100 in PbTe, by ∼0.2  Å at 300 K, producing a split Pb-Te pair distribution. We present an extended x-ray absorption fine structure spectroscopy (EXAFS) study of PbTe (and Tl doped PbTe) to determine if Pb or Te is off center. EXAFS provides sensitive r- or k-space phase information which can differentiate between a split peak for the Pb-Te distribution (indicative of off-center Pb) and a thermally broadened peak. We find no evidence for a split peak for Pb-Te or Te-Pb. At 300 K, the vibration amplitude for Pb-Te (or Te-Pb) is large; this thermally induced disorder is indicative of weak bonds, and the large disorder is consistent with the low thermal conductivity at 300 K. We also find evidence of an anharmonic potential for the nearest Pb-Te bonds, consistent with the overall anharmonicity found for the phonon modes. This effect is modeled by a "skew" factor (C3) which significantly improves the fit of the Pb-Te and Te-Pb peaks for the high temperature EXAFS data; C3 becomes significant above approximately 150-200 K. The consequences of these results will be discussed.

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.

[Fine stereo structure for natural organic molecules, a preliminary study. II. Melting point influenced by structure factors].

PubMed

Lu, Y; Zheng, Q; Lu, D; Ma, P; Chen, Y

1995-06-01

Crystal structures of two compounds from Tripterygium wilfordii Hook f. have been determined by X-ray diffraction method. Structure factors influencing melting point of solid state have been analysed. Crystal class (or space group), recrystallization solvent, force between molecules and fine changes of molecular structures will all cause melting point changes of crystal substance.

Laboratory-size three-dimensional water-window x-ray microscope with Wolter type I mirror optics

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

Ohsuka, Shinji; The Graduate School for the Creation of New Photonics Industries, 1955-1 Kurematsu-cho, Nishi-ku, Hamamatsu-City, 431-1202; Ohba, Akira

2016-01-28

We constructed a laboratory-size three-dimensional water-window x-ray microscope that combines wide-field transmission x-ray microscopy with tomographic reconstruction techniques. It consists of an electron-impact x-ray source emitting oxygen Kα x-rays, Wolter type I grazing incidence mirror optics, and a back-illuminated CCD for x-ray imaging. A spatial resolution limit better than 1.0 line pairs per micrometer was obtained for two-dimensional transmission images, and 1-μm-scale three-dimensional fine structures were resolved.

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.

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.

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

X-ray source development for EXAFS measurements on the National Ignition Facility.

PubMed

Coppari, F; Thorn, D B; Kemp, G E; Craxton, R S; Garcia, E M; Ping, Y; Eggert, J H; Schneider, M B

2017-08-01

Extended X-ray absorption Fine Structure (EXAFS) measurements require a bright, spectrally smooth, and broad-band x-ray source. In a laser facility, such an x-ray source can be generated by a laser-driven capsule implosion. In order to optimize the x-ray emission, different capsule types and laser irradiations have been tested at the National Ignition Facility (NIF). A crystal spectrometer is used to disperse the x-rays and high efficiency image plate detectors are used to measure the absorption spectra in transmission geometry. EXAFS measurements at the K-edge of iron at ambient conditions have been obtained for the first time on the NIF laser, and the requirements for optimization have been established.

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.

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.

Dissecting Diffuse X-ray Emission in 30 Doradus with T-ReX

NASA Astrophysics Data System (ADS)

Townsley, Leisa K.; Broos, Patrick

2017-08-01

30 Doradus (the Tarantula Nebula) offers us a microscope on starburst astrophysics, having endured 25 Myrs of the birth and death of the most massive stars known. Across 30 Dor's 250-pc extent, stellar winds and supernovae have carved its ISM into an amazing display of arcs, pillars, and bubbles. For over 40 years, we have also known that 30 Dor is a bright X-ray emitter, so its familiar stars and cold ISM structures suffer irradiation by multi-million-degree plasmas. The 2-Ms Chandra X-ray Visionary Project ``The Tarantula -- Revealed by X-rays'' (T-ReX) exploits Chandra's fine spatial resolution and the ACIS-I field of view to study ISM interfaces on 1--10 pc scales across the entire 30 Dor complex. Here we give preliminary results from ongoing analyses of these data, focusing on the diffuse X-ray emission. Massive star winds and cavity supernovae over the millenia have contributed to a broad mix of X-ray-emitting plasmas and absorbing columns, showing that 30 Dor's hot ISM is just as complex and confusing as that seen at colder temperatures.

Overview of nanoscale NEXAFS performed with soft X-ray microscopes.

PubMed

Guttmann, Peter; Bittencourt, Carla

2015-01-01

Today, in material science nanoscale structures are becoming more and more important. Not only for the further miniaturization of semiconductor devices like carbon nanotube based transistors, but also for newly developed efficient energy storage devices, gas sensors or catalytic systems nanoscale and functionalized materials have to be analysed. Therefore, analytical tools like near-edge X-ray absorption fine structure (NEXAFS) spectroscopy has to be applied on single nanostructures. Scanning transmission X-ray microscopes (STXM) as well as full-field transmission X-ray microscopes (TXM) allow the required spatial resolution to study individual nanostructures. In the soft X-ray energy range only STXM was used so far for NEXAFS studies. Due to its unique setup, the TXM operated by the Helmholtz-Zentrum Berlin (HZB) at the electron storage ring BESSY II is the first one in the soft X-ray range which can be used for NEXAFS spectroscopy studies which will be shown in this review. Here we will give an overview of the different microscopes used for NEXAFS studies and describe their advantages and disadvantages for different samples.

A wavelet analysis for the X-ray absorption spectra of molecules

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

Penfold, T. J.; Ecole polytechnique Federale de Lausanne, Laboratoire de chimie et biochimie computationnelles, ISIC, FSB-BCH, CH-1015 Lausanne; SwissFEL, Paul Scherrer Inst, CH-5232 Villigen

2013-01-07

We present a Wavelet transform analysis for the X-ray absorption spectra of molecules. In contrast to the traditionally used Fourier transform approach, this analysis yields a 2D correlation plot in both R- and k-space. As a consequence, it is possible to distinguish between different scattering pathways at the same distance from the absorbing atom and between the contributions of single and multiple scattering events, making an unambiguous assignment of the fine structure oscillations for complex systems possible. We apply this to two previously studied transition metal complexes, namely iron hexacyanide in both its ferric and ferrous form, and a rheniummore » diimine complex, [ReX(CO){sub 3}(bpy)], where X = Br, Cl, or ethyl pyridine (Etpy). Our results demonstrate the potential advantages of using this approach and they highlight the importance of multiple scattering, and specifically the focusing phenomenon to the extended X-ray absorption fine structure (EXAFS) spectra of these complexes. We also shed light on the low sensitivity of the EXAFS spectrum to the Re-X scattering pathway.« less

Adjustable Grazing-Incidence X-Ray Optics

NASA Technical Reports Server (NTRS)

O'Dell, Stephen L.; Reid, Paul B.

2015-01-01

With its unique subarcsecond imaging performance, NASA's Chandra X-ray Observatory illustrates the importance of fine angular resolution for x-ray astronomy. Indeed, the future of x-ray astronomy relies upon x-ray telescopes with comparable angular resolution but larger aperture areas. Combined with the special requirements of nested grazing-incidence optics, mass, and envelope constraints of space-borne telescopes render such advances technologically and programmatically challenging. The goal of this technology research is to enable the cost-effective fabrication of large-area, lightweight grazing-incidence x-ray optics with subarcsecond resolution. Toward this end, the project is developing active x-ray optics using slumped-glass mirrors with thin-film piezoelectric arrays for correction of intrinsic or mount-induced distortions.

Optimizing soft X-ray NEXAFS spectroscopy in the laboratory

NASA Astrophysics Data System (ADS)

Mantouvalou, I.; Jonas, A.; Witte, K.; Jung, R.; Stiel, H.; Kanngießer, B.

2017-05-01

Near edge X-ray absorption fine structure (NEXAFS) spectroscopy in the soft X-ray range is feasible in the laboratory using laser-produced plasma sources. We present a study using seven different target materials for optimized data analysis. The emission spectra of the materials with atomic numbers ranging from Z = 6 to Z = 79 show distinct differences, rendering the adapted selection of a suitable target material for specialized experiments feasible. For NEXAFS spectroscopy a 112.5 nm thick polyimide film is investigated as a reference exemplifying the superiority of quasi-continuum like emission spectra.

Reply to Comment on Axial oxygen-centered lattice instabilities in YBa[sub 2]Cu[sub 3]O[sub 7]: An application of the analysis of extended x-ray-absorption fine structure in anharmonic systems' ''

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

Mustre de Leon, J.; Batistic, I.; Bishop, A.R.

1993-05-01

We assert that the one-site Cu(1)-O(4) model, suggested in the Comment by Thomsen and Cardona [Phys. Rev. B 47, 12 320 (1993)] is inconsistent with polarized x-ray-absorption fine-structure and diffraction results. We also show that the two-site Cu(1)-O(4) distribution is not inconsistent with optical measurements, although a rigid double-well modeling of this distribution is [Phys. Rev. Lett. 68, 3236 (1992)].

High-resolution x-ray imaging using a structured scintillator

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

Hormozan, Yashar, E-mail: hormozan@kth.se; Sychugov, Ilya; Linnros, Jan

2016-02-15

Purpose: In this study, the authors introduce a new generation of finely structured scintillators with a very high spatial resolution (a few micrometers) compared to conventional scintillators, yet maintaining a thick absorbing layer for improved detectivity. Methods: Their concept is based on a 2D array of high aspect ratio pores which are fabricated by ICP etching, with spacings (pitches) of a few micrometers, on silicon and oxidation of the pore walls. The pores were subsequently filled by melting of powdered CsI(Tl), as the scintillating agent. In order to couple the secondary emitted photons of the back of the scintillator arraymore » to a CCD device, having a larger pixel size than the pore pitch, an open optical microscope with adjustable magnification was designed and implemented. By imaging a sharp edge, the authors were able to calculate the modulation transfer function (MTF) of this finely structured scintillator. Results: The x-ray images of individually resolved pores suggest that they have been almost uniformly filled, and the MTF measurements show the feasibility of a few microns spatial resolution imaging, as set by the scintillator pore size. Compared to existing techniques utilizing CsI needles as a structured scintillator, their results imply an almost sevenfold improvement in resolution. Finally, high resolution images, taken by their detector, are presented. Conclusions: The presented work successfully shows the functionality of their detector concept for high resolution imaging and further fabrication developments are most likely to result in higher quantum efficiencies.« less

X-ray source development for EXAFS measurements on the National Ignition Facility

DOE PAGES

Coppari, F.; Thorn, D. B.; Kemp, G. E.; ...

2017-08-28

We present that extended X-ray absorption Fine Structure (EXAFS) measurements require a bright, spectrally smooth, and broad-band x-ray source. In a laser facility, such an x-ray source can be generated by a laser-driven capsule implosion. In order to optimize the x-ray emission, different capsule types and laser irradiations have been tested at the National Ignition Facility (NIF). A crystal spectrometer is used to disperse the x-rays and high efficiency image plate detectors are used to measure the absorption spectra in transmission geometry. Finally, EXAFS measurements at the K-edge of iron at ambient conditions have been obtained for the first timemore » on the NIF laser, and the requirements for optimization have been established.« less

Electronic structure and x-ray magnetic circular dichroism in Mn-doped topological insulators Bi2Se3 and Bi2Te3

NASA Astrophysics Data System (ADS)

Antonov, V. N.; Bekenov, L. V.; Uba, S.; Ernst, A.

2017-12-01

We studied the structural, electronic, and magnetic properties of Mn-doped topological insulators Bi2Se3 and Bi2Te3 within the density-functional theory (DFT) using the generalized gradient approximation (GGA) in the framework of the fully relativistic spin-polarized Dirac linear muffin-tin orbital band-structure method. The x-ray absorption spectra (XAS) and x-ray magnetic circular dichroism at the Mn K and L2 ,3 edges were investigated theoretically from first principles. The calculated results are in good agreement with experimental data. The complex fine structure of the Mn L2 ,3 XAS in Mn-doped Bi2Se3 and Bi2Te3 was found to be not compatible with a pure Mn3 + valency state. Its interpretation demands mixed valent states. The theoretically calculated x-ray emission spectra at the Mn K and L2 ,3 edges are also presented and analyzed.

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.

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.

Penetrating view of nano-structures in Aleochara verna spermatheca and flagellum by hard X-ray microscopy

NASA Astrophysics Data System (ADS)

Zhang, Kai; Li, De-E.; Hong, You-Li; Zhu, Pei-Ping; Yuan, Qing-Xi; Huang, Wan-Xia; Gao, Kun; Zhou, Hong-Zhang; Wu, Zi-Yu

2013-07-01

A penetrating view of the three-dimensional nanostructure of female spermatheca and male flagellum in the species Aleochara verna is obtained with 100-nm resolution using a hard X-ray microscope, which provides a fast noninvasive imaging technology for insect morphology. Through introducing Zernike phase contrast and heavy metal staining, images taken at 8 keV displayed sufficient contrast for observing nanoscale fine structures, such as the spermatheca cochleate duct and the subapex of the flagellum, which have some implications for the study of the sperm transfer process and genital evolution in insects. This work shows that both the spatial resolution and the contrast characteristic of hard X-ray microscopy are quite promising for insect morphology studies and, particularly, provide an attractive alternative to the destructive techniques used for investigating internal soft tissues.

Reflectivity Around the Gold M-Edges of X-ray Reflector of the Soft X-Ray Telescope Onboard ASTRO-H

NASA Technical Reports Server (NTRS)

Kurashimaa, Sho; Furuzawa, Akihiro; Sato, Toshiki; Kikuchia, Naomichi; Nakaniwaa, Nozomi; Maeda, Yoshitomo; Ishida, Manabu; Izuka, Ryo; Okajima, Takashi; Mori, Hideyuki;

Near-edge X-ray absorption spectra for metallic Cu and Mn

NASA Astrophysics Data System (ADS)

Greaves, G. N.; Durham, P. J.; Diakun, G.; Quinn, P.

1981-11-01

The measurement of X-ray absorption fine structure of metals- both in the extended region (EXAFS) as well as in the near edge region (XANES)-has been widely discussed (see refs 1-6 for Cu and refs 7-9 for Mn). The recent availability of intense X-ray fluxes from storage rings has usually been exploited for EXAFS leaving the XANES often with poorer resolution than earlier work performed on conventional sources (for example, compare the near edge structure for copper in ref. 1 with refs 3 or 6). In addition, whilst the theory and analysis of EXAFS is relatively well-established2,10, a theory for the strong scattering regime near to the absorption edge has only recently been developed11. We report here the first high resolution XANES spectra for Cu and Mn which were performed at the SRS storage ring at Daresbury. Although both metals have close-packed structures consisting of atoms of similar size their local atomic structure is different in detail. Significant differences are found in their respective XANES reflecting the senstivity of this region of the X-ray absorption fine structure to the local atomic structure. Spectra for the two metals have been analysed using the new multiple scattering formalism. This is a real space calculation and unlike a conventional band structure approach it does not require structural periodicity but works from the local arrangement of atoms.

Enhanced renal image contrast by ethanol fixation in phase-contrast X-ray computed tomography.

PubMed

Shirai, Ryota; Kunii, Takuya; Yoneyama, Akio; Ooizumi, Takahito; Maruyama, Hiroko; Lwin, Thet Thet; Hyodo, Kazuyuki; Takeda, Tohoru

2014-07-01

Phase-contrast X-ray imaging using a crystal X-ray interferometer can depict the fine structures of biological objects without the use of a contrast agent. To obtain higher image contrast, fixation techniques have been examined with 100% ethanol and the commonly used 10% formalin, since ethanol causes increased density differences against background due to its physical properties and greater dehydration of soft tissue. Histological comparison was also performed. A phase-contrast X-ray system was used, fitted with a two-crystal X-ray interferometer at 35 keV X-ray energy. Fine structures, including cortex, tubules in the medulla, and the vessels of ethanol-fixed kidney could be visualized more clearly than that of formalin-fixed tissues. In the optical microscopic images, shrinkage of soft tissue and decreased luminal space were observed in ethanol-fixed kidney; and this change was significantly shown in the cortex and outer stripe of the outer medulla. The ethanol fixation technique enhances image contrast by approximately 2.7-3.2 times in the cortex and the outer stripe of the outer medulla; the effect of shrinkage and the physical effect of ethanol cause an increment of approximately 78% and 22%, respectively. Thus, the ethanol-fixation technique enables the image contrast to be enhanced in phase-contrast X-ray imaging.

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

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.

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

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.

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

Characterization of CuHal-intercalated carbon nanotubes with x-ray absorption spectroscopy combined with x-ray photoelectron and resonant photoemission spectroscopies

NASA Astrophysics Data System (ADS)

Brzhezinskaya, M.; Generalov, A.; Vinogdradov, A.; Eliseev, A.

2013-04-01

Encapsulated single-walled carbon nanotubes (SWCNTs) with inner channels filled by different compounds present the new class of composite materials. Such CNTs give opportunity to form 1D nanocrystals as well as quantum nanowires with new physical and chemical properties inside the tubes. The present study is aimed to characterize the possible chemical interaction between CuHal (Hal=I, Cl, Br) and SWCNTs in CuHal@SWCNTs and electronic structure of the latter using high-resolution near edge X-ray absorption fine structure (NEXAFS) spectroscopy combined with high-resolution X-ray photoelectron spectroscopy and resonant photoemission spectroscopy. The present study has shown that there is a chemical interaction between the filler and π-electron subsystem of CNTs which is accompanied by changes of the atomic and electronic structure of the filler during the encapsulating it inside CNTs.

In situ X-ray probing reveals fingerprints of surface platinum oxide.

