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

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

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

Chemical imaging analysis of the brain with X-ray methods

NASA Astrophysics Data System (ADS)

Collingwood, Joanna F.; Adams, Freddy

2017-04-01

Cells employ various metal and metalloid ions to augment the structure and the function of proteins and to assist with vital biological processes. In the brain they mediate biochemical processes, and disrupted metabolism of metals may be a contributing factor in neurodegenerative disorders. In this tutorial review we will discuss the particular role of X-ray methods for elemental imaging analysis of accumulated metal species and metal-containing compounds in biological materials, in the context of post-mortem brain tissue. X-rays have the advantage that they have a short wavelength and can penetrate through a thick biological sample. Many of the X-ray microscopy techniques that provide the greatest sensitivity and specificity for trace metal concentrations in biological materials are emerging at synchrotron X-ray facilities. Here, the extremely high flux available across a wide range of soft and hard X-rays, combined with state-of-the-art focusing techniques and ultra-sensitive detectors, makes it viable to undertake direct imaging of a number of elements in brain tissue. The different methods for synchrotron imaging of metals in brain tissues at regional, cellular, and sub-cellular spatial resolution are discussed. Methods covered include X-ray fluorescence for elemental imaging, X-ray absorption spectrometry for speciation imaging, X-ray diffraction for structural imaging, phase contrast for enhanced contrast imaging and scanning transmission X-ray microscopy for spectromicroscopy. Two- and three-dimensional (confocal and tomographic) imaging methods are considered as well as the correlation of X-ray microscopy with other imaging tools.

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.

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

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

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.

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.

Multifractal Analysis of Seismically Induced Soft-Sediment Deformation Structures Imaged by X-Ray Computed Tomography

NASA Astrophysics Data System (ADS)

Nakashima, Yoshito; Komatsubara, Junko

Unconsolidated soft sediments deform and mix complexly by seismically induced fluidization. Such geological soft-sediment deformation structures (SSDSs) recorded in boring cores were imaged by X-ray computed tomography (CT), which enables visualization of the inhomogeneous spatial distribution of iron-bearing mineral grains as strong X-ray absorbers in the deformed strata. Multifractal analysis was applied to the two-dimensional (2D) CT images with various degrees of deformation and mixing. The results show that the distribution of the iron-bearing mineral grains is multifractal for less deformed/mixed strata and almost monofractal for fully mixed (i.e. almost homogenized) strata. Computer simulations of deformation of real and synthetic digital images were performed using the egg-beater flow model. The simulations successfully reproduced the transformation from the multifractal spectra into almost monofractal spectra (i.e. almost convergence on a single point) with an increase in deformation/mixing intensity. The present study demonstrates that multifractal analysis coupled with X-ray CT and the mixing flow model is useful to quantify the complexity of seismically induced SSDSs, standing as a novel method for the evaluation of cores for seismic risk assessment.

Remote X-Ray Diffraction and X-Ray Fluorescence Analysis on Planetary Surfaces

NASA Technical Reports Server (NTRS)

Blake, David F.; DeVincenzi, D. (Technical Monitor)

1999-01-01

The legacy of planetary X-ray Diffraction (XRD) and X-ray Fluorescence (XRF) began in 1960 when W. Parish proposed an XRD instrument for deployment on the moon. The instrument was built and flight qualified, but the Lunar XRD program was cancelled shortly before the first human landing in 1969. XRF chemical data have been collected in situ by surface landers on Mars (Viking 1 & 2, Pathfinder) and Venus (Venera 13 & 14). These highly successful experiments provide critical constraints on our current understanding of surface processes and planetary evolution. However, the mineralogy, which is more critical to planetary surface science than simple chemical analysis, will remain unknown or will at best be imprecisely constrained until X-ray diffraction (XRD) data are collected. Recent progress in X-ray detector technology allows the consideration of simultaneous XRD (mineralogic analysis) and high-precision XRF (elemental analysis) in systems miniaturized to the point where they can be mounted on fixed landers or small robotic rovers. There is a variety of potential targets for XRD/XRF equipped landers within the solar system, the most compelling of which are the poles of the moon, the southern highlands of Mars and Europa.

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

Application of x-ray absorption fine structure (XAFS) to local-order analysis in Fe-Cr maghemite-like materials

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

Montero-Cabrera, M. E., E-mail: elena.montero@cimav.edu.mx; Fuentes-Cobas, L. E.; Macías-Ríos, E.

2015-07-23

The maghemite-like oxide system γ-Fe{sub 2-x}Cr{sub x}O{sub 3} (x=0.75, 1 and 1.25) was studied by X-ray absorption fine structure (XAFS) and by synchrotron radiation X-ray diffraction (XRD). Measurements were performed at the Stanford Synchrotron Radiation Lightsource at room temperature, at beamlines 2-1, 2-3 and 4-3. High-resolution XRD patterns were processed by means of the Rietveld method. In cases of atoms being neighbors in the Periodic Table, the order/disorder degree of the considered solutions is indiscernible by “normal” (absence of “anomalous scattering”) diffraction experiments. Thus, maghemite-like materials were investigated by XAFS in both Fe and Cr K-edges to clarify, via short-rangemore » structure characterization, the local ordering of the investigated system. Athena and Artemis graphic user interfaces for IFEFFIT and FEFF8.4 codes were employed for XAFS spectra interpretation. Pre-edge decomposition and theoretical modeling of X-ray absorption near edge structure (XANES) transitions were performed. By analysis of the Cr K-edge XANES, it has been confirmed that Cr is located in an octahedral environment. Fitting of the extended X-ray absorption fine structure (EXAFS) spectra was performed under the consideration that the central atom of Fe is allowed to occupy octa- and tetrahedral positions, while Cr occupies only octahedral ones. Coordination number of neighboring atoms, interatomic distances and their quadratic deviation average were determined for x=1, by fitting simultaneously the EXAFS spectra of both Fe and Cr K-edges. The results of fitting the experimental spectra with theoretical standards showed that the cation vacancies tend to follow a regular pattern within the structure of the iron-chromium maghemite (FeCrO{sub 3})« less

AUSPEX: a graphical tool for X-ray diffraction data analysis.

PubMed

Thorn, Andrea; Parkhurst, James; Emsley, Paul; Nicholls, Robert A; Vollmar, Melanie; Evans, Gwyndaf; Murshudov, Garib N

2017-09-01

In this paper, AUSPEX, a new software tool for experimental X-ray data analysis, is presented. Exploring the behaviour of diffraction intensities and the associated estimated uncertainties facilitates the discovery of underlying problems and can help users to improve their data acquisition and processing in order to obtain better structural models. The program enables users to inspect the distribution of observed intensities (or amplitudes) against resolution as well as the associated estimated uncertainties (sigmas). It is demonstrated how AUSPEX can be used to visually and automatically detect ice-ring artefacts in integrated X-ray diffraction data. Such artefacts can hamper structure determination, but may be difficult to identify from the raw diffraction images produced by modern pixel detectors. The analysis suggests that a significant portion of the data sets deposited in the PDB contain ice-ring artefacts. Furthermore, it is demonstrated how other problems in experimental X-ray data caused, for example, by scaling and data-conversion procedures can be detected by AUSPEX.

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

NASA Astrophysics Data System (ADS)

Murphy, Michael Wayne

2010-06-01

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

Improving packaged food quality and safety. Part 1: synchrotron X-ray analysis.

PubMed

López-Rubio, A; Hernandez-Muñoz, P; Catala, R; Gavara, R; Lagarón, J M

2005-10-01

The objective was to demonstrate, as an example of an application, the potential of synchrotron X-ray analysis to detect morphological alterations that can occur in barrier packaging materials and structures. These changes can affect the packaging barrier characteristics when conventional food preservation treatments are applied to packaged food. The paper presents the results of a number of experiments where time-resolved combined wide-angle X-ray scattering and small-angle X-ray scattering analysis as a function of temperature and humidity were applied to ethylene-vinyl alcohol co-polymers (EVOH), polypropylene (PP)/EVOH/PP structures, aliphatic polyketone terpolymer (PK) and amorphous polyamide (aPA) materials. A comparison between conventional retorting and high-pressure processing treatments in terms of morphologic alterations are also presented for EVOH. The impact of retorting on the EVOH structure contrasts with the good behaviour of the PK during this treatment and with that of aPA. However, no significant structural changes were observed by wide-angle X-ray scattering in the EVOH structures after high-pressure processing treatment. These structural observations have also been correlated with oxygen permeability measurements that are of importance when guaranteeing the intended levels of safety and quality of packaged food.

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.

Micro X-ray diffraction analysis of thin films using grazing-exit conditions.

PubMed

Noma, T; Iida, A

1998-05-01

An X-ray diffraction technique using a hard X-ray microbeam for thin-film analysis has been developed. To optimize the spatial resolution and the surface sensitivity, the X-ray microbeam strikes the sample surface at a large glancing angle while the diffracted X-ray signal is detected with a small (grazing) exit angle. Kirkpatrick-Baez optics developed at the Photon Factory were used, in combination with a multilayer monochromator, for focusing X-rays. The focused beam size was about 10 x 10 micro m. X-ray diffraction patterns of Pd, Pt and their layered structure were measured. Using a small exit angle, the signal-to-background ratio was improved due to a shallow escape depth. Under the grazing-exit condition, the refraction effect of diffracted X-rays was observed, indicating the possibility of surface sensitivity.

VETA-I x ray test analysis

NASA Technical Reports Server (NTRS)

Brissenden, R. J. V.; Chartas, G.; Freeman, M. D.; Hughes, J. P.; Kellogg, E. M.; Podgorski, W. A.; Schwartz, D. A.; Zhao, P.

1992-01-01

This interim report presents some definitive results from our analysis of the VETA-I x-ray testing data. It also provides a description of the hardware and software used in the conduct of the VETA-I x-ray test program performed at the MSFC x-ray Calibration Facility (XRCF). These test results also serve to supply data and information to include in the TRW final report required by DPD 692, DR XC04. To provide an authoritative compendium of results, we have taken nine papers as published in the SPIE Symposium, 'Grazing Incidence X-ray/EUV Optics for Astronomy and Projection Lithography' and have reproduced them as the content of this report.

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.

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.

Room temperature neutron crystallography of drug resistant HIV-1 protease uncovers limitations of X-ray structural analysis at 100K

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

Gerlits, Oksana O.; Keen, David A.; Blakeley, Matthew P.

HIV-1 protease inhibitors are crucial for treatment of HIV-1/AIDS, but their effectiveness is thwarted by rapid emergence of drug resistance. To better understand binding of clinical inhibitors to resistant HIV-1 protease, we used room-temperature joint X-ray/neutron (XN) crystallography to obtain an atomic-resolution structure of the protease triple mutant (V32I/I47V/V82I) in complex with amprenavir. The XN structure reveals a D+ ion located midway between the inner Oδ1 oxygen atoms of the catalytic aspartic acid residues. Comparison of the current XN structure with our previous XN structure of the wild-type HIV-1 protease-amprenavir complex suggests that the three mutations do not significantly altermore » the drug–enzyme interactions. This is in contrast to the observations in previous 100 K X-ray structures of these complexes that indicated loss of interactions by the drug with the triple mutant protease. These findings, thus, uncover limitations of structural analysis of drug binding using X-ray structures obtained at 100 K.« less

Room temperature neutron crystallography of drug resistant HIV-1 protease uncovers limitations of X-ray structural analysis at 100K

DOE PAGES

Gerlits, Oksana O.; Keen, David A.; Blakeley, Matthew P.; ...

2017-02-14

HIV-1 protease inhibitors are crucial for treatment of HIV-1/AIDS, but their effectiveness is thwarted by rapid emergence of drug resistance. To better understand binding of clinical inhibitors to resistant HIV-1 protease, we used room-temperature joint X-ray/neutron (XN) crystallography to obtain an atomic-resolution structure of the protease triple mutant (V32I/I47V/V82I) in complex with amprenavir. The XN structure reveals a D+ ion located midway between the inner Oδ1 oxygen atoms of the catalytic aspartic acid residues. Comparison of the current XN structure with our previous XN structure of the wild-type HIV-1 protease-amprenavir complex suggests that the three mutations do not significantly altermore » the drug–enzyme interactions. This is in contrast to the observations in previous 100 K X-ray structures of these complexes that indicated loss of interactions by the drug with the triple mutant protease. These findings, thus, uncover limitations of structural analysis of drug binding using X-ray structures obtained at 100 K.« less

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.

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.

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.

Computed microtomography and X-ray fluorescence analysis for comprehensive analysis of structural changes in bone.

PubMed

Buzmakov, Alexey; Chukalina, Marina; Nikolaev, Dmitry; Schaefer, Gerald; Gulimova, Victoria; Saveliev, Sergey; Tereschenko, Elena; Seregin, Alexey; Senin, Roman; Prun, Victor; Zolotov, Denis; Asadchikov, Victor

2013-01-01

This paper presents the results of a comprehensive analysis of structural changes in the caudal vertebrae of Turner's thick-toed geckos by computer microtomography and X-ray fluorescence analysis. We present algorithms used for the reconstruction of tomographic images which allow to work with high noise level projections that represent typical conditions dictated by the nature of the samples. Reptiles, due to their ruggedness, small size, belonging to the amniote and a number of other valuable features, are an attractive model object for long-orbital experiments on unmanned spacecraft. Issues of possible changes in their bone tissue under the influence of spaceflight are the subject of discussions between biologists from different laboratories around the world.

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

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.

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 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.

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.

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.

TES X-ray microcalorimeters for X-ray astronomy and material analysis

NASA Astrophysics Data System (ADS)

Mitsuda, Kazuhisa

2016-11-01

TES X-ray microcalorimeter arrays provide not only high-energy resolution (FWHM < 10eV) in X-ray spectroscopy but also imaging and high-counting-rate capabilities. They are very promising spectrometer for X-ray astronomy and material analysis. In this paper, we report our recent progress. For material analysis, we have fabricated 8 × 8 format array with a fast signal response ( 40 μs) and proved the energy resolution of 5.8 eV FWHM at 5.9 keV. We developed common biasing scheme to reduce number of wirings from room temperature to the cryogenic stage. From measurements using the newly-designed common-bias SQUID array amplifier chips, and from numerical simulations, we demonstrated that signal cross talks due to the common bias is enough small. For space applications, we are developing frequency-division signal multiplexing system. We have fabricated a baseband feedback system and demonstrated that the noise added by the feedback system is about 4 eV FWHM equivalent for 16 ch multiplexing system. The digital to analog converter (DAC) dominates the noise, and needs be reduced by a factor of four for future astronomy missions.

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

X-ray microtomography analysis of soil structure deformation caused by centrifugation

NASA Astrophysics Data System (ADS)

Schlüter, Steffen; Leuther, Frederic; Vogler, Steffen; Vogel, Hans-Jörg

2016-04-01

Centrifugation provides a fast method to measure soil water retention curves over a wide moisture range. However, deformation of soil structure may occur at high angular velocities in the centrifuge. The objective of this study was to capture these changes in soil structure with X-ray microtomography and to measure local deformations via digital volume correlation. Two samples were investigated that differ in texture and rock content. A detailed analysis of the pore space reveals an interplay between shrinkage due to drying and soil compaction due to compression. Macroporosity increases at moderate angular velocity because of crack formation due to moisture release. At higher angular velocities, corresponding to capillary pressure of <-100kPa, macroporosity decreases again because of structure deformation due to compression. While volume changes due to swelling clay minerals are immanent to any drying process, the compaction of soil is a specific drawback of the centrifugation method. A new protocol for digital volume correlation was developed to analyze the spatial heterogeneity of deformation. In both samples the displacement of soil constituents is highest in the top part of the sample and exhibits high lateral variability explained by the spatial distribution of macropores in the sample. Centrifugation should therefore only be applied after the completion of all other hydraulic or thermal experiments, or any other analysis that depends on the integrity of soil structure.

X-ray microtomography analysis of soil structure deformation caused by centrifugation

NASA Astrophysics Data System (ADS)

Schlüter, S.; Leuther, F.; Vogler, S.; Vogel, H.-J.

2016-01-01

Centrifugation provides a fast method to measure soil water retention curves over a wide moisture range. However, deformation of soil structure may occur at high angular velocities in the centrifuge. The objective of this study was to capture these changes in soil structure with X-ray microtomography and to measure local deformations via digital volume correlation. Two samples were investigated that differ in texture and rock content. A detailed analysis of the pore space reveals an interplay between shrinkage due to drying and soil compaction due to compression. Macroporosity increases at moderate angular velocity because of crack formation due to moisture release. At higher angular velocities, corresponding to capillary pressure of ψ < -100 kPa, macroporosity decreases again because of structure deformation due to compression. While volume changes due to swelling clay minerals are immanent in any drying process, the compaction of soil is a specific drawback of the centrifugation method. A new protocol for digital volume correlation was developed to analyze the spatial heterogeneity of deformation. In both samples the displacement of soil constituents is highest in the top part of the sample and exhibits high lateral variability explained by the spatial distribution of macropores in the sample. Centrifugation should therefore only be applied after the completion of all other hydraulic or thermal experiments, or any other analysis that depends on the integrity of soil structure.

X-ray CT analysis of pore structure in sand

NASA Astrophysics Data System (ADS)

Mukunoki, Toshifumi; Miyata, Yoshihisa; Mikami, Kazuaki; Shiota, Erika

2016-06-01

The development of microfocused X-ray computed tomography (CT) devices enables digital imaging analysis at the pore scale. The applications of these devices are diverse in soil mechanics, geotechnical and geoenvironmental engineering, petroleum engineering, and agricultural engineering. In particular, the imaging of the pore space in porous media has contributed to numerical simulations for single-phase and multiphase flows or contaminant transport through the pore structure as three-dimensional image data. These obtained results are affected by the pore diameter; therefore, it is necessary to verify the image preprocessing for the image analysis and to validate the pore diameters obtained from the CT image data. Moreover, it is meaningful to produce the physical parameters in a representative element volume (REV) and significant to define the dimension of the REV. This paper describes the underlying method of image processing and analysis and discusses the physical properties of Toyoura sand for the verification of the image analysis based on the definition of the REV. On the basis of the obtained verification results, a pore-diameter analysis can be conducted and validated by a comparison with the experimental work and image analysis. The pore diameter is deduced from Young-Laplace's law and a water retention test for the drainage process. The results from previous study and perforated-pore diameter originally proposed in this study, called the voxel-percolation method (VPM), are compared in this paper. In addition, the limitations of the REV, the definition of the pore diameter, and the effectiveness of the VPM for an assessment of the pore diameter are discussed.

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.

In Situ Mineralogical Analysis of Planetary Materials Using X-Ray Diffraction and X-Ray Fluorescence

NASA Technical Reports Server (NTRS)

Sarrazin, P.; Blake, D.; Vaniman, D.; Chang, Sherwood (Technical Monitor)

1996-01-01

Remote observations of Mars have led scientists to believe that its early climate was similar to that of the early Earth, having had abundant liquid water and a dense atmosphere. One of the most fascinating questions of recent times is whether simple bacterial life developed on Mars (as it did on the Earth) during this early element period. Analyses of SNC meteorites have broadened considerably our knowledge of the chemistry of certain types of Martian rocks, underscoring the tantalizing possibility of early hydrothermal systems and even of ancient bacterial life. Detailed analyses of SNC meteorites in Terrestrial laboratories utilize the most sophisticated organic, isotopic and microscopic techniques in existence. Indeed; it is unlikely that the key biogenic indicators used in McKay et al (ibid) could be identified by a remote instrument on the surface of Mars. As a result, it is probable that any robotic search for evidence of an ancient Martian biosphere will have as its focus the identification of key minerals in likely host rocks rather than the direct detection of organic or isotopic biomarkers. Even on a sample return mission, mineralogical screening will be utilized to choose the most likely candidate rocks. X-ray diffraction (XRD) is the only technique that can provide a direct determination of the crystal structures of the phases present within a sample. When many different crystalline phases are present, quantitative analysis is better constrained if used in conjunction with a determination of elemental composition, obtainable by X-ray fluorescence (XRF) using the same X-ray source as for XRD. For planetary surface analysis, a remote instrument combining XRD and XRF could be used for mineralogical characterization of both soils and rocks. We are designing a remote XRD/XRF instrument with this objective in mind. The instrument concept pays specific attention to constraints in sample preparation, weight, volume, power, etc. Based on the geometry of a

Empirical studies of solar flares: Comparison of X-ray and H alpha filtergrams and analysis of the energy balance of the X-ray plasma

NASA Technical Reports Server (NTRS)

Moore, R. L.

1979-01-01

The physics of solar flares was investigated through a combined analysis of X-ray filtergrams of the high temperature coronal component of flares and H alpha filtergrams of the low temperature chromospheric component. The data were used to study the magnetic field configuration and its changes in solar flares, and to examine the chromospheric location and structure of X-ray bright points (XPB) and XPB flares. Each topic and the germane data are discussed. The energy balance of the thermal X-ray plasma in flares, while not studied, is addressed.

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.

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.

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

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.

Simultaneous Neutron and X-ray Tomography for Quantitative analysis of Geological Samples

NASA Astrophysics Data System (ADS)

LaManna, J.; Hussey, D. S.; Baltic, E.; Jacobson, D. L.

2016-12-01

Multiphase flow is a critical area of research for shale gas, oil recovery, underground CO2 sequestration, geothermal power, and aquifer management. It is critical to understand the porous structure of the geological formations in addition to the fluid/pore and fluid/fluid interactions. Difficulties for analyzing flow characteristics of rock cores are in obtaining 3D distribution information on the fluid flow and maintaining the cores in a state for other analysis methods. Two powerful non-destructive methods for obtaining 3D structural and compositional information are X-ray and neutron tomography. X-ray tomography produces information on density and structure while neutrons excel at acquiring the liquid phase and produces compositional information. These two methods can offer strong complementary information but are typically conducted at separate times and often at different facilities. This poses issues for obtaining dynamic and stochastic information as the sample will change between analysis modes. To address this, NIST has developed a system that allows for multimodal, simultaneous tomography using thermal neutrons and X-rays by placing a 90 keVp micro-focus X-ray tube 90° to the neutron beam. High pressure core holders that simulate underground conditions have been developed to facilitate simultaneous tomography. These cells allow for the control of confining pressure, axial load, temperature, and fluid flow through the core. This talk will give an overview the simultaneous neutron and x-ray tomography capabilities at NIST, the benefits of multimodal imaging, environmental equipment for geology studies, and several case studies that have been conducted at NIST.

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.

Kinetic products in coordination networks: ab initio X-ray powder diffraction analysis.

PubMed

Martí-Rujas, Javier; Kawano, Masaki

2013-02-19

Porous coordination networks are materials that maintain their crystal structure as molecular "guests" enter and exit their pores. They are of great research interest with applications in areas such as catalysis, gas adsorption, proton conductivity, and drug release. As with zeolite preparation, the kinetic states in coordination network preparation play a crucial role in determining the final products. Controlling the kinetic state during self-assembly of coordination networks is a fundamental aspect of developing further functionalization of this class of materials. However, unlike for zeolites, there are few structural studies reporting the kinetic products made during self-assembly of coordination networks. Synthetic routes that produce the necessary selectivity are complex. The structural knowledge obtained from X-ray crystallography has been crucial for developing rational strategies for design of organic-inorganic hybrid networks. However, despite the explosive progress in the solid-state study of coordination networks during the last 15 years, researchers still do not understand many chemical reaction processes because of the difficulties in growing single crystals suitable for X-ray diffraction: Fast precipitation can lead to kinetic (metastable) products, but in microcrystalline form, unsuitable for single crystal X-ray analysis. X-ray powder diffraction (XRPD) routinely is used to check phase purity, crystallinity, and to monitor the stability of frameworks upon guest removal/inclusion under various conditions, but rarely is used for structure elucidation. Recent advances in structure determination of microcrystalline solids from ab initio XRPD have allowed three-dimensional structure determination when single crystals are not available. Thus, ab initio XRPD structure determination is becoming a powerful method for structure determination of microcrystalline solids, including porous coordination networks. Because of the great interest across scientific

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

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

Investigation of internal structure of fine granules by microtomography using synchrotron X-ray radiation.

PubMed

Noguchi, Shuji; Kajihara, Ryusuke; Iwao, Yasunori; Fujinami, Yukari; Suzuki, Yoshio; Terada, Yasuko; Uesugi, Kentaro; Miura, Keiko; Itai, Shigeru

2013-03-10

Computed tomography (CT) using synchrotron X-ray radiation was evaluated as a non-destructive structural analysis method for fine granules. Two kinds of granules have been investigated: a bromhexine hydrochloride (BHX)-layered Celphere CP-102 granule coated with pH-sensitive polymer Kollicoat Smartseal 30-D, and a wax-matrix granule constructed from acetaminophen (APAP), dibasic calcium phosphate dehydrate, and aminoalkyl methacrylate copolymer E (AMCE) manufactured by melt granulation. The diameters of both granules were 200-300 μm. CT analysis of CP-102 granule could visualize the laminar structures of BHX and Kollicoat layers, and also visualize the high talc-content regions in the Kollicoat layer that could not be detected by scanning electron microscopy. Moreover, CT analysis using X-ray energies above the absorption edge of Br specifically enhanced the contrast in the BHX layer. As for granules manufactured by melt granulation, CT analysis revealed that they had a small inner void space due to a uniform distribution of APAP and other excipients. The distribution of AMCE revealed by CT analysis was also found to involve in the differences of drug dissolution from the granules as described previously. These observations demonstrate that CT analysis using synchrotron X-ray radiation is a powerful method for the detailed internal structure analysis of fine granules. Copyright © 2013 Elsevier B.V. All rights reserved.

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

A long-term space astrophysics research program: An x-ray perspective of the components and structure of galaxies

NASA Technical Reports Server (NTRS)

Fabbiano, G.

1995-01-01

X-ray studies of galaxies by the Smithsonian Astrophysical Observatory (SAO) and MIT are described. Activities at SAO include ROSAT PSPC x-ray data reduction and analysis pipeline; x-ray sources in nearby Sc galaxies; optical, x-ray, and radio study of ongoing galactic merger; a radio, far infrared, optical, and x-ray study of the Sc galaxy NGC247; and a multiparametric analysis of the Einstein sample of early-type galaxies. Activities at MIT included continued analysis of observations with ROSAT and ASCA, and continued development of new approaches to spectral analysis with ASCA and AXAF. Also, a new method for characterizing structure in galactic clusters was developed and applied to ROSAT images of a large sample of clusters. An appendix contains preprints generated by the research.

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

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

The 16th International Conference on X-ray Absorption Fine Structure (XAFS16)

NASA Astrophysics Data System (ADS)

Grunwaldt, J.-D.; Hagelstein, M.; Rothe, J.

2016-05-01

This preface of the proceedings volume of the 16th International Conference on X- ray Absorption Fine Structure (XAFS16) gives a glance on the five days of cutting-edge X-ray science which were held in Karlsruhe, Germany, August 23 - 28, 2015. In addition, several satellite meetings took place in Hamburg, Berlin and Stuttgart, a Sino-German workshop, three data analysis tutorials as well as special symposia on industrial catalysis and XFELs were held at the conference venue.

Analysis of Soil Structure Turnover with Garnet Particles and X-Ray Microtomography

PubMed Central

Vogel, Hans-Jörg

2016-01-01

Matter turnover in soil is tightly linked to soil structure which governs the heterogeneous distribution of habitats, reaction sites and pathways in soil. Thereby, the temporal dynamics of soil structure alteration is deemed to be important for essential ecosystem functions of soil but very little is known about it. A major reason for this knowledge gap is the lack of methods to study soil structure turnover directly at microscopic scales. Here we devise a conceptual approach and an image processing workflow to study soil structure turnover by labeling some initial state of soil structure with small garnet particles and tracking their fate with X-ray microtomography. The particles adhere to aggregate boundaries at the beginning of the experiment but gradually change their position relative to the nearest pore as structure formation progresses and pores are destructed or newly formed. A new metric based on the contact distances between particles and pores is proposed that allows for a direct quantification of soil structure turnover rates. The methodology is tested for a case study about soil compaction of a silty loam soil during stepwise increase of bulk density (ρ = {1.1, 1.3, 1.5} g/cm3). We demonstrate that the analysis of mean contact distances provides genuinely new insights about changing diffusion pathways that cannot be inferred neither from conventional pore space attributes (porosity, mean pore size, pore connectivity) nor from deformation analysis with digital image correlation. This structure labeling approach to quantify soil structure turnover provides a direct analogy to stable isotope labeling for the analysis of matter turnover and can be readily combined with each other. PMID:27453995

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.

Enabling liquid solvent structure analysis using hard x-ray absorption spectroscopy with a transferrable microfluidic reactor

NASA Astrophysics Data System (ADS)

Zheng, Jian; Zhang, Wei; Wang, Feng; Yu, Xiao-Ying

2018-05-01

In this paper, a vacuum compatible microfluidic device, system for analysis at the liquid vacuum interface, is integrated to hard x-ray absorption spectroscopy to obtain the local structure of K3[Fe(CN)6] in aqueous solutions with three concentrations of 0.5 M, 0.05 M, and 0.005 M. The solutions were sealed in a microchannel 500 µm wide and 300 µm deep in a portable microfluidic device. The Fe K-edge x-ray absorption spectra indicate a presence of Fe(III) in the complex in water, with an octahedral geometry coordinated with 6 C atoms in the first shell with a distance of ~1.92 Å and 6 N atoms in the second shell with a distance of ~3.10 Å. Varying the concentration has no observable influence on the structure of K3[Fe(CN)6]. Our results demonstrate the feasibility of using microfluidic based liquid cells in large synchrotron facilities. Using portable microfludic reactors provides a viable approach to enable multifaceted measurements of liquids in the future.

Enabling liquid solvent structure analysis using hard x-ray absorption spectroscopy with a transferrable microfluidic reactor.

PubMed

Zheng, Jian; Zhang, Wei; Wang, Feng; Yu, Xiao-Ying

2018-05-10

In this paper, a vacuum compatible microfluidic device, system for analysis at the liquid vacuum interface, is integrated to hard x-ray absorption spectroscopy to obtain the local structure of K 3 [Fe(CN) 6 ] in aqueous solutions with three concentrations of 0.5 M, 0.05 M, and 0.005 M. The solutions were sealed in a microchannel 500 µm wide and 300 µm deep in a portable microfluidic device. The Fe K-edge x-ray absorption spectra indicate a presence of Fe(III) in the complex in water, with an octahedral geometry coordinated with 6 C atoms in the first shell with a distance of ~1.92 Å and 6 N atoms in the second shell with a distance of ~3.10 Å. Varying the concentration has no observable influence on the structure of K 3 [Fe(CN) 6 ]. Our results demonstrate the feasibility of using microfluidic based liquid cells in large synchrotron facilities. Using portable microfludic reactors provides a viable approach to enable multifaceted measurements of liquids in the future.

Enabling liquid solvent structure analysis using hard x-ray absorption spectroscopy with a transferrable microfluidic reactor

DOE PAGES

Zheng, Jian; Zhang, Wei; Wang, Feng; ...

2018-04-11

In this study, a vacuum compatible microfluidic device, system for analysis at the liquid vacuum interface, is integrated to hard x-ray absorption spectroscopy to obtain the local structure of K 3[Fe(CN) 6] in aqueous solutions with three concentrations of 0.5 M, 0.05 M, and 0.005 M. The solutions were sealed in a microchannel 500 µm wide and 300 µm deep in a portable microfluidic device. The Fe K-edge x-ray absorption spectra indicate a presence of Fe(III) in the complex in water, with an octahedral geometry coordinated with 6 C atoms in the first shell with a distance of ~1.92 Åmore » and 6 N atoms in the second shell with a distance of ~3.10 Å. Varying the concentration has no observable influence on the structure of K 3[Fe(CN) 6]. Our results demonstrate the feasibility of using microfluidic based liquid cells in large synchrotron facilities. Using portable microfludic reactors provides a viable approach to enable multifaceted measurements of liquids in the future.« less

Enabling liquid solvent structure analysis using hard x-ray absorption spectroscopy with a transferrable microfluidic reactor

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

Zheng, Jian; Zhang, Wei; Wang, Feng

In this study, a vacuum compatible microfluidic device, system for analysis at the liquid vacuum interface, is integrated to hard x-ray absorption spectroscopy to obtain the local structure of K 3[Fe(CN) 6] in aqueous solutions with three concentrations of 0.5 M, 0.05 M, and 0.005 M. The solutions were sealed in a microchannel 500 µm wide and 300 µm deep in a portable microfluidic device. The Fe K-edge x-ray absorption spectra indicate a presence of Fe(III) in the complex in water, with an octahedral geometry coordinated with 6 C atoms in the first shell with a distance of ~1.92 Åmore » and 6 N atoms in the second shell with a distance of ~3.10 Å. Varying the concentration has no observable influence on the structure of K 3[Fe(CN) 6]. Our results demonstrate the feasibility of using microfluidic based liquid cells in large synchrotron facilities. Using portable microfludic reactors provides a viable approach to enable multifaceted measurements of liquids in the future.« less

Enabling liquid solvent structure analysis using hard x-ray absorption spectroscopy with a transferrable microfluidic reactor

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

Zheng, Jian; Zhang, Wei; Wang, Feng

In this paper, a vacuum compatible microfluidic device, System for Analysis at the Liquid Vacuum Interface (SALVI), is integrated to hard x-ray absorption spectroscopy (XAS) to obtain the local structure of K3[Fe(CN)6] in aqueous solutions with three concentrations of 0.5 M, 0.05 M, and 0.005 M. The solutions were sealed in a microchannel of 500 μm wide and 300 µm deep in a portable microfluidic device. The Fe K-edge x-ray absorption spectra show that the complex in water is Fe(III). The complex is present with octahedral geometry coordinated with 6 C atoms in the first shell with a distance ofmore » ~1.92 Å and 6 N atoms in the second shell with a distance of ~3.10 Å. Varying the concentration has no observable influence on the structure of K3[Fe(CN)6]. Our results demonstrate the feasibility of using microfluidic based liquid cells in large synchrotron facilities and it is a viable approach to enable multifaceted measurements of liquids in the future.« less

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

NASA Astrophysics Data System (ADS)

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

2017-11-01

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

Analysis of the Central X-ray Source in DG Tau

NASA Astrophysics Data System (ADS)

Schneider, P. Christian; Schmitt, Jürgen H. M. M.

As a stellar X-ray source DG Tau shows two rather unusual features: A resolved X-ray jet [2] and an X-ray spectrum best described by two thermal components with different absorbing column densities, a so called "two-absorber X-ray (TAX)" morphology [1, 2]. In an effort to understand the properties of the central X-ray source in DG Tau a detailed position analysis was carried out.

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}}*).

Wavelet transform analysis of the small-scale X-ray structure of the cluster Abell 1367

NASA Technical Reports Server (NTRS)

Grebeney, S. A.; Forman, W.; Jones, C.; Murray, S.

1995-01-01

We have developed a new technique based on a wavelet transform analysis to quantify the small-scale (less than a few arcminutes) X-ray structure of clusters of galaxies. We apply this technique to the ROSAT position sensitive proportional counter (PSPC) and Einstein high-resolution imager (HRI) images of the central region of the cluster Abell 1367 to detect sources embedded within the diffuse intracluster medium. In addition to detecting sources and determining their fluxes and positions, we show that the wavelet analysis allows a characterization of the sources extents. In particular, the wavelet scale at which a given source achieves a maximum signal-to-noise ratio in the wavelet images provides an estimate of the angular extent of the source. To account for the widely varying point response of the ROSAT PSPC as a function of off-axis angle requires a quantitative measurement of the source size and a comparison to a calibration derived from the analysis of a Deep Survey image. Therefore, we assume that each source could be described as an isotropic two-dimensional Gaussian and used the wavelet amplitudes, at different scales, to determine the equivalent Gaussian Full Width Half-Maximum (FWHM) (and its uncertainty) appropriate for each source. In our analysis of the ROSAT PSPC image, we detect 31 X-ray sources above the diffuse cluster emission (within a radius of 24 min), 16 of which are apparently associated with cluster galaxies and two with serendipitous, background quasars. We find that the angular extents of 11 sources exceed the nominal width of the PSPC point-spread function. Four of these extended sources were previously detected by Bechtold et al. (1983) as 1 sec scale features using the Einstein HRI. The same wavelet analysis technique was applied to the Einstein HRI image. We detect 28 sources in the HRI image, of which nine are extended. Eight of the extended sources correspond to sources previously detected by Bechtold et al. Overall, using both the

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.

X-ray near-field speckle: implementation and critical analysis

PubMed Central

Lu, Xinhui; Mochrie, S. G. J.; Narayanan, S.; Sandy, A. R.; Sprung, M.

2011-01-01

The newly introduced coherence-based technique of X-ray near-field speckle (XNFS) has been implemented at 8-ID-I at the Advanced Photon Source. In the near-field regime of high-brilliance synchrotron X-rays scattered from a sample of interest, it turns out that, when the scattered radiation and the main beam both impinge upon an X-ray area detector, the measured intensity shows low-contrast speckles, resulting from interference between the incident and scattered beams. A micrometer-resolution XNFS detector with a high numerical aperture microscope objective has been built and its capability for studying static structures and dynamics at longer length scales than traditional far-field X-ray scattering techniques is demonstrated. Specifically, the dynamics of dilute silica and polystyrene colloidal samples are characterized. This study reveals certain limitations of the XNFS technique, especially in the characterization of static structures, which is discussed. PMID:21997906

Microstructure Analysis of Bismuth Absorbers for Transition-Edge Sensor X-ray Microcalorimeters

NASA Astrophysics Data System (ADS)

Yan, Daikang; Divan, Ralu; Gades, Lisa M.; Kenesei, Peter; Madden, Timothy J.; Miceli, Antonino; Park, Jun-Sang; Patel, Umeshkumar M.; Quaranta, Orlando; Sharma, Hemant; Bennett, Douglas A.; Doriese, William B.; Fowler, Joseph W.; Gard, Johnathon D.; Hays-Wehle, James P.; Morgan, Kelsey M.; Schmidt, Daniel R.; Swetz, Daniel S.; Ullom, Joel N.

2018-03-01

Given its large X-ray stopping power and low specific heat capacity, bismuth (Bi) is a promising absorber material for X-ray microcalorimeters and has been used with transition-edge sensors (TESs) in the past. However, distinct X-ray spectral features have been observed in TESs with Bi absorbers deposited with different techniques. Evaporated Bi absorbers are widely reported to have non-Gaussian low-energy tails, while electroplated ones do not show this feature. In this study, we fabricated Bi absorbers with these two methods and performed microstructure analysis using scanning electron microscopy and X-ray diffraction microscopy. The two types of material showed the same crystallographic structure, but the grain size of the electroplated Bi was about 40 times larger than that of the evaporated Bi. This distinction in grain size is likely to be the cause of their different spectral responses.

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.

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

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

TOPICAL REVIEW: Human soft tissue analysis using x-ray or gamma-ray techniques

NASA Astrophysics Data System (ADS)

Theodorakou, C.; Farquharson, M. J.

2008-06-01

This topical review is intended to describe the x-ray techniques used for human soft tissue analysis. X-ray techniques have been applied to human soft tissue characterization and interesting results have been presented over the last few decades. The motivation behind such studies is to provide improved patient outcome by using the data obtained to better understand a disease process and improve diagnosis. An overview of theoretical background as well as a complete set of references is presented. For each study, a brief summary of the methodology and results is given. The x-ray techniques include x-ray diffraction, x-ray fluorescence, Compton scattering, Compton to coherent scattering ratio and attenuation measurements. The soft tissues that have been classified using x-rays or gamma rays include brain, breast, colon, fat, kidney, liver, lung, muscle, prostate, skin, thyroid and uterus.

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.

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.

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.

Structural analysis of polymer thin films using GISAXS in the tender X-ray region: Concept and design of GISAXS experiments using the tender X-ray energy at BL-15A2 at the Photon Factory

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

Takagi, H., E-mail: takagih@post.kek.jp; Igarashi, N.; Mori, T.

If small angle X-ray scattering (SAXS) utilizing the soft X-ray region is available, advanced and unique experiments, which differ from traditional SAXS methods, can be realized. For example, grazing-incidence small angle X-ray scattering (GISAXS) using hard X-ray is a powerful tool for understanding the nanostructure in both vertical and lateral directions of thin films, while GISAXS utilizing the tender X-ray region (SX-GISAXS) enables depth-resolved analysis as well as a standard GISAXS analysis in thin films. Thus, at BL-15A2 at the Photon Factory, a dedicated diffractometer for SX-GISAXS (above 2.1 keV) was constructed. This diffractometer is composed of four vacuum chambers andmore » can be converted into the vacuum state from the sample chamber in front of the detector surface. Diffractions are clearly observed until 12th peak when measuring collagen by SAXS with an X-ray energy of 2.40 keV and a camera length of 825 mm. Additionally, we conducted the model experiment using SX-GISAXS with an X-ray energy of 2.40 keV to confirm that a poly(methyl methacrylate)-poly(n-butyl acrylate) block copolymer thin film has a microphase-separated structure in the thin film, which is composed of lamellae aligned both parallel and perpendicular to the substrate surface. Similarly, in a polystyrene-poly(methyl methacrylate) block copolymer thin film, SX-GISAXS with 3.60 keV and 5.73 keV revealed that hexagonally packed cylinders are aligned parallel to the substrate surface. The incident angle dependence of the first order peak position of the q{sub z} direction obtained from experiments at various incident X-ray energies agrees very well with the theoretical one calculated from the distorted wave Born approximation.« less

Development of a micro-X-ray fluorescence system based on polycapillary X-ray optics for non-destructive analysis of archaeological objects

NASA Astrophysics Data System (ADS)

Cheng, Lin; Ding, Xunliang; Liu, Zhiguo; Pan, Qiuli; Chu, Xuelian

2007-08-01

A new micro-X-ray fluorescence (micro-XRF) system based on rotating anode X-ray generator and polycapillary X-ray optics has been set up in XOL Lab, BNU, China, in order to be used for analysis of archaeological objects. The polycapillary X-ray optics used here can focus the primary X-ray beam down to tens of micrometers in diameter that allows for non-destructive and local analysis of sub-mm samples with minor/trace level sensitivity. The analytical characteristics and potential of this micro-XRF system in archaeological research are discussed. Some described uses of this instrument include studying Chinese ancient porcelain.

Structural analysis of jewelry from the Moche tomb of the `lady of Cao' by X-ray digital radiography

NASA Astrophysics Data System (ADS)

Azeredo, S. R.; Cesareo, R.; Franco, R.; Fernandez, A.; Bustamante, A.; Lopes, R. T.

2018-04-01

Nose ornaments from the tomb of the `Lady of Cao', a mummified woman representative of the Moche culture and dated to the third-or-fourth century AD, were analyzed by X-ray digital radiography. These spectacular gold and silver jewels are some of the most sophisticated metalworking ever produced in ancient America. The Mochecivilization flourished along the north coast of present-day Peru, between the Andes and the Pacific Ocean, approximately between 100 and 600 AD. The Moche were very sophisticated artisans and metal smiths, being considered the finest producers of jewels and artifacts of the region. A portable X-ray digital radiography (XDR) system consisting of a flat panel detector with high resolution image and a mini X-ray tube was used for the structural analysis of the Moche jewels aiming at inferring different joining methods of the silver-gold sheets. The radiographic analysis showed some differences in the joint of the silver-and-gold sheets. Presence of filler material and adhesive for joining the silver-and-gold sheets was visible as well as silver-gold junctions without filler material (or with a material invisible in radiography). Furthermore, the technique demonstrated the advantage of using a portable XDR micro system when the sample cannot be brought to the laboratory.