PubMed

Friebel, Daniel; Miller, Daniel J; O'Grady, Christopher P; Anniyev, Toyli; Bargar, John; Bergmann, Uwe; Ogasawara, Hirohito; Wikfeldt, Kjartan Thor; Pettersson, Lars G M; Nilsson, Anders

2011-01-07

In situ X-ray absorption spectroscopy (XAS) at the Pt L(3) edge is a useful probe for Pt-O interactions at polymer electrolyte membrane fuel cell (PEMFC) cathodes. We show that XAS using the high energy resolution fluorescence detection (HERFD) mode, applied to a well-defined monolayer Pt/Rh(111) sample where the bulk penetrating hard X-rays probe only surface Pt atoms, provides a unique sensitivity to structure and chemical bonding at the Pt-electrolyte interface. Ab initio multiple-scattering calculations using the FEFF code and complementary extended X-ray absorption fine structure (EXAFS) results indicate that the commonly observed large increase of the white-line at high electrochemical potentials on PEMFC cathodes originates from platinum oxide formation, whereas previously proposed chemisorbed oxygen-containing species merely give rise to subtle spectral changes.

Characterizing phosphorus speciation of Chesapeake Bay sediments using chemical extraction, 31P NMR, and X-ray absorption fine structure spectroscopy.

PubMed

Li, Wei; Joshi, Sunendra R; Hou, Guangjin; Burdige, David J; Sparks, Donald L; Jaisi, Deb P

2015-01-06

Nutrient contamination has been one of the lingering issues in the Chesapeake Bay because the bay restoration is complicated by temporally and seasonally variable nutrient sources and complex interaction between imported and regenerated nutrients. Differential reactivity of sedimentary phosphorus (P) pools in response to imposed biogeochemical conditions can record past sediment history and therefore a detailed sediment P speciation may provide information on P cycling particularly the stability of a P pool and the formation of one pool at the expense of another. This study examined sediment P speciation from three sites in the Chesapeake Bay: (i) a North site in the upstream bay, (ii) a middle site in the central bay dominated by seasonally hypoxic bottom water, and (iii) a South site at the bay-ocean boundary using a combination of sequential P extraction (SEDEX) and spectroscopic techniques, including (31)P NMR, P X-ray absorption near edge structure spectroscopy (XANES), and Fe extended X-ray absorption fine structure (EXAFS). Results from sequential P extraction reveal that sediment P is composed predominantly of ferric Fe-bound P and authigenic P, which was further confirmed by solid-state (31)P NMR, XANES, and EXAFS analyses. Additionally, solution (31)P NMR results show that the sediments from the middle site contain high amounts of organic P such as monoesters and diesters, compared to the other two sites, but that these compounds rapidly decrease with sediment depth indicating remineralized P could have precipitated as authigenic P. Fe EXAFS enabled to identify the changes in Fe mineral composition and P sinks in response to imposed redox condition in the middle site sediments. The presence of lepidocrocite, vermiculite, and Fe smectite in the middle site sediments indicates that some ferric Fe minerals can still be present along with pyrite and vivianite, and that ferric Fe-bound P pool can be a major P sink in anoxic sediments. These results provide

Accurate Modeling of X-ray Extinction by Interstellar Grains

NASA Astrophysics Data System (ADS)

Hoffman, John; Draine, B. T.

2016-02-01

Interstellar abundance determinations from fits to X-ray absorption edges often rely on the incorrect assumption that scattering is insignificant and can be ignored. We show instead that scattering contributes significantly to the attenuation of X-rays for realistic dust grain size distributions and substantially modifies the spectrum near absorption edges of elements present in grains. The dust attenuation modules used in major X-ray spectral fitting programs do not take this into account. We show that the consequences of neglecting scattering on the determination of interstellar elemental abundances are modest; however, scattering (along with uncertainties in the grain size distribution) must be taken into account when near-edge extinction fine structure is used to infer dust mineralogy. We advertise the benefits and accuracy of anomalous diffraction theory for both X-ray halo analysis and near edge absorption studies. We present an open source Fortran suite, General Geometry Anomalous Diffraction Theory (GGADT), that calculates X-ray absorption, scattering, and differential scattering cross sections for grains of arbitrary geometry and composition.

ACCURATE MODELING OF X-RAY EXTINCTION BY INTERSTELLAR GRAINS

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

Hoffman, John; Draine, B. T., E-mail: jah5@astro.princeton.edu, E-mail: draine@astro.princeton.edu

Interstellar abundance determinations from fits to X-ray absorption edges often rely on the incorrect assumption that scattering is insignificant and can be ignored. We show instead that scattering contributes significantly to the attenuation of X-rays for realistic dust grain size distributions and substantially modifies the spectrum near absorption edges of elements present in grains. The dust attenuation modules used in major X-ray spectral fitting programs do not take this into account. We show that the consequences of neglecting scattering on the determination of interstellar elemental abundances are modest; however, scattering (along with uncertainties in the grain size distribution) must bemore » taken into account when near-edge extinction fine structure is used to infer dust mineralogy. We advertise the benefits and accuracy of anomalous diffraction theory for both X-ray halo analysis and near edge absorption studies. We present an open source Fortran suite, General Geometry Anomalous Diffraction Theory (GGADT), that calculates X-ray absorption, scattering, and differential scattering cross sections for grains of arbitrary geometry and composition.« less

Scanning electron microscopy/energy dispersive spectrometry fixedbeam or overscan x-ray microanalysis of particles can miss the real structure: x-ray spectrum image mapping reveals the true nature

NASA Astrophysics Data System (ADS)

Newbury, Dale E.; Ritchie, Nicholas W. M.

2013-05-01

The typical strategy for analysis of a microscopic particle by scanning electron microscopy/energy dispersive spectrometry x-ray microanalysis (SEM/EDS) is to use a fixed beam placed at the particle center or to continuously overscan to gather an "averaged" x-ray spectrum. While useful, such strategies inevitably concede any possibility of recognizing microstructure within the particle, and such fine scale structure is often critical for understanding the origins, behavior, and fate of particles. Elemental imaging by x-ray mapping has been a mainstay of SEM/EDS analytical practice for many years, but the time penalty associated with mapping with older EDS technology has discouraged its general use and reserved it more for detailed studies that justified the time investment. The emergence of the high throughput, high peak stability silicon drift detector (SDD-EDS) has enabled a more effective particle mapping strategy: "flash" x-ray spectrum image maps can now be recorded in seconds that capture the spatial distribution of major (concentration, C > 0.1 mass fraction) and minor (0.01 <= C <= 0.1) constituents. New SEM/SDD-EDS instrument configurations feature multiple SDDs that view the specimen from widely spaced azimuthal angles. Multiple, simultaneous measurements from different angles enable x-ray spectrometry and mapping that can minimize the strong geometric effects of particles. The NIST DTSA-II software engine is a powerful aid for quantitatively analyzing EDS spectra measured individually as well as for mapping information (available free for Java platforms at: http://www.cstl.nist.gov/div837/837.02/epq/dtsa2/index.html).

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.

X-ray absorption investigation of local structural disorder in Ni 1-xFe x (x=0.10, 0.20, 0.35, and 0.50) alloys

DOE PAGES

Zhang, Fuxiang X.; Jin, Ke; Zhao, Shijun; ...

2017-04-27

Defect energetics in structural materials has long been recognized to be affected by specific alloy compositions. Significantly enhanced radiation resistance has recently been observed in concentrated solid-solution alloys. However, the link between local structural disorder and modified defect dynamics in solid solutions remains unclear. To reveal the atomic-level lattice distortion, the local structures of Ni and Fe in Ni 1-xFe x (x=0.1, 0.2, 0.35 and 0.5) solid solution alloys were measured with extended X-ray absorption fine structure (EXAFS) technique. The lattice constant and the first-neighbor distances increase with the increase of Fe content in the solid solutions. EXAFS measurements havemore » revealed that the bond length of Fe with surrounding atoms is 0.01-0.03 larger than that of Ni in the alloy systems. Debye-Waller factor of the Fe-Fe bonds in all the systems is also slightly larger than that of the Ni-Ni bond. EXAFS fitting suggests that the local structural disorder is enhanced with the addition of Fe elements in the solid solution. The local bonding environments from ab initio calculation are in good agreement with the experimental results, which suggest that the Fe has a larger first-neighbor bonding distance than that of Ni, and thus Ni atom inside the Ni-Fe solid solution alloys undergoes compressive strain.« less

X-ray absorption investigation of local structural disorder in Ni 1-xFe x (x=0.10, 0.20, 0.35, and 0.50) alloys

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

Zhang, Fuxiang X.; Jin, Ke; Zhao, Shijun

Defect energetics in structural materials has long been recognized to be affected by specific alloy compositions. Significantly enhanced radiation resistance has recently been observed in concentrated solid-solution alloys. However, the link between local structural disorder and modified defect dynamics in solid solutions remains unclear. To reveal the atomic-level lattice distortion, the local structures of Ni and Fe in Ni 1-xFe x (x=0.1, 0.2, 0.35 and 0.5) solid solution alloys were measured with extended X-ray absorption fine structure (EXAFS) technique. The lattice constant and the first-neighbor distances increase with the increase of Fe content in the solid solutions. EXAFS measurements havemore » revealed that the bond length of Fe with surrounding atoms is 0.01-0.03 larger than that of Ni in the alloy systems. Debye-Waller factor of the Fe-Fe bonds in all the systems is also slightly larger than that of the Ni-Ni bond. EXAFS fitting suggests that the local structural disorder is enhanced with the addition of Fe elements in the solid solution. The local bonding environments from ab initio calculation are in good agreement with the experimental results, which suggest that the Fe has a larger first-neighbor bonding distance than that of Ni, and thus Ni atom inside the Ni-Fe solid solution alloys undergoes compressive strain.« less

Effect of aluminum on the local structure of silicon in zeolites as studied by Si K edge X-ray absorption near-edge fine structure: spectra simulation with a non-muffin tin atomic background.

PubMed

Bugaev, Lusegen A; Bokhoven, Jeroen A van; Khrapko, Valerii V

2009-04-09

Experimental Si K edge X-ray absorption near-edge fine structure (XANES) of zeolite faujasite, mordenite, and beta are interpreted by means of the FEFF8 code, replacing the theoretical atomic background mu(0) by a background that was extracted from an experimental spectrum. To some extent, this diminished the effect of the inaccuracy introduced by the MT potential and accounted for the intrinsic loss of photoelectrons. The agreement of the theoretical and experimental spectra at energies above the white lines enabled us to identify structural distortion around silicon, which occurs with increasing aluminum content. The Si K edge XANES spectra are very sensitive to slight distortions in the silicon coordination. Placing an aluminum atom on a nearest neighboring T site causes a distortion in the silicon tetrahedron, shortening one of the silicon-oxygen bonds relative to the other three.

High resolution projection X-ray microscope equipped with fluorescent X-ray analyzer and its applications

NASA Astrophysics Data System (ADS)

Minami, K.; Saito, Y.; Kai, H.; Shirota, K.; Yada, K.

2009-09-01

We have newly developed an open type fine-focus X-ray tube "TX-510" to realize a spatial resolution of 50nm and to radiate low energy characteristic X-rays for giving high absorption contrast to images of microscopic organisms. The "TX-510" employs a ZrO/W(100) Schottky emitter and an "In-Lens Field Emission Gun". The key points of the improvements are (1) reduced spherical aberration coefficient of magnetic objective lens, (2) easy and accurate focusing, (3) newly designed astigmatism compensator, (4) segmented thin film target for interchanging the target materials by electron beam shift and (5) fluorescent X-ray analysis system.

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}}*).

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.

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.

Soft x-ray absorption spectra of ilmenite family.

PubMed

Agui, A; Mizumaki, M; Saitoh, Y; Matsushita, T; Nakatani, T; Fukaya, A; Torikai, E

2001-03-01

We have carried out soft x-ray absorption spectroscopy to study the electronic structure of ilmenite family, such as MnTiO3, FeTiO3, and CoTiO3 at the soft x-ray beamline, BL23SU, at the SPring-8. The Ti and M L2,3 absorption spectra of MTiO3 (M=Mn, Fe, and Co) show spectra of Ti4+ and M2+ electron configurations, respectively. Except the Fe L2,3 spectrum, those spectra were understood within the O(h) symmetry around the transition metal ions. The Fe L3-edge spectrum clearly shows a doublet peak at the L3 edge, which is attributed to Fe2+ state, moreover the very high-resolution the L-edge spectra of transition metals show fine structures. The spectra of those ilmenites are compared.

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.

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

Extended x-ray absorption fine structure measurements of quasi-isentropically compressed vanadium targets on the OMEGA laser

NASA Astrophysics Data System (ADS)

Yaakobi, B.; Boehly, T. R.; Sangster, T. C.; Meyerhofer, D. D.; Remington, B. A.; Allen, P. G.; Pollaine, S. M.; Lorenzana, H. E.; Lorenz, K. T.; Hawreliak, J. A.

2008-06-01

The use of in situ extended x-ray absorption fine structure (EXAFS) for characterizing nanosecond laser-shocked vanadium, titanium, and iron has recently been demonstrated. These measurements are extended to laser-driven, quasi-isentropic compression experiments (ICE). The radiation source (backlighter) for EXAFS in all of these experiments is obtained by imploding a spherical target on the OMEGA laser [T. R. Boehly et al., Rev. Sci. Instrum. 66, 508 (1995)]. Isentropic compression (where the entropy is kept constant) enables to reach high compressions at relatively low temperatures. The absorption spectra are used to determine the temperature and compression in a vanadium sample quasi-isentropically compressed to pressures of up to ˜0.75Mbar. The ability to measure the temperature and compression directly is unique to EXAFS. The drive pressure is calibrated by substituting aluminum for the vanadium and interferometrically measuring the velocity of the back target surface by the velocity interferometer system for any reflector (VISAR). The experimental results obtained by EXAFS and VISAR agree with each other and with the simulations of a hydrodynamic code. The role of a shield to protect the sample from impact heating is studied. It is shown that the shield produces an initial weak shock that is followed by a quasi-isentropic compression at a relatively low temperature. The role of radiation heating from the imploding target as well as from the laser-absorption region is studied. The results show that in laser-driven ICE, as compared with laser-driven shocks, comparable compressions can be achieved at lower temperatures. The EXAFS results show important details not seen in the VISAR results.

Spin and orbital states in single-layered La2-xCaxCoO4 studied by doping- and temperature-dependent near-edge x-ray absorption fine structure

NASA Astrophysics Data System (ADS)

Merz, M.; Fuchs, D.; Assmann, A.; Uebe, S.; v. Löhneysen, H.; Nagel, P.; Schuppler, S.

2011-07-01

The doping-dependent valence, orbital, and spin-state configurations of single-layered La2-xCaxCoO4 (x=0, 0.5, 1, and 1.5) were investigated with temperature-dependent near-edge x-ray absorption fine structure at the Co L2,3 and O K edges. The spectra show that in La2CoO4, the superexchange between neighboring Co2+ HS states is responsible for the strong antiferromagnetism. With increasing hole doping, the superexchange interactions between Co2+ HS ions are rapidly reduced by interlaced nonmagnetic Co3+ LS. For La1.5Ca0.5CoO4, the low Néel temperature of the samples together with the 50% Co2+ HS and 50% Co3+ LS configuration suggests a checkerboard arrangement of these ions. The spin blockade resulting from this arrangement naturally explains the high resistivity of La1.5Ca0.5CoO4. Upon further doping, Co2+ HS ions are replaced by Co3+ HS, and for LaCaCoO4 a mixture of Co3+ LS and Co3+ HS occurs. Superexchange via configuration fluctuation processes between these two species seems to induce long-range ferromagnetism, while the superexchange between adjacent Co3+ HS neighbors may lead to a competing antiferromagnetic exchange. For a doping content beyond x=1, Co4+ HS is introduced to the system at the expense of Co3+ LS, and a t2g double exchange between Co3+ HS and Co4+ HS is established, which further enhances ferromagnetic interactions and reduces resistivity. No indications for a Co3+ IS state are found throughout the La2-xCaxCoO4 doping series.

Cr/B 4C multilayer mirrors: Study of interfaces and X-ray reflectance

DOE PAGES

Burcklen, C.; Soufli, R.; Gullikson, E.; ...

2016-03-24

Here, we present an experimental study of the effect of layer interfaces on the x-ray reflectance in Cr/B 4C multilayer interference coatings with layer thicknesses ranging from 0.7 nm to 5.4 nm. The multilayers were deposited by magnetron sputtering and by ion beam sputtering. Grazing incidence x-ray reflectometry, soft x-ray reflectometry, and transmission electron microscopy reveal asymmetric multilayer structures with a larger B 4C-on-Cr interface, which we modeled with a 1–1.5 nm thick interfacial layer. Reflectance measurements in the vicinity of the Cr L 2,3 absorption edge demonstrate fine structure that is not predicted by simulations using the currently tabulatedmore » refractive index (optical constants) values for Cr.« less

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.

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.

X-Ray Absorption Microspectroscopy with Electrostatic Force Microscopy and its Application to Chemical States Mapping

NASA Astrophysics Data System (ADS)

Ishii, M.; Rigopoulos, N.; Poolton, N. R. J.; Hamilton, B.

2007-02-01

A new technique named X-EFM that measures the x-ray absorption fine structure (XAFS) of nanometer objects was developed. In X-EFM, electrostatic force microscopy (EFM) is used as an x-ray absorption detector, and photoionization induced by x-ray absorption of surface electron trapping sites is detected by EFM. An EFM signal with respect to x-ray photon energy provides the XAFS spectra of the trapping sites. We adopted X-EFM to observe Si oxide thin films. An edge jump shift intrinsic to the X-EFM spectrum was found, and it was explained with a model where an electric field between the trapping site and probe deepens the energy level of the inner-shell. A scanning probe under x-rays with fixed photon energy provided the chemical state mapping on the surface.

Vanadium K-edge X-ray absorption spectroscopy of bromoperoxidase from Ascophyllum nodosum

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

Arber, J.M.; de Boer, E.; Garner, C.D.