X-ray fluorescence analysis of low concentrations metals in geological samples and technological products

NASA Astrophysics Data System (ADS)

Lagoida, I. A.; Trushin, A. V.

2016-02-01

For the past several years many nuclear physics methods of quantitative elemental analysis have been designed. Many of these methods have applied in different devices which have become useful and effective instrument in many industrial laboratories. Methods of a matter structure analysis are based on the intensity detection of the X-ray radiation from the nuclei of elements which are excited by external X-ray source. The production of characteristic X-rays involves transitions of the orbital electrons of atoms in the target material between allowed orbits, or energy states, associated with ionization of the inner atomic shells. One of these methods is X-ray fluorescence analysis, which is widespread in metallurgical and processing industries and is used to identify and measure the concentration of the elements in ores and minerals on a conveyor belt. Samples of copper ore with known concentrations of elements, were taken from the Ural deposit. To excite the characteristic X-rays radionuclide sources 109Cd, with half-life 461.4 days were used. After finding the calibration coefficients, control measurements of samples and averaging of overall samples were made. The measurement error did not exceed 3%.

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

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

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

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

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.

Characterization of ceramic powders by an X-ray measuring method

NASA Technical Reports Server (NTRS)

Ziegler, B.

1983-01-01

X-ray line broadening analysis gives quantitative data on structural changes of ceramic powders after different processing steps. Various Al2O3 powders were investigated and the following points are discussed on the basis of these results: X-ray line broadening analysis, structural changes during grinding, structural changes during annealing, influence of structural properties on sintering behavior and application of line broadening analysis to quality control of powders.

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

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.

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.

Production, purification, crystallization and preliminary X-ray analysis of adeno-associated virus serotype 8

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

Lane, Michael Douglas; Nam, Hyun-Joo; Padron, Eric

2005-06-01

The production, purification, crystallization and preliminary X-ray crystallographic analysis of adeno-associated virus serotype 8 is reported. Adeno-associated viruses (AAVs) are actively being developed for clinical gene-therapy applications and the efficiencies of the vectors could be significantly improved by a detailed understanding of their viral capsid structures and the structural determinants of their tissue-transduction interactions. AAV8 is ∼80% identical to the more widely studied AAV2, but its liver-transduction efficiency is significantly greater than that of AAV2 and other serotypes. The production, purification, crystallization and preliminary X-ray crystallographic analysis of AAV8 viral capsids are reported. The crystals diffract X-rays to 3.0 Åmore » resolution using synchrotron radiation and belong to the hexagonal space group P6{sub 3}22, with unit-cell parameters a = 257.5, c = 443.5 Å. The unit cell contains two viral particles, with ten capsid viral protein monomers per crystallographic asymmetric unit.« less

Healing X-ray scattering images

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

Liu, Jiliang; Lhermitte, Julien; Tian, Ye

X-ray scattering images contain numerous gaps and defects arising from detector limitations and experimental configuration. Here, we present a method to heal X-ray scattering images, filling gaps in the data and removing defects in a physically meaningful manner. Unlike generic inpainting methods, this method is closely tuned to the expected structure of reciprocal-space data. In particular, we exploit statistical tests and symmetry analysis to identify the structure of an image; we then copy, average and interpolate measured data into gaps in a way that respects the identified structure and symmetry. Importantly, the underlying analysis methods provide useful characterization of structuresmore » present in the image, including the identification of diffuseversussharp features, anisotropy and symmetry. The presented method leverages known characteristics of reciprocal space, enabling physically reasonable reconstruction even with large image gaps. The method will correspondingly fail for images that violate these underlying assumptions. The method assumes point symmetry and is thus applicable to small-angle X-ray scattering (SAXS) data, but only to a subset of wide-angle data. Our method succeeds in filling gaps and healing defects in experimental images, including extending data beyond the original detector borders.« less

Healing X-ray scattering images

DOE PAGES

Liu, Jiliang; Lhermitte, Julien; Tian, Ye; ...

2017-05-24

X-ray scattering images contain numerous gaps and defects arising from detector limitations and experimental configuration. Here, we present a method to heal X-ray scattering images, filling gaps in the data and removing defects in a physically meaningful manner. Unlike generic inpainting methods, this method is closely tuned to the expected structure of reciprocal-space data. In particular, we exploit statistical tests and symmetry analysis to identify the structure of an image; we then copy, average and interpolate measured data into gaps in a way that respects the identified structure and symmetry. Importantly, the underlying analysis methods provide useful characterization of structuresmore » present in the image, including the identification of diffuseversussharp features, anisotropy and symmetry. The presented method leverages known characteristics of reciprocal space, enabling physically reasonable reconstruction even with large image gaps. The method will correspondingly fail for images that violate these underlying assumptions. The method assumes point symmetry and is thus applicable to small-angle X-ray scattering (SAXS) data, but only to a subset of wide-angle data. Our method succeeds in filling gaps and healing defects in experimental images, including extending data beyond the original detector borders.« less

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.

Spectroscopic analysis of solar and cosmic X-ray spectra. 1: The nature of cosmic X-ray spectra and proposed analytical techniques

NASA Technical Reports Server (NTRS)

Walker, A. B. C., Jr.

1975-01-01

Techniques for the study of the solar corona are reviewed as an introduction to a discussion of modifications required for the study of cosmic sources. Spectroscopic analysis of individual sources and the interstellar medium is considered. The latter was studied via analysis of its effect on the spectra of selected individual sources. The effects of various characteristics of the ISM, including the presence of grains, molecules, and ionization, are first discussed, and the development of ISM models is described. The expected spectral structure of individual cosmic sources is then reviewed with emphasis on supernovae remnants and binary X-ray sources. The observational and analytical requirements imposed by the characteristics of these sources are identified, and prospects for the analysis of abundances and the study of physical parameters within them are assessed. Prospects for the spectroscopic study of other classes of X-ray sources are also discussed.

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 source assembly having enhanced output stability, and fluid stream analysis applications thereof

DOEpatents

Radley, Ian [Glenmont, NY; Bievenue, Thomas J [Delmar, NY; Burdett, John H [Charlton, NY; Gallagher, Brian W [Guilderland, NY; Shakshober, Stuart M [Hudson, NY; Chen, Zewu [Schenectady, NY; Moore, Michael D [Alplaus, NY

2008-06-08

An x-ray source assembly and method of operation are provided having enhanced output stability. The assembly includes an anode having a source spot upon which electrons impinge and a control system for controlling position of the anode source spot relative to an output structure. The control system can maintain the anode source spot location relative to the output structure notwithstanding a change in one or more operating conditions of the x-ray source assembly. One aspect of the disclosed invention is most amenable to the analysis of sulfur in petroleum-based fuels.

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

Observation of Structure of Surfaces and Interfaces by Synchrotron X-ray Diffraction: Atomic-Scale Imaging and Time-Resolved Measurements

NASA Astrophysics Data System (ADS)

Wakabayashi, Yusuke; Shirasawa, Tetsuroh; Voegeli, Wolfgang; Takahashi, Toshio

2018-06-01

The recent developments in synchrotron optics, X-ray detectors, and data analysis algorithms have enhanced the capability of the surface X-ray diffraction technique. This technique has been used to clarify the atomic arrangement around surfaces in a non-contact and nondestructive manner. An overview of surface X-ray diffraction, from the historical development to recent topics, is presented. In the early stage of this technique, surface reconstructions of simple semiconductors or metals were studied. Currently, the surface or interface structures of complicated functional materials are examined with sub-Å resolution. As examples, the surface structure determination of organic semiconductors and of a one-dimensional structure on silicon are presented. A new frontier is time-resolved interfacial structure analysis. A recent observation of the structure and dynamics of the electric double layer of ionic liquids, and an investigation of the structural evolution in the wettability transition on a TiO2 surface that utilizes a newly designed time-resolved surface diffractometer, are presented.

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

3D X-ray ultra-microscopy of bone tissue.

PubMed

Langer, M; Peyrin, F

2016-02-01

We review the current X-ray techniques with 3D imaging capability at the nano-scale: transmission X-ray microscopy, ptychography and in-line phase nano-tomography. We further review the different ultra-structural features that have so far been resolved: the lacuno-canalicular network, collagen orientation, nano-scale mineralization and their use as basis for mechanical simulations. X-ray computed tomography at the micro-metric scale is increasingly considered as the reference technique in imaging of bone micro-structure. The trend has been to push towards increasingly higher resolution. Due to the difficulty of realizing optics in the hard X-ray regime, the magnification has mainly been due to the use of visible light optics and indirect detection of the X-rays, which limits the attainable resolution with respect to the wavelength of the visible light used in detection. Recent developments in X-ray optics and instrumentation have allowed to implement several types of methods that achieve imaging that is limited in resolution by the X-ray wavelength, thus enabling computed tomography at the nano-scale. We review here the X-ray techniques with 3D imaging capability at the nano-scale: transmission X-ray microscopy, ptychography and in-line phase nano-tomography. Further, we review the different ultra-structural features that have so far been resolved and the applications that have been reported: imaging of the lacuno-canalicular network, direct analysis of collagen orientation, analysis of mineralization on the nano-scale and use of 3D images at the nano-scale to drive mechanical simulations. Finally, we discuss the issue of going beyond qualitative description to quantification of ultra-structural features.

IPC two-color analysis of x ray galaxy clusters

NASA Technical Reports Server (NTRS)

White, Raymond E., III

1990-01-01

The mass distributions were determined of several clusters of galaxies by using X ray surface brightness data from the Einstein Observatory Imaging Proportional Counter (IPC). Determining cluster mass distributions is important for constraining the nature of the dark matter which dominates the mass of galaxies, galaxy clusters, and the Universe. Galaxy clusters are permeated with hot gas in hydrostatic equilibrium with the gravitational potentials of the clusters. Cluster mass distributions can be determined from x ray observations of cluster gas by using the equation of hydrostatic equilibrium and knowledge of the density and temperature structure of the gas. The x ray surface brightness at some distance from the cluster is the result of the volume x ray emissivity being integrated along the line of sight in the cluster.

Difficult macromolecular structures determined using X-ray diffraction techniques.

PubMed

Hernández-Santoyo, Alejandra

2012-07-01

Macromolecular crystallography has been, for the last few decades, the main source of structural information of biological macromolecular systems and it is one of the most powerful techniques for the analysis of enzyme mechanisms and macromolecular interactions at the atomic level. In addition, it is also an extremely powerful tool for drug design. Recent technological and methodological developments in macromolecular X-ray crystallography have allowed solving structures that until recently were considered difficult or even impossible, such as structures at atomic or subatomic resolution or large macromolecular complexes and assemblies at low resolution. These developments have also helped to solve the 3D-structure of macromolecules from twin crystals. Recently, this technique complemented with cryo-electron microscopy and neutron crystallography has provided the structure of large macromolecular machines with great precision allowing understanding of the mechanisms of their function.

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 ( ...

Spectral structure of a polycapillary lens shaped X-ray beam

NASA Astrophysics Data System (ADS)

Gogolev, A. S.; Filatov, N. A.; Uglov, S. R.; Hampai, D.; Dabagov, S. B.

2018-04-01

Polycapillary X-ray optics is widely used in X-ray analysis techniques to create a small secondary source, for instance, or to deliver X-rays to the point of interest with minimum intensity losses [1]. The main characteristics of the analytical devices on its base are the size and divergence of the focused or translated beam. In this work, we used the photon-counting pixel detector ModuPIX to study the parameters for polycapillary focused X-ray tube radiation as well as the energy and spatial dependences of radiation at the focus. We have characterized the high-speed spectral camera ModuPIX, which is a single Timepix device with a fast parallel readout allowing up to 850 frames per second with 256 × 256 pixels and a 55 μm pitch defined by the frame frequency. By means of the silicon monochromator the energy response function is measured in clustering mode by the energy scan over total X-ray tube spectrum.

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

Time-resolved structural studies at synchrotrons and X-ray free electron lasers: opportunities and challenges

PubMed Central

Neutze, Richard; Moffat, Keith

2012-01-01

X-ray free electron lasers (XFELs) are potentially revolutionary X-ray sources because of their very short pulse duration, extreme peak brilliance and high spatial coherence, features that distinguish them from today’s synchrotron sources. We review recent time-resolved Laue diffraction and time-resolved wide angle X-ray scattering (WAXS) studies at synchrotron sources, and initial static studies at XFELs. XFELs have the potential to transform the field of time-resolved structural biology, yet many challenges arise in devising and adapting hardware, experimental design and data analysis strategies to exploit their unusual properties. Despite these challenges, we are confident that XFEL sources are poised to shed new light on ultrafast protein reaction dynamics. PMID:23021004

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.

Oxyanion Induced Variations in Domain Structure for Amorphous Cobalt Oxide Oxygen Evolving Catalysts, Resolved by X-ray Pair Distribution Function Analysis

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

Kwon, Gihan; Kokhan, Oleksandr; Han, Ali

Amorphous thin film oxygen evolving catalysts, OECs, of first-row transition metals show promise to serve as self-assembling photoanode materials in solar-driven, photoelectrochemical `artificial leaf' devices. This report demonstrates the ability to use high-energy X-ray scattering and atomic pair distribution function analysis, PDF, to resolve structure in amorphous metal oxide catalyst films. The analysis is applied here to resolve domain structure differences induced by oxyanion substitution during the electrochemical assembly of amorphous cobalt oxide catalyst films, Co-OEC. PDF patterns for Co-OEC films formed using phosphate, Pi, methylphosphate, MPi, and borate, Bi, electrolyte buffers show that the resulting domains vary in sizemore » following the sequence Pi < MPi < Bi. The increases in domain size for CoMPi and CoBi were found to be correlated with increases in the contributions from bilayer and trilayer stacked domains having structures intermediate between those of the LiCoOO and CoO(OH) mineral forms. The lattice structures and offset stacking of adjacent layers in the partially stacked CoMPi and CoBi domains were best matched to those in the LiCoOO layered structure. The results demonstrate the ability of PDF analysis to elucidate features of domain size, structure, defect content and mesoscale organization for amorphous metal oxide catalysts that are not readily accessed by other X-ray techniques. Finally, PDF structure analysis is shown to provide a way to characterize domain structures in different forms of amorphous oxide catalysts, and hence provide an opportunity to investigate correlations between domain structure and catalytic activity.« less

Oxyanion Induced Variations in Domain Structure for Amorphous Cobalt Oxide Oxygen Evolving Catalysts, Resolved by X-ray Pair Distribution Function Analysis

DOE PAGES

Kwon, Gihan; Kokhan, Oleksandr; Han, Ali; ...

2015-12-01

Amorphous thin film oxygen evolving catalysts, OECs, of first-row transition metals show promise to serve as self-assembling photoanode materials in solar-driven, photoelectrochemical `artificial leaf' devices. This report demonstrates the ability to use high-energy X-ray scattering and atomic pair distribution function analysis, PDF, to resolve structure in amorphous metal oxide catalyst films. The analysis is applied here to resolve domain structure differences induced by oxyanion substitution during the electrochemical assembly of amorphous cobalt oxide catalyst films, Co-OEC. PDF patterns for Co-OEC films formed using phosphate, Pi, methylphosphate, MPi, and borate, Bi, electrolyte buffers show that the resulting domains vary in sizemore » following the sequence Pi < MPi < Bi. The increases in domain size for CoMPi and CoBi were found to be correlated with increases in the contributions from bilayer and trilayer stacked domains having structures intermediate between those of the LiCoOO and CoO(OH) mineral forms. The lattice structures and offset stacking of adjacent layers in the partially stacked CoMPi and CoBi domains were best matched to those in the LiCoOO layered structure. The results demonstrate the ability of PDF analysis to elucidate features of domain size, structure, defect content and mesoscale organization for amorphous metal oxide catalysts that are not readily accessed by other X-ray techniques. Finally, PDF structure analysis is shown to provide a way to characterize domain structures in different forms of amorphous oxide catalysts, and hence provide an opportunity to investigate correlations between domain structure and catalytic activity.« less

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.

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.

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

Observations of the structure and evolution of solar flares with a soft X-ray telescope

NASA Technical Reports Server (NTRS)

Vorpahl, J. A.; Gibson, E. G.; Landecker, P. B.; Mckenzie, D. L.; Underwood, J. M.

1975-01-01

Soft X ray flare events were observed with the S-056 X-ray telescope that was part of the ATM complement of instruments aboard SKYLAB. Analyses of these data are reported. The observations are summarized and a detailed discussion of the X-ray flare structures is presented. The data indicated that soft X-ray emitted by a flare come primarily from an intense well-defined core surrounded by a region of fainter, more diffuse emission. An analysis of flare evolution indicates evidence for preliminary heating and energy release prior to the main phase of the flare. Core features are found to be remarkably stable and retain their shape throughout a flare. Most changes in the overall configuration seem to be result of the appearance, disappearance or change in brightness of individual features, rather than the restructuring or reorientation of these features. Brief comparisons with several theories are presented.

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

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

PubMed

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

2016-03-07

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

X-ray source assembly having enhanced output stability, and fluid stream analysis applications thereof

DOEpatents

Radley, Ian; Bievenue, Thomas J.; Burdett Jr., John H.; Gallagher, Brian W.; Shakshober, Stuart M.; Chen, Zewu; Moore, Michael D.

2007-04-24

An x-ray source assembly (2700) and method of operation are provided having enhanced output stability. The assembly includes an anode (2125) having a source spot upon which electrons (2120) impinge and a control system (2715/2720) for controlling position of the anode source spot relative to an output structure. The control system can maintain the anode source spot location relative to the output structure (2710) notwithstanding a change in one or more operating conditions of the x-ray source assembly. One aspect of the disclosed invention is most amenable to the analysis of sulfur in petroleum-based fuels.

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

Quantitative Analysis Of Three-dimensional Branching Systems From X-ray Computed Microtomography Data

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

McKinney, Adriana L.; Varga, Tamas

Branching structures such as lungs, blood vessels and plant roots play a critical role in life. Growth, structure, and function of these branching structures have an immense effect on our lives. Therefore, quantitative size information on such structures in their native environment is invaluable for studying their growth and the effect of the environment on them. X-ray computed tomography (XCT) has been an effective tool for in situ imaging and analysis of branching structures. We developed a costless tool that approximates the surface and volume of branching structures. Our methodology of noninvasive imaging, segmentation and extraction of quantitative information ismore » demonstrated through the analysis of a plant root in its soil medium from 3D tomography data. XCT data collected on a grass specimen was used to visualize its root structure. A suite of open-source software was employed to segment the root from the soil and determine its isosurface, which was used to calculate its volume and surface. This methodology of processing 3D data is applicable to other branching structures even when the structure of interest is of similar x-ray attenuation to its environment and difficulties arise with sample segmentation.« less

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

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.

Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)

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

Hura, Greg L.; Menon, Angeli L.; Hammel, Michal

2009-07-20

We present an efficient pipeline enabling high-throughput analysis of protein structure in solution with small angle X-ray scattering (SAXS). Our SAXS pipeline combines automated sample handling of microliter volumes, temperature and anaerobic control, rapid data collection and data analysis, and couples structural analysis with automated archiving. We subjected 50 representative proteins, mostly from Pyrococcus furiosus, to this pipeline and found that 30 were multimeric structures in solution. SAXS analysis allowed us to distinguish aggregated and unfolded proteins, define global structural parameters and oligomeric states for most samples, identify shapes and similar structures for 25 unknown structures, and determine envelopes formore » 41 proteins. We believe that high-throughput SAXS is an enabling technology that may change the way that structural genomics research is done.« less

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

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

NASA Astrophysics Data System (ADS)

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

2008-10-01

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

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

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.

Combined analysis of 1,3-benzodioxoles by crystalline sponge X-ray crystallography and laser desorption ionization mass spectrometry.

PubMed

Hayashi, Yukako; Ohara, Kazuaki; Taki, Rika; Saeki, Tomomi; Yamaguchi, Kentaro

2018-03-12

The crystalline sponge (CS) method, which employs single-crystal X-ray diffraction to determine the structure of an analyte present as a liquid or an oil and having a low melting point, was used in combination with laser desorption ionization mass spectrometry (LDI-MS). 1,3-Benzodioxole derivatives were encapsulated in CS and their structures were determined by combining X-ray crystallography and MS. After the X-ray analysis, the CS was subjected to imaging mass spectrometry (IMS) with an LDI spiral-time-of-flight mass spectrometer (TOF-MS). The ion detection area matched the microscopic image of the encapsulated CS. In addition, the accumulated 1D mass spectra showed that fragmentation of the guest molecule (hereafter, guest) can be easily visualized without any interference from the fragment ions of CS except for two strong ion peaks derived from the tridentate ligand TPT (2,4,6-tris(4-pyridyl)-1,3,5-triazine) of the CS and its fragment. X-ray analysis clearly showed the presence of the guest as well as the π-π, CH-halogen, and CH-O interactions between the guest and the CS framework. However, some guests remained randomly diffused in the nanopores of CS. In addition, the detection limit was less than sub-pmol order based on the weight and density of CS determined by X-ray analysis. Spectroscopic data, such as UV-vis and NMR, also supported the encapsulation of the guest through the interaction between the guest and CS components. The results denote that the CS-LDI-MS method, which combines CS, X-ray analysis and LDI-MS, is effective for structure determination.

Surface modification of platinum by laser-produced X-rays

NASA Astrophysics Data System (ADS)

Latif, Hamid; Shahid Rafique, M.; Khaleeq-ur-Rahaman, M.; Sattar, Abdul; Anjum, S.; Usman, A.; Zaheer, S.; Rawat, R. S.