Bromoperoxidase from Ascophyllum nodusum was the first vanadium-containing enzyme to be isolated. X-ray absorption spectra have now been collected in order to investigate the coordination of vanadium in the native, native plus bromide, native plus hydrogen peroxide, and dithionite-reduced forms of the enzyme. The edge and X-ray absorption near-edge structures show that, in the four samples studied, it is only on reduction of the native enzyme that the metal site is substantially altered. In addition, these data are consistent with the presence of vanadium(IV) in the reduced enzyme and vanadium(V) in the other samples. Extended X-ray absorption fine structure datamore » confirm that there are structural changes at the metal site on reduction of the native enzyme, notably a lengthening of the average inner-shell distance, and the presence of terminal oxygen together with histidine and oxygen-donating residues.« less

Soft X-ray spectroscopy of nanoparticles by velocity map imaging

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

Kostko, O.; Xu, B.; Jacobs, M. I.

Velocity map imaging (VMI), a technique traditionally used to study chemical dynamics in the gas phase, is applied to study X-ray photoemission from aerosol nanoparticles. Soft X-rays from the Advanced Light Source synchrotron, probe a beam of nanoparticles, and the resulting photoelectrons are velocity mapped to obtain their kinetic energy distributions. A new design of the VMI spectrometer is described. The spectrometer is benchmarked by measuring vacuum ultraviolet photoemission from gas phase xenon and squalene nanoparticles followed by measurements using soft X-rays. It is demonstrated that the photoelectron distribution from X-ray irradiated squalene nanoparticles is dominated by secondary electrons. Bymore » scanning the photon energies and measuring the intensities of these secondary electrons, a near edge X-ray absorption fine structure (NEXAFS) spectrum is obtained. The NEXAFS technique is used to obtain spectra of aqueous nanoparticles at the oxygen K edge. By varying the position of the aqueous nanoparticle beam relative to the incident X-ray beam, evidence is presented such that the VMI technique allows for NEXAFS spectroscopy of water in different physical states. Finally, we discuss the possibility of applying VMI methods to probe liquids and solids via X-ray spectroscopy.« less

Soft X-ray spectroscopy of nanoparticles by velocity map imaging

DOE PAGES

Kostko, O.; Xu, B.; Jacobs, M. I.; ...

2017-05-05

Velocity map imaging (VMI), a technique traditionally used to study chemical dynamics in the gas phase, is applied to study X-ray photoemission from aerosol nanoparticles. Soft X-rays from the Advanced Light Source synchrotron, probe a beam of nanoparticles, and the resulting photoelectrons are velocity mapped to obtain their kinetic energy distributions. A new design of the VMI spectrometer is described. The spectrometer is benchmarked by measuring vacuum ultraviolet photoemission from gas phase xenon and squalene nanoparticles followed by measurements using soft X-rays. It is demonstrated that the photoelectron distribution from X-ray irradiated squalene nanoparticles is dominated by secondary electrons. Bymore » scanning the photon energies and measuring the intensities of these secondary electrons, a near edge X-ray absorption fine structure (NEXAFS) spectrum is obtained. The NEXAFS technique is used to obtain spectra of aqueous nanoparticles at the oxygen K edge. By varying the position of the aqueous nanoparticle beam relative to the incident X-ray beam, evidence is presented such that the VMI technique allows for NEXAFS spectroscopy of water in different physical states. Finally, we discuss the possibility of applying VMI methods to probe liquids and solids via X-ray spectroscopy.« less

Inelastic losses in X-ray absorption theory

NASA Astrophysics Data System (ADS)

Campbell, Luke Whalin

There is a surprising lack of many body effects observed in XAS (X-ray Absorption Spectroscopy) experiments. While collective excitations and other satellite effects account for between 20% and 40% of the spectral weight of the core hole and photoelectron excitation spectrum, the only commonly observed many body effect is a relatively structureless amplitude reduction to the fine structure, typically no more than a 10% effect. As a result, many particle effects are typically neglected in the XAS codes used to predict and interpret modern experiments. To compensate, the amplitude reduction factor is simply fitted to experimental data. In this work, a quasi-boson model is developed to treat the case of XAS, when the system has both a photoelectron and a core hole. We find that there is a strong interference between the extrinsic and intrinsic losses. The interference reduces the excitation amplitudes at low energies where the core hole and photo electron induced excitations tend to cancel. At high energies, the interference vanishes, and the theory reduces to the sudden approximation. The x-ray absorption spectrum including many-body excitations is represented by a convolution of the one-electron absorption spectrum with an energy dependent spectral function. The latter has an asymmetric quasiparticle peak and broad satellite structure. The net result is a phasor sum, which yields the many body amplitude reduction and phase shift of the fine structure oscillations (EXAFS), and possibly additional satellite structure. Calculations for several cases of interest are found to be in reasonable agreement with experiment. Edge singularity effects and deviations from the final state rule arising from this theory are also discussed. The ab initio XAS code FEFF has been extended for calculations of the many body amplitude reduction and phase shift in x-ray spectroscopies. A new broadened plasmon pole self energy is added. The dipole matrix elements are modified to include a

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.

Effect of oxygen impurities on properties of the ternary superconductor SnMo/sub 6/S/sub 8/: Extended x-ray-absorption fine-structure determination of bond distances and local-density cluster calculations

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

Guenzburger, D.; Ellis, D.E.; Montano, P.A.

1985-10-01

Electronic structure calculations were performed for clusters representing the Chevrel-phase SnMo/sub 6/S/sub 8/, with and without oxygen doping. In order to obtain the local structure around the Sn atom, extended x-ray-absorption fine-structure (EXAFS) measurements were made with synchro- tron radiation. The interatomic distances obtained experimentally were used in the calculations. The effect of oxygen doping on the Moessbauer isomer shift and quadrupole splitting values of /sup 119/Sn was investigated theoretically and compared with reported experimental values. The effect of oxygen substitution on the density of states at the Fermi energy of the (Mo/sub 6/S/sub 8/)/sup 2 -/ cluster was alsomore » studied. The results suggest that oxygen doping does not alter significantly the electronic structure of SnMo/sub 6/S/sub 8/.« less

Advancing X-ray scattering metrology using inverse genetic algorithms.

PubMed

Hannon, Adam F; Sunday, Daniel F; Windover, Donald; Kline, R Joseph

2016-01-01

We compare the speed and effectiveness of two genetic optimization algorithms to the results of statistical sampling via a Markov chain Monte Carlo algorithm to find which is the most robust method for determining real space structure in periodic gratings measured using critical dimension small angle X-ray scattering. Both a covariance matrix adaptation evolutionary strategy and differential evolution algorithm are implemented and compared using various objective functions. The algorithms and objective functions are used to minimize differences between diffraction simulations and measured diffraction data. These simulations are parameterized with an electron density model known to roughly correspond to the real space structure of our nanogratings. The study shows that for X-ray scattering data, the covariance matrix adaptation coupled with a mean-absolute error log objective function is the most efficient combination of algorithm and goodness of fit criterion for finding structures with little foreknowledge about the underlying fine scale structure features of the nanograting.

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.

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.

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

Surface complexation and precipitate geometry for aqueous Zn(II) sorption on ferrihydrite I: X-ray absorption extended fine structure spectroscopy analysis

USGS Publications Warehouse

Waychunas, G.A.; Fuller, C.C.; Davis, J.A.

2002-01-01

"Two-line" ferrihydrite samples precipitated and then exposed to a range of aqueous Zn solutions (10-5 to 10-3 M), and also coprecipitated in similar Zn solutions (pH 6.5), have been examined by Zn and Fe K-edge X-ray absorption spectroscopy. Typical Zn complexes on the surface have Zn-O distances of 1.97(0.2) A?? and coordination numbers of about 4.0(0.5), consistent with tetrahedral oxygen coordination. This contrasts with Zn-O distances of 2.11(.02) A?? and coordination numbers of 6 to 7 in the aqueous Zn solutions used in sample preparation. X-ray absorption extended fine structure spectroscopy (EXAFS) fits to the second shell of cation neighbors indicate as many as 4 Zn-Fe neighbors at 3.44(.04) A?? in coprecipitated samples, and about two Zn-Fe neighbors at the same distance in adsorption samples. In both sets of samples, the fitted coordination number of second shell cations decreases as sorption density increases, indicating changes in the number and type of available complexing sites or the onset of competitive precipitation processes. Comparison of our results with the possible geometries for surface complexes and precipitates suggests that the Zn sorption complexes are inner sphere and at lowest adsorption densities are bidentate, sharing apical oxygens with adjacent edge-sharing Fe(O,OH)6 octahedra. Coprecipitation samples have complexes with similar geometry, but these are polydentate, sharing apices with more than two adjacent edge-sharing Fe(O,OH)6 polyhedra. The results are inconsistent with Zn entering the ferrihydrite structure (i.e., solid solution formation) or formation of other Zn-Fe precipitates. The fitted Zn-Fe coordination numbers drop with increasing Zn density with a minimum of about 0.8(.2) at Zn/(Zn + Fe) of 0.08 or more. This change appears to be attributable to the onset of precipitation of zinc hydroxide polymers with mainly tetrahedral Zn coordination. At the highest loadings studied, the nature of the complexes changes further

Atomic-scale distortion of optically activated Sm dopants identified with site-selective X-ray absorption spectroscopy

NASA Astrophysics Data System (ADS)

Ishii, Masashi; Crowe, Iain F.; Halsall, Matthew P.; Hamilton, Bruce; Hu, Yongfeng; Sham, Tsun-Kong; Harako, Susumu; Zhao, Xin-Wei; Komuro, Shuji

2013-10-01

The local structure of luminescent Sm dopants was investigated using an X-ray absorption fine-structure technique with X-ray-excited optical luminescence. Because this technique evaluates X-ray absorption from luminescence, only optically active sites are analyzed. The Sm L3 near-edge spectrum contains split 5d states and a shake-up transition that are specific to luminescent Sm. Theoretical calculations using cluster models identified an atomic-scale distortion that can reproduce the split 5d states. The model with C4v local symmetry and compressive bond length of Sm-O of a six-fold oxygen (SmO6) cluster is most consistent with the experimental results.

X-ray phase-contrast imaging of the breast—advances towards clinical implementation

PubMed Central

Herzen, J; Willner, M; Grandl, S; Scherer, K; Bamberg, F; Reiser, M F; Pfeiffer, F; Hellerhoff, K

2014-01-01

Breast cancer constitutes about one-quarter of all cancers and is the leading cause of cancer death in women. To reduce breast cancer mortality, mammographic screening programmes have been implemented in many Western countries. However, these programmes remain controversial because of the associated radiation exposure and the need for improvement in terms of diagnostic accuracy. Phase-contrast imaging is a new X-ray-based technology that has been shown to provide enhanced soft-tissue contrast and improved visualization of cancerous structures. Furthermore, there is some indication that these improvements of image quality can be maintained at reduced radiation doses. Thus, X-ray phase-contrast mammography may significantly contribute to advancements in early breast cancer diagnosis. Feasibility studies of X-ray phase-contrast breast CT have provided images that allow resolution of the fine structure of tissue that can otherwise only be obtained by histology. This implies that X-ray phase-contrast imaging may also lead to the development of entirely new (micro-) radiological applications. This review provides a brief overview of the physical characteristics of this new technology and describes recent developments towards clinical implementation of X-ray phase-contrast imaging of the breast. PMID:24452106

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.

Scanning Transmission X-ray Microscopy: Applications in Atmospheric Aerosol Research

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

Moffet, Ryan C.; Tivanski, Alexei V.; Gilles, Mary K.

Scanning transmission x-ray microscopy (STXM) combines x-ray microscopy and near edge x-ray absorption fine structure spectroscopy (NEXAFS). This combination provides spatially resolved bonding and oxidation state information. While there are reviews relevant to STXM/NEXAFS applications in other environmental fields (and magnetic materials) this chapter focuses on atmospheric aerosols. It provides an introduction to this technique in a manner approachable to non-experts. It begins with relevant background information on synchrotron radiation sources and a description of NEXAFS spectroscopy. The bulk of the chapter provides a survey of STXM/NEXAFS aerosol studies and is organized according to the type of aerosol investigated. Themore » purpose is to illustrate the current range and recent growth of scientific investigations employing STXM-NEXAFS to probe atmospheric aerosol morphology, surface coatings, mixing states, and atmospheric processing.« less

Structural changes of green roof growing substrate layer studied by X-ray CT

NASA Astrophysics Data System (ADS)

Jelinkova, Vladimira; Sacha, Jan; Dohnal, Michal; Snehota, Michal

2017-04-01

Increasing interest in green infrastructure linked with newly implemented legislation/rules/laws worldwide opens up research potential for field of soil hydrology. A better understanding of function of engineered soils involved in green infrastructure solutions such as green roofs or rain garden is needed. A soil layer is considered as a highly significant component of the aforesaid systems. In comparison with a natural soil, the engineered soil is assumed to be the more challenging case due to rapid structure changes early stages after its build-up. The green infrastructure efficiency depends on the physical and chemical properties of the soil, which are, in the case of engineered soils, a function of its initial composition and subsequent soil formation processes. The project presented in this paper is focused on fundamental processes in the relatively thick layer of engineered soil. The initial structure development, during which the pore geometry is altered by the growth of plant roots, water influx, solid particles translocation and other soil formation processes, is investigated with the help of noninvasive imaging technique  X-ray computed tomography. The soil development has been studied on undisturbed soil samples taken periodically from green roof test system during early stages of its life cycle. Two approaches and sample sizes were employed. In the first approach, undisturbed samples (volume of about 63 cm3) were taken each time from the test site and scanned by X-ray CT. In the second approach, samples (volume of about 630 cm3) were permanently installed at the test site and has been repeatedly removed to perform X-ray CT imaging. CT-derived macroporosity profiles reveal significant temporal changes of soil structure. Clogging of pores by fine particles and fissures development are two most significant changes that would affect the green roof system efficiency. This work has been supported by the Ministry of Education, Youth and Sports within

X-ray Absorption Study of Graphene Oxide and Transition Metal Oxide Nanocomposites.

PubMed

Gandhiraman, Ram P; Nordlund, Dennis; Javier, Cristina; Koehne, Jessica E; Chen, Bin; Meyyappan, M

2014-08-14

The surface properties of the electrode materials play a crucial role in determining the performance and efficiency of energy storage devices. Graphene oxide and nanostructures of 3d transition metal oxides were synthesized for construction of electrodes in supercapacitors, and the electronic structure and oxidation states were probed using near-edge X-ray absorption fine structure. Understanding the chemistry of graphene oxide would provide valuable insight into its reactivity and properties as the graphene oxide transformation to reduced-graphene oxide is a key step in the synthesis of the electrode materials. Polarized behavior of the synchrotron X-rays and the angular dependency of the near-edge X-ray absorption fine structures (NEXAFS) have been utilized to study the orientation of the σ and π bonds of the graphene oxide and graphene oxide-metal oxide nanocomposites. The core-level transitions of individual metal oxides and that of the graphene oxide nanocomposite showed that the interaction of graphene oxide with the metal oxide nanostructures has not altered the electronic structure of either of them. As the restoration of the π network is important for good electrical conductivity, the C K edge NEXAFS spectra of reduced graphene oxide nanocomposites confirms the same through increased intensity of the sp 2 -derived unoccupied states π* band. A pronounced angular dependency of the reduced sample and the formation of excitonic peaks confirmed the formation of extended conjugated network.

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

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

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%.

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.

[Based on Curing Age of Calcined Coal Gangue Fine Aggregate Mortar of X-Ray Diffraction and Scanning Electron Microscopy Analysis].

PubMed

Dong, Zuo-chao; Xia, Jun-wu; Duan, Xiao-mu; Cao, Ji-chang

2016-03-01

By using X-ray diffraction (XRD) and environmental scanning electron microscope (SEM) analysis method, we stud- ied the activity of coal gangue fine aggregate under different calcination temperature. In view of the activity of the highest-700 degrees C high temperature calcined coal gangue fine aggregate mortar of hydration products, microstructure and strength were discussed in this paper, and the change laws of mortar strength with curing age (3, 7, 14, 28, 60 and 90 d) growth were analyzed. Test results showed that coal gangue fine aggregate with the increase of calcination temperature, the active gradually increases. When the calcination temperature reaches 700 degrees C, the activity of coal gangue fine aggregate is the highest. When calcining temperature continues to rise, activity falls. After 700 degrees C high temperature calcined coal gangue fine aggregate has obvious ash activity, the active components of SiO2 and Al2 O3 can be with cement hydration products in a certain degree of secondary hydration reaction. Through on the top of the activity of different curing age 700 degrees C high temperature calcined coal gangue fine aggregate mortar, XRD and SEM analysis showed that with the increase of curing age, secondary hydration reaction will be more fully, and the amount of hydration products also gradually increases. Compared with the early ages of the cement mortar, the products are more stable hydration products filling in mortar microscopic pore, which can further improve the microstructure of mortar, strengthen the interface performance of the mortar. The mortar internal structure is more uniform, calcined coal gangue fine aggregate and cement mortar are more of a strong continuous whole, which increase the later strength of hardened cement mortar, 700 degrees C high temperature calcined coal gangue fine aggregate pozzolanic effect is obvious.

Synchrotron X-ray microscopy and spectroscopy analysis of iron in hemochromatosis liver and intestines

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

Ko, J .Y. Peter; Sham, Tsun-Kong; Chakrabarti, Subrata

2009-12-01

Hemochromatosis is a genetic disorder that causes body to store excess iron in organs such as heart or liver. Distribution of iron, as well as copper, zinc and calcium, and chemical identity of iron in hemochromatosis liver and intestine were investigated by X-ray microprobe experiments, which consist of X-ray microscopy and micro-X-ray absorption fine structure. Our results show that iron concentration in hemochromatosis liver tissue is high, while much less Fe is found in intestinal tissue. Moreover, chemical identity of Fe in hemochromatosis liver can be identified. X-ray microprobe experiments allows for examining elemental distribution at an excellent spatial resolution.more » Moreover, chemical identity of element of interest can be obtained.« less

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.

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

Study of the Role of Vortex Annihilation in the Mechanism of Neutron and X-Ray Production in the Plasma Focus.