2014-11-01

Laser-induced plasma is used as an X-ray source for the growth of hillocks like nanostructures on platinum surface. To generate X-rays, plasma is produced by Nd:YAG laser, which is operated at second harmonics (λ = 532 nm, E = 400 mJ). Analytical grade 5 N pure Al, Cu and W are used as laser targets for X-rays production. X-rays produced from Al, Cu and W plasmas are used to irradiate three analytical grade (5 N pure) platinum substrates, respectively, under the vacuum ∼10-4 torr. XRD analysis shows considerable structural changes in the exposed platinum. The decrement in reflection intensities, increment in dislocation line density, change in d-spacing and disturbance in the periodicity of planes evidently prove these structural changes. Atomic force microscope AFM topographic analysis of the platinum exposed to X-rays emitted from Al, Cu and W targets showed that nanometer-size hillocks are produced on the platinum surface irrespective of the source. It has also been observed that due to these hillocks, the roughness of the surface has increased. Conductivity of hillocks produced from X-rays produced by Al, Cu and W targets is compared and it is shown that the hillocks produced by Al target X-rays have better conductivity compared to the hillocks produced by X-rays from Cu and W 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.

X-Ray Astronomy

NASA Technical Reports Server (NTRS)

Wu, S. T.

2000-01-01

Dr. S. N. Zhang has lead a seven member group (Dr. Yuxin Feng, Mr. XuejunSun, Mr. Yongzhong Chen, Mr. Jun Lin, Mr. Yangsen Yao, and Ms. Xiaoling Zhang). This group has carried out the following activities: continued data analysis from space astrophysical missions CGRO, RXTE, ASCA and Chandra. Significant scientific results have been produced as results of their work. They discovered the three-layered accretion disk structure around black holes in X-ray binaries; their paper on this discovery is to appear in the prestigious Science magazine. They have also developed a new method for energy spectral analysis of black hole X-ray binaries; four papers on this topics were presented at the most recent Atlanta AAS meeting. They have also carried Monte-Carlo simulations of X-ray detectors, in support to the hardware development efforts at Marshall Space Flight Center (MSFC). These computation-intensive simulations have been carried out entirely on the computers at UAH. They have also carried out extensive simulations for astrophysical applications, taking advantage of the Monte-Carlo simulation codes developed previously at MSFC and further improved at UAH for detector simulations. One refereed paper and one contribution to conference proceedings have been resulted from this effort.

Monochromatic computed microtomography using laboratory and synchrotron sources and X-ray fluorescence analysis for comprehensive analysis of structural changes in bones.

PubMed

Buzmakov, Alexey; Chukalina, Marina; Nikolaev, Dmitry; Gulimova, Victoriya; Saveliev, Sergey; Tereschenko, Elena; Seregin, Alexey; Senin, Roman; Zolotov, Denis; Prun, Victor; Shaefer, Gerald; Asadchikov, Victor

2015-06-01

A combination of X-ray tomography at different wavelengths and X-ray fluorescence analysis was applied in the study of two types of bone tissue changes: prolonged presence in microgravity conditions and age-related bone growth. The proximal tail vertebrae of geckos were selected for investigation because they do not bear the supporting load in locomotion, which allows them to be considered as an independent indicator of gravitational influence. For the vertebrae of geckos no significant differences were revealed in the elemental composition of the flight samples and the synchronous control samples. In addition, the gecko bone tissue samples from the jaw apparatus, spine and shoulder girdle were measured. The dynamics of structural changes in the bone tissue growth was studied using samples of a human fetal hand. The hands of human fetuses of 11-15 weeks were studied. Autonomous zones of calcium accumulation were found not only in individual fingers but in each of the investigated phalanges. The results obtained are discussed.

Studying Ultradisperse Diamond Structure within Explosively Synthesized Samples via X-Ray Techniques

NASA Astrophysics Data System (ADS)

Sharkov, M. D.; Boiko, M. E.; Ivashevskaya, S. N.; Belyakova, N. S.

2013-08-01

XRD (X-Ray Diffraction) and SAXS (Small-Angle X-Ray Scattering) data have been measured for a pair of samples produced with the help of explosives. XRD peaks have shown the both samples to contain crystal diamond components as well as graphite ones. Basing on SAXS analysis, possible presence of grains with radii up to 30-50 nm within all the samples has been shown. Structure components with fractal dimension between 1 and 2 in the sample have been detected, this fact being in agreement with the assumption of diamond grain coating similarity to onion shells. In order to broad rocking curves analysis, the standard SAXS treatment technique has been complemented by a Fourier filtering procedure. For the sample #1, rocking curve components corresponding to individual interplanar distances with magnitudes from 5 nm up to 15 nm have been separated. A hypothesis relating these values to the distances between concentric onion-like shells of diamond grains has been formulated.

Handbook Of X-ray Astronomy

NASA Astrophysics Data System (ADS)

Arnaud, Keith A.; Smith, R. K.; Siemiginowska, A.; Edgar, R. J.; Grant, C. E.; Kuntz, K. D.; Schwartz, D. A.

2011-09-01

This poster advertises a book to be published in September 2011 by Cambridge University Press. Written for graduate students, professional astronomers and researchers who want to start working in this field, this book is a practical guide to x-ray astronomy. The handbook begins with x-ray optics, basic detector physics and CCDs, before focussing on data analysis. It introduces the reduction and calibration of x-ray data, scientific analysis, archives, statistical issues and the particular problems of highly extended sources. The book describes the main hardware used in x-ray astronomy, emphasizing the implications for data analysis. The concepts behind common x-ray astronomy data analysis software are explained. The appendices present reference material often required during data analysis.

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

SOLEIL shining on the solution-state structure of biomacromolecules by synchrotron X-ray footprinting at the Metrology beamline.

PubMed

Baud, A; Aymé, L; Gonnet, F; Salard, I; Gohon, Y; Jolivet, P; Brodolin, K; Da Silva, P; Giuliani, A; Sclavi, B; Chardot, T; Mercère, P; Roblin, P; Daniel, R

2017-05-01

Synchrotron X-ray footprinting complements the techniques commonly used to define the structure of molecules such as crystallography, small-angle X-ray scattering and nuclear magnetic resonance. It is remarkably useful in probing the structure and interactions of proteins with lipids, nucleic acids or with other proteins in solution, often better reflecting the in vivo state dynamics. To date, most X-ray footprinting studies have been carried out at the National Synchrotron Light Source, USA, and at the European Synchrotron Radiation Facility in Grenoble, France. This work presents X-ray footprinting of biomolecules performed for the first time at the X-ray Metrology beamline at the SOLEIL synchrotron radiation source. The installation at this beamline of a stopped-flow apparatus for sample delivery, an irradiation capillary and an automatic sample collector enabled the X-ray footprinting study of the structure of the soluble protein factor H (FH) from the human complement system as well as of the lipid-associated hydrophobic protein S3 oleosin from plant seed. Mass spectrometry analysis showed that the structural integrity of both proteins was not affected by the short exposition to the oxygen radicals produced during the irradiation. Irradiated molecules were subsequently analysed using high-resolution mass spectrometry to identify and locate oxidized amino acids. Moreover, the analyses of FH in its free state and in complex with complement C3b protein have allowed us to create a map of reactive solvent-exposed residues on the surface of FH and to observe the changes in oxidation of FH residues upon C3b binding. Studies of the solvent accessibility of the S3 oleosin show that X-ray footprinting offers also a unique approach to studying the structure of proteins embedded within membranes or lipid bodies. All the biomolecular applications reported herein demonstrate that the Metrology beamline at SOLEIL can be successfully used for synchrotron X-ray footprinting of

A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions

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

Murray, Thomas D.; Johns Hopkins University School of Medicine, Baltimore, MD 21205; Lyubimov, Artem Y.

A highly X-ray-transparent, silicon nitride-based device has been designed and fabricated to harvest protein microcrystals for high-resolution X-ray diffraction data collection using microfocus beamlines and XFELs. Microcrystals present a significant impediment to the determination of macromolecular structures by X-ray diffraction methods. Although microfocus synchrotron beamlines and X-ray free-electron lasers (XFELs) can enable the collection of interpretable diffraction data from microcrystals, there is a need for efficient methods of harvesting small volumes (<2 µl) of microcrystals grown under common laboratory formats and delivering them to an X-ray beam source under native growth conditions. One approach that shows promise in overcoming themore » challenges intrinsic to microcrystal analysis is to pair so-called ‘fixed-target’ sample-delivery devices with microbeam-based X-ray diffraction methods. However, to record weak diffraction patterns it is necessary to fabricate devices from X-ray-transparent materials that minimize background scattering. Presented here is the design of a new micro-diffraction device consisting of three layers fabricated from silicon nitride, photoresist and polyimide film. The chip features low X-ray scattering and X-ray absorption properties, and uses a customizable blend of hydrophobic and hydrophilic surface patterns to help localize microcrystals to defined regions. Microcrystals in their native growth conditions can be loaded into the chips with a standard pipette, allowing data collection at room temperature. Diffraction data collected from hen egg-white lysozyme microcrystals (10–15 µm) loaded into the chips yielded a complete, high-resolution (<1.6 Å) data set sufficient to determine a high-quality structure by molecular replacement. The features of the chip allow the rapid and user-friendly analysis of microcrystals grown under virtually any laboratory format at microfocus synchrotron beamlines and XFELs.« less

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

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

A novel spinal kinematic analysis using X-ray imaging and vicon motion analysis: a case study.

PubMed

Noh, Dong K; Lee, Nam G; You, Joshua H

2014-01-01

This study highlights a novel spinal kinematic analysis method and the feasibility of X-ray imaging measurements to accurately assess thoracic spine motion. The advanced X-ray Nash-Moe method and analysis were used to compute the segmental range of motion in thoracic vertebra pedicles in vivo. This Nash-Moe X-ray imaging method was compared with a standardized method using the Vicon 3-dimensional motion capture system. Linear regression analysis showed an excellent and significant correlation between the two methods (R2 = 0.99, p < 0.05), suggesting that the analysis of spinal segmental range of motion using X-ray imaging measurements was accurate and comparable to the conventional 3-dimensional motion analysis system. Clinically, this novel finding is compelling evidence demonstrating that measurements with X-ray imaging are useful to accurately decipher pathological spinal alignment and movement impairments in idiopathic scoliosis (IS).

BL-Lacs in X-Ray Outburst

NASA Technical Reports Server (NTRS)

Remillard, Ronald A.; Urry, C. Megan; Aharonian, Felix; Pian, Elena; Sambruna, Rita; Coppi, Paolo

2000-01-01

We conducted a multifrequency campaign for the TeV blazar Markarian 421 in 1998 April. The campaign started from a pronounced high-amplitude flare recorded by BeppoSAX and Whipple; the Advanced Satellite for Cosmology and Astrophysics (ASCA) observation started three days later. In the X-ray data, we detected multiple flares, occurring on timescales of about one day. ASCA data clearly reveal spectral variability. The comparison of the data from ASCA, the Extreme Ultraviolet Explorer, and the Rossi X-Ray Timing Explorer indicates that the variability amplitudes in the low-energy synchrotron component are larger at higher photon energies. In TeV and gamma-rays, large intraday variations-which were correlated with the X-ray flux-were observed when results from three Cerenkov telescopes were combined. The rms variability of TeV and gamma-rays was similar to that observed in hard X-rays, above ten keV. The X-ray light curve reveals flares that are almost symmetric for most cases, implying that the dominant timescale is the light crossing time through the emitting region. The structure function analysis based on the continuous X-ray light curve of seven days indicates that the characteristic timescale is approx. 0.5 days. The analysis of ASCA light curves in various energy bands appears to show both soft (positive) and hard (negative) lags. These may not be real, as systematic effects could also produce these lags, which are all much smaller than an orbit. If the lags of both signs are real, these imply that the particle acceleration and X-ray cooling timescales are similar.

Improving material identification by combining x-ray and neutron tomography

NASA Astrophysics Data System (ADS)

LaManna, Jacob M.; Hussey, Daniel S.; Baltic, Eli; Jacobson, David L.

2017-09-01

X-rays and neutrons provide complementary non-destructive probes for the analysis of structure and chemical composition of materials. Contrast differences between the modes arise due to the differences in interaction with matter. Due to the high sensitivity to hydrogen, neutrons excel at separating liquid water or hydrogenous phases from the underlying structure while X-rays resolve the solid structure. Many samples of interest, such as fluid flow in porous materials or curing concrete, are stochastic or slowly changing with time which makes analysis of sequential imaging with X-rays and neutrons difficult as the sample may change between scans. To alleviate this issue, NIST has developed a system for simultaneous X-ray and neutron tomography by orienting a 90 keVpeak micro-focus X-ray tube orthogonally to a thermal neutron beam. This system allows for non-destructive, multimodal tomography of dynamic or stochastic samples while penetrating through sample environment equipment such as pressure and flow vessels. Current efforts are underway to develop methods for 2D histogram based segmentation of reconstructed volumes. By leveraging the contrast differences between X-rays and neutrons, greater histogram peak separation can occur in 2D vs 1D enabling improved material identification.

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

PubMed

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

2018-04-13

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

A nearly on-axis spectroscopic system for simultaneously measuring UV-visible absorption and X-ray diffraction in the SPring-8 structural genomics beamline.

PubMed

Sakaguchi, Miyuki; Kimura, Tetsunari; Nishida, Takuma; Tosha, Takehiko; Sugimoto, Hiroshi; Yamaguchi, Yoshihiro; Yanagisawa, Sachiko; Ueno, Go; Murakami, Hironori; Ago, Hideo; Yamamoto, Masaki; Ogura, Takashi; Shiro, Yoshitsugu; Kubo, Minoru

2016-01-01

UV-visible absorption spectroscopy is useful for probing the electronic and structural changes of protein active sites, and thus the on-line combination of X-ray diffraction and spectroscopic analysis is increasingly being applied. Herein, a novel absorption spectrometer was developed at SPring-8 BL26B2 with a nearly on-axis geometry between the X-ray and optical axes. A small prism mirror was placed near the X-ray beamstop to pass the light only 2° off the X-ray beam, enabling spectroscopic analysis of the X-ray-exposed volume of a crystal during X-ray diffraction data collection. The spectrometer was applied to NO reductase, a heme enzyme that catalyzes NO reduction to N2O. Radiation damage to the heme was monitored in real time during X-ray irradiation by evaluating the absorption spectral changes. Moreover, NO binding to the heme was probed via caged NO photolysis with UV light, demonstrating the extended capability of the spectrometer for intermediate analysis.

X-ray irradiation-induced structural changes on Single Wall Carbon Nanotubes

NASA Astrophysics Data System (ADS)

Bardi, N.; Jurewicz, I.; King, A. K.; Alkhorayef, M. A.; Bradley, D.; Dalton, A. B.

2017-11-01

Dosimetry devices based on Carbon Nanotubes are a promising new technology. In particular using devices based on single wall Carbon Nanotubes may offer a tissue equivalent response with the possibility for device miniaturisation, high scale manufacturing and low cost. An important precursor to device fabrication requires a quantitative study of the effects of X-ray radiation on the physical and chemical properties of the individual nanotubes. In this study, we concentrate on the effects of relatively low doses, 20 cGy and 45 cGy , respectively. We use a range of characterization techniques including scanning electron microscopy, Raman spectroscopy and X-ray photoelectron spectroscopy to quantify the effects of the radiation dose on inherent properties of the nanotubes. Specifically we find that the radiation exposure results in a reduction in the sp2 nature of the nanotube bond structure. Moreover, our analysis indicates that the exposure results in nanotubes that have an increased defect density which ultimately effects the electrical properties of the nanotubes.

Impact of Oriented Clay Particles on X-Ray Spectroscopy Analysis

NASA Astrophysics Data System (ADS)

Lim, A. J. M. S.; Syazwani, R. N.; Wijeyesekera, D. C.

2016-07-01

Understanding the engineering properties of the mineralogy and microfabic of clayey soils is very complex and thus very difficult for soil characterization. Micromechanics of soils recognize that the micro structure and mineralogy of clay have a significant influence on its engineering behaviour. To achieve a more reliable quantitative evaluation of clay mineralogy, a proper sample preparation technique for quantitative clay mineral analysis is necessary. This paper presents the quantitative evaluation of elemental analysis and chemical characterization of oriented and random oriented clay particles using X-ray spectroscopy. Three different types of clays namely marine clay, bentonite and kaolin clay were studied. The oriented samples were prepared by placing the dispersed clay in water and left to settle on porous ceramic tiles by applying a relatively weak suction through a vacuum pump. Images form a Scanning Electron Microscope (SEM) was also used to show the comparison between the orientation patterns of both the sample preparation techniques. From the quantitative analysis of the X-ray spectroscopy, oriented sampling method showed more accuracy in identifying mineral deposits, because it produced better peak intensity on the spectrum and more mineral content can be identified compared to randomly oriented samples.

Energetic electron processes fluorescence effects for structured nanoparticles X-ray analysis and nuclear medicine applications

NASA Astrophysics Data System (ADS)

Taborda, A.; Desbrée, A.; Carvalho, A.; Chaves, P. C.; Reis, M. A.

2016-08-01

Superparamagnetic iron oxide (SPIO) nanoparticles are widely used as contrast agents for nuclear magnetic resonance imaging (MRI), and can be modified for improved imaging or to become tissue-specific or even protein-specific. The knowledge of their detailed elemental composition characterisation and potential use in nuclear medicine applications, is, therefore, an important issue. X-ray fluorescence techniques such as particle induced X-ray emission (PIXE) or X-ray fluorescence spectrometry (XRF), can be used for elemental characterisation even in problematic situations where very little sample volume is available. Still, the fluorescence coefficient of Fe is such that, during the decay of the inner-shell ionised atomic structure, keV Auger electrons are produced in excess to X-rays. Since cross-sections for ionisation induced by keV electrons, for low atomic number atoms, are of the order of 103 barn, care should be taken to account for possible fluorescence effects caused by Auger electrons, which may lead to the wrong quantification of elements having atomic number lower than the atomic number of Fe. Furthermore, the same electron processes will occur in iron oxide nanoparticles containing 57Co, which may be used for nuclear medicine therapy purposes. In the present work, simple approximation algorithms are proposed for the quantitative description of radiative and non-radiative processes associated with Auger electrons cascades. The effects on analytical processes and nuclear medicine applications are quantified for the case of iron oxide nanoparticles, by calculating both electron fluorescence emissions and energy deposition on cell tissues where the nanoparticles may be embedded.

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

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

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

2009-08-27

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

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

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

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

2009-04-29

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

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.

Au133(SPh-tBu)52 nanomolecules: X-ray crystallography, optical, electrochemical, and theoretical analysis.

PubMed

Dass, Amala; Theivendran, Shevanuja; Nimmala, Praneeth Reddy; Kumara, Chanaka; Jupally, Vijay Reddy; Fortunelli, Alessandro; Sementa, Luca; Barcaro, Giovanni; Zuo, Xiaobing; Noll, Bruce C

2015-04-15

Crystal structure determination has revolutionized modern science in biology, chemistry, and physics. However, the difficulty in obtaining periodic crystal lattices which are needed for X-ray crystal analysis has hindered the determination of atomic structure in nanomaterials, known as the "nanostructure problem". Here, by using rigid and bulky ligands, we have overcome this limitation and successfully solved the X-ray crystallographic structure of the largest reported thiolated gold nanomolecule, Au133S52. The total composition, Au133(SPh-tBu)52, was verified using high resolution electrospray ionization mass spectrometry (ESI-MS). The experimental and simulated optical spectra show an emergent surface plasmon resonance that is more pronounced than in the slightly larger Au144(SCH2CH2Ph)60. Theoretical analysis indicates that the presence of rigid and bulky ligands is the key to the successful crystal formation.

X-ray structure determination and deuteration of nattokinase.

PubMed

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

2013-11-01

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

X-ray structure determination and deuteration of nattokinase

PubMed Central

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

2013-01-01

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

"X-Ray Transients in Star-Forming Regions" and "Hard X-Ray Emission from X-Ray Bursters"

NASA Technical Reports Server (NTRS)

Halpern, Jules P.; Kaaret, Philip

1999-01-01

This grant funded work on the analysis of data obtained with the Burst and Transient Experiment (BATSE) on the Compton Gamma-Ray Observatory. The goal of the work was to search for hard x-ray transients in star forming regions using the all-sky hard x-ray monitoring capability of BATSE. Our initial work lead to the discovery of a hard x-ray transient, GRO J1849-03. Follow-up observations of this source made with the Wide Field Camera on BeppoSAX showed that the source should be identified with the previously known x-ray pulsar GS 1843-02 which itself is identified with the x-ray source X1845-024 originally discovered with the SAS-3 satellite. Our identification of the source and measurement of the outburst recurrence time, lead to the identification of the source as a Be/X-ray binary with a spin period of 94.8 s and an orbital period of 241 days. The funding was used primarily for partial salary and travel support for John Tomsick, then a graduate student at Columbia University. John Tomsick, now Dr. Tomsick, received his Ph.D. from Columbia University in July 1999, based partially on results obtained under this investigation. He is now a postdoctoral research scientist at the University of California, San Diego.

Control of the Low-energy X-rays by Using MCNP5 and Numerical Analysis for a New Concept Intra-oral X-ray Imaging System

NASA Astrophysics Data System (ADS)

Huh, Jangyong; Ji, Yunseo; Lee, Rena

2018-05-01

An X-ray control algorithm to modulate the X-ray intensity distribution over the FOV (field of view) has been developed by using numerical analysis and MCNP5, a particle transport simulation code on the basis of the Monte Carlo method. X-rays, which are widely used in medical diagnostic imaging, should be controlled in order to maximize the performance of the X-ray imaging system. However, transporting X-rays, like a liquid or a gas is conveyed through a physical form such as pipes, is not possible. In the present study, an X-ray control algorithm and technique to uniformize the Xray intensity projected on the image sensor were developed using a flattening filter and a collimator in order to alleviate the anisotropy of the distribution of X-rays due to intrinsic features of the X-ray generator. The proposed method, which is combined with MCNP5 modeling and numerical analysis, aimed to optimize a flattening filter and a collimator for a uniform distribution of X-rays. Their size and shape were estimated from the method. The simulation and the experimental results both showed that the method yielded an intensity distribution over an X-ray field of 6×4 cm2 at SID (source to image-receptor distance) of 5 cm with a uniformity of more than 90% when the flattening filter and the collimator were mounted on the system. The proposed algorithm and technique are not only confined to flattening filter development but can also be applied for other X-ray related research and development efforts.