DTIC Science & Technology

This paper shows that an understanding of the nature of the x-ray and neutron producing processes in the plasma focus requires a study of the ’fine...structure’ of the plasma focus and that this fine structure study requires diagnostic techniques with spacial resolution down to 50 micrometers and

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

A balloon-borne payload for imaging hard X-rays and gamma rays from solar flares

NASA Technical Reports Server (NTRS)

Crannell, Carol J.; Dennis, Brian R.; Orwig, Larry E.; Schmahl, Edward J.; Lang, Frederic L.; Starr, Richard; Norris, Jay P.; Greene, Michael E.; Hurford, Gordon J.; Johnson, W. N.

1991-01-01

Hard X-rays and gamma rays provide direct evidence of the roles of accelerated particles in solar flares. An approach that employs a spatial Fourier-transform technique for imaging the sources of these emissions is described, and the development of a balloon-borne imaging device based on this instrumental technique is presented. The detectors, together with the imaging optics, are sensitive to hard X-ray and gamma-ray emission in the energy-range from 20 to 700 keV. This payload, scheduled for its first flight in June 1992, will provide 11-arc second angular resolution and millisecond time resolution with a whole-sun field of view. For subsequent flights, the effective detector area can be increased by as much as a factor of four, and imaging optics with angular resolution as fine as 2 arcsec can be added to the existing gondola and metering structures.

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

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 ( ...

Evaluation of multiple-scale 3D characterization for coal physical structure with DCM method and synchrotron X-ray CT.

PubMed

Wang, Haipeng; Yang, Yushuang; Yang, Jianli; Nie, Yihang; Jia, Jing; Wang, Yudan

2015-01-01

Multiscale nondestructive characterization of coal microscopic physical structure can provide important information for coal conversion and coal-bed methane extraction. In this study, the physical structure of a coal sample was investigated by synchrotron-based multiple-energy X-ray CT at three beam energies and two different spatial resolutions. A data-constrained modeling (DCM) approach was used to quantitatively characterize the multiscale compositional distributions at the two resolutions. The volume fractions of each voxel for four different composition groups were obtained at the two resolutions. Between the two resolutions, the difference for DCM computed volume fractions of coal matrix and pores is less than 0.3%, and the difference for mineral composition groups is less than 0.17%. This demonstrates that the DCM approach can account for compositions beyond the X-ray CT imaging resolution with adequate accuracy. By using DCM, it is possible to characterize a relatively large coal sample at a relatively low spatial resolution with minimal loss of the effect due to subpixel fine length scale structures.

Three-dimensional imaging of nanoscale materials by using coherent x-rays

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

Miao, Jianwei

sufficiently fine scale on the Ewald sphere, the 3D structure of the object is determined by the 2D spherical pattern. We confirmed the theoretical analysis by performing 3D numerical reconstructions of a sodium silicate glass structure at 2 A resolution from a 2D spherical diffraction pattern alone. As X-ray free electron lasers are under rapid development worldwide, ankylography may open up a new horizon to obtain the 3D structure of a non-crystalline specimen from a single pulse and allow time-resolved 3D structure determination of disordered materials.« less

Real time observation of mouse fetal skeleton using a high resolution X-ray synchrotron

PubMed Central

Chang, Dong Woo; Kim, Bora; Shin, Jae Hoon; Yun, Young Min; Je, Jung Ho; Hwu, Yeu kuang; Yoon, Jung Hee

2011-01-01

The X-ray synchrotron is quite different from conventional radiation sources. This technique may expand the capabilities of conventional radiology and be applied in novel manners for special cases. To evaluate the usefulness of X-ray synchrotron radiation systems for real time observations, mouse fetal skeleton development was monitored with a high resolution X-ray synchrotron. A non-monochromatized X-ray synchrotron (white beam, 5C1 beamline) was employed to observe the skeleton of mice under anesthesia at embryonic day (E)12, E14, E15, and E18. At the same time, conventional radiography and mammography were used to compare with X-ray synchrotron. After synchrotron radiation, each mouse was sacrificed and stained with Alizarin red S and Alcian blue to observe bony structures. Synchrotron radiation enabled us to view the mouse fetal skeleton beginning at gestation. Synchrotron radiation systems facilitate real time observations of the fetal skeleton with greater accuracy and magnification compared to mammography and conventional radiography. Our results show that X-ray synchrotron systems can be used to observe the fine structures of internal organs at high magnification. PMID:21586868

Low-dose x-ray tomography through a deep convolutional neural network

DOE PAGES

Yang, Xiaogang; De Andrade, Vincent; Scullin, William; ...

2018-02-07

Synchrotron-based X-ray tomography offers the potential of rapid large-scale reconstructions of the interiors of materials and biological tissue at fine resolution. However, for radiation sensitive samples, there remain fundamental trade-offs between damaging samples during longer acquisition times and reducing signals with shorter acquisition times. We present a deep convolutional neural network (CNN) method that increases the acquired X-ray tomographic signal by at least a factor of 10 during low-dose fast acquisition by improving the quality of recorded projections. Short exposure time projections enhanced with CNN show similar signal to noise ratios as compared with long exposure time projections and muchmore » lower noise and more structural information than low-dose fats acquisition without CNN. We optimized this approach using simulated samples and further validated on experimental nano-computed tomography data of radiation sensitive mouse brains acquired with a transmission X-ray microscopy. We demonstrate that automated algorithms can reliably trace brain structures in datasets collected with low dose-CNN. As a result, this method can be applied to other tomographic or scanning based X-ray imaging techniques and has great potential for studying faster dynamics in specimens.« less

Low-dose x-ray tomography through a deep convolutional neural network

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

Yang, Xiaogang; De Andrade, Vincent; Scullin, William

Synchrotron-based X-ray tomography offers the potential of rapid large-scale reconstructions of the interiors of materials and biological tissue at fine resolution. However, for radiation sensitive samples, there remain fundamental trade-offs between damaging samples during longer acquisition times and reducing signals with shorter acquisition times. We present a deep convolutional neural network (CNN) method that increases the acquired X-ray tomographic signal by at least a factor of 10 during low-dose fast acquisition by improving the quality of recorded projections. Short exposure time projections enhanced with CNN show similar signal to noise ratios as compared with long exposure time projections and muchmore » lower noise and more structural information than low-dose fats acquisition without CNN. We optimized this approach using simulated samples and further validated on experimental nano-computed tomography data of radiation sensitive mouse brains acquired with a transmission X-ray microscopy. We demonstrate that automated algorithms can reliably trace brain structures in datasets collected with low dose-CNN. As a result, this method can be applied to other tomographic or scanning based X-ray imaging techniques and has great potential for studying faster dynamics in specimens.« less

X-ray absorption spectroscopic studies of mononuclear non-heme iron enzymes

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

Westre, Tami E.

Fe-K-edge X-ray absorption spectroscopy (XAS) has been used to investigate the electronic and geometric structure of the iron active site in non-heme iron enzymes. A new theoretical extended X-ray absorption fine structure (EXAFS) analysis approach, called GNXAS, has been tested on data for iron model complexes to evaluate the utility and reliability of this new technique, especially with respect to the effects of multiple-scattering. In addition, a detailed analysis of the 1s→3d pre-edge feature has been developed as a tool for investigating the oxidation state, spin state, and geometry of iron sites. Edge and EXAFS analyses have then been appliedmore » to the study of non-heme iron enzyme active sites.« less

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.

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.

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

X-ray fluorescence - a non-destructive tool in investigation of Czech fine and applied art objects

NASA Astrophysics Data System (ADS)

Trojek, T.; Musílek, L.

2017-08-01

A brief review of application of X-ray fluorescence analysis (XRFA) to fine and applied arts related to Czech cultural heritage is presented. The Department of Dosimetry and Application of Ionising Radiation of CTU-FNSPE has used XRFA in collaboration with various Czech institutions dealing with cultural history for many kinds of artefacts, (e.g., Roman and medieval brass, gemstones and noble metals from the sceptre of one of the faculties of the Charles University in Prague, millefiori beads, etc.). In some cases, a combination of various other techniques alongside XRFA was used for enhancing our knowledge of a measured object.

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.

Structural Characterization of Poorly-Crystalline Scorodite, Iron (III)-arsenate Co-precipitates and Uranium Millneutralized Raffinate Solids using X-ray Absorption Fine Structure Spectroscopy

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

Chen, N.; Jiang, D; Cutler, J

X-ray absorption fine structure (XAFS) is used to characterize the mineralogy of the iron(III)-arsenate(V) precipitates produced during the raffinate (aqueous effluent) neutralization process at the McClean Lake uranium mill in northern Saskatchewan, Canada. To facilitate the structural characterization of the precipitated solids derived from the neutralized raffinate, a set of reference compounds were synthesized and analyzed. The reference compounds include crystalline scorodite, poorly-crystalline scorodite, iron(III)-arsenate co-precipitates obtained under different pH conditions, and arsenate-adsorbed on goethite. The poorly-crystalline scorodite (prepared at pH 4 with Fe/As = 1) has similar As local structure as that of crystalline scorodite. Both As and Femore » K-edge XAFS of poorly-crystalline scorodite yield consistent results on As-Fe (or Fe-As) shell. From As K-edge analysis the As-Fe shell has an inter-atomic distance of 3.33 {+-} 0.02 A and coordination number of 3.2; while from Fe K-edge analysis the Fe-As distance and coordination number are 3.31 {+-} 0.02 A and 3.8, respectively. These are in contrast with the typical arsenate adsorption on bidentate binuclear sites on goethite surfaces, where the As-Fe distance is 3.26 {+-} 0.03 A and coordination number is close to 2. A similar local structure identified in the poorly-crystalline scorodite is also found in co-precipitation solids (Fe(III)/As(V) = 3) when precipitated at the same pH (pH = 4): As-Fe distance 3.30 {+-} 0.03 A and coordination number 3.9; while at pH = 8 the co-precipitate has As-Fe distance of 3.27 {+-} 0.03 A and coordination number about 2, resembling more closely the adsorption case. The As local structure in the two neutralized raffinate solid series (precipitated at pH values up to 7) closely resembles that in the poorly-crystalline scorodite. All of the raffinate solids have the same As-Fe inter-atomic distance as that in the poorly-crystalline scorodite, and a systematic

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…

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.

Fine structure of the K X-ray absorption spectra of titanium in some hydrides, borides, and silicides (in Russian)

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

Vainshtein, �. E.; Zhurakovskii, E. A.

1959-08-01

X-ray spectral analyses confirmed the hypothesis on the metal-like state of hydrogen in tithnium hydrides. Experiments with titunium borides and silicides indicate the special character and degree of the 3d--level participation in the metallic'' bond between the atoms of various complexes. The structure of metalloid elements becomes more complicated with an increase in the specific number of boron and silicon atoms and the bond between the atoms tends to become covalent. (R.V.J.)

A Geometric and Electrostatic Study of the [4Fe-4S] Cluster of Adenosine-5´-Phosphosulfate Reductase from Broken Symmetry Density Functional Calculations and Extended X-ray Absorption Fine Structure Spectroscopy

PubMed Central

Bhave, Devayani P.; Han, Wen-Ge; Pazicni, Samuel; Penner-Hahn, James E.; Carroll, Kate S.; Noodleman, Louis

2011-01-01

Adenosine-5’-phosphosulfate reductase (APSR) is an iron-sulfur protein that catalyses the reduction of adenosine-5’-phosphosulfate (APS) to sulfite. APSR coordinates to a [4Fe-4S] cluster via a conserved CC-X~80-CXXC motif and the cluster is essential for catalysis. Despite extensive functional, structural and spectroscopic studies, the exact role of the iron-sulfur cluster in APS reduction remains unknown. To gain an understanding into the role of the cluster, density functional theory (DFT) analysis and extended X-ray fine structure spectroscopy (EXAFS) have been performed to reveal insights into the coordination, geometry and electrostatics of the [4Fe-4S] cluster. XANES data confirms that the cluster is in the [4Fe-4S]2+ state in both native and substrate-bound APSR while EXAFS data recorded at ~0.1 Å resolution indicates that there is no significant change in the structure of the [4Fe-4S] cluster between the native and substrate-bound forms of the protein. On the other hand, DFT calculations provide an insight into the subtle differences between the geometry of the cluster in the native and APS-bound forms of APSR. A comparison between models with and without the tandem cysteine pair coordination of the cluster suggests a role for the unique coordination in facilitating a compact geometric structure and ‘fine-tuning’ the electronic structure to prevent reduction of the cluster. Further, calculations using models in which residue Lys144 is mutated to Ala confirm the finding that Lys144 serves as a crucial link in the interactions involving the [4Fe-4S] cluster and APS. PMID:21678934

Diamond sensors and polycapillary lenses for X-ray absorption spectroscopy.

PubMed

Ravel, B; Attenkofer, K; Bohon, J; Muller, E; Smedley, J

2013-10-01

Diamond sensors are evaluated as incident beam monitors for X-ray absorption spectroscopy experiments. These single crystal devices pose a challenge for an energy-scanning experiment using hard X-rays due to the effect of diffraction from the crystalline sensor at energies which meet the Bragg condition. This problem is eliminated by combination with polycapillary lenses. The convergence angle of the beam exiting the lens is large compared to rocking curve widths of the diamond. A ray exiting one capillary from the lens meets the Bragg condition for any reflection at a different energy from the rays exiting adjacent capillaries. This serves to broaden each diffraction peak over a wide energy range, allowing linear measurement of incident intensity over the range of the energy scan. Extended X-ray absorption fine structure data are measured with a combination of a polycapillary lens and a diamond incident beam monitor. These data are of comparable quality to data measured without a lens and with an ionization chamber monitoring the incident beam intensity.

600 eV falcon-linac thomson x-ray source

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

Crane, J K; LeSage, G P; Ditmire, T

2000-12-15

stockpile stewardship. Another x-ray diagnostic technique, extended x-ray absorption fine structure (EXAFS) spectroscopy, can be used to measure small-scale structural changes to understand the underlying atomic physics associated with the formation of defects. [2]« less

X-ray absorption spectroscopy study on SiC-side interface structure of SiO2–SiC formed by thermal oxidation in dry oxygen

NASA Astrophysics Data System (ADS)

Isomura, Noritake; Kosaka, Satoru; Kataoka, Keita; Watanabe, Yukihiko; Kimoto, Yasuji

2018-06-01

Extended X-ray absorption fine structure (EXAFS) spectroscopy is demonstrated to measure the fine atomic structure of SiO2–SiC interfaces. The SiC-side of the interface can be measured by fabricating thin SiO2 films and using SiC-selective EXAFS measurements. Fourier transforms of the oscillations of the EXAFS spectra correspond to radial-structure functions and reveal a new peak of the first nearest neighbor of Si for m-face SiC, which does not appear in measurements of the Si-face. This finding suggests that the m-face interface could include a structure with shorter Si–C distances. Numerical calculations provide additional support for this finding.

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

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.

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

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.

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.

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

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.

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.

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.

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.

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

GPU-accelerated depth map generation for X-ray simulations of complex CAD geometries

NASA Astrophysics Data System (ADS)

Grandin, Robert J.; Young, Gavin; Holland, Stephen D.; Krishnamurthy, Adarsh

2018-04-01

Interactive x-ray simulations of complex computer-aided design (CAD) models can provide valuable insights for better interpretation of the defect signatures such as porosity from x-ray CT images. Generating the depth map along a particular direction for the given CAD geometry is the most compute-intensive step in x-ray simulations. We have developed a GPU-accelerated method for real-time generation of depth maps of complex CAD geometries. We preprocess complex components designed using commercial CAD systems using a custom CAD module and convert them into a fine user-defined surface tessellation. Our CAD module can be used by different simulators as well as handle complex geometries, including those that arise from complex castings and composite structures. We then make use of a parallel algorithm that runs on a graphics processing unit (GPU) to convert the finely-tessellated CAD model to a voxelized representation. The voxelized representation can enable heterogeneous modeling of the volume enclosed by the CAD model by assigning heterogeneous material properties in specific regions. The depth maps are generated from this voxelized representation with the help of a GPU-accelerated ray-casting algorithm. The GPU-accelerated ray-casting method enables interactive (> 60 frames-per-second) generation of the depth maps of complex CAD geometries. This enables arbitrarily rotation and slicing of the CAD model, leading to better interpretation of the x-ray images by the user. In addition, the depth maps can be used to aid directly in CT reconstruction algorithms.

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

Homogeneity of Pb(Zr ,Ti)O3 thin films by chemical solution deposition: Extended x-ray absorption fine structure spectroscopy study of zirconium local environment

NASA Astrophysics Data System (ADS)

Malic, Barbara; Arcon, Iztok; Kodre, Alojz; Kosec, Marija

2006-09-01

Sols for Pb(Zr0.53Ti0.47)O3 (PZT) thin films were prepared by 2-methoxyethanol route from lead acetate, titanium n-propoxide, and zirconium n-propoxide, the latter either unmodified or modified with acetylacetone or acetic acid in a 2/1 molar ratio and deposited on sapphire (0001). By Zr K-edge extended x-ray absorption fine structure (EXAFS) spectroscopy, the structural changes in the Zr local environment, induced by the addition of the two modifiers, were followed from the synthesis of the PZT sol to the transition to the amorphous film. In the unmodified PZT sol segregation of Zr species occurs from the original dimers present in the Zr propoxide solution in 2-methoxyethanol. The immediate neighborhood of Zr atoms changes markedly at the transition from the sol to the amorphous film: the local structure around Zr atoms is similar to the one found in tetragonal zirconia particles. The modification of Zr propoxide with acetylacetone in 2-methoxyethanol results in Zr monomers. In PZT sol, clustering of Zr species is observed continuing into the amorphous film. By modification with acetic acid the original dimeric structure of the Zr precursor is retained in the PZT sol and further in the amorphous film. Selective modification of Zr propoxide with acetic acid therefore results in a more homogeneous distribution of Zr atoms in the PZT sol and amorphous film than in both as-received and acetylacetone-modified Zr propoxide.

X-ray coherent scattering tomography of textured material (Conference Presentation)

NASA Astrophysics Data System (ADS)

Zhu, Zheyuan; Pang, Shuo

2017-05-01

Small-angle X-ray scattering (SAXS) measures the signature of angular-dependent coherently scattered X-rays, which contains richer information in material composition and structure compared to conventional absorption-based computed tomography. SAXS image reconstruction method of a 2 or 3 dimensional object based on computed tomography, termed as coherent scattering computed tomography (CSCT), enables the detection of spatially-resolved, material-specific isotropic scattering signature inside an extended object, and provides improved contrast for medical diagnosis, security screening, and material characterization applications. However, traditional CSCT methods assumes materials are fine powders or amorphous, and possess isotropic scattering profiles, which is not generally true for all materials. Anisotropic scatters cannot be captured using conventional CSCT method and result in reconstruction errors. To obtain correct information from the sample, we designed new imaging strategy which incorporates extra degree of detector motion into X-ray scattering tomography for the detection of anisotropic scattered photons from a series of two-dimensional intensity measurements. Using a table-top, narrow-band X-ray source and a panel detector, we demonstrate the anisotropic scattering profile captured from an extended object and the reconstruction of a three-dimensional object. For materials possessing a well-organized crystalline structure with certain symmetry, the scatter texture is more predictable. We will also discuss the compressive schemes and implementation of data acquisition to improve the collection efficiency and accelerate the imaging process.

The New Hard X-ray Mission

NASA Astrophysics Data System (ADS)

Pareschi, Giovanni; Tagliaferri, Gianpiero; Argan, Andrea; Bellazzini, Ronaldo; Catalano, Osvaldo; Costa, Enrico; Cusumano, Giancarlo; Fiore, Fabrizio; Fiorini, Carlo; Malaguti, Giuseppe; Matt, Giorgio; Mereghetti, Sandro; Micela, Giuseppina; Perola, Giuseppe Cesare; Villa, Gabriele

2010-07-01

The Italian New Hard X-ray Mission (NHXM) is an evolution of the HEXIT-Sat concept, extending up to 80 keV the fine imaging capability today available only at E<10 keV, with the further addition of photoelectric imaging polarimetry. NHXM consists of four identical mirrors, with a 10 m focal length, achieved after launch by means of a deployable structure. Three of the four telescopes will have at their focus three identical spectro-imaging cameras, while a X-ray imaging polarimeter will be placed at the focus of the fourth. In order to ensure a low and stable background, NHXM will be place on a low Earth equatorial orbit. NHXM will provide a real breakthrough on a number of hot astrophysical issues, broadly falling under two main topics: i) censing the black holes in the Universe and probing the physics of accretion in the most diverse conditions; ii) investigating the particle acceleration mechanisms at work in different contexts, and the effects of radiative transfer in highly magnetized plasmas and strong gravitational fields.

Novel applications of X-ray photoelectron spectroscopy on unsupported nanoparticles

NASA Astrophysics Data System (ADS)

Kostko, Oleg; Xu, Bo; Jacobs, Michael I.; Ahmed, Musahid

X-ray photoelectron spectroscopy (XPS) is a powerful technique for chemical analysis of surfaces. We will present novel results of XPS on unsupported, gas-phase nanoparticles using a velocity-map imaging (VMI) spectrometer. This technique allows for probes of both the surfaces of nanoparticles via XPS as well as their interiors via near edge X-ray absorption fine structure (NEXAFS) spectroscopy. A recent application of this technique has confirmed that arginine's guanidinium group exists in a protonated state even in strongly basic solution. Moreover, the core-level photoelectron spectroscopy can provide information on the effective attenuation length (EAL) of low kinetic energy electrons. This contradictory value is important for determining the probing depth of XPS and in photolithography. A new method for determining EALs will be presented.

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

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

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.

Nonlinear resonance scattering of femtosecond X-ray pulses on atoms in plasmas

NASA Astrophysics Data System (ADS)

Rosmej, F. B.; Astapenko, V. A.; Lisitsa, V. S.; Moroz, N. N.

2017-11-01

It is shown that for sufficiently short pulses the resonance scattering probability becomes a nonlinear function of the pulse duration. For fs X-ray pulses scattered on atoms in plasmas maxima and minima develop in the nonlinear regime whereas in the limit of long pulses the probability becomes linear and turns over into the standard description of the electromagnetic pulse scattering. Numerical calculations are carried out in terms of a generalized scattering probability for the total time of pulse duration including fine structure splitting and ion Doppler broadening in hot plasmas. For projected X-ray monocycles, the generalized nonlinear approach differs by 1-2 orders of magnitude from the standard theory.

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

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.

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.

X-ray absorption spectroscopy study of Gd3+-loaded ultra-short carbon nanotubes

NASA Astrophysics Data System (ADS)

Ma, Q.; Jebb, M.; Tweedle, M. F.; Wilson, L. J.

2013-04-01

We present an x-ray absorption spectroscopy study of the local structure around the Gd3+ion loaded in ultra short (20-100 nm) carbon nanotubes (GNTs). X-ray Gd L3 absorption near edge structure data shows that the 31.2-μM GNT suspension exhibits a clear characteristic of hydration at the [GdOn] cluster. Extended x-ray absorption fine structure data show that the Gd3+ ion is coordinated by about 9 oxygen ions and that this first coordination shell exhibits an asymmetry similar to that found in triclinic Gd-acetate or Gd[C2H3O2]3·4H2O or GdAc. After correction for the asymmetry using the cumulant of the third order, the Gd-O bond distance is found to be 2.345 Å, instead of 2.406 Å for a symmetrical (or Gaussian) distribution. It is shorter than that in the Gd-containing MRI contrast agents currently in clinical uses. This may account in part for high proton relaxivity observed for the GNT suspension.

High resolution x-ray fluorescence spectroscopy - a new technique for site- and spin-selectivity

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

Wang, Xin

1996-12-01

X-ray spectroscopy has long been used to elucidate electronic and structural information of molecules. One of the weaknesses of x-ray absorption is its sensitivity to all of the atoms of a particular element in a sample. Through out this thesis, a new technique for enhancing the site- and spin-selectivity of the x-ray absorption has been developed. By high resolution fluorescence detection, the chemical sensitivity of K emission spectra can be used to identify oxidation and spin states; it can also be used to facilitate site-selective X-ray Absorption Near Edge Structure (XANES) and site-selective Extended X-ray Absorption Fine Structure (EXAFS). Themore » spin polarization in K fluorescence could be used to generate spin selective XANES or spin-polarized EXAFS, which provides a new measure of the spin density, or the nature of magnetic neighboring atoms. Finally, dramatic line-sharpening effects by the combination of absorption and emission processes allow observation of structure that is normally unobservable. All these unique characters can enormously simplify a complex x-ray spectrum. Applications of this novel technique have generated information from various transition-metal model compounds to metalloproteins. The absorption and emission spectra by high resolution fluorescence detection are interdependent. The ligand field multiplet model has been used for the analysis of K{alpha} and K{beta} emission spectra. First demonstration on different chemical states of Fe compounds has shown the applicability of site selectivity and spin polarization. Different interatomic distances of the same element in different chemical forms have been detected using site-selective EXAFS.« less

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.

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.

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.

Tin Oxide Crystals Exposed by Low-Energy {110} Facets for Enhanced Electrochemical Heavy Metal Ions Sensing: X-ray Absorption Fine Structure Experimental Combined with Density-Functional Theory Evidence.

PubMed

Jin, Zhen; Yang, Meng; Chen, Shao-Hua; Liu, Jin-Huai; Li, Qun-Xiang; Huang, Xing-Jiu

2017-02-21

Herein, we revealed that the electrochemical behaviors on the detection of heavy metal ions (HMIs) would largely rely on the exposed facets of SnO 2 nanoparticles. Compared to the high-energy {221} facet, the low-energy {110} facet of SnO 2 possessed better electrochemical performance. The adsorption/desorption tests, density-functional theory (DFT) calculations, and X-ray absorption fine structure (XAFS) studies showed that the lower barrier energy of surface diffusion on {110} facet was critical for the superior electrochemical property, which was favorable for the ions diffusion on the electrode, and further leading the enhanced electrochemical performance. Through the combination of experiments and theoretical calculations, a reliable interpretation of the mechanism for electroanalysis of HMIs with nanomaterials exposed by different crystal facets has been provided. Furthermore, it provides a deep insight into understanding the key factor to improve the electrochemical performance for HMIs detection, so as to design high-performance electrochemical sensors.

X-ray absorption spectroscopy and neutron diffraction study of the perovskite-type rare-earth cobaltites

NASA Astrophysics Data System (ADS)

Sikolenko, V.; Efimova, E.; Franz, A.; Ritter, C.; Troyanchuk, I. O.; Karpinsky, D.; Zubavichus, Y.; Veligzhanin, A.; Tiutiunnikov, S. I.; Sazonov, A.; Efimov, V.

2018-05-01

Correlations between local and long-range structure distortions in the perovskite-type RE1-xSrxCoO3-δ (RE = La, Pr, Nd; x = 0.0 and 0.5) compounds have been studied at room temperature by extended X-ray absorption fine structure (EXAFS) at the Co K-edge and high-resolution neutron powder diffraction (NPD). The use of two complementary experimental techniques allowed us to explore the influence of the type of rare-earth element and strontium substitution on unusual behavior of static and dynamic features of both the Co-O bond lengths.

Local structural and chemical ordering of nanosized Pt3±δCo probed by multiple-scattering x-ray absorption spectroscopy

NASA Astrophysics Data System (ADS)

Greco, Giorgia; Witkowska, Agnieszka; Principi, Emiliano; Minicucci, Marco; di Cicco, Andrea

2011-04-01

This work reports a detailed investigation of the local structure and chemical disorder of a Pt3±δCo thin film and Pt3±δCo nanoparticles. We have used a combination of techniques including x-ray absorption spectroscopy (XAS), x-ray diffraction (XRD), and high-resolution transmission electron microscopy (TEM). High-quality XAS spectra at the Co K edge and Pt L3 edge have been analyzed using double-edge multiple-scattering data analysis. Structural extended x-ray absorption fine structure (EXAFS) refinements have been performed accounting for the reduction of the coordination numbers and degeneracy of three-atom configurations, resulting from the measured size distribution and stoichiometry. The important effect of chemical ordering on pair and three-atom configurations has been studied using computer simulations based on a simple model accounting for substitutional disorder, defined by an order parameter s. It has been found that individual EXAFS signals related to the minority species (Co) are extremely sensitive to substitutional disorder so their intensities, especially those of the collinear three-atom configurations, can be used as a measure of the ordering level. The thin film has been found to be chemically disordered (s⩽0.4), in agreement with previous estimates. The Pt3±δCo nanoalloy has been found to be partially ordered (s=0.6±0.1) while the local structure around Co atoms is characterized by a higher level of structural disorder as compared to the bulk-like thin film. The robust approach for nanomaterial characterization used in this work combining different techniques can, in principle, be applied for structural refinements of any binary nanocrystalline functional system.

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

Alternative difference analysis scheme combining R-space EXAFS fit with global optimization XANES fit for X-ray transient absorption spectroscopy.

PubMed

Zhan, Fei; Tao, Ye; Zhao, Haifeng

2017-07-01

Time-resolved X-ray absorption spectroscopy (TR-XAS), based on the laser-pump/X-ray-probe method, is powerful in capturing the change of the geometrical and electronic structure of the absorbing atom upon excitation. TR-XAS data analysis is generally performed on the laser-on minus laser-off difference spectrum. Here, a new analysis scheme is presented for the TR-XAS difference fitting in both the extended X-ray absorption fine-structure (EXAFS) and the X-ray absorption near-edge structure (XANES) regions. R-space EXAFS difference fitting could quickly provide the main quantitative structure change of the first shell. The XANES fitting part introduces a global non-derivative optimization algorithm and optimizes the local structure change in a flexible way where both the core XAS calculation package and the search method in the fitting shell are changeable. The scheme was applied to the TR-XAS difference analysis of Fe(phen) 3 spin crossover complex and yielded reliable distance change and excitation population.

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.

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.

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

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.

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.

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).

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

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.

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.

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

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

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.

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

Electronic structure of nickel silicide in subhalf-micron lines and blanket films: An x-ray absorption fine structures study at the Ni and Si L3,2 edge

NASA Astrophysics Data System (ADS)

Naftel, S. J.; Coulthard, I.; Sham, T. K.; Xu, D.-X.; Erickson, L.; Das, S. R.

1999-05-01

We report a Ni and Si L3,2-edge x-ray absorption near edge structures (XANES) study of nickel-silicon interaction in submicron (0.15 and 0.2 μm) lines on a n-Si(100) wafer as well as a series of well characterized Ni-Si blanket films. XANES measurements recorded in both total electron yield and soft x-ray fluorescence yield indicate that under the selected silicidation conditions, the more desirable low resistivity phase, NiSi, is indeed the dominant phase in the subhalf-micron lines although the formation of this phase is less complete as the line becomes narrower and this is accompanied by a Ni rich surface.

Effect of Fe-substitution on the structure and magnetism of single crystals Mn2-xFexBO4

NASA Astrophysics Data System (ADS)

Platunov, M. S.; Kazak, N. V.; Knyazev, Yu. V.; Bezmaternykh, L. N.; Moshkina, E. M.; Trigub, A. L.; Veligzhanin, A. A.; Zubavichus, Y. V.; Solovyov, L. A.; Velikanov, D. A.; Ovchinnikov, S. G.

2017-10-01

Single crystalline Mn2-xFexBO4 with x = 0.3, 0.5, 0.7 grown by the flux method have been studied by means of X-ray diffraction and X-ray absorption spectroscopy at both Mn and Fe K edges. The compounds were found to crystallize in an orthorhombic warwickite structure (sp. gr. Pnam). The lattice parameters change linearly with x thus obeying the Vegard's law. The Fe3+ substitution for Mn3+ has been deduced from the X-ray absorption near-edge structure (XANES) spectra. Two energy positions of the absorption edges have been observed in Mn K-edge XANES spectra indicating the presence of manganese in two different oxidation states. Extended X-ray absorption fine structure (EXAFS) analysis has shown the reduction of local structural distortions upon Fe substitution. The magnetization data have revealed a spin-glass transition at TSG = 11, 14 and 18 K for x = 0.3, 0.5 and 0.7, respectively.

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.

Novel silica stabilization method for the analysis of fine nanocrystals using coherent X-ray diffraction imaging

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

Monteforte, Marianne; Estandarte, Ana K.; Chen, Bo

2016-06-23

High-energy X-ray Bragg coherent diffraction imaging (BCDI) is a well established synchrotron-based technique used to quantitatively reconstruct the three-dimensional morphology and strain distribution in nanocrystals. The BCDI technique has become a powerful analytical tool for quantitative investigations of nanocrystals, nanotubes, nanorods and more recently biological systems. BCDI has however typically failed for fine nanocrystals in sub-100?nm size regimes ? a size routinely achievable by chemical synthesis ? despite the spatial resolution of the BCDI technique being 20?30?nm. The limitations of this technique arise from the movement of nanocrystals under illumination by the highly coherent beam, which prevents full diffraction datamore » sets from being acquired. A solution is provided here to overcome this problem and extend the size limit of the BCDI technique, through the design of a novel stabilization method by embedding the fine nanocrystals into a silica matrix. Chemically synthesized FePt nanocrystals of maximum dimension 20?nm and AuPd nanocrystals in the size range 60?65?nm were investigated with BCDI measurement at beamline 34-ID-C of the APS, Argonne National Laboratory. Novel experimental methodologies to elucidate the presence of strain in fine nanocrystals are a necessary pre-requisite in order to better understand strain profiles in engineered nanocrystals for novel device development.« less

Novel silica stabilization method for the analysis of fine nanocrystals using coherent X-ray diffraction imaging.

PubMed

Monteforte, Marianne; Estandarte, Ana K; Chen, Bo; Harder, Ross; Huang, Michael H; Robinson, Ian K

2016-07-01

High-energy X-ray Bragg coherent diffraction imaging (BCDI) is a well established synchrotron-based technique used to quantitatively reconstruct the three-dimensional morphology and strain distribution in nanocrystals. The BCDI technique has become a powerful analytical tool for quantitative investigations of nanocrystals, nanotubes, nanorods and more recently biological systems. BCDI has however typically failed for fine nanocrystals in sub-100 nm size regimes - a size routinely achievable by chemical synthesis - despite the spatial resolution of the BCDI technique being 20-30 nm. The limitations of this technique arise from the movement of nanocrystals under illumination by the highly coherent beam, which prevents full diffraction data sets from being acquired. A solution is provided here to overcome this problem and extend the size limit of the BCDI technique, through the design of a novel stabilization method by embedding the fine nanocrystals into a silica matrix. Chemically synthesized FePt nanocrystals of maximum dimension 20 nm and AuPd nanocrystals in the size range 60-65 nm were investigated with BCDI measurement at beamline 34-ID-C of the APS, Argonne National Laboratory. Novel experimental methodologies to elucidate the presence of strain in fine nanocrystals are a necessary pre-requisite in order to better understand strain profiles in engineered nanocrystals for novel device development.

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.

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

Atomic and electronic structure of Mo6S9-xIx nanowires

NASA Astrophysics Data System (ADS)

Meden, A.; Kodre, A.; Padeznik Gomilsek, J.; Arcon, I.; Vilfan, I.; Vrbanic, D.; Mrzel, A.; Mihailovic, D.