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.

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

NASA Astrophysics Data System (ADS)

Shrivastava, B. D.

2012-05-01

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

Monochromatic computed microtomography using laboratory and synchrotron sources and X-ray fluorescence analysis for comprehensive analysis of structural changes in bones1

PubMed Central

Buzmakov, Alexey; Chukalina, Marina; Nikolaev, Dmitry; Gulimova, Victoriya; Saveliev, Sergey; Tereschenko, Elena; Seregin, Alexey; Senin, Roman; Zolotov, Denis; Prun, Victor; Shaefer, Gerald; Asadchikov, Victor

2015-01-01

A combination of X-ray tomography at different wavelengths and X-ray fluorescence analysis was applied in the study of two types of bone tissue changes: prolonged presence in microgravity conditions and age-related bone growth. The proximal tail vertebrae of geckos were selected for investigation because they do not bear the supporting load in locomotion, which allows them to be considered as an independent indicator of gravitational influence. For the vertebrae of geckos no significant differences were revealed in the elemental composition of the flight samples and the synchronous control samples. In addition, the gecko bone tissue samples from the jaw apparatus, spine and shoulder girdle were measured. The dynamics of structural changes in the bone tissue growth was studied using samples of a human fetal hand. The hands of human fetuses of 11–15 weeks were studied. Autonomous zones of calcium accumulation were found not only in individual fingers but in each of the investigated phalanges. The results obtained are discussed. PMID:26089762

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.

Synchrotron X-Ray Diffraction Analysis of Meteorites in Thin Section: Preliminary Results

NASA Technical Reports Server (NTRS)

Treiman, A. H.; Lanzirotti, A.; Xirouchakis, D.

2004-01-01

X-ray diffraction is the pre-eminent technique for mineral identification and structure determination, but is difficult to apply to grains in thin section, the standard meteorite preparation. Bright focused X-ray beams from synchrotrons have been used extensively in mineralogy and have been applied to extraterrestrial particles. The intensity and small spot size achievable in synchrotron X-ray beams makes them useful for study of materials in thin sections. Here, we describe Synchrotron X-ray Diffraction (SXRD) in thin section as done at the National Synchrotron Light Source, and cite examples of its value for studies of meteorites in thin section.

Comparison of dissimilarity measures for cluster analysis of X-ray diffraction data from combinatorial libraries

NASA Astrophysics Data System (ADS)

Iwasaki, Yuma; Kusne, A. Gilad; Takeuchi, Ichiro

2017-12-01

Machine learning techniques have proven invaluable to manage the ever growing volume of materials research data produced as developments continue in high-throughput materials simulation, fabrication, and characterization. In particular, machine learning techniques have been demonstrated for their utility in rapidly and automatically identifying potential composition-phase maps from structural data characterization of composition spread libraries, enabling rapid materials fabrication-structure-property analysis and functional materials discovery. A key issue in development of an automated phase-diagram determination method is the choice of dissimilarity measure, or kernel function. The desired measure reduces the impact of confounding structural data issues on analysis performance. The issues include peak height changes and peak shifting due to lattice constant change as a function of composition. In this work, we investigate the choice of dissimilarity measure in X-ray diffraction-based structure analysis and the choice of measure's performance impact on automatic composition-phase map determination. Nine dissimilarity measures are investigated for their impact in analyzing X-ray diffraction patterns for a Fe-Co-Ni ternary alloy composition spread. The cosine, Pearson correlation coefficient, and Jensen-Shannon divergence measures are shown to provide the best performance in the presence of peak height change and peak shifting (due to lattice constant change) when the magnitude of peak shifting is unknown. With prior knowledge of the maximum peak shifting, dynamic time warping in a normalized constrained mode provides the best performance. This work also serves to demonstrate a strategy for rapid analysis of a large number of X-ray diffraction patterns in general beyond data from combinatorial libraries.

A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions

DOE PAGES

Murray, Thomas D.; Lyubimov, Artem Y.; Ogata, Craig M.; ...

2015-08-11

Microcrystals present a significant impediment to the determination of macromolecular structures by X-ray diffraction methods. Although microfocus synchrotron beamlines and X-ray free-electron lasers (XFELs) can enable the collection of interpretable diffraction data from microcrystals, there is a need for efficient methods of harvesting small volumes (<2 µl) of microcrystals grown under common laboratory formats and delivering them to an X-ray beam source under native growth conditions. One approach that shows promise in overcoming the challenges intrinsic to microcrystal analysis is to pair so-called `fixed-target' sample-delivery devices with microbeam-based X-ray diffraction methods. However, to record weak diffraction patterns it is necessarymore » to fabricate devices from X-ray-transparent materials that minimize background scattering. Presented here is the design of a new micro-diffraction device consisting of three layers fabricated from silicon nitride, photoresist and polyimide film. The chip features low X-ray scattering and X-ray absorption properties, and uses a customizable blend of hydrophobic and hydrophilic surface patterns to help localize microcrystals to defined regions. Microcrystals in their native growth conditions can be loaded into the chips with a standard pipette, allowing data collection at room temperature. Diffraction data collected from hen egg-white lysozyme microcrystals (10–15 µm) loaded into the chips yielded a complete, high-resolution (<1.6 Å) data set sufficient to determine a high-quality structure by molecular replacement. In addition, the features of the chip allow the rapid and user-friendly analysis of microcrystals grown under virtually any laboratory format at microfocus synchrotron beamlines and XFELs.« less

A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions

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

Murray, Thomas D.; Lyubimov, Artem Y.; Ogata, Craig M.

Microcrystals present a significant impediment to the determination of macromolecular structures by X-ray diffraction methods. Although microfocus synchrotron beamlines and X-ray free-electron lasers (XFELs) can enable the collection of interpretable diffraction data from microcrystals, there is a need for efficient methods of harvesting small volumes (<2 µl) of microcrystals grown under common laboratory formats and delivering them to an X-ray beam source under native growth conditions. One approach that shows promise in overcoming the challenges intrinsic to microcrystal analysis is to pair so-called `fixed-target' sample-delivery devices with microbeam-based X-ray diffraction methods. However, to record weak diffraction patterns it is necessarymore » to fabricate devices from X-ray-transparent materials that minimize background scattering. Presented here is the design of a new micro-diffraction device consisting of three layers fabricated from silicon nitride, photoresist and polyimide film. The chip features low X-ray scattering and X-ray absorption properties, and uses a customizable blend of hydrophobic and hydrophilic surface patterns to help localize microcrystals to defined regions. Microcrystals in their native growth conditions can be loaded into the chips with a standard pipette, allowing data collection at room temperature. Diffraction data collected from hen egg-white lysozyme microcrystals (10–15 µm) loaded into the chips yielded a complete, high-resolution (<1.6 Å) data set sufficient to determine a high-quality structure by molecular replacement. In addition, the features of the chip allow the rapid and user-friendly analysis of microcrystals grown under virtually any laboratory format at microfocus synchrotron beamlines and XFELs.« less

A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions

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

Murray, Thomas D.; Lyubimov, Artem Y.; Ogata, Craig M.

Microcrystals present a significant impediment to the determination of macromolecular structures by X-ray diffraction methods. Although microfocus synchrotron beamlines and X-ray free-electron lasers (XFELs) can enable the collection of interpretable diffraction data from microcrystals, there is a need for efficient methods of harvesting small volumes (<2µl) of microcrystals grown under common laboratory formats and delivering them to an X-ray beam source under native growth conditions. One approach that shows promise in overcoming the challenges intrinsic to microcrystal analysis is to pair so-called `fixed-target' sample-delivery devices with microbeam-based X-ray diffraction methods. However, to record weak diffraction patterns it is necessary tomore » fabricate devices from X-ray-transparent materials that minimize background scattering. Presented here is the design of a new micro-diffraction device consisting of three layers fabricated from silicon nitride, photoresist and polyimide film. The chip features low X-ray scattering and X-ray absorption properties, and uses a customizable blend of hydrophobic and hydrophilic surface patterns to help localize microcrystals to defined regions. Microcrystals in their native growth conditions can be loaded into the chips with a standard pipette, allowing data collection at room temperature. Diffraction data collected from hen egg-white lysozyme microcrystals (10–15µm) loaded into the chips yielded a complete, high-resolution (<1.6Å) data set sufficient to determine a high-quality structure by molecular replacement. The features of the chip allow the rapid and user-friendly analysis of microcrystals grown under virtually any laboratory format at microfocus synchrotron beamlines and XFELs.« less

A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions

PubMed Central

Murray, Thomas D.; Lyubimov, Artem Y.; Ogata, Craig M.; Vo, Huy; Uervirojnangkoorn, Monarin; Brunger, Axel T.; Berger, James M.

2015-01-01

Microcrystals present a significant impediment to the determination of macromolecular structures by X-ray diffraction methods. Although microfocus synchrotron beamlines and X-ray free-electron lasers (XFELs) can enable the collection of interpretable diffraction data from microcrystals, there is a need for efficient methods of harvesting small volumes (<2 µl) of microcrystals grown under common laboratory formats and delivering them to an X-ray beam source under native growth conditions. One approach that shows promise in overcoming the challenges intrinsic to microcrystal analysis is to pair so-called ‘fixed-target’ sample-delivery devices with microbeam-based X-ray diffraction methods. However, to record weak diffraction patterns it is necessary to fabricate devices from X-ray-transparent materials that minimize background scattering. Presented here is the design of a new micro-diffraction device consisting of three layers fabricated from silicon nitride, photoresist and polyimide film. The chip features low X-ray scattering and X-ray absorption properties, and uses a customizable blend of hydrophobic and hydrophilic surface patterns to help localize microcrystals to defined regions. Microcrystals in their native growth conditions can be loaded into the chips with a standard pipette, allowing data collection at room temperature. Diffraction data collected from hen egg-white lysozyme microcrystals (10–15 µm) loaded into the chips yielded a complete, high-resolution (<1.6 Å) data set sufficient to determine a high-quality structure by molecular replacement. The features of the chip allow the rapid and user-friendly analysis of microcrystals grown under virtually any laboratory format at microfocus synchrotron beamlines and XFELs. PMID:26457423

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

X-ray Crystallographic Structure of Thermophilic Rhodopsin

PubMed Central

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

2016-01-01

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

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).

Synchrotron x-ray modification of nanoparticle superlattice formation

NASA Astrophysics Data System (ADS)

Lu, Chenguang; Akey, Austin J.; Herman, Irving P.

2012-09-01

The synchrotron x-ray radiation used to perform small angle x-ray scattering (SAXS) during the formation of three-dimensional nanoparticle superlattices by drop casting nanoparticle solutions affects the structure and the local crystalline order of the resulting films. The domain size decreases due to the real-time SAXS analysis during drying and more macroscopic changes are visible to the eye.

Analysis of sculptures using XRF and X-ray radiography

NASA Astrophysics Data System (ADS)

Calza, C.; Oliveira, D. F.; Freitas, R. P.; Rocha, H. S.; Nascimento, J. R.; Lopes, R. T.

2015-11-01

This work reports the analysis of two sacred images on polychrome wood using X-ray Radiography and Energy Dispersive X-Ray Fluorescence. The first case is the analysis of a sculpture portraying Saint Sebastian, the patron saint of Rio de Janeiro, which is considered the second most ancient sacred image of Brazil. This sculpture was made in Portugal and was transported to Brazil by Estácio Sá, founder of the city of Rio de Janeiro, in 1565. Nowadays, it is located on the main altar of the Church of Capuchin Friars. The second case is the analysis of a sculpture representing Our Lady of Conception, which is located in the D. João VI Museum (EBA/UFRJ, Rio de Janeiro). The objective of these analyses was to evaluate the general conditions of the sculptures, identifying possible problems and internal damages, areas that revealed signs of previous retouchings and the materials and pigments employed by the artists, in order to assist its restoration procedures. EDXRF measurements were carried out with a portable system, developed at the Nuclear Instrumentation Laboratory, consisting of a Si-PIN XR-100CR detector from Amptek and an Oxford TF3005 X-ray tube with W anode. An X-ray source, a CR System GE CR50P and IP detectors were used to perform the radiographs. The XRF analysis of the sculptures identified the original pigments in both cases and the radiographic images revealed details of the manufacture; restored regions; extensive use of lead white; presence of cracks on the wood; use of nails and spikes, etc.

Phase-contrast x-ray computed tomography for biological imaging

NASA Astrophysics Data System (ADS)

Momose, Atsushi; Takeda, Tohoru; Itai, Yuji

1997-10-01

We have shown so far that 3D structures in biological sot tissues such as cancer can be revealed by phase-contrast x- ray computed tomography using an x-ray interferometer. As a next step, we aim at applications of this technique to in vivo observation, including radiographic applications. For this purpose, the size of view field is desired to be more than a few centimeters. Therefore, a larger x-ray interferometer should be used with x-rays of higher energy. We have evaluated the optimal x-ray energy from an aspect of does as a function of sample size. Moreover, desired spatial resolution to an image sensor is discussed as functions of x-ray energy and sample size, basing on a requirement in the analysis of interference fringes.

Proton-Induced X-Ray Emission Analysis of Crematorium Emissions

NASA Astrophysics Data System (ADS)

Ali, Salina; Nadareski, Benjamin; Safiq, Alexandrea; Smith, Jeremy; Yoskowitz, Josh; Labrake, Scott; Vineyard, Michael

2013-10-01

There has been considerable concern in recent years about possible mercury emissions from crematoria. We have performed a particle-induced X-ray emission (PIXE) analysis of atmospheric aerosol samples collected on the roof of the crematorium at Vale Cemetery in Schenectady, NY, to address this concern. The samples were collected with a nine-stage cascade impactor that separates the particulate matter according to particle size. The aerosol samples were bombarded with 2.2-MeV protons from the Union College 1.1-MV Pelletron Accelerator. The emitted X-rays were detected with a silicon drift detector and the X-ray energy spectra were analyzed using GUPIX software to determine the elemental concentrations. We measured significant concentrations of sulfur, phosphorus, potassium, calcium, and iron, but essentially no mercury. The lower limit of detection for mercury in this experiment was approximately 0.2 ng/m3. We will describe the experimental procedure, discuss the PIXE analysis, and present preliminary results.

Coherent convergent-beam time-resolved X-ray diffraction

PubMed Central

Spence, John C. H.; Zatsepin, Nadia A.; Li, Chufeng

2014-01-01

The use of coherent X-ray lasers for structural biology allows the use of nanometre diameter X-ray beams with large beam divergence. Their application to the structure analysis of protein nanocrystals and single particles raises new challenges and opportunities. We discuss the form of these coherent convergent-beam (CCB) hard X-ray diffraction patterns and their potential use for time-resolved crystallography, normally achieved by Laue (polychromatic) diffraction, for which the monochromatic laser radiation of a free-electron X-ray laser is unsuitable. We discuss the possibility of obtaining single-shot, angle-integrated rocking curves from CCB patterns, and the dependence of the resulting patterns on the focused beam coordinate when the beam diameter is larger or smaller than a nanocrystal, or smaller than one unit cell. We show how structure factor phase information is provided at overlapping interfering orders and how a common phase origin between different shots may be obtained. Their use in refinement of the phase-sensitive intensity between overlapping orders is suggested. PMID:24914153

Au133(SPh-tBu)52 Nanomolecules: X-ray Crystallography, Optical, Electrochemical, and Theoretical Analysis

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

Dass, Amala; Theivendran, Shevanuja; Nimmala, Praneeth Reddy

2015-04-15

Crystal structure determination has revolutionized modern science in biology, chemistry, and physics. However, the difficulty in obtaining periodic crystal lattices which are needed for X-ray crystal analysis has hindered the determination of atomic structure in nanomaterials, known as the “nanostructure problem”. Here, by using rigid and bulky ligands, we have overcome this limitation and successfully solved the X-ray crystallographic structure of the largest reported thiolated gold nanomolecule, Au133S52. The total composition, Au133(SPh-tBu)52, was verified using high resolution electrospray ionization mass spectrometry (ESI-MS). The experimental and simulated optical spectra show an emergent surface plasmon resonance that is more pronounced than inmore » the slightly larger Au144(SCH2CH2Ph)60. Theoretical analysis indicates that the presence of rigid and bulky ligands is the key to the successful crystal formation.« less

Au 133 (SPh - t Bu) 52 Nanomolecules: X-ray Crystallography, Optical, Electrochemical, and Theoretical Analysis

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

Dass, Amala; Theivendran, Shevanuja; Nimmala, Praneeth Reddy

2015-04-15

Crystal structure determination has revolutionized modern science in biology, chemistry, and physics. However, the difficulty in obtaining periodic crystal lattices which are needed for X-ray crystal analysis has hindered the determination of atomic structure in nanomaterials, known as the "nanostructure problem". Here, by using rigid and bulky ligands, we have overcome this limitation and successfully solved the X-ray crystallographic structure of the largest reported thiolated gold nanomolecule, Au133S52. The total composition, Au-133(SPh-tBu)(52), was verified using high resolution electrospray ionization mass spectrometry (ESI-MS). The experimental and simulated optical spectra show an emergent surface plasmon resonance that is more pronounced than inmore » the slightly larger Au-144(SCH2CH2Ph)(60). Theoretical analysis indicates that the presence of rigid and bulky ligands is the key to the successful crystal formation.« less

Anisotropy enhanced X-ray scattering from solvated transition metal complexes

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

Biasin, Elisa; van Driel, Tim B.; Levi, Gianluca

Time-resolved X-ray scattering patterns from photoexcited molecules in solution are in many cases anisotropic at the ultrafast time scales accessible at X-ray free-electron lasers (XFELs). This anisotropy arises from the interaction of a linearly polarized UV–Vis pump laser pulse with the sample, which induces anisotropic structural changes that can be captured by femtosecond X-ray pulses. In this work, a method for quantitative analysis of the anisotropic scattering signal arising from an ensemble of molecules is described, and it is demonstrated how its use can enhance the structural sensitivity of the time-resolved X-ray scattering experiment. This method is applied on time-resolvedmore » X-ray scattering patterns measured upon photoexcitation of a solvated di-platinum complex at an XFEL, and the key parameters involved are explored. Here it is shown that a combined analysis of the anisotropic and isotropic difference scattering signals in this experiment allows a more precise determination of the main photoinduced structural change in the solute,i.e.the change in Pt—Pt bond length, and yields more information on the excitation channels than the analysis of the isotropic scattering only. Finally, it is discussed how the anisotropic transient response of the solvent can enable the determination of key experimental parameters such as the instrument response function.« less

Anisotropy enhanced X-ray scattering from solvated transition metal complexes

DOE PAGES

Biasin, Elisa; van Driel, Tim B.; Levi, Gianluca; ...

2018-02-13

Time-resolved X-ray scattering patterns from photoexcited molecules in solution are in many cases anisotropic at the ultrafast time scales accessible at X-ray free-electron lasers (XFELs). This anisotropy arises from the interaction of a linearly polarized UV–Vis pump laser pulse with the sample, which induces anisotropic structural changes that can be captured by femtosecond X-ray pulses. In this work, a method for quantitative analysis of the anisotropic scattering signal arising from an ensemble of molecules is described, and it is demonstrated how its use can enhance the structural sensitivity of the time-resolved X-ray scattering experiment. This method is applied on time-resolvedmore » X-ray scattering patterns measured upon photoexcitation of a solvated di-platinum complex at an XFEL, and the key parameters involved are explored. Here it is shown that a combined analysis of the anisotropic and isotropic difference scattering signals in this experiment allows a more precise determination of the main photoinduced structural change in the solute,i.e.the change in Pt—Pt bond length, and yields more information on the excitation channels than the analysis of the isotropic scattering only. Finally, it is discussed how the anisotropic transient response of the solvent can enable the determination of key experimental parameters such as the instrument response function.« less

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.

Analysis of the X-ray emission of nine Swift afterglows

NASA Astrophysics Data System (ADS)

Panaitescu, A.; Mészáros, P.; Gehrels, N.; Burrows, D.; Nousek, J.

2006-03-01

The X-ray light curves of nine Swift XRT afterglows (050126, 050128, 050219A, 050315, 050318, 050319, 050401, 050408 and 050505) display a complex behaviour: a steep t-3.0+/-0.3 decay until ~400 s, followed by a significantly slower t-0.65+/-0.20 fall-off, which at 0.2-2 day after the burst evolves into a t-1.7+/-0.5 decay. We consider three possible models for the geometry of relativistic blast-waves (spherical outflows, non-spreading jets and spreading jets), two possible dynamical regimes for the forward shock (adiabatic and fully radiative), and we take into account a possible angular structure of the outflow and delayed energy injection in the blast-wave to identify the models which reconcile the X-ray light-curve decay with the slope of the X-ray continuum for each of the above three afterglow phases. By piecing together the various models for each phase in a way that makes physical sense, we identify possible models for the entire X-ray afterglow. The major conclusion of this work is that a long-lived episode of energy injection in the blast-wave, during which the shock energy increases at t1.0+/-0.5, is required for five afterglows and could be at work in the other four as well. For some afterglows, there may be other mechanisms that can explain the t < 400 s fast falling-off X-ray light curve (e.g. the large-angle gamma-ray burst emission), the 400 s to 5 h slow decay (e.g. a structured outflow), or the steepening at 0.2-2 day (e.g. a jet-break, a collimated outflow transiting from a wind with a r-3 radial density profile to a homogeneous or outward-increasing density region). Optical observations in conjunction with the X-ray can distinguish among these various models. Our simple tests allow the determination of the location of the cooling frequency relative to the X-ray domain and, thus, of the index of the electron power-law distribution with energy in the blast-wave. The resulting indices are clearly inconsistent with a universal value.

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.