2005-09-01

Moybdenum-based subnanometre diameter nanowires are easy to synthesize and disperse, and they exhibit a variety of functional properties in which they are superior to other one-dimensional materials. However, further progress in the understanding of physical properties and the development of new and specific applications have so far been impeded by the fact that their structure was not accurately known. Here we report on a combination of systematic x-ray diffraction and extended x-ray absorption fine structure experiments, and first-principles theoretical structure calculations, which are used to determine the atomic skeletal structure of individual Mo6S9-xIx (MoSIx) nanowires, their packing arrangement within bundles and their electronic band structure. From this work we conclude that the variations in functional properties appear to arise from different stoichiometry, not skeletal structure. A supplementary data file is available from http://stacks.iop.org/0957-4484/16/1578

Structural characterization of poorly-crystalline scorodite, iron(III)-arsenate co-precipitates and uranium mill neutralized raffinate solids using X-ray absorption fine structure spectroscopy

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

Chen, N; Jiang, D T; Cutler, J

X-ray absorption fine structure (XAFS) is used to characterize the mineralogy of the iron(III)-arsenate(V) precipitates produced during the raffinate (aqueous effluent) neutralization process at the McClean Lake uranium mill in northern Saskatchewan, Canada. To facilitate the structural characterization of the precipitated solids derived from the neutralized raffinate, a set of reference compounds were synthesized and analyzed. The reference compounds include crystalline scorodite, poorly-crystalline scorodite, iron(III)-arsenate co-precipitates obtained under different pH conditions, and arsenate-adsorbed on goethite. The poorly-crystalline scorodite (prepared at pH 4 with Fe/As = 1) has similar As local structure as that of crystalline scorodite. Both As and Femore » K-edge XAFS of poorly-crystalline scorodite yield consistent results on As-Fe (or Fe-As) shell. From As K-edge analysis the As-Fe shell has an inter-atomic distance of 3.33 ± 0.02 Å and coordination number of 3.2; while from Fe K-edge analysis the Fe-As distance and coordination number are 3.31 ± 0.02 Å and 3.8, respectively. These are in contrast with the typical arsenate adsorption on bidentate binuclear sites on goethite surfaces, where the As-Fe distance is 3.26 ± 0.03 Å and coordination number is close to 2. A similar local structure identified in the poorly-crystalline scorodite is also found in co-precipitation solids (Fe(III)/As(V) = 3) when precipitated at the same pH (pH = 4): As-Fe distance 3.30 ± 0.03 Å and coordination number 3.9; while at pH = 8 the co-precipitate has As-Fe distance of 3.27 ± 0.03 Å and coordination number about 2, resembling more closely the adsorption case. The As local structure in the two neutralized raffinate solid series (precipitated at pH values up to 7) closely resembles that in the poorly-crystalline scorodite. All of the raffinate solids have the same As-Fe inter-atomic distance as that in the poorly-crystalline scorodite, and a systematic

Interaction between Eu(III) and graphene oxide nanosheets investigated by batch and extended X-ray absorption fine structure spectroscopy and by modeling techniques.

PubMed

Sun, Yubing; Wang, Qi; Chen, Changlun; Tan, Xiaoli; Wang, Xiangke

2012-06-05

The interaction mechanism between Eu(III) and graphene oxide nanosheets (GONS) was investigated by batch and extended X-ray absorption fine structure (EXAFS) spectroscopy and by modeling techniques. The effects of pH, ionic strength, and temperature on Eu(III) adsorption on GONS were evaluated. The results indicated that ionic strength had no effect on Eu(III) adsorption on GONS. The maximum adsorption capacity of Eu(III) on GONS at pH 6.0 and T = 298 K was calculated to be 175.44 mg·g(-1), much higher than any currently reported. The thermodynamic parameters calculated from temperature-dependent adsorption isotherms suggested that Eu(III) adsorption on GONS was an endothermic and spontaneous process. Results of EXAFS spectral analysis indicated that Eu(III) was bound to ∼6-7 O atoms at a bond distance of ∼2.44 Å in the first coordination shell. The value of Eu-C bond distance confirmed the formation of inner-sphere surface complexes on GONS. Surface complexation modeling gave an excellent fit with the predominant mononuclear monodentate >SOEu(2+) and binuclear bidentate (>SO)(2)Eu(2)(OH)(2)(2+) complexes. This paper highlights the application of GONS as a suitable material for the preconcentration and removal of trivalent lanthanides and actinides from aqueous solutions in environmental pollution management.

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.

Quick-scanning x-ray absorption spectroscopy system with a servo-motor-driven channel-cut monochromator with a temporal resolution of 10 ms.

PubMed

Nonaka, T; Dohmae, K; Araki, T; Hayashi, Y; Hirose, Y; Uruga, T; Yamazaki, H; Mochizuki, T; Tanida, H; Goto, S

2012-08-01

We have developed a quick-scanning x-ray absorption fine structure (QXAFS) system and installed it at the recently constructed synchrotron radiation beamline BL33XU at the SPring-8. Rapid acquisition of high-quality QXAFS data was realized by combining a servo-motor-driven Si channel-cut monochromator with a tapered undulator. Two tandemly aligned monochromators with channel-cut Si(111) and Si(220) crystals covered energy ranges of 4.0-28.2 keV and 6.6-46.0 keV, respectively. The system allows the users to adjust instantly the energy ranges of scans, the starting angles of oscillations, and the frequencies. The channel-cut crystals are cooled with liquid nitrogen to enable them to withstand the high heat load from the undulator radiation. Deformation of the reflecting planes is reduced by clamping each crystal with two cooling blocks. Performance tests at the Cu K-edge demonstrated sufficiently high data quality for x-ray absorption near-edge structure and extended x-ray absorption fine-structure analyses with temporal resolutions of up to 10 and 25 ms, respectively.

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.

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

X-ray absorption spectroscopy and EPR studies of oriented spinach thylakoid preparations

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

Andrews, J.C.

In this study, oriented Photosystem II (PS II) particles from spinach chloroplasts are studied with electron paramagnetic resonance (EPR) and x-ray absorption spectroscopy (XAS) to determine more details of the structure of the oxygen evolving complex (OEC). The nature of halide binding to Mn is also studied with Cl K-edge and Mn EXAFS (extended x-ray absorption fine structure) of Mn-Cl model compounds, and with Mn EXAFS of oriented PS II in which Br has replaced Cl. Attention is focused on the following: photosynthesis and the oxygen evolving complex; determination of mosaic spread in oriented photosystem II particles from signal IImore » EPR measurement; oriented EXAFS--studies of PS II in the S{sub 2} state; structural changes in PS II as a result of treatment with ammonia: EPR and XAS studies; studies of halide binding to Mn: Cl K-edge and Mn EXAFS of Mn-Cl model compounds and Mn EXAFS of oriented Br-treated photosystem II.« less

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.

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.

Probing the Li Insertion Mechanism of ZnFe 2O 4 in Li-Ion Batteries: A Combined X-Ray Diffraction, Extended X-Ray Absorption Fine Structure, and Density Functional Theory Study [Probing the Li insertion mechanism of ZnFe 2O 4 in Li ion batteries: A combined XRD, EXAFS, and DFT study

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

Zhang, Yiman; Pelliccione, Christopher J.; Brady, Alexander B.

Here, we report an extensive study on fundamental properties that determine the functional electrochemistry of ZnFe 2O 4 spinel (theoretical capacity of 1000 mAh/g). For the first time, the reduction mechanism is followed through a combination of in situ X-ray diffraction data, synchrotron based powder diffraction, and ex-situ extended X-ray absorption fine structure allowing complete visualization of reduction products irrespective of their crystallinity. The first 0.5 electron equivalents (ee) do not significantly change the starting crystal structure. Subsequent lithiation results in migration of Zn 2+ ions from 8a tetrahedral sites into vacant 16c sites. Density functional theory shows that Limore » + ions insert into 16c site initially and then 8a site with further lithiation. Fe metal is formed over the next eight ee of reduction with no evidence of concurrent Zn 2+ reduction to Zn metal. Despite the expected formation of LiZn alloy from the electron count, we find no evidence for this phase under the tested conditions. Additionally, upon oxidation to 3 V, we observe an FeO phase with no evidence of Fe 2O 3. Electrochemistry data show higher electron equivalent transfer than can be accounted for solely based on ZnFe 2O 4 reduction indicating excess capacity ascribed to carbon reduction or surface electrolyte interphase formation.« less

Probing the Li Insertion Mechanism of ZnFe 2O 4 in Li-Ion Batteries: A Combined X-Ray Diffraction, Extended X-Ray Absorption Fine Structure, and Density Functional Theory Study [Probing the Li insertion mechanism of ZnFe 2O 4 in Li ion batteries: A combined XRD, EXAFS, and DFT study

DOE PAGES

Zhang, Yiman; Pelliccione, Christopher J.; Brady, Alexander B.; ...

2017-04-24

Here, we report an extensive study on fundamental properties that determine the functional electrochemistry of ZnFe 2O 4 spinel (theoretical capacity of 1000 mAh/g). For the first time, the reduction mechanism is followed through a combination of in situ X-ray diffraction data, synchrotron based powder diffraction, and ex-situ extended X-ray absorption fine structure allowing complete visualization of reduction products irrespective of their crystallinity. The first 0.5 electron equivalents (ee) do not significantly change the starting crystal structure. Subsequent lithiation results in migration of Zn 2+ ions from 8a tetrahedral sites into vacant 16c sites. Density functional theory shows that Limore » + ions insert into 16c site initially and then 8a site with further lithiation. Fe metal is formed over the next eight ee of reduction with no evidence of concurrent Zn 2+ reduction to Zn metal. Despite the expected formation of LiZn alloy from the electron count, we find no evidence for this phase under the tested conditions. Additionally, upon oxidation to 3 V, we observe an FeO phase with no evidence of Fe 2O 3. Electrochemistry data show higher electron equivalent transfer than can be accounted for solely based on ZnFe 2O 4 reduction indicating excess capacity ascribed to carbon reduction or surface electrolyte interphase formation.« less

Capillary Optics Based X-Ray Micro-Imaging Elemental Analysis

NASA Astrophysics Data System (ADS)

Hampai, D.; Dabagov, S. B.; Cappuccio, G.; Longoni, A.; Frizzi, T.; Cibin, G.

2010-04-01

A rapidly developed during the last few years micro-X-ray fluorescence spectrometry (μXRF) is a promising multi-elemental technique for non-destructive analysis. Typically it is rather hard to perform laboratory μXRF analysis because of the difficulty of producing an original small-size X-ray beam as well as its focusing. Recently developed for X-ray beam focusing polycapillary optics offers laboratory X-ray micro probes. The combination of polycapillary lens and fine-focused micro X-ray tube can provide high intensity radiation flux on a sample that is necessary in order to perform the elemental analysis. In comparison to a pinhole, an optimized "X-ray source-op tics" system can result in radiation density gain of more than 3 orders by the value. The most advanced way to get that result is to use the confocal configuration based on two X-ray lenses, one for the fluorescence excitation and the other for the detection of secondary emission from a sample studied. In case of X-ray capillary microfocusing a μXRF instrument designed in the confocal scheme allows us to obtain a 3D elemental mapping. In this work we will show preliminary results obtained with our prototype, a portable X-ray microscope for X-ray both imaging and fluorescence analysis; it enables μXRF elemental mapping simultaneously with X-ray imaging. A prototype of compact XRF spectrometer with a spatial resolution less than 100 μm has been designed.

Simultaneous Speciation, Structure, and Equilibrium Constant Determination in the Ni2+-EDTA-CN- Ternary System via High-Resolution Laboratory X-ray Absorption Fine Structure Spectroscopy and Theoretical Calculations.

PubMed

Bajnóczi, Éva G; Németh, Zoltán; Vankó, György

2017-11-20

Even quite simple chemical systems can involve many components and chemical states, and sometimes it can be very difficult to differentiate them by their hardly separable physical-chemical properties. The Ni II -EDTA-CN - (EDTA = ethylenediaminetetraacetic acid) ternary system is a good example for this problem where, in spite of its fairly simple components and numerous investigations, several molecular combinations can exist, all of them not having been identified unambiguously yet. In order to achieve a detailed understanding of the reaction steps and chemical equilibria, methods are required in which the structural transitions in the different reaction steps can be followed via element-selective complex spectral feature sets. With the help of our recently developed von Hámos type high-resolution laboratory X-ray absorption spectrometer, both the structural variations and stability constants of the forming complexes were determined from the same measurement series, proving that X-ray absorption spectroscopy can be considered as a multifaced, table-top tool in coordination chemistry. Furthermore, with the help of theoretical calculations, independent structural evidence was also given for the formation of the [NiEDTA(CN)] 3- mixed complex.

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.

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.

Alternative difference analysis scheme combining R -space EXAFS fit with global optimization XANES fit for X-ray transient absorption spectroscopy

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

Zhan, Fei; Tao, Ye; Zhao, Haifeng

Time-resolved X-ray absorption spectroscopy (TR-XAS), based on the laser-pump/X-ray-probe method, is powerful in capturing the change of the geometrical and electronic structure of the absorbing atom upon excitation. TR-XAS data analysis is generally performed on the laser-on minus laser-off difference spectrum. Here, a new analysis scheme is presented for the TR-XAS difference fitting in both the extended X-ray absorption fine-structure (EXAFS) and the X-ray absorption near-edge structure (XANES) regions.R-space EXAFS difference fitting could quickly provide the main quantitative structure change of the first shell. The XANES fitting part introduces a global non-derivative optimization algorithm and optimizes the local structure changemore » in a flexible way where both the core XAS calculation package and the search method in the fitting shell are changeable. The scheme was applied to the TR-XAS difference analysis of Fe(phen) 3spin crossover complex and yielded reliable distance change and excitation population.« less

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.

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.

Thin-film X-ray filters on microstructured substrates and their thermophysical properties

NASA Astrophysics Data System (ADS)

Mitrofanov, A. V.

2018-02-01

It is shown that structured substrates having micron- or submicron-sized through holes and coated with an ultrathin organic film can be used for the fabrication of thin-film X-ray filters via direct growth of functional layers on a substrate by sputter deposition, without additional complex processing steps. An optimised process is considered for the fabrication of X-ray filters on support structures in the form of electroplated fine nickel grids and on track-etched polymer membranes with micron- and submicrondiameter through pores. 'Optimisation' is here taken to mean matching the sputter deposition conditions with the properties of substrates so as to avoid overheating. The filters in question are intended for both imaging and single-channel detectors operating in the soft X-ray and vacuum UV spectral regions, at wavelengths from 10 to 60 nm. Thermal calculations are presented for the heating of ultrathin layers of organic films and thin-film support substrates during the sputter deposition of aluminium or other functional materials. The paper discusses approaches for cooling thinfilm composites during the sputter deposition process and the service of the filters in experiments and gives a brief overview of the works that utilised filters produced by the described technique on microstructured substrates, including orbital solar X-ray research in the framework of the CORONAS programme and laboratory laser plasma experiments.

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.

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.

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

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.

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

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

X-ray absorption spectroscopic studies of the active sites of nickel- and copper-containing metalloproteins

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

Tan, Grace O.

1993-06-01

X-ray absorption spectroscopy (XAS) is a useful tool for obtaining structural and chemical information about the active sites of metalloproteins and metalloenzymes. Information may be obtained from both the edge region and the extended X-ray absorption fine structure (EXAFS) or post-edge region of the K-edge X-ray absorption spectrum of a metal center in a compound. The edge contains information about the valence electronic structure of the atom that absorbs the X-rays. It is possible in some systems to infer the redox state of the metal atom in question, as well as the geometry and nature of ligands connected to it,more » from the features in the edge in a straightforward manner. The EXAFS modulations, being produced by the backscattering of the ejected photoelectron from the atoms surrounding the metal atom, provide, when analyzed, information about the number and type of neighbouring atoms, and the distances at which they occur. In this thesis, analysis of both the edge and EXAFS regions has been used to gain information about the active sites of various metalloproteins. The metalloproteins studied were plastocyanin (Pc), laccase and nickel carbon monoxide dehydrogenase (Ni CODH). Studies of Cu(I)-imidazole compounds, related to the protein hemocyanin, are also reported here.« less

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

Characterization of the Cu(Π) and Zn(Π) binding to the Amyloid-β short peptides by both the Extended X-ray Absorption Fine Structure and the Synchrotron Radiation Circular Dichroism spectroscopy

NASA Astrophysics Data System (ADS)

Zhang, Zhiyin; Sun, Shuaishuai; Xu, Jianhua; Zhang, Jing; Huang, Yan; Zhang, Bingbing; Tao, Ye

2013-04-01

Alzheimer's disease (AD) is a progressive and devastating neurodegenerative pathology, clinically characterized by dementia, cognitive impairment, personality disorders and memory loss. It is generally accepted that, misfolding of Aβ peptides is the key element in pathogenesis and the secondary structure of Aβ can be changed to major β-strand with reasons unknown yet. Many studies have shown that the misfolding may be linked with some biometals, mainly copper and zinc ions. To characterize interactions of Aβ and metal ions, we utilized both the extended X-ray fine structure spectroscopy (EXAFS) and the synchrotron radiation circular dichroism spectroscopy (SRCD). Aβ (13-22), Aβ (13-21), Aβ (E22G) and Aβ(HH-AA) were selected to study the mechanism of copper and zinc binding to Aβ. We found that Cu interaction with H13 and H14 residues led to the disappearance of the PPΠ, while the Cu binding E22 residue caused a remarkable conformation change to β-sheet enrichment. The Zn ion, in contrast, made little effect on the conformation and it coordinated to only one histidine (H residue) or not.

XAFS SPECTROSCOPY ANALYSIS OF SELECTED HAP ELEMENTS IN FINE PM DERIVED FROM COAL COMBUSTION

EPA Science Inventory

X-ray absorption fine structure (XAFS) spectroscopy has been used to investigate the valence states and molecular structures of sulfur (S), chromium (Cr), arsenic (As), and zinc (Zn) in fine particulate matter (PM) separated from coal flyash produced in a realistic combustion sys...

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…

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

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

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.

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

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.

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

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

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

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

Reactor for tracking catalyst nanoparticles in liquid at high temperature under a high-pressure gas phase with X-ray absorption spectroscopy.

PubMed

Nguyen, Luan; Tao, Franklin Feng

2018-02-01

Structure of catalyst nanoparticles dispersed in liquid phase at high temperature under gas phase of reactant(s) at higher pressure (≥5 bars) is important for fundamental understanding of catalytic reactions performed on these catalyst nanoparticles. Most structural characterizations of a catalyst performing catalysis in liquid at high temperature under gas phase at high pressure were performed in an ex situ condition in terms of characterizations before or after catalysis since, from technical point of view, access to the catalyst nanoparticles during catalysis in liquid phase at high temperature under high pressure reactant gas is challenging. Here we designed a reactor which allows us to perform structural characterization using X-ray absorption spectroscopy including X-ray absorption near edge structure spectroscopy and extended X-ray absorption fine structure spectroscopy to study catalyst nanoparticles under harsh catalysis conditions in terms of liquid up to 350 °C under gas phase with a pressure up to 50 bars. This reactor remains nanoparticles of a catalyst homogeneously dispersed in liquid during catalysis and X-ray absorption spectroscopy characterization.

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.

Development of high-resolution x-ray CT system using parallel beam geometry

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

Yoneyama, Akio, E-mail: akio.yoneyama.bu@hitachi.com; Baba, Rika; Hyodo, Kazuyuki

2016-01-28

For fine three-dimensional observations of large biomedical and organic material samples, we developed a high-resolution X-ray CT system. The system consists of a sample positioner, a 5-μm scintillator, microscopy lenses, and a water-cooled sCMOS detector. Parallel beam geometry was adopted to attain a field of view of a few mm square. A fine three-dimensional image of birch branch was obtained using a 9-keV X-ray at BL16XU of SPring-8 in Japan. The spatial resolution estimated from the line profile of a sectional image was about 3 μm.

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

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

The Focusing Optics X-ray Solar Imager

NASA Astrophysics Data System (ADS)

Glesener, L.; Christe, S.; Krucker, S.; Ishikawa, S.; Ramsey, B.; Takahashi, T.; Saito, S.; Lin, R. P.

2012-12-01

Measurements of the nonthermal energies and occurrence frequencies of nanoflares are important for understanding the overall flare contribution to coronal heating. Nanoflares have been observed to be ubiquitous in the quiet Sun in extreme ultraviolet and soft X-ray wavelengths, but so far remain undetected at nonthermal hard X-ray (HXR) energies, likely due to the insufficient sensitivity of current instruments. The Focusing Optics X-ray Solar Imager (FOXSI) sounding rocket payload has been designed for high sensitivity in the 5-15 keV range by combining grazing-incidence HXR optics with fine-resolution silicon strip detectors. FOXSI will make the first measurement of nonthermal HXR from accelerated electrons in nanoflares, and will also measure hot (5-10 MK) components of active region temperatures. FOXSI is scheduled for a first flight in October 2012, and the first results of this flight will be presented.

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

An IAEA multi-technique X-ray spectrometry endstation at Elettra Sincrotrone Trieste: benchmarking results and interdisciplinary applications.

PubMed

Karydas, Andreas Germanos; Czyzycki, Mateusz; Leani, Juan José; Migliori, Alessandro; Osan, Janos; Bogovac, Mladen; Wrobel, Pawel; Vakula, Nikita; Padilla-Alvarez, Roman; Menk, Ralf Hendrik; Gol, Maryam Ghahremani; Antonelli, Matias; Tiwari, Manoj K; Caliri, Claudia; Vogel-Mikuš, Katarina; Darby, Iain; Kaiser, Ralf Bernd

2018-01-01

The International Atomic Energy Agency (IAEA) jointly with the Elettra Sincrotrone Trieste (EST) operates a multipurpose X-ray spectrometry endstation at the X-ray Fluorescence beamline (10.1L). The facility has been available to external users since the beginning of 2015 through the peer-review process of EST. Using this collaboration framework, the IAEA supports and promotes synchrotron-radiation-based research and training activities for various research groups from the IAEA Member States, especially those who have limited previous experience and resources to access a synchrotron radiation facility. This paper aims to provide a broad overview about various analytical capabilities, intrinsic features and performance figures of the IAEA X-ray spectrometry endstation through the measured results. The IAEA-EST endstation works with monochromatic X-rays in the energy range 3.7-14 keV for the Elettra storage ring operating at 2.0 or 2.4 GeV electron energy. It offers a combination of different advanced analytical probes, e.g. X-ray reflectivity, X-ray absorption fine-structure measurements, grazing-incidence X-ray fluorescence measurements, using different excitation and detection geometries, and thereby supports a comprehensive characterization for different kinds of nanostructured and bulk materials.

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.

Quantitative determination of the lateral density and intermolecular correlation between proteins anchored on the membrane surfaces using grazing incidence small-angle X-ray scattering and grazing incidence X-ray fluorescence.

PubMed

Abuillan, Wasim; Vorobiev, Alexei; Hartel, Andreas; Jones, Nicola G; Engstler, Markus; Tanaka, Motomu

2012-11-28

As a physical model of the surface of cells coated with densely packed, non-crystalline proteins coupled to lipid anchors, we functionalized the surface of phospholipid membranes by coupling of neutravidin to biotinylated lipid anchors. After the characterization of fine structures perpendicular to the plane of membrane using specular X-ray reflectivity, the same membrane was characterized by grazing incidence small angle X-ray scattering (GISAXS). Within the framework of distorted wave Born approximation and two-dimensional Percus-Yevick function, we can analyze the form and structure factors of the non-crystalline, membrane-anchored proteins for the first time. As a new experimental technique to quantify the surface density of proteins on the membrane surface, we utilized grazing incidence X-ray fluorescence (GIXF). Here, the mean intermolecular distance between proteins from the sulfur peak intensities can be calculated by applying Abelé's matrix formalism. The characteristic correlation distance between non-crystalline neutravidin obtained by the GISAXS analysis agrees well with the intermolecular distance calculated by GIXF, suggesting a large potential of the combination of GISAXS and GIXF in probing the lateral density and correlation of non-crystalline proteins displayed on the membrane surface.

Sub-atomic dimensional metrology: developments in the control of x-ray interferometers

NASA Astrophysics Data System (ADS)

Yacoot, Andrew; Kuetgens, Ulrich

2012-07-01

Within the European Metrology Research Programme funded project NANOTRACE, the nonlinearity of the next generation of optical interferometers has been measured using x-ray interferometry. The x-ray interferometer can be regarded as a ruler or translation stage whose graduations or displacement steps are based on the lattice spacing of the crystallographic planes from which the x-rays are diffracted: in this case the graduations are every 192 pm corresponding to the spacing between the (2 2 0) planes in silicon. Precise displacement of the x-ray interferometer's monolithic translation stage in steps corresponding to discrete numbers of x-ray fringes requires servo positioning capability at the picometre level. To achieve this very fine control, a digital control system has been developed which has opened up the potential for advances in metrology using x-ray interferometry that include quadrature counting of x-ray fringes.

KMC-1: a high resolution and high flux soft x-ray beamline at BESSY.

PubMed

Schaefers, F; Mertin, M; Gorgoi, M

2007-12-01

The crystal monochromator beamline KMC-1 at a BESSY II bending magnet covers the energy range from soft (1.7 keV) to hard x-rays (12 keV) employing the (n,-n) double crystal arrangement with constant beam offset. The monochromator is equipped with three sets of crystals, InSb, Si (111), and Si (422) which are exchangeable in situ within a few minutes. Beamline and monochromator have been optimized for high flux and high resolution. This could be achieved by (1) a windowless setup under ultrahigh-vacuum conditions up to the experiment, (2) by the use of only three optical elements to minimize reflection losses, (3) by collecting an unusually large horizontal radiation fan (6 mrad) with the toroidal premirror, and (4) the optimization of the crystal optics to the soft x-ray range necessitating quasibackscattering crystal geometry (theta(Bragg,max)=82 degrees) delivering crystal limited resolution. The multipurpose beamline is in use for a variety of user facilities such as extended x-ray absorption fine structure, ((Bio-)EXAFS) near-edge x-ray absorption fine structure (NEXAFS), absorption and fluorescence spectroscopy. Due to the windowless UHV setup the k edges of the technologically and biologically important elements such as Si, P, and S are accessible. In addition to these experiments this beamline is now extensively used for photoelectron spectroscopy at high kinetic energies. Photon flux in the 10(11)-10(12) photons/s range and beamline resolving powers of more than E/DeltaE approximately 100.000 have been measured at selected energies employing Si (nnn) high order radiation in quasibackscattering geometry, thus photoelectron spectroscopy with a total instrumental resolution of about 150 meV is possible. This article describes the design features of the beamline and reports some experimental results in the above mentioned fields.

KMC-1: A high resolution and high flux soft x-ray beamline at BESSY

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

Schaefers, F.; Mertin, M.; Gorgoi, M.

2007-12-15

The crystal monochromator beamline KMC-1 at a BESSY II bending magnet covers the energy range from soft (1.7 keV) to hard x-rays (12 keV) employing the (n,-n) double crystal arrangement with constant beam offset. The monochromator is equipped with three sets of crystals, InSb, Si (111), and Si (422) which are exchangeable in situ within a few minutes. Beamline and monochromator have been optimized for high flux and high resolution. This could be achieved by (1) a windowless setup under ultrahigh-vacuum conditions up to the experiment, (2) by the use of only three optical elements to minimize reflection losses, (3)more » by collecting an unusually large horizontal radiation fan (6 mrad) with the toroidal premirror, and (4) the optimization of the crystal optics to the soft x-ray range necessitating quasibackscattering crystal geometry ({theta}{sub Bragg,max}=82 deg.) delivering crystal limited resolution. The multipurpose beamline is in use for a variety of user facilities such as extended x-ray absorption fine structure, ((Bio-)EXAFS) near-edge x-ray absorption fine structure (NEXAFS), absorption and fluorescence spectroscopy. Due to the windowless UHV setup the k edges of the technologically and biologically important elements such as Si, P, and S are accessible. In addition to these experiments this beamline is now extensively used for photoelectron spectroscopy at high kinetic energies. Photon flux in the 10{sup 11}-10{sup 12} photons/s range and beamline resolving powers of more than E/{delta}E{approx_equal}100.000 have been measured at selected energies employing Si (nnn) high order radiation in quasibackscattering geometry, thus photoelectron spectroscopy with a total instrumental resolution of about 150 meV is possible. This article describes the design features of the beamline and reports some experimental results in the above mentioned fields.« less

Systematic oxidation of polystyrene by ultraviolet-ozone, characterized by near-edge X-ray absorption fine structure and contact angle.

PubMed

Klein, Robert J; Fischer, Daniel A; Lenhart, Joseph L

2008-08-05

The process of implanting oxygen in polystyrene (PS) via exposure to ultraviolet-ozone (UV-O) was systematically investigated using the characterization technique of near-edge X-ray absorption fine structure (NEXAFS). Samples of PS exposed to UV-O for 10-300 s and washed with isopropanol were analyzed using the carbon and oxygen K-edge NEXAFS partial electron yields, using various retarding bias voltages to depth-profile the oxygen penetration into the surface. Evaluation of reference polymers provided a scale to quantify the oxygen concentration implanted by UV-O treatment. We find that ozone initially reacts with the double bonds on the phenyl rings, forming carbonyl groups, but within 1 min of exposure, the ratio of double to single oxygen bonds stabilizes at a lower value. Oxygen penetrates the film with relative ease, creating a fairly uniform distribution of oxygen within at least the first 4 nm (the effective depth probed by NEXAFS here). Before oxygen accumulates in large concentrations, however, it preferentially degrades the uppermost layer of the film by removing oxygenated low-molecular-weight oligomers. The failure to accumulate high concentrations of oxygen is seen in the nearly constant carbon edge jump, the low concentration of oxygen even at 5 min exposure (58% of that in poly(4-acetoxystyrene), the polymer with the most similarities to UV-O-treated PS), and the relatively high contact angles. At 5 min exposure the oxygen concentration contains ca. 7 atomic % oxygen. The oxygen species that are implanted consist predominantly of single O-C bonds and double O=C bonds but also include a small fraction of O-H. UV-O treatment leads a plateau after 2 min exposure in the water contact angle hysteresis, at a value of 67 +/- 2 degrees , due primarily to chemical heterogeneity. Annealing above T(g) allows oxygenated species to move short distances away from the surface but not diffuse further than 1-2 nm.

Applications of “Tender” Energy (1-5 keV) X-ray Absorption Spectroscopy in Life Sciences

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

Northrup, Paul; Leri, Alessandra; Tappero, Ryan

The “tender” energy range of 1 to 5 keV, between the energy ranges of most “hard” (>5 keV) and “soft” (<1 keV) synchrotron X-ray facilities, offers some unique opportunities for synchrotron-based X-ray absorption fine structure spectroscopy in life sciences. In particular the K absorption edges of Na through Ca offer opportunities to study local structure, speciation, and chemistry of many important biological compounds, structures and processes. This is an area of largely untapped science, in part due to a scarcity of optimized facilities. Such measurements also entail unique experimental challenges. Lastly, this brief review describes the technique, its experimental challenges,more » recent progress in development of microbeam measurement capabilities, and several highlights illustrating applications in life sciences.« less

Applications of “Tender” Energy (1-5 keV) X-ray Absorption Spectroscopy in Life Sciences

DOE PAGES

Northrup, Paul; Leri, Alessandra; Tappero, Ryan

2016-02-15

The “tender” energy range of 1 to 5 keV, between the energy ranges of most “hard” (>5 keV) and “soft” (<1 keV) synchrotron X-ray facilities, offers some unique opportunities for synchrotron-based X-ray absorption fine structure spectroscopy in life sciences. In particular the K absorption edges of Na through Ca offer opportunities to study local structure, speciation, and chemistry of many important biological compounds, structures and processes. This is an area of largely untapped science, in part due to a scarcity of optimized facilities. Such measurements also entail unique experimental challenges. Lastly, this brief review describes the technique, its experimental challenges,more » recent progress in development of microbeam measurement capabilities, and several highlights illustrating applications in life sciences.« less

Soft X-ray Spectromicroscopy of Polymers

NASA Astrophysics Data System (ADS)

Ade, Harald

1997-03-01

The development of Near Edge X-ray Absorption Fine Structure (NEXAFS) microscopy^1 and linear dichroism microscopy^2 over the last few years utilizing the X1-Scanning Transmission X-ray Microscope (X1-STXM) at the National Synchrotron Light Source provides excellent specificity to various functional groups and moieties in organic molecules and polymeric materials at a spatial resolution of 50 nm. This chemical specificity can be utilized to map the distribution of various compounds in a material, or to micro-chemically analyze small sample areas. Examples of applications include the study of various phase-separated polymers (polyurethanes, liquid crystalline polyesters), multicomponent polymer blends, polymer laminates, and other organic materials such as coal^3. Linear dichroism microscopy furthermore explores the polarization dependence of NEXAFS in (partially) oriented materials, and can determine the orientation of specific functional groups. Applications of linear dichroism microscopy have focused so far on determining the relative degree of radial orientation in Kevlar fibers^3. ^1 H. Ade, X. Zhang, S. Cameron, C. Costello, J. Kirz, and S. Williams, Science 258, 972 (1992). ^2 H. Ade and B. Hsiao, Science 262, 1427 (1993). ^3 Acknowledgement: My callaborators are B. Hsiao, S. Subramoney, B. Wood, I. Plotzker, E. Rightor, G. Mitchell, C. Sloop, D.-J. Liu, S.-C. Liu, J. Marti, C. Zimba, A. P. Smith, R. Spontak, R. Fornes, R. Gilbert, C. Cody, A. Hitchcock and S. Urquhart. The X1-STXM is built and maintained by J. Kirz and C. Jacobsen and their groups. Work supported by: NSF Young Investigator Award (DMR-9458060), DuPont Young Professor Grant, and Dow Chemical.

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

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.

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.

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

Lanthanide complexes of macrocyclic polyoxovanadates by VO4 units: synthesis, characterization, and structure elucidation by X-ray crystallography and EXAFS spectroscopy.

PubMed

Nishio, Masaki; Inami, Shinnosuke; Katayama, Misaki; Ozutsumi, Kazuhiko; Hayashi, Yoshihito

2012-01-16

Reactions of a tetravanadate anion, [V(4)O(12)](4-), with a series of lanthanide(III) salts yield three types of lanthanide complexes of macrocyclic polyoxovanadates: (Et(4)N)(6)[Ln(III)V(9)O(27)] [Ln = Nd (1), Sm (2), Eu (3), Gd (4), Tb (5), Dy (6)], (Et(4)N)(5)[(H(2)O)Ho(III)(V(4)O(12))(2)] (7), and (Et(4)N)(7)[Ln(III)V(10)O(30)] [Ln = Er (8), Tm (9), Yb (10), Lu (11)]. Lanthanide complexes 1-11 are isolated and characterized by IR, elemental analysis, single-crystal X-ray diffraction, and extended X-ray absorption fine structure spectroscopy (EXAFS). Lanthanide complexes 1-6 are composed of a square-antiprism eight-coordinated Ln(III) center with a macrocyclic polyoxovanadate that is constructed from nine VO(4) tetrahedra through vertex sharing. The structure of 7 is composed of a seven-coordinated Ho(III) center, which exhibits a capped trigonal-prism coordination environment by the sandwiching of two cyclic tetravanadates with a capping H(2)O ligand. Lanthanide complexes 8-11 have a six-coordinated Ln(III) center with a 10-membered vanadate ligand. The structural trend to adopt a larger coordination number for a larger lanthanide ion among the three types of structures is accompanied by a change in the vanadate ring sizes. These lanthanide complexes are examined by EXAFS spectroscopies on lanthanide L(III) absorption edges, and the EXAFS oscillations of each of the samples in the solid state and in acetonitrile are identical. The Ln-O and Ln···V bond lengths obtained from fits of the EXAFS data are consistent with the data from the single-crystal X-ray studies, reflecting retention of the structures in acetonitrile.

[CuCl(n)](2-n) ion-pair species in 1-ethyl-3-methylimidazolium chloride ionic liquid-water mixtures: ultraviolet-visible, X-ray absorption fine structure, and density functional theory characterization.