X-Ray Emission from the Soft X-Ray Transient Aquila X-1

NASA Technical Reports Server (NTRS)

Tavani, Marco

1998-01-01

Aquila X-1 is the most prolific of soft X-ray transients. It is believed to contain a rapidly spinning neutron star sporadically accreting near the Eddington limit from a low-mass companion star. The interest in studying the repeated X-ray outbursts from Aquila X-1 is twofold: (1) studying the relation between optical, soft and hard X-ray emission during the outburst onset, development and decay; (2) relating the spectral component to thermal and non-thermal processes occurring near the magnetosphere and in the boundary layer of a time-variable accretion disk. Our investigation is based on the BATSE monitoring of Aquila X-1 performed by our group. We observed Aquila X-1 in 1997 and re-analyzed archival information obtained in April 1994 during a period of extraordinary outbursting activity of the source in the hard X-ray range. Our results allow, for the first time for this important source, to obtain simultaneous spectral information from 2 keV to 200 keV. A black body (T = 0.8 keV) plus a broken power-law spectrum describe accurately the 1994 spectrum. Substantial hard X-ray emission is evident in the data, confirming that the accretion phase during sub-Eddington limit episodes is capable of producing energetic hard emission near 5 x 10(exp 35) ergs(exp -1). A preliminary paper summarizes our results, and a more comprehensive account is being written. We performed a theoretical analysis of possible emission mechanisms, and confirmed that a non-thermal emission mechanism triggered in a highly sheared magnetosphere at the accretion disk inner boundary can explain the hard X-ray emission. An anticorrelation between soft and hard X-ray emission is indeed prominently observed as predicted by this model.

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

PubMed

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

2018-01-16

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

The Mapping X-ray Fluorescence Spectrometer (MapX)

NASA Astrophysics Data System (ADS)

Sarrazin, P.; Blake, D. F.; Marchis, F.; Bristow, T.; Thompson, K.

2017-12-01

Many planetary surface processes leave traces of their actions as features in the size range 10s to 100s of microns. The Mapping X-ray Fluorescence Spectrometer (MapX) will provide elemental imaging at 100 micron spatial resolution, yielding elemental chemistry at a scale where many relict physical, chemical, or biological features can be imaged and interpreted in ancient rocks on planetary bodies and planetesimals. MapX is an arm-based instrument positioned on a rock or regolith with touch sensors. During an analysis, an X-ray source (tube or radioisotope) bombards the sample with X-rays or alpha-particles / gamma-rays, resulting in sample X-ray Fluorescence (XRF). X-rays emitted in the direction of an X-ray sensitive CCD imager pass through a 1:1 focusing lens (X-ray micro-pore Optic (MPO)) that projects a spatially resolved image of the X-rays onto the CCD. The CCD is operated in single photon counting mode so that the energies and positions of individual X-ray photons are recorded. In a single analysis, several thousand frames are both stored and processed in real-time. Higher level data products include single-element maps with a lateral spatial resolution of 100 microns and quantitative XRF spectra from ground- or instrument- selected Regions of Interest (ROI). XRF spectra from ROI are compared with known rock and mineral compositions to extrapolate the data to rock types and putative mineralogies. When applied to airless bodies and implemented with an appropriate radioisotope source for alpha-particle excitation, MapX will be able to analyze biogenic elements C, N, O, P, S, in addition to the cations of the rock-forming elements >Na, accessible with either X-ray or gamma-ray excitation. The MapX concept has been demonstrated with a series of lab-based prototypes and is currently under refinement and TRL maturation.

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.

Analysis of X-ray structures of matrix metalloproteinases via chaotic map clustering.

PubMed

Giangreco, Ilenia; Nicolotti, Orazio; Carotti, Angelo; De Carlo, Francesco; Gargano, Gianfranco; Bellotti, Roberto

2010-10-08

Matrix metalloproteinases (MMPs) are well-known biological targets implicated in tumour progression, homeostatic regulation, innate immunity, impaired delivery of pro-apoptotic ligands, and the release and cleavage of cell-surface receptors. With this in mind, the perception of the intimate relationships among diverse MMPs could be a solid basis for accelerated learning in designing new selective MMP inhibitors. In this regard, decrypting the latent molecular reasons in order to elucidate similarity among MMPs is a key challenge. We describe a pairwise variant of the non-parametric chaotic map clustering (CMC) algorithm and its application to 104 X-ray MMP structures. In this analysis electrostatic potentials are computed and used as input for the CMC algorithm. It was shown that differences between proteins reflect genuine variation of their electrostatic potentials. In addition, the analysis has been also extended to analyze the protein primary structures and the molecular shapes of the MMP co-crystallised ligands. The CMC algorithm was shown to be a valuable tool in knowledge acquisition and transfer from MMP structures. Based on the variation of electrostatic potentials, CMC was successful in analysing the MMP target family landscape and different subsites. The first investigation resulted in rational figure interpretation of both domain organization as well as of substrate specificity classifications. The second made it possible to distinguish the MMP classes, demonstrating the high specificity of the S1' pocket, to detect both the occurrence of punctual mutations of ionisable residues and different side-chain conformations that likely account for induced-fit phenomena. In addition, CMC demonstrated a potential comparable to the most popular UPGMA (Unweighted Pair Group Method with Arithmetic mean) method that, at present, represents a standard clustering bioinformatics approach. Interestingly, CMC and UPGMA resulted in closely comparable outcomes, but often

CIAO: A Modern Data Analysis System for X-Ray Astronomy

NASA Astrophysics Data System (ADS)

Fruscione, Antonella

2017-08-01

It is now eighteen years after launch and Chandra continues to produce spectacular results!A portion of the success is to be attributed to the data analysis software CIAO (Chandra Interactive Analysis of Observations) that the Chandra X-Ray Center (CXC) continues to improve and release year after year.CIAO is downloaded more than 1200 times a year and it is used by a wide variety of users around the world: from novice to experienced X-ray astronomers, high school, undergraduate and graduate students, archival users (many new to X-ray or Chandra data), users with extensive resources and others from smaller countries and institutions.The scientific goals and kinds of datasets and analysis cover a wide range: observations spanning from days to years, different instrument configurations and different kinds of targets, from pointlike stars and quasars, to fuzzy galaxies and clusters, to moving solar objects. These different needs and goals require a variety of specialized software and careful and detailed documentation which is what the CIAO software provides. In general, we strive to build a software system which is easy for beginners, yet powerful for advanced users.The complexity of the Chandra data require a flexible data analysis system which provides an environment where the users can apply our tools, but can also explore and construct their own applications. The main purpose of this talk is to present CIAO as a modern data analysis system for X-ray data analysis.CIAO has grown tremendously over the years and we will highlight (a) the most recent advancements with a particular emphasis on the newly developed high-level scripts which simplify the analysis steps for the most common cases making CIAO more accessible to all users - including beginners and users who are not X-ray astronomy specialists, (b) the python-based Sherpa modelling and fitting application and the new stand-alone version openly developed and distributed on Github and (c) progress on methods to

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.

Temporal characteristic analysis of laser-modulated pulsed X-ray source for space X-ray communication

NASA Astrophysics Data System (ADS)

Hang, Shuang; Liu, Yunpeng; Li, Huan; Tang, Xiaobin; Chen, Da

2018-04-01

X-ray communication (XCOM) is a new communication type and is expected to realize high-speed data transmission in some special communication scenarios, such as deep space communication and blackout communication. This study proposes a high-speed modulated X-ray source scheme based on the laser-to-X-ray conversion. The temporal characteristics of the essential components of the proposed laser-modulated pulsed X-ray source (LMPXS) were analyzed to evaluate its pulse emission performance. Results show that the LMPXS can provide a maximum modulation rate up to 100 Mbps which is expected to significantly improve the data rate of XCOM.

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.

The active site structure of tetanus neurotoxin resolved by multiple scattering analysis in X-Ray absorption spectroscopy.

PubMed Central

Meneghini, C; Morante, S

1998-01-01

A detailed study of the x-ray absorption spectrum of tetanus neurotoxin in the K-edge EXAFS region of the zinc absorber is presented that allows the complete identification of the amino acid residues coordinated to the zinc active site. A very satisfactory interpretation of the experimental data can be given if multiple scattering contributions are included in the analysis. Comparing the absorption spectrum of tetanus neurotoxin to that of two other structurally similar zinc-endopeptidases, thermolysin and astacin, in which the zinc coordination mode is known from crystallographic data, we conclude that in tetanus neurotoxin, besides a water molecule, zinc is coordinated to two histidines and a tyrosine. PMID:9746536

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.

Evaluating structure in thin block copolymer films with soft x-rays (Conference Presentation)

NASA Astrophysics Data System (ADS)

Sunday, Daniel; Liman, Christopher; Hannon, Adam F.; Ren, Jiaxing; Chen, Xuanxuan; Suh, Hyo Seon; de Pablo, Juan J.; Nealey, Paul F.; Kline, R. Joseph

2017-03-01

The semiconductor industry is evaluating a variety of approaches for the cost efficient production of future processing and memory generations. Amongst the technologies being explored are multiple patterning steps, extreme ultraviolet (EUV) lithography, multiple-beam electron beam lithography and the directed self-assembly (DSA) of block copolymers (BCPs). BCP DSA utilizes a chemical or topographical template to induce long range order in a thin film of BCP which enhances the resolution of the original pattern. The characterization of buried structure within a DSA BCP film is challenging due to the lack of contrast between the organic materials. Critical-dimension small angle x-ray scattering (CDSAXS) measurements were performed on DSA BCP films, using soft X-rays to tune the contrast, in order to understand the relationship between template structure and film morphology.1 The results of these measurements show that as the width of the guiding stripe widens the arrangement of the BCP on the guiding stripe inverts, shifting from the A block being centered on the guiding stripe to the B block being centered on the guiding stripe. The initial results of integration of mean field simulations into the analysis of scattering data will also be discussed. In addition to examining the BCP structure with CDSAXS, soft X-ray reflectivity2 measurements were performed on BCP to better understand the relationship between interface width for systems with alternative architectures (triblocks) and additives (polymers/ionic liquids). The addition of a selectively associating additive increases the interaction parameter between the two blocks, resulting in the reduction of the interface width and access to smaller pitches. The use of soft X-ray reflectivity allows the evaluation of the distribution of the additive. (1) Sunday, D. F.; Hammond, M. R.; Wang, C.; Wu, W.; Delongchamp, D. M.; Tjio, M.; Cheng, J. Y.; Kline, R. J.; Pitera, J. W. Determination of the Internal Morphology of

Normal incidence X-ray telescope power spectra of X-ray emission from solar active regions. I - Observations. II - Theory

NASA Technical Reports Server (NTRS)

Gomez, Daniel O.; Martens, Petrus C. H.; Golub, Leon

1993-01-01

Fourier analysis is applied to very high resolution image of coronal active regions obtained by the Normal Incidence X-Ray Telescope is used to find a broad isotropic power-law spectrum of the spatial distribution of soft X-ray intensities. Magnetic structures of all sizes are present down to the resolution limit of the instrument. Power spectra for the X-ray intensities of a sample of topologically different active regions are found which fall off with increasing wavenumber as 1/k-cubed. A model is presented that relates the basic features of coronal magnetic fluctuations to the subphotospheric hydrodynamic turbulence that generates them. The model is used to find a theoretical power spectrum for the X-ray intensity which falls off with increasing wavenumber as 1/k-cubed. The implications of a turbulent regime in active regions are discussed.

Investigating the local structure of B-site cations in (1-x)BaTiO3-xBiScO3 and (1-x)PbTiO3-xBiScO3 using X-ray absorption spectroscopy

NASA Astrophysics Data System (ADS)

Blanchard, Peter E. R.; Grosvenor, Andrew P.

2018-05-01

The structural properties of (1-x)BaTiO3-xBiScO3 and (1-x)PbTiO3-xBiScO3 were investigated using powder X-ray diffraction and X-ray absorption spectroscopy. Diffraction measurements confirmed that substituting small amounts of BiScO3 into BaTiO3 initially stabilizes a cubic phase at x = 0.2 before impurity phases begin to form at x = 0.5. BiScO3 substitution also resulted in noticeable changes in the local coordination environment of Ti4+. X-ray absorption near-edge spectroscopy (XANES) analysis showed that replacing Ti4+ with Sc3+ results in an increase in the off-centre displacement of Ti4+ cations. Surprisingly, BiScO3 substitution has no effect on the displacement of the Ti4+ cation in the (1-x)PbTiO3-xBiScO3 solid solution.

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

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.

X-ray peak profile analysis of zinc oxide nanoparticles formed by simple precipitation method

NASA Astrophysics Data System (ADS)

Pelicano, Christian Mark; Rapadas, Nick Joaquin; Magdaluyo, Eduardo

2017-12-01

Zinc oxide (ZnO) nanoparticles were successfully synthesized by a simple precipitation method using zinc acetate and tetramethylammonium hydroxide. The synthesized ZnO nanoparticles were characterized by X-ray Diffraction analysis (XRD) and Transmission Electron Microscopy (TEM). The XRD result revealed a hexagonal wurtzite structure for the ZnO nanoparticles. The TEM image showed spherical nanoparticles with an average crystallite size of 6.70 nm. For x-ray peak analysis, Williamson-Hall (W-H) and Size-Strain Plot (SSP) methods were applied to examine the effects of crystallite size and lattice strain on the peak broadening of the ZnO nanoparticles. Based on the calculations, the estimated crystallite sizes and lattice strains obtained are in good agreement with each other.

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.

Au36(SPh)24 nanomolecules: X-ray crystal structure, optical spectroscopy, electrochemistry, and theoretical analysis.

PubMed

Nimmala, Praneeth Reddy; Knoppe, Stefan; Jupally, Vijay Reddy; Delcamp, Jared H; Aikens, Christine M; Dass, Amala

2014-12-11

The physicochemical properties of gold:thiolate nanomolecules depend on their crystal structure and the capping ligands. The effects of protecting ligands on the crystal structure of the nanomolecules are of high interest in this area of research. Here we report the crystal structure of an all aromatic thiophenolate-capped Au36(SPh)24 nanomolecule, which has a face-centered cubic (fcc) core similar to other nanomolecules such as Au36(SPh-tBu)24 and Au36(SC5H9)24 with the same number of gold atoms and ligands. The results support the idea that a stable core remains intact even when the capping ligand is varied. We also correct our earlier assignment of "Au36(SPh)23" which was determined based on MALDI mass spectrometry which is more prone to fragmentation than ESI mass spectrometry. We show that ESI mass spectrometry gives the correct assignment of Au36(SPh)24, supporting the X-ray crystal structure. The electronic structure of the title compound was computed at different levels of theory (PBE, LDA, and LB94) using the coordinates extracted from the single crystal X-ray diffraction data. The optical and electrochemical properties were determined from experimental data using UV-vis spectroscopy, cyclic voltammetry, and differential pulse voltammetry. Au36(SPh)24 shows a broad electrochemical gap near 2 V, a desirable optical gap of ∼1.75 eV for dye-sensitized solar cell applications, as well as appropriately positioned electrochemical potentials for many electrocatalytic reactions.

Periodicity Analysis of X-ray Light Curves of SS 433

NASA Astrophysics Data System (ADS)

Wang, J. Y.; Lu, X. L.; Zhao, Q. W.; Dong, D. Q.; Lao, B. Q.; Lu, Y.; Wei, Y. H.; Wu, X. C.; An, T.

2016-03-01

SS 433 is the only X-ray binary to date that was detected to have a pair of well-collimated jets, and its orbital period, super orbital period, and nutation period were all detected at the same time. The study on the periodic X-ray variabilities is helpful for understanding its dynamic process of the central engine and the correlation with other bands. In the present paper, two time series analysis techniques, Lomb-Scargle periodogram and weighted wavelet Z-transform, are employed to search for the periodicities from the Swift/BAT (Burst Alert Telescope)(15--50 keV) and RXTE/ASM (Rossi X-Ray Timing Explorer/All-Sky Monitor)(1.5--3, 3--5 and 5--12 keV) light curves of SS 433, and the Monte Carlo simulation is performed. For the 15--50 keV energy band, five significant periodic signals are detected, which are P_1(˜6.29 d), P_2 (˜6.54 d), P_3 (˜13.08 d), P_4 (˜81.50 d), and P_5 (˜162.30 d). For the 3--5 and 5--12 keV energy bands, periodic signals P_3 (˜13 d) and P_5 (˜162 d) are detected in both energy bands. However, for the 1.5--3 keV energy band, no significant periodic signal is detected. P_5 has the strongest periodic signal in the power spectrum for all the energy bands of 3--5, 5--12, and 15--50 keV, and it is consistent with that obtained by previous study in optical band. Further, due to the existence of relativistic radio jets, the X-ray and optical band variability of P_5 (˜162 d) is probably related to the precession of the relativistic jets. High coherence between X-ray and optical light curves may also imply that the X-ray and optical emissions are of the same physical origin. P_3 shows a good agreement with the orbital period (˜13.07 d) first obtained by previous study, and P_2 and P_4 are the high frequency harmonic components of P_3 and P_5, respectively. P_1 is detected from the power spectrum of 15--50 keV energy band only, and it is consistent with the systematic nutation period. As the power of energy band decreases (from hard X-ray to

Miniature x-ray source

DOEpatents

Trebes, James E.; Stone, Gary F.; Bell, Perry M.; Robinson, Ronald B.; Chornenky, Victor I.

2002-01-01

A miniature x-ray source capable of producing broad spectrum x-ray emission over a wide range of x-ray energies. The miniature x-ray source comprises a compact vacuum tube assembly containing a cathode, an anode, a high voltage feedthru for delivering high voltage to the anode, a getter for maintaining high vacuum, a connection for an initial vacuum pump down and crimp-off, and a high voltage connection for attaching a compact high voltage cable to the high voltage feedthru. At least a portion of the vacuum tube wall is highly x-ray transparent and made, for example, from boron nitride. The compact size and potential for remote operation allows the x-ray source, for example, to be placed adjacent to a material sample undergoing analysis or in proximity to the region to be treated for medical applications.

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.

Analysis of synthetic diamond single crystals by X-ray topography and double-crystal diffractometry

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

Prokhorov, I. A., E-mail: igor.prokhorov@mail.ru; Ralchenko, V. G.; Bolshakov, A. P.

2013-12-15

Structural features of diamond single crystals synthesized under high pressure and homoepitaxial films grown by chemical vapor deposition (CVD) have been analyzed by double-crystal X-ray diffractometry and topography. The conditions of a diffraction analysis of diamond crystals using Ge monochromators have been optimized. The main structural defects (dislocations, stacking faults, growth striations, second-phase inclusions, etc.) formed during crystal growth have been revealed. The nitrogen concentration in high-pressure/high-temperature (HPHT) diamond substrates is estimated based on X-ray diffraction data. The formation of dislocation bundles at the film-substrate interface in the epitaxial structures has been revealed by plane-wave topography; these dislocations are likelymore » due to the relaxation of elastic macroscopic stresses caused by the lattice mismatch between the substrate and film. The critical thicknesses of plastic relaxation onset in CVD diamond films are calculated. The experimental techniques for studying the real diamond structure in optimizing crystal-growth technology are proven to be highly efficient.« less

The supramolecular structure of bone: X-ray scattering analysis and lateral structure modeling

PubMed Central

Zhou, Hong-Wen; Burger, Christian; Wang, Hao; Hsiao, Benjamin S.; Chu, Benjamin; Graham, Lila

2016-01-01

The evolution of vertebrates required a key development in supramolecular evolution: internally mineralized collagen fibrils. In bone, collagen molecules and mineral crystals form a nanocomposite material comparable to cast iron in tensile strength, but several times lighter and more flexible. Current understanding of the internal nanoscale structure of collagen fibrils, derived from studies of rat tail tendon (RTT), does not explain how nucleation and growth of mineral crystals can occur inside a collagen fibril. Experimental obstacles encountered in studying bone have prevented a solution to this problem for several decades. This report presents a lateral packing model for collagen molecules in bone fibrils, based on the unprecedented observation of multiple resolved equatorial reflections for bone tissue using synchrotron small-angle X-ray scattering (SAXS; ∼1 nm resolution). The deduced structure for pre-mineralized bone fibrils includes features that are not present in RTT: spatially discrete microfibrils. The data are consistent with bone microfibrils similar to pentagonal Smith microfibrils, but are not consistent with the (nondiscrete) quasi-hexagonal microfibrils reported for RTT. These results indicate that collagen fibrils in bone and tendon differ in their internal structure in a manner that allows bone fibrils, but not tendon fibrils, to internally mineralize. In addition, the unique pattern of collagen cross-link types and quantities in mineralized tissues can be can be accounted for, in structural/functional terms, based on a discrete microfibril model. PMID:27599731

Structural investigations of Pu{sup III} phosphate by X-ray diffraction, MAS-NMR and XANES spectroscopy

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

Popa, Karin; Raison, Philippe E., E-mail: philippe.raison@ec.europa.eu; Martel, Laura

2015-10-15

PuPO{sub 4} was prepared by a solid state reaction method and its crystal structure at room temperature was solved by powder X-ray diffraction combined with Rietveld refinement. High resolution XANES measurements confirm the +III valence state of plutonium, in agreement with valence bond derivation. The presence of the americium (as β{sup −} decay product of plutonium) in the +III oxidation state was determined based on XANES spectroscopy. High resolution solid state {sup 31}P NMR agrees with the XANES results and the presence of a solid-solution. - Graphical abstract: A full structural analysis of PuPO{sub 4} based on Rietveld analysis ofmore » room temperature X-ray diffraction data, XANES and MAS NMR measurements was performed. - Highlights: • The crystal structure of PuPO{sub 4} monazite is solved. • In PuPO{sub 4} plutonium is strictly trivalent. • The presence of a minute amount of Am{sup III} is highlighted. • We propose PuPO{sub 4} as a potential reference material for spectroscopic and microscopic studies.« less

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.

How little data is enough? Phase-diagram analysis of sparsity-regularized X-ray computed tomography

PubMed Central

Jørgensen, J. S.; Sidky, E. Y.

2015-01-01

We introduce phase-diagram analysis, a standard tool in compressed sensing (CS), to the X-ray computed tomography (CT) community as a systematic method for determining how few projections suffice for accurate sparsity-regularized reconstruction. In CS, a phase diagram is a convenient way to study and express certain theoretical relations between sparsity and sufficient sampling. We adapt phase-diagram analysis for empirical use in X-ray CT for which the same theoretical results do not hold. We demonstrate in three case studies the potential of phase-diagram analysis for providing quantitative answers to questions of undersampling. First, we demonstrate that there are cases where X-ray CT empirically performs comparably with a near-optimal CS strategy, namely taking measurements with Gaussian sensing matrices. Second, we show that, in contrast to what might have been anticipated, taking randomized CT measurements does not lead to improved performance compared with standard structured sampling patterns. Finally, we show preliminary results of how well phase-diagram analysis can predict the sufficient number of projections for accurately reconstructing a large-scale image of a given sparsity by means of total-variation regularization. PMID:25939620

How little data is enough? Phase-diagram analysis of sparsity-regularized X-ray computed tomography.

PubMed

Jørgensen, J S; Sidky, E Y

2015-06-13

We introduce phase-diagram analysis, a standard tool in compressed sensing (CS), to the X-ray computed tomography (CT) community as a systematic method for determining how few projections suffice for accurate sparsity-regularized reconstruction. In CS, a phase diagram is a convenient way to study and express certain theoretical relations between sparsity and sufficient sampling. We adapt phase-diagram analysis for empirical use in X-ray CT for which the same theoretical results do not hold. We demonstrate in three case studies the potential of phase-diagram analysis for providing quantitative answers to questions of undersampling. First, we demonstrate that there are cases where X-ray CT empirically performs comparably with a near-optimal CS strategy, namely taking measurements with Gaussian sensing matrices. Second, we show that, in contrast to what might have been anticipated, taking randomized CT measurements does not lead to improved performance compared with standard structured sampling patterns. Finally, we show preliminary results of how well phase-diagram analysis can predict the sufficient number of projections for accurately reconstructing a large-scale image of a given sparsity by means of total-variation regularization.

Airborne particulate matter (PM) filter analysis and modeling by total reflection X-ray fluorescence (TXRF) and X-ray standing wave (XSW).

PubMed

Borgese, L; Salmistraro, M; Gianoncelli, A; Zacco, A; Lucchini, R; Zimmerman, N; Pisani, L; Siviero, G; Depero, L E; Bontempi, E

2012-01-30

This work is presented as an improvement of a recently introduced method for airborne particulate matter (PM) filter analysis [1]. X-ray standing wave (XSW) and total reflection X-ray fluorescence (TXRF) were performed with a new dedicated laboratory instrumentation. The main advantage of performing both XSW and TXRF, is the possibility to distinguish the nature of the sample: if it is a small droplet dry residue, a thin film like or a bulk sample. Another advantage is related to the possibility to select the angle of total reflection to make TXRF measurements. Finally, the possibility to switch the X-ray source allows to measure with more accuracy lighter and heavier elements (with a change in X-ray anode, for example from Mo to Cu). The aim of the present study is to lay the theoretical foundation of the new proposed method for airborne PM filters quantitative analysis improving the accuracy and efficiency of quantification by means of an external standard. The theoretical model presented and discussed demonstrated that airborne PM filters can be considered as thin layers. A set of reference samples is prepared in laboratory and used to obtain a calibration curve. Our results demonstrate that the proposed method for quantitative analysis of air PM filters is affordable and reliable without the necessity to digest filters to obtain quantitative chemical analysis, and that the use of XSW improve the accuracy of TXRF analysis. Copyright © 2011 Elsevier B.V. All rights reserved.

CIAO: CHANDRA/X-RAY DATA ANALYSIS FOR EVERYONE

NASA Astrophysics Data System (ADS)

McDowell, Jonathan; CIAO Team

2018-01-01

Eighteen years after the launch of Chandra, the archive is full of scientifically rich data and new observations continue. Improvements in recent years to the data analysis package CIAO (Chandra Interactive Analysis of Observations) and its extensive accompanying documentation make it easier for astronomers without a specialist background in high energy astrophysics to take advantage of this resource.The CXC supports hundreds of CIAO users around the world at all levels of training from high school and undergraduate students to the most experienced X-ray astronomers. In general, we strive to provide a software system which is easy for beginners, yet powerful for advanced users.Chandra data cover a range of instrument configurations and types of target (pointlike, extended and moving), requiring a flexible data analysis system. In addition to CIAO tools using the familiar FTOOLS/IRAF-style parameter interface, CIAO includes applications such as the Sherpa fitting engine which provide access to the data via Python scripting.In this poster we point prospective (and existing!) users to the high level Python scripts now provided to reprocess Chandra or other X-ray mission data, determine source fluxes and upper limits, and estimate backgrounds; and to the latest documentation including the CIAO Gallery, a new entry point featuring the system's different capabilities.This work has been supported by NASA under contract NAS 8-03060 to the Smithsonian Astrophysical Observatory for operation of the Chandra X-ray Center.

Production, purification, crystallization and preliminary X-ray structural studies of adeno-associated virus serotype 5

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

DiMattia, Michael; Govindasamy, Lakshmanan; Levy, Hazel C.

2005-10-01

The production, purification, crystallization and preliminary crystallographic analysis of empty adeno-associated virus serotype 5 capsids are reported. Adeno-associated virus serotype 5 (AAV5) is under development for gene-therapy applications for the treatment of cystic fibrosis. To elucidate the structural features of AAV5 that control its enhanced transduction of the apical surface of airway epithelia compared with other AAV serotypes, X-ray crystallographic studies of the viral capsid have been initiated. The production, purification, crystallization and preliminary crystallographic analysis of empty AAV5 viral capsids are reported. The crystals diffract X-rays to beyond 3.2 Å resolution using synchrotron radiation and belong to the orthorhombicmore » space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 264.7, b = 447.9, c = 629.7 Å. There is one complete T = 1 viral capsid per asymmetric unit. The orientation and position of the viral capsid in the asymmetric unit have been determined by rotation and translation functions, respectively, and the AAV5 structure determination is in progress.« less

Lunar elemental analysis obtained from the Apollo gamma-ray and X-ray remote sensing experiment

NASA Technical Reports Server (NTRS)

Trombka, J. I.; Arnold, J. R.; Adler, I.; Metzger, A. E.; Reedy, R. C.

1974-01-01

Gamma ray and X-ray spectrometers carried in the service module of the Apollo 15 and 16 spacecraft were employed for compositional mapping of the lunar surface. The measurements involved the observation of the intensity and characteristics energy distribution of gamma rays and X-rays emitted from the lunar surface. A large scale compositional map of over 10 percent of the lunar surface was obtained from an analysis of the observed spectra. The objective of the X-ray experiment was to measure the K spectral lines from Mg, Al, and Si. Spectra were obtained and the data were reduced to Al/Si and Mg/Si intensity ratios and ultimately to chemical ratios. The objective of the gamma-ray experiment was to measure the natural and cosmic ray induced activity emission spectrum. At this time, the elemental abundances for Th, U, K, Fe, Ti, Si, and O have been determined over a number of major lunar regions.

Thermal analysis on x-ray tube for exhaust process

NASA Astrophysics Data System (ADS)

Kumar, Rakesh; Rao Ratnala, Srinivas; Veeresh Kumar, G. B.; Shivakumar Gouda, P. S.

2018-02-01

It is great importance in the use of X-rays for medical purposes that the dose given to both the patient and the operator is carefully controlled. There are many types of the X- ray tubes used for different applications based on their capacity and power supplied. In present thesis maxi ray 165 tube is analysed for thermal exhaust processes with ±5% accuracy. Exhaust process is usually done to remove all the air particles and to degasify the insert under high vacuum at 2e-05Torr. The tube glass is made up of Pyrex material, 95%Tungsten and 5%rhenium is used as target material for which the melting point temperature is 3350°C. Various materials are used for various parts; during the operation of X- ray tube these waste gases are released due to high temperature which in turn disturbs the flow of electrons. Thus, before using the X-ray tube for practical applications it has to undergo exhaust processes. Initially we build MX 165 model to carry out thermal analysis, and then we simulate the bearing temperature profiles with FE model to match with test results with ±5%accuracy. At last implement the critical protocols required for manufacturing processes like MF Heating, E-beam, Seasoning and FT.

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

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

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 standing wave analysis of nanostructures using partially coherent radiation

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

Tiwari, M. K., E-mail: mktiwari@rrcat.gov.in; Das, Gangadhar; Bedzyk, M. J.

2015-09-07

The effect of longitudinal (or temporal) coherence on total reflection assisted x-ray standing wave (TR-XSW) analysis of nanoscale materials is quantitatively demonstrated by showing how the XSW fringe visibility can be strongly damped by decreasing the spectral resolution of the incident x-ray beam. The correction for nonzero wavelength dispersion (δλ ≠ 0) of the incident x-ray wave field is accounted for in the model computations of TR-XSW assisted angle dependent fluorescence yields of the nanostructure coatings on x-ray mirror surfaces. Given examples include 90 nm diameter Au nanospheres deposited on a Si(100) surface and a 3 nm thick Zn layer trapped on top amore » 100 nm Langmuir-Blodgett film coating on a Au mirror surface. Present method opens up important applications, such as enabling XSW studies of large dimensioned nanostructures using conventional laboratory based partially coherent x-ray sources.« less

Optical and X-ray studies of Compact X-ray Binaries in NGC 5904

NASA Astrophysics Data System (ADS)

Bhalotia, Vanshree; Beck-Winchatz, Bernhard

2018-06-01

Due to their high stellar densities, globular cluster systems trigger various dynamical interactions, such as the formation of compact X-ray binaries. Stellar collisional frequencies have been correlated to the number of X-ray sources detected in various clusters and we hope to measure this correlation for NGC 5904. Optical fluxes of sources from archival HST images of NGC 5904 have been measured using a DOLPHOT PSF photometry in the UV, optical and near-infrared. We developed a data analysis pipeline to process the fluxes of tens of thousands of objects using awk, python and DOLPHOT. We plot color magnitude diagrams in different photometric bands in order to identify outliers that could be X-ray binaries, since they do not evolve the same way as singular stars. Aligning previously measured astrometric data for X-ray sources in NGC 5904 from Chandra with archival astrometric data from HST will filter out the outlier objects that are not X-ray producing, and provide a sample of compact binary systems that are responsible for X-ray emission in NGC 5904. Furthermore, previously measured X-ray fluxes of NGC 5904 from Chandra have also been used to measure the X-ray to optical flux ratio and identify the types of compact X-ray binaries responsible for the X-ray emissions in NGC 5904. We gratefully acknowledge the support from the Illinois Space Grant Consortium.

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.

Recent results of synchrotron radiation induced total reflection X-ray fluorescence analysis at HASYLAB, beamline L

NASA Astrophysics Data System (ADS)

Streli, C.; Pepponi, G.; Wobrauschek, P.; Jokubonis, C.; Falkenberg, G.; Záray, G.; Broekaert, J.; Fittschen, U.; Peschel, B.

2006-11-01

At the Hamburger Synchrotronstrahlungslabor (HASYLAB), Beamline L, a vacuum chamber for synchrotron radiation-induced total reflection X-ray fluorescence analysis, is now available which can easily be installed using the adjustment components for microanalysis present at this beamline. The detector is now in the final version of a Vortex silicon drift detector with 50-mm 2 active area from Radiant Detector Technologies. With the Ni/C multilayer monochromator set to 17 keV extrapolated detection limits of 8 fg were obtained using the 50-mm 2 silicon drift detector with 1000 s live time on a sample containing 100 pg of Ni. Various applications are presented, especially of samples which are available in very small amounts: As synchrotron radiation-induced total reflection X-ray fluorescence analysis is much more sensitive than tube-excited total reflection X-ray fluorescence analysis, the sampling time of aerosol samples can be diminished, resulting in a more precise time resolution of atmospheric events. Aerosols, directly sampled on Si reflectors in an impactor were investigated. A further application was the determination of contamination elements in a slurry of high-purity Al 2O 3. No digestion is required; the sample is pipetted and dried before analysis. A comparison with laboratory total reflection X-ray fluorescence analysis showed the higher sensitivity of synchrotron radiation-induced total reflection X-ray fluorescence analysis, more contamination elements could be detected. Using the Si-111 crystal monochromator also available at beamline L, XANES measurements to determine the chemical state were performed. This is only possible with lower sensitivity as the flux transmitted by the crystal monochromator is about a factor of 100 lower than that transmitted by the multilayer monochromator. Preliminary results of X-ray absorption near-edge structure measurements for As in xylem sap from cucumber plants fed with As(III) and As(V) are reported. Detection limits

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

13.1 micrometers hard X-ray focusing by a new type monocapillary X-ray optic designed for common laboratory X-ray source

NASA Astrophysics Data System (ADS)

Sun, Xuepeng; zhang, Xiaoyun; Zhu, Yu; Wang, Yabing; Shang, Hongzhong; Zhang, Fengshou; Liu, Zhiguo; Sun, Tianxi

2018-04-01

A new type of monocapillary X-ray optic, called 'two bounces monocapillary X-ray optics' (TBMXO), is proposed for generating a small focal spot with high power-density gain for micro X-ray analysis, using a common laboratory X-ray source. TBMXO is consists of two parts: an ellipsoidal part and a tapered part. Before experimental testing, the TBMXO was simulated by the ray tracing method in MATLAB. The simulated results predicted that the proposed TBMXO would produce a smaller focal spot with higher power-density gain than the ellipsoidal monocapillary X-ray optic (EMXO). In the experiment, the TBMXO performance was tested by both an optical device and a Cu target X-ray tube with focal spot of 100 μm. The results indicated that the TBMXO had a slope error of 57.6 μrad and a 13.1 μm focal spot and a 1360 gain in power density were obtained.

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

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

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

NASA Astrophysics Data System (ADS)

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

2011-03-01

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

Bone geometry, structure and mineral distribution using Dual energy X ray Absorptiometry (DXA)

NASA Technical Reports Server (NTRS)

Whalen, Robert; Cleek, Tammy

1993-01-01

Dual energy x-ray absorptiometry (DXA) is currently the most widely used method of analyzing regional and whole body changes in bone mineral content (BMC) and areal (g/sq cm) bone mineral density (BMD). However, BMC and BMD do not provide direct measures of long bone geometry, structure, or strength nor do regional measurements detect localized changes in other regions of the same bone. The capabilities of DXA can be enhanced significantly by special processing of pixel BMC data which yields cross-sectional geometric and structural information. We have extended this method of analysis in order to develop non-uniform structural beam models of long bones.

Periodicity Analysis of X-ray Light Curves of SS 433

NASA Astrophysics Data System (ADS)

Wang, Jun-yi; Lu, Xiang-long; Zhao, Qiu-wen; Dong, Dian-qiao; Lao, Bao-qiang; Lu, Yang; Wei, Yan-heng; Wu, Xiao-cong; An, Tao

2017-01-01

SS 433 is sofar the unique X-ray binary that has the simultaneously detected orbital period, super-orbital period, and nutation period, as well as a bidirectional spiral jet. The study on its X-ray light variability is helpful for understanding the dynamic process of the system, and the correlations between the different wavebands. In this paper, two time-series analysis techniques, i.e., the Lomb-Scargle periodogram and weighted wavelet Z-transform, are employed to search for the periods in the Swift/BAT (Burst Alert Telescope) (15-50 keV) and RXTE/ASM (Rose X-ray Timing Explorer/All Sky Monitor) (1.5-3, 3- 4, and 5-12 keV) light curves of SS 433, and the Monte Carlo simulation is performed for the obtained periodical components. For the 15-50 keV energy band, five significant periodical components are detected, which are P1(∼6.29 d), P2 (∼6.54 d), P3 (∼13.08 d), P4 (∼81.50 d), and P5 (∼162.30 d). For the 3-5 and 5-12 keV energy bands, the periodical components P3 (∼13 d) and P5 (∼162 d) are detected in both energy bands. However, for the 1.5-3 keV energy band, no significant periodic signal is detected. P5 is the strongest periodic signal in the power spectrum for all the energy bands of 3-5, 5-12, and 15-50 keV, and it is consistent with the previous result obtained from the study of optical light curves. Furthermore, in combination with the radio spiral jet of SS 433, it is suggested that the X-ray and optical variability of P5 (∼162 d) is probably related to the precession of its relativistic jet. The high correlation between the X-ray and optical light curves may also imply that the X-ray and optical radiations are of the same physical origin. P3 shows a good agreement with the orbital period (∼13.07 d) obtained by the previous study, and P2 and P4 are respectively the high-frequency harmonics of P3 and P5. P1 is detected only in the power spectrum of the 15-50 keV energy band, and it is consistent with the nutation period of the system. As

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

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

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

2016-07-15

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

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.

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

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

Molybdenum X-Ray Absorption Edges from 200 – 20,000 eV, The Benefits of Soft X-Ray Spectroscopy for Chemical Speciation

PubMed Central

George, Simon J.; Drury, Owen B.; Fu, Juxia; Friedrich, Stephan; Doonan, Christian J.; George, Graham N.; White, Jonathan M.; Young, Charles G.; Cramer, Stephen P.

2009-01-01

We have surveyed the chemical utility of the near-edge structure of molybdenum x-ray absorption edges from the hard x-ray K-edge at 20,000 eV down to the soft x-ray M4,5-edges at ~230 eV. We compared, for each edge, the spectra of two tetrahedral anions, MoO4 and MoS42-. We used three criteria for assessing near-edge structure of each edge: (i) the ratio of the observed chemical shift between MoO42- and MoS42- and the linewidth, (ii) the chemical information from analysis of the near-edge structure and (iii) the ease of measurement using fluorescence detection. Not surprisingly, the K-edge was by far the easiest to measure, but it contained the least information. The L2,3-edges, although harder to measure, had benefits with regard to selection rules and chemical speciation in that they had both a greater chemical shift as well as detailed lineshapes which could be theoretically analyzed in terms of Mo ligand field, symmetry, and covalency. The soft x-ray M2,3-edges were perhaps the least useful, in that they were difficult to measure using fluorescence detection and had very similar information content to the corresponding L2,3-edges. Interestingly, the soft x-ray, low energy (~230 eV) M4,5-edges had greatest potential chemical sensitivity and using our high resolution superconducting tunnel junction (STJ) fluorescence detector they appear to be straightforward to measure. The spectra were amenable to analysis using both the TT-multiplet approach and FEFF. The results using FEFF indicate that the sharp near-edge peaks arise from 3d → 5p transitions, while the broad edge structure has predominately 3d → 4f character. A proper understanding of the dependence of these soft x-ray spectra on ligand field and site geometry is necessary before a complete assessment of the utility of the Mo M4,5-edges can be made. This work includes crystallographic characterization of sodium tetrathiomolybdate. PMID:19041140

X ray microscope assembly and alignment support and advanced x ray microscope design and analysis

NASA Technical Reports Server (NTRS)

Shealy, David L.

1991-01-01

Considerable efforts have been devoted recently to the design, analysis, fabrication, and testing of spherical Schwarzschild microscopes for soft x ray application in microscopy and projection lithography. The spherical Schwarzschild microscope consists of two concentric spherical mirrors configured such that the third order spherical aberration and coma are zero. Since multilayers are used on the mirror substrates for x ray applications, it is desirable to have only two reflecting surfaces in a microscope. In order to reduce microscope aberrations and increase the field of view, generalized mirror surface profiles have been considered in this investigation. Based on incoherent and sine wave modulation transfer function (MTF) calculations, the object plane resolution of a microscope has been analyzed as a function of the object height and numerical aperture (NA) of the primary for several spherical Schwarzschild, conic, and aspherical head reflecting two mirror microscope configurations.

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.

Crystallization and preliminary X-ray analysis of copper amine oxidase from Escherichia coli K-12.

PubMed

Roh, J H; Suzuki, H; Kumagai, H; Yamashita, M; Azakami, H; Murooka, Y; Mikami, B

1994-05-13

Copper-containing monoamine oxidase (MAO) from Escherichia coli was overproduced in the periplasmic space by expression of the cloned gene. The purified MAO has been crystallized by means of the hanging drop technique using sodium citrate as a precipitant. The crystals belong to the orthorhombic system, space group P2(1)2(1)2(1), with unit cell dimensions of a = 136.1 A, b = 168.4 A and c = 81.6 A. The asymmetric unit contains one molecule of MAO, with a crystal volume per protein mass (Vm) of 2.88 A3/Da and a solvent content of 58% by volume. The crystals diffract X-rays to a resolution limit of at least 2.7 A and are resistant to X-ray radiation damage. They appear to be suitable for X-ray structure analysis.

XAP, a program for deconvolution and analysis of complex X-ray spectra

USGS Publications Warehouse

Quick, James E.; Haleby, Abdul Malik

1989-01-01

The X-ray analysis program (XAP) is a spectral-deconvolution program written in BASIC and specifically designed to analyze complex spectra produced by energy-dispersive X-ray analytical systems (EDS). XAP compensates for spectrometer drift, utilizes digital filtering to remove background from spectra, and solves for element abundances by least-squares, multiple-regression analysis. Rather than base analyses on only a few channels, broad spectral regions of a sample are reconstructed from standard reference spectra. The effects of this approach are (1) elimination of tedious spectrometer adjustments, (2) removal of background independent of sample composition, and (3) automatic correction for peak overlaps. Although the program was written specifically to operate a KEVEX 7000 X-ray fluorescence analytical system, it could be adapted (with minor modifications) to analyze spectra produced by scanning electron microscopes, electron microprobes, and probes, and X-ray defractometer patterns obtained from whole-rock powders.

Analysis of coke beverages by total-reflection X-ray fluorescence

NASA Astrophysics Data System (ADS)

Fernández-Ruiz, Ramón; von Bohlen, Alex; Friedrich K, E. Josue; Redrejo, M. J.

2018-07-01

The influence of the organic content, sample preparation process and the morphology of the depositions of two types of Coke beverage, traditional and light Coke, have been investigated by mean of Total-reflection X-ray Fluorescence (TXRF) spectrometry. Strong distortions of the nominal concentration values, up to 128% for P, have been detected in the analysis of traditional Coke by different preparation methods. These differences have been correlated with the edge X-ray energies of the elements analyzed being more pronounced for the lighter elements. The influence of the organic content (mainly sugar) was evaluated comparing traditional and light Coke analytical TXRF results. Three sample preparation methods have been evaluated as follows: direct TXRF analysis of the sample only adding internal standard, TXRF analysis after open vessel acid digestion and TXRF analysis after high pressure and temperature microwave-assisted acid digestion. Strong correlations were detected between quantitative results, methods of preparation and energies of the X-ray absorption edges of quantified elements. In this way, a decay behavior for the concentration differences between preparation methods and the energies of the X-ray absorption edges of each element were observed. The observed behaviors were modeled with exponential decay functions obtaining R2 correlation coefficients from 0.989 to 0.992. The strong absorption effect observed, and even possible matrix effect, can be explained by the inherent high organic content of the evaluated samples and also by the morphology and average thickness of the TXRF depositions observed. As main conclusion of this work, the analysis of light elements in samples with high organic content by TXRF, i.e. medical, biological, food or any other organic matrixes should be taken carefully. In any case, the direct analysis is not recommended and a previous microwave-assisted acid digestion, or similar, is mandatory, for the correct elemental

Image analysis of the AXAF VETA-I x ray mirror

NASA Technical Reports Server (NTRS)

Freeman, Mark D.; Hughes, John P; Vanspeybroeck, L.; Weisskopf, M.; Bilbro, J.

1992-01-01

Initial core scan data of the VETA-I x-ray mirror proved disappointing, showing considerable unpredicted image structure and poor measured FWHM. 2-D core scans were performed, providing important insight into the nature of the distortion. Image deconvolutions using a ray traced model PSF was performed successfully to reinforce our conclusion regarding the origin of the astigmatism. A mechanical correction was made to the optical structure, and the mirror was tested successfully (FWHM 0.22 arcsec) as a result.

PyXRF: Python-based X-ray fluorescence analysis package

NASA Astrophysics Data System (ADS)

Li, Li; Yan, Hanfei; Xu, Wei; Yu, Dantong; Heroux, Annie; Lee, Wah-Keat; Campbell, Stuart I.; Chu, Yong S.

2017-09-01

We developed a python-based fluorescence analysis package (PyXRF) at the National Synchrotron Light Source II (NSLS-II) for the X-ray fluorescence-microscopy beamlines, including Hard X-ray Nanoprobe (HXN), and Submicron Resolution X-ray Spectroscopy (SRX). This package contains a high-level fitting engine, a comprehensive commandline/ GUI design, rigorous physics calculations, and a visualization interface. PyXRF offers a method of automatically finding elements, so that users do not need to spend extra time selecting elements manually. Moreover, PyXRF provides a convenient and interactive way of adjusting fitting parameters with physical constraints. This will help us perform quantitative analysis, and find an appropriate initial guess for fitting. Furthermore, we also create an advanced mode for expert users to construct their own fitting strategies with a full control of each fitting parameter. PyXRF runs single-pixel fitting at a fast speed, which opens up the possibilities of viewing the results of fitting in real time during experiments. A convenient I/O interface was designed to obtain data directly from NSLS-II's experimental database. PyXRF is under open-source development and designed to be an integral part of NSLS-II's scientific computation library.

Solar X-ray Astronomy Sounding Rocket Program

NASA Technical Reports Server (NTRS)

Moses, J. Daniel

1989-01-01

Several broad objectives were pursued by the development and flight of the High Resolution Soft X-Ray Imaging Sounding Rocket Payload, followed by the analysis of the resulting data and by comparison with both ground based and space based observations from other investigators. The scientific objectives were: to study the thermal equilibrium of active region loop systems by analyzing the X-ray observations to determine electron temperatures, densities, and pressures; by recording the changes in the large scale coronal structures from the maximum and descending phases of Cycle 21 to the ascending phase of Cycle 22; and to extend the study of small scale coronal structures through the minimum of Cycle 21 with new emphasis on correlative observations.

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.

X-ray photoemission study of NiS2-xSex (x=0.0 1.2)

NASA Astrophysics Data System (ADS)

Krishnakumar, S. R.; Sarma, D. D.

2003-10-01

Electronic structure of NiS2-xSex system has been investigated for various compositions (x) using x-ray photoemission spectroscopy. An analysis of the core-level as well as the valence-band spectra of NiS2 in conjunction with many-body cluster calculations provides a quantitative description of the electronic structure of this compound. With increasing Se content, the on-site Coulomb correlation strength (U) does not change, while the bandwidth W of the system increases, driving the system from a covalent insulating state to a pd-metallic state.

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

Dual-energy x-ray image decomposition by independent component analysis

NASA Astrophysics Data System (ADS)

Jiang, Yifeng; Jiang, Dazong; Zhang, Feng; Zhang, Dengfu; Lin, Gang

2001-09-01

The spatial distributions of bone and soft tissue in human body are separated by independent component analysis (ICA) of dual-energy x-ray images. It is because of the dual energy imaging modelí-s conformity to the ICA model that we can apply this method: (1) the absorption in body is mainly caused by photoelectric absorption and Compton scattering; (2) they take place simultaneously but are mutually independent; and (3) for monochromatic x-ray sources the total attenuation is achieved by linear combination of these two absorption. Compared with the conventional method, the proposed one needs no priori information about the accurate x-ray energy magnitude for imaging, while the results of the separation agree well with the conventional one.

Solid state parameters, structure elucidation, High Resolution X-Ray Diffraction (HRXRD), phase matching, thermal and impedance analysis on L-Proline trichloroacetate (L-PTCA) NLO single crystals.

PubMed

Kalaiselvi, P; Raj, S Alfred Cecil; Jagannathan, K; Vijayan, N; Bhagavannarayana, G; Kalainathan, S

2014-11-11

Nonlinear optical single crystal of L-Proline trichloroacetate (L-PTCA) was successfully grown by Slow Evaporation Solution Technique (SEST). The grown crystals were subjected to single crystal X-ray diffraction analysis to confirm the structure. From the single crystal XRD data, solid state parameters were determined for the grown crystal. The crystalline perfection has been evaluated using high resolution X-ray diffractometer. The frequencies of various functional groups were identified from FTIR spectral analysis. The percentage of transmittance was obtained from UV Visible spectral analysis. TGA-DSC measurements indicate the thermal stability of the crystal. The dielectric constant, dielectric loss and ac conductivity were measured by the impedance analyzer. The DC conductivity was calculated by the cole-cole plot method. Copyright © 2014 Elsevier B.V. All rights reserved.

Photo-Darkening Kinetics and Structural Anisotropic Modifications in the Chalcogenide Glass Arsenic Trisulfide: a Study of Kinetic X-Ray Absorption Spectroscopy

NASA Astrophysics Data System (ADS)

Lee, Jay Min

1990-08-01

The purpose of the study is to investigate the mechanisms involved with photo-induced atomic structural modifications in the chalcogenide glass As_2 S_3. This glass exhibits the reversible effects of photo-darkening followed by thermal bleaching. We observed the time behavior of photo-induced properties under the influence of linearly polarized band -gap light. In a macroscopic optical investigation, we monitor optical changes in the photo-darkening process, and in a local structural probe we study kinetic (or time -resolved dispersive) x-ray absorption spectroscopy. Our observations center on kinetic phenomena and structural modifications induced by polarized excitation of lone-pair orbitals in the chalcogenide glass. Experimental results include the following observations: (i) The polarity of the optically induced anisotropy is critically dependent on the intensity and the polarization of the band-gap irradiation beam. (ii) The near edge peak height in x-ray absorption spectra shows subtle but sensitive change during the photo-darkening process. (iii) Photon intensity dependent dichroic kinetics reflect a connection between the optically probed macroscopic property and the x-ray probed local anisotropic structure. Analysis of the x-ray absorption results includes a computer simulation of the polarized absorption spectra. These results suggest that specific structural units tend to orient themselves with respect to the photon polarization. A substantial part of the analysis involves a major effort in dealing with the x-ray kinetic data manipulation and the experimental difficulties caused by a synchrotron instability problem. Based on our observations, we propose a possible mechanism for the observed photo-structural modifications. Through a model of computer relaxed photo-darkening kinetics, we support the notion that a twisting of a specific intermediate range order structure is responsible for local directional variations and global network distortions. In the

The temperature and density structures of an X-ray flare during the decay phase. [Skylab observations

NASA Technical Reports Server (NTRS)

Silk, J. K.; Kahler, S. W.; Krieger, A. S.; Vaiana, G. S.

1976-01-01

The X-ray flare of 9 August 1973 was characterized by a spatially small kernel structure which persisted throughout its duration. The decay phase of this flare was observed in the objective grating mode of the X-ray telescope aboard the Skylab. Data analysis was carried out by scanning the images with a microdensitometer, converting the density arrays to energy using laboratory film calibration data and taking cross sections of the energy images. The 9 August flare shows two distinct periods in its decay phase, involving both cooling and material loss. The objective grating observations reveal that the two phenomena are separated in time. During the earlier phase of the flare decay, the distribution of emission measure as a function of temperature is changing, the high temperature component of the distribution being depleted relative to the cooler body of plasma. As the decay continues, the emission measure distribution stabilizes and the flux diminishes as the amount of material at X-ray emitting temperatures decreases.

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.

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

Atmospheric electron x-ray spectrometer

NASA Technical Reports Server (NTRS)

Feldman, Jason E. (Inventor); George, Thomas (Inventor); Wilcox, Jaroslava Z. (Inventor)

2002-01-01

The present invention comprises an apparatus for performing in-situ elemental analyses of surfaces. The invention comprises an atmospheric electron x-ray spectrometer with an electron column which generates, accelerates, and focuses electrons in a column which is isolated from ambient pressure by a:thin, electron transparent membrane. After passing through the membrane, the electrons impinge on the sample in atmosphere to generate characteristic x-rays. An x-ray detector, shaping amplifier, and multi-channel analyzer are used for x-ray detection and signal analysis. By comparing the resultant data to known x-ray spectral signatures, the elemental composition of the surface can be determined.

Long Periodic Structure of a Room-Temperature Ionic Liquid by High-Pressure Small-Angle X-Ray Scattering and Wide-Angle X-Ray Scattering: 1-Decyl-3-Methylimidazolium Chloride.

PubMed

Abe, Hiroshi; Hamaya, Nozomu; Koyama, Yoshihiro; Kishimura, Hiroaki; Takekiyo, Takahiro; Yoshimura, Yukihiro; Wakabayashi, Daisuke; Funamori, Nobumasa; Matsuishi, Kiyoto

2018-04-23

The Bragg reflections of 1-decyl-3-methylimidazolium chloride ([C 10 mim][Cl]), a room-temperature ionic liquid, are observed in a lowly scattered wavevector (q) region using high-pressure (HP) small-angle X-ray scattering methods. The HP crystal of [C 10 mim][Cl] was characterized by an extremely long periodic structure. The peak position at the lowest q (1.4 nm -1 ) was different from that of the prepeak observed in the liquid state (2.3 nm -1 ). Simultaneously, Bragg reflections at high-q were detected using HP wide-angle X-ray scattering. The longest lattice constant was estimated to be 4.3 nm using structural analysis. The crystal structure of HP differed from that of the low-temperature (LT) crystal and the LT liquid crystal. With increasing pressure, Bragg reflections in the high-q component became much broader, and were accompanied by phase transition, although those in the low-q component were observed to be relatively sharp. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Application toward Confocal Full-Field Microscopic X-ray Absorption Near Edge Structure Spectroscopy.

PubMed

Tack, Pieter; Vekemans, Bart; Laforce, Brecht; Rudloff-Grund, Jennifer; Hernández, Willinton Y; Garrevoet, Jan; Falkenberg, Gerald; Brenker, Frank; Van Der Voort, Pascal; Vincze, Laszlo

2017-02-07

Using X-ray absorption near edge structure (XANES) spectroscopy, information on the local chemical structure and oxidation state of an element of interest can be acquired. Conventionally, this information can be obtained in a spatially resolved manner by scanning a sample through a focused X-ray beam. Recently, full-field methods have been developed to obtain direct 2D chemical state information by imaging a large sample area. These methods are usually in transmission mode, thus restricting the use to thin and transmitting samples. Here, a fluorescence method is displayed using an energy-dispersive pnCCD detector, the SLcam, characterized by measurement times far superior to what is generally applicable. Additionally, this method operates in confocal mode, thus providing direct 3D spatially resolved chemical state information from a selected subvolume of a sample, without the need of rotating a sample. The method is applied to two samples: a gold-supported magnesia catalyst (Au/MgO) and a natural diamond containing Fe-rich inclusions. Both samples provide XANES spectra that can be overlapped with reference XANES spectra, allowing this method to be used for fingerprinting and linear combination analysis of known XANES reference compounds.

Surface studies of solids using integral X-ray-induced photoemission yield

PubMed Central

Stoupin, Stanislav; Zhernenkov, Mikhail; Shi, Bing

2016-01-01

X-ray induced photoemission yield contains structural information complementary to that provided by X-ray Fresnel reflectivity, which presents an advantage to a wide variety of surface studies if this information is made easily accessible. Photoemission in materials research is commonly acknowledged as a method with a probing depth limited by the escape depth of the photoelectrons. Here we show that the integral hard-X-ray-induced photoemission yield is modulated by the Fresnel reflectivity of a multilayer structure and carries structural information that extends well beyond the photoelectron escape depth. A simple electric self-detection of the integral photoemission yield and Fourier data analysis permit extraction of thicknesses of individual layers. The approach does not require detection of the reflected radiation and can be considered as a framework for non-invasive evaluation of buried layers with hard X-rays under grazing incidence. PMID:27874041

Surface studies of solids using integral x-ray-induced photoemission yield

DOE PAGES

Stoupin, Stanislav; Zhernenkov, Mikhail; Shi, Bing

2016-11-22

X-ray induced photoemission yield contains structural information complementary to that provided by X-ray Fresnel reflectivity, which presents an advantage to a wide variety of surface studies if this information is made easily accessible. Photoemission in materials research is commonly acknowledged as a method with a probing depth limited by the escape depth of the photoelectrons. Here we show that the integral hard-X-ray-induced photoemission yield is modulated by the Fresnel reflectivity of a multilayer structure and carries structural information that extends well beyond the photoelectron escape depth. A simple electric self-detection of the integral photoemission yield and Fourier data analysis permitmore » extraction of thicknesses of individual layers. The approach does not require detection of the reflected radiation and can be considered as a framework for non-invasive evaluation of buried layers with hard X-rays under grazing incidence.« less

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.

Risk factors and visual fatigue of baggage X-ray security screeners: a structural equation modelling analysis.

PubMed

Yu, Rui-Feng; Yang, Lin-Dong; Wu, Xin

2017-05-01

This study identified the risk factors influencing visual fatigue in baggage X-ray security screeners and estimated the strength of correlations between those factors and visual fatigue using structural equation modelling approach. Two hundred and five X-ray security screeners participated in a questionnaire survey. The result showed that satisfaction with the VDT's physical features and the work environment conditions were negatively correlated with the intensity of visual fatigue, whereas job stress and job burnout had direct positive influences. The path coefficient between the image quality of VDT and visual fatigue was not significant. The total effects of job burnout, job stress, the VDT's physical features and the work environment conditions on visual fatigue were 0.471, 0.469, -0.268 and -0.251 respectively. These findings indicated that both extrinsic factors relating to VDT and workplace environment and psychological factors including job burnout and job stress should be considered in the workplace design and work organisation of security screening tasks to reduce screeners' visual fatigue. Practitioner Summary: This study identified the risk factors influencing visual fatigue in baggage X-ray security screeners and estimated the strength of correlations between those factors and visual fatigue. The findings were of great importance to the workplace design and the work organisation of security screening tasks to reduce screeners' visual fatigue.

Production, Purification, Crystallization and Preliminary X-ray Structural Studies of Adeno-Associated Virus Serotype 5

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

DiMattia,M.; Govindasamy, L.; Levy, H.

2005-01-01

Adeno-associated virus serotype 5 (AAV5) is under development for gene-therapy applications for the treatment of cystic fibrosis. To elucidate the structural features of AAV5 that control its enhanced transduction of the apical surface of airway epithelia compared with other AAV serotypes, X-ray crystallographic studies of the viral capsid have been initiated. The production, purification, crystallization and preliminary crystallographic analysis of empty AAV5 viral capsids are reported. The crystals diffract X-rays to beyond 3.2 Angstroms resolution using synchrotron radiation and belong to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 264.7, b = 447.9, c =more » 629.7 Angstroms. There is one complete T = 1 viral capsid per asymmetric unit. The orientation and position of the viral capsid in the asymmetric unit have been determined by rotation and translation functions, respectively, and the AAV5 structure determination is in progress.« less

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

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.

Coherent diffraction imaging analysis of shape-controlled nanoparticles with focused hard X-ray free-electron laser pulses.

PubMed

Takahashi, Yukio; Suzuki, Akihiro; Zettsu, Nobuyuki; Oroguchi, Tomotaka; Takayama, Yuki; Sekiguchi, Yuki; Kobayashi, Amane; Yamamoto, Masaki; Nakasako, Masayoshi

2013-01-01

We report the first demonstration of the coherent diffraction imaging analysis of nanoparticles using focused hard X-ray free-electron laser pulses, allowing us to analyze the size distribution of particles as well as the electron density projection of individual particles. We measured 1000 single-shot coherent X-ray diffraction patterns of shape-controlled Ag nanocubes and Au/Ag nanoboxes and estimated the edge length from the speckle size of the coherent diffraction patterns. We then reconstructed the two-dimensional electron density projection with sub-10 nm resolution from selected coherent diffraction patterns. This method enables the simultaneous analysis of the size distribution of synthesized nanoparticles and the structures of particles at nanoscale resolution to address correlations between individual structures of components and the statistical properties in heterogeneous systems such as nanoparticles and cells.

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

OSO-8 soft X-ray wheel experiment: Data analysis

NASA Technical Reports Server (NTRS)

Kraushaar, W. L.

1982-01-01

The soft X-ray experiment hardware and its operation are described. The device included six X-ray proportional counters, two of which, numbers 1 and 4, were pressurized with on-board methane gas supplies. Number 4 developed an excessive leak rate early in the mission and was turned off on 1975 day number 282 except for brief (typically 2-hour) periods up to day 585 after which it as left off. Counter 1 worked satisfactorily until 1975 day number 1095 (January 1, 1978) at which time the on-board methane supply was depleted. The other four counters were sealed and all except number 3 worked satisfactorily throughout the mission which terminated with permanent satellie shut-down on day 1369. This was the first large area thin-window, gas-flow X-ray detector to be flown in orbit. The background problems were severe and consumed a very large portion of the data analysis effort. These background problems were associated with the Earth's trapped electron belts.

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.

Synthesis, X-ray structure, magnetic resonance, and DFT analysis of a soluble copper(II) phthalocyanine lacking C-H bonds.

PubMed

Moons, Hans; Łapok, Łukasz; Loas, Andrei; Van Doorslaer, Sabine; Gorun, Sergiu M

2010-10-04

The synthesis, crystal structure, and electronic properties of perfluoro-isopropyl-substituted perfluorophthalocyanine bearing a copper atom in the central cavity (F(64)PcCu) are reported. While most halogenated phthalocyanines do not exhibit long-term order sufficient to form large single crystals, this is not the case for F(64)PcCu. Its crystal structure was determined by X-ray analysis and linked to the electronic properties determined by electron paramagnetic resonance (EPR). The findings are corroborated by density functional theory (DFT) computations, which agree well with the experiment. X-band continuous-wave EPR spectra of undiluted F(64)PcCu powder, indicate the existence of isolated metal centers. The electron-withdrawing effect of the perfluoroalkyl (R(f)) groups significantly enhances the complexes solubility in organic solvents like alcohols, including via their axial coordination. This coordination is confirmed by X-band (1)H HYSCORE experiments and is also seen in the solid state via the X-ray structure. Detailed X-band CW-EPR, X-band Davies and Mims ENDOR, and W-band electron spin-echo-detected EPR studies of F(64)PcCu in ethanol allow the determination of the principal g values and the hyperfine couplings of the metal, nitrogen, and fluorine nuclei. Comparison of the g and metal hyperfine values of F(64)PcCu and other PcCu complexes in different matrices reveals a dominant effect of the matrix on these EPR parameters, while variations in the ring substituents have only a secondary effect. The relatively strong axial coordination occurs despite the diminished covalency of the C-N bonds and potentially weakening Jahn-Teller effects. Surprisingly, natural abundance (13)C HYSCORE signals could be observed for a frozen ethanol solution of F(64)PcCu. The (13)C nuclei contributing to the HYSCORE spectra could be identified as the pyrrole carbons by means of DFT. Finally, (19)F ENDOR and easily observable paramagnetic NMR were found to relate well to the

Electronic structure measurements of metal-organic solar cell dyes using x-ray absorption spectroscopy

NASA Astrophysics Data System (ADS)

Johnson, Phillip S.

The focus of this thesis is twofold: to report the results of X-ray absorption studies of metal-organic dye molecules for dye-sensitized solar cells and to provide a basic training manual on X-ray absorption spectroscopy techniques and data analysis. The purpose of our research on solar cell dyes is to work toward an understanding of the factors influencing the electronic structure of the dye: the choice of the metal, its oxidation state, ligands, and cage structure. First we study the effect of replacing Ru in several common dye structures by Fe. First-principles calculations and X-ray absorption spectroscopy at the C 1s and N 1s edges are combined to investigate transition metal dyes in octahedral and square planar N cages. Octahedral molecules are found to have a downward shift in the N 1s-to-pi* transition energy and an upward shift in C 1s-to-pi* transition energy when Ru is replaced by Fe, explained by an extra transfer of negative charge from Fe to the N ligands compared to Ru. For the square planar molecules, the behavior is more complex because of the influence of axial ligands and oxidation state. Next