PubMed

Li, Guosheng; Camaioni, Donald M; Amonette, James E; Zhang, Z Conrad; Johnson, Timothy J; Fulton, John L

2010-10-07

We studied the coordination environment about Cu(II) in a pure ionic liquid, 1-ethyl-3-methylimidazolium chloride ([EMIM]Cl), and in binary mixtures of this compound with water across the entire range of compositions, using a combination of X-ray absorption fine structure (XAFS), ultraviolet-visible (UV-vis) spectroscopy, and electronic structure calculations. Our results show a series of stages in the ion pairing of the divalent cation, Cu(II), including the contact ion pairing of Cu(2+) with multiple Cl(-) ligands to form various CuCl(n)((2-n)) polyanions, as well as the subsequent solvation and ion pairing of the polychlorometallate anion with the EMIM(+) cation. Ion-pair formation is strongly promoted in [EMIM]Cl by the low dielectric constant and by the extensive breakdown of the water hydrogen-bond network in [EMIM]Cl-water mixtures. The CuCl(4)(2-) species dominates in the [EMIM]Cl solvent, and calculations along with spectroscopy show that its geometry distorts to C(2) symmetry compared to D(2d) in the gas phase. These results are important in understanding catalysis and separation processes involving transition metals in ionic liquid systems.

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.

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.

New trends in space x-ray optics

NASA Astrophysics Data System (ADS)

Hudec, R.; Maršíková, V.; Pína, L.; Inneman, A.; Skulinová, M.

2017-11-01

The X-ray optics is a key element of various X-ray telescopes, X-ray microscopes, as well as other X-ray imaging instruments. The grazing incidence X-ray lenses represent the important class of X-ray optics. Most of grazing incidence (reflective) X-ray imaging systems used in astronomy but also in other (laboratory) applications are based on the Wolter 1 (or modified) arrangement. But there are also other designs and configurations proposed, used and considered for future applications both in space and in laboratory. The Kirkpatrick-Baez (K-B) lenses as well as various types of Lobster-Eye optics and MCP/Micropore optics serve as an example. Analogously to Wolter lenses, the X-rays are mostly reflected twice in these systems to create focal images. Various future projects in X-ray astronomy and astrophysics will require large segments with multiple thin shells or foils. The large Kirkpatrick-Baez modules, as well as the large Lobster-Eye X-ray telescope modules in Schmidt arrangement may serve as examples. All these space projects will require high quality and light segmented shells (bent or flat foils) with high X-ray reflectivity and excellent mechanical stability. The Multi Foil Optics (MFO) approach represent a promising alternative for both LE and K-B X-ray optical modules. Several types of reflecting substrates may be considered for these applications, with emphasis on thin float glass sheets and, more recently, high quality silicon wafers. This confirms the importance of non- Wolter X-ray optics designs for the future. Future large space X-ray telescopes (such as IXO) require precise and light-weight X-ray optics based on numerous thin reflecting shells. Novel approaches and advanced technologies are to be exploited and developed. In this contribution, we refer on results of tested X-ray mirror shells produced by glass thermal forming (GTF) and by shaping Si wafers. Both glass foils and Si wafers are commercially available, have excellent surface

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.

Synthesis and x-ray characterization of cobalt phosphide (Co₂P) nanorods for the oxygen reduction reaction

DOE PAGES

Doan-Nguyen, Vicky V.T.; Su, Dong; Zhang, Sen; ...

2015-07-14

Low temperature fuel cells are clean, effective alternative fuel conversion technology. Oxygen reduction reaction (ORR) at the fuel cell cathode has required Pt as the electrocatalyst for high activity and selectivity of the four-electron reaction pathway. Targeting a less expensive, earth abundant alternative, we have developed the synthesis of cobalt phosphide (Co₂P) nanorods for ORR. Characterization techniques that include total X-ray scattering and extended X-ray absorption fine structure revealed a deviation of the nanorods from bulk crystal structure with a contraction along the b orthorhombic lattice parameter. The carbon supported nanorods have comparable activity but are remarkably more stable thanmore » conventional Pt catalysts for the oxygen reduction reaction in alkaline environments.« less

Specimen charging in X-ray absorption spectroscopy: correction of total electron yield data from stabilized zirconia in the energy range 250-915 eV.

PubMed

Vlachos, Dimitrios; Craven, Alan J; McComb, David W

2005-03-01

The effects of specimen charging on X-ray absorption spectroscopy using total electron yield have been investigated using powder samples of zirconia stabilized by a range of oxides. The stabilized zirconia powder was mixed with graphite to minimize the charging but significant modifications of the intensities of features in the X-ray absorption near-edge fine structure (XANES) still occurred. The time dependence of the charging was measured experimentally using a time scan, and an algorithm was developed to use this measured time dependence to correct the effects of the charging. The algorithm assumes that the system approaches the equilibrium state by an exponential decay. The corrected XANES show improved agreement with the electron energy-loss near-edge fine structure obtained from the same samples.

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.

Full-Field Calcium K-Edge X-ray Absorption Near-Edge Structure Spectroscopy on Cortical Bone at the Micron-Scale: Polarization Effects Reveal Mineral Orientation.

PubMed

Hesse, Bernhard; Salome, Murielle; Castillo-Michel, Hiram; Cotte, Marine; Fayard, Barbara; Sahle, Christoph J; De Nolf, Wout; Hradilova, Jana; Masic, Admir; Kanngießer, Birgit; Bohner, Marc; Varga, Peter; Raum, Kay; Schrof, Susanne

2016-04-05

Here, we show results on X-ray absorption near edge structure spectroscopy in both transmission and X-ray fluorescence full-field mode (FF-XANES) at the calcium K-edge on human bone tissue in healthy and diseased conditions and for different tissue maturation stages. We observe that the dominating spectral differences originating from different tissue regions, which are well pronounced in the white line and postedge structures are associated with polarization effects. These polarization effects dominate the spectral variance and must be well understood and modeled before analyzing the very subtle spectral variations related to the bone tissue variations itself. However, these modulations in the fine structure of the spectra can potentially be of high interest to quantify orientations of the apatite crystals in highly structured tissue matrices such as bone. Due to the extremely short wavelengths of X-rays, FF-XANES overcomes the limited spatial resolution of other optical and spectroscopic techniques exploiting visible light. Since the field of view in FF-XANES is rather large the acquisition times for analyzing the same region are short compared to, for example, X-ray diffraction techniques. Our results on the angular absorption dependence were verified by both site-matched polarized Raman spectroscopy, which has been shown to be sensitive to the orientation of bone building blocks and by mathematical simulations of the angular absorbance dependence. As an outlook we further demonstrate the polarization based assessment of calcium-containing crystal orientation and specification of calcium in a beta-tricalcium phosphate (β-Ca3(PO4)2 scaffold implanted into ovine bone. Regarding the use of XANES to assess chemical properties of Ca in human bone tissue our data suggest that neither the anatomical site (tibia vs jaw) nor pathology (healthy vs necrotic jaw bone tissue) affected the averaged spectral shape of the XANES spectra.

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.

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

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.

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.

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.

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.

X-ray absorption spectroscopy and X-ray photoelectron spectroscopy studies of CaSO 4:Dy thermoluminescent phosphors

NASA Astrophysics Data System (ADS)

Bakshi, A. K.; Jha, S. N.; Olivi, L.; Phase, D. M.; Kher, R. K.; Bhattacharyya, D.

2007-11-01

Extended X-ray absorption fine structure (EXAFS) measurements have been carried out on CaSO4:Dy phosphor samples at the Dy L3 edge with synchrotron radiation. Measurements were carried out on a set of samples which were subjected to post-preparation annealing at different temperatures and for different cycles. The EXAFS data have been analysed to find the Dy-S and Dy-O bond lengths in the neighbourhood of the Dy atoms in a CaSO4 matrix. The observations from EXAFS measurements were verified with XANES and XPS techniques. On the basis of these measurements, efforts were made to explain the loss of thermoluminescence sensitivity of CaSO4:Dy phosphors after repeated cycles of annealing at 400 °C in air for 1 h.

Pt and Ru X-ray absorption spectroscopy of PtRu anode catalysts in operating direct methanol fuel cells.

PubMed

Stoupin, Stanislav; Chung, Eun-Hyuk; Chattopadhyay, Soma; Segre, Carlo U; Smotkin, Eugene S

2006-05-25

In situ X-ray absorption spectroscopy, ex situ X-ray fluorescence, and X-ray powder diffraction enabled detailed core analysis of phase segregated nanostructured PtRu anode catalysts in an operating direct methanol fuel cell (DMFC). No change in the core structures of the phase segregated catalyst was observed as the potential traversed the current onset potential of the DMFC. The methodology was exemplified using a Johnson Matthey unsupported PtRu (1:1) anode catalyst incorporated into a DMFC membrane electrode assembly. During DMFC operation the catalyst is essentially metallic with half of the Ru incorporated into a face-centered cubic (FCC) Pt alloy lattice and the remaining half in an amorphous phase. The extended X-ray absorption fine structure (EXAFS) analysis suggests that the FCC lattice is not fully disordered. The EXAFS indicates that the Ru-O bond lengths were significantly shorter than those reported for Ru-O of ruthenium oxides, suggesting that the phases in which the Ru resides in the catalysts are not similar to oxides.

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.

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

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

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.

Hard X-ray Optics Technology Development for Astronomy at the Marshall Space Flight Center

NASA Technical Reports Server (NTRS)

Gubarev, Mikhail; Ramsey, Brian; Kilaru, Kiranmayee

2009-01-01

Grazing-incidence telescopes based on Wolter 1 geometry have delivered impressive advances in astrophysics at soft-x-ray wavelengths, while the hard xray region remains relatively unexplored at fine angular resolution and high sensitivities. The ability to perform ground-breaking science in the hard-x-ray energy range had been the motivation for technology developments aimed at fabricating low-cost, light-weight, high-quality x-ray mirrors. Grazing-incidence x-ray optics for high-energy astrophysical applications is being developed at MSFC using the electroform-nickel replication process.

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)

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.

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.

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

Morphology, stability, and X-ray absorption spectroscopic study of iron oxide (Hematite) nanoparticles prepared by micelle nanolithography

NASA Astrophysics Data System (ADS)

Bera, Anupam; Bhattacharya, Atanu; Tiwari, N.; Jha, S. N.; Bhattacharyya, D.

2018-03-01

Currently, considerable effort is being made towards synthesis and characterization of iron oxide nanoparticles. In this article, we report on the preparation and characterization of iron oxide nanoparticle (NP) arrays supported on natively oxidized Si(100) surface. The NPs are synthesized by reverse micelle nanolithography technique and are then deposited onto natively oxidized Si(100) surface via spin-coating. Plasma oxidation followed by high temperature annealing results in a unimodal size distribution of pseudohexagonally-ordered array of iron oxide NPs (with ∼14 nm mean diameter and ∼5 nm mean height). High temperature annealing does not fragment the NPs. Particles are sinter-resistant: the unimodal arrays are robust with respect to thermal treatment. X-ray absorption spectroscopy (XAS), including X-ray Absorption Near Edge Structure (XANES) and Extended X-ray Absorption Fine Structure (EXAFS), reveals that structure of the iron oxide particle resembles closely the hematite α-Fe2O3 structure. Furthermore, with the help of EXAFS spectra, we eliminate the possibility of γ-Fe2O3, Fe3O4, FeO and FeO(OH) structures for the NPs.

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

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

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

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.

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

Active Galactic Nuclei and X-ray Ovservations

NASA Astrophysics Data System (ADS)

Vasylenko, A. A.; Zhdanov, V. I.; Fedorova, E. V.

2016-11-01

Active galactic nuclei (AGN) are the brightest objects in the Universe and their brightness is mainly caused by accretion of m atter onto supermassive black holes (SMBH). This is the common reason of the AGN activity. However, every AGN has differences and fine features, which are the subject of an intensive investigation. The occurrence of such highly-relativistic objects as SMBH residing at the AGN core makes them an excellent laboratory for testing the fundamental physical theories. The X-rays and gamma-rays generated in a corona of an accretion disc around SMBH yield valuable information for these tests, the radiation in the range of 1-100 keV being at present the most informative source. However, there are a number of obstacles for such a study due to different physical processes that complicate the interpretation of observations in different bands of the electromagnetic radiation. In this paper, we review the current concepts concerning the structure of AGNs with a focus on the central part of these objects th at require relativistic theories for their understanding. The basic notions of the unified AGN schemes are considered; some modifications are reviewed. The paper contains the following sections. I. Introduction; II. Observational manifestations and classification of galaxies with active nuclei (II.A. Optical observations; II.B. Radio observations; II.C. X-ray data; II.D Infrared data; II.E. AGN anatomy with multywave data); III. AGN "central machine"; III.A. Black holes; III.B. Accretion disc types; III.C. Corona; III.D. AGN unified scheme); IV. Simulation X-ray AGN spectra (IV.A. The power-law contimuum and the exponential cut-off; IV.B. The absorption of X-rays; IV.C. Reflection; IV.D. Fe K a line; IV.E. Spin paradigm); V. AGN as a laboratory to test the fundamental interactions (V.A. Strong gravitational fields; V.B. Dynamic dark energy near compact astrophysical objects

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.

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.

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.

X-ray absorption near-edge spectroscopy in bioinorganic chemistry: Application to M–O2 systems

PubMed Central

Sarangi, Ritimukta

2012-01-01

Metal K-edge X-ray absorption spectroscopy (XAS) has been extensively applied to bioinorganic chemistry to obtain geometric structure information on metalloprotein and biomimetic model complex active sites by analyzing the higher energy extended X-ray absorption fine structure (EXAFS) region of the spectrum. In recent years, focus has been on developing methodologies to interpret the lower energy K-pre-edge and rising-edge regions (XANES) and using it for electronic structure determination in complex bioinorganic systems. In this review, the evolution and progress of 3d-transition metal K-pre-edge and rising-edge methodology development is presented with particular focus on applications to bioinorganic systems. Applications to biomimetic transition metal–O2 intermediates (M = Fe, Co, Ni and Cu) are reviewed, which demonstrate the power of the method as an electronic structure determination technique and its impact in understanding the role of supporting ligands in tuning the electronic configuration of transition metal–O2 systems. PMID:23525635

X-ray transparent microfluidic chips for high-throughput screening and optimization of in meso membrane protein crystallization

PubMed Central

Schieferstein, Jeremy M.; Pawate, Ashtamurthy S.; Wan, Frank; Sheraden, Paige N.; Broecker, Jana; Ernst, Oliver P.; Gennis, Robert B.

2017-01-01

Elucidating and clarifying the function of membrane proteins ultimately requires atomic resolution structures as determined most commonly by X-ray crystallography. Many high impact membrane protein structures have resulted from advanced techniques such as in meso crystallization that present technical difficulties for the set-up and scale-out of high-throughput crystallization experiments. In prior work, we designed a novel, low-throughput X-ray transparent microfluidic device that automated the mixing of protein and lipid by diffusion for in meso crystallization trials. Here, we report X-ray transparent microfluidic devices for high-throughput crystallization screening and optimization that overcome the limitations of scale and demonstrate their application to the crystallization of several membrane proteins. Two complementary chips are presented: (1) a high-throughput screening chip to test 192 crystallization conditions in parallel using as little as 8 nl of membrane protein per well and (2) a crystallization optimization chip to rapidly optimize preliminary crystallization hits through fine-gradient re-screening. We screened three membrane proteins for new in meso crystallization conditions, identifying several preliminary hits that we tested for X-ray diffraction quality. Further, we identified and optimized the crystallization condition for a photosynthetic reaction center mutant and solved its structure to a resolution of 3.5 Å. PMID:28469762

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

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

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.

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.

A novel x-ray detector design with higher DQE and reduced aliasing: Theoretical analysis of x-ray reabsoprtion in detector converter material

NASA Astrophysics Data System (ADS)

Nano, Tomi; Escartin, Terenz; Karim, Karim S.; Cunningham, Ian A.

2016-03-01

The ability to improve visualization of structural information in digital radiography without increasing radiation exposures requires improved image quality across all spatial frequencies, especially at high frequencies. The detective quantum efficiency (DQE) as a function of spatial frequency quantifies image quality given by an x-ray detector. We present a method of increasing DQE at high spatial frequencies by improving the modulation transfer function (MTF) and reducing noise aliasing. The Apodized Aperature Pixel (AAP) design uses a detector with micro-elements to synthesize desired pixels and provide higher DQE than conventional detector designs. A cascaded system analysis (CSA) that incorporates x-ray interactions is used for comparison of the theoretical MTF, noise power spectrum (NPS), and DQE. Signal and noise transfer through the converter material is shown to consist of correlated an uncorrelated terms. The AAP design was shown to improve the DQE of both material types that have predominantly correlated transfer (such as CsI) and predominantly uncorrelated transfer (such as Se). Improvement in the MTF by 50% and the DQE by 100% at the sampling cut-off frequency is obtained when uncorrelated transfer is prevalent through the converter material. Optimizing high-frequency DQE results in improved image contrast and visualization of small structures and fine-detail.

An X-ray absorption spectroscopy study of the inversion degree in zinc ferrite nanocrystals dispersed on a highly porous silica aerogel matrix.

PubMed

Carta, D; Marras, C; Loche, D; Mountjoy, G; Ahmed, S I; Corrias, A

2013-02-07

The structural properties of zinc ferrite nanoparticles with spinel structure dispersed in a highly porous SiO(2) aerogel matrix were compared with a bulk zinc ferrite sample. In particular, the details of the cation distribution between the octahedral (B) and tetrahedral (A) sites of the spinel structure were determined using X-ray absorption spectroscopy. The analysis of both the X-ray absorption near edge structure and the extended X-ray absorption fine structure indicates that the degree of inversion of the zinc ferrite spinel structures varies with particle size. In particular, in the bulk microcrystalline sample, Zn(2+) ions are at the tetrahedral sites and trivalent Fe(3+) ions occupy octahedral sites (normal spinel). When particle size decreases, Zn(2+) ions are transferred to octahedral sites and the degree of inversion is found to increase as the nanoparticle size decreases. This is the first time that a variation of the degree of inversion with particle size is observed in ferrite nanoparticles grown within an aerogel matrix.

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.

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.

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

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

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.

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.

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.

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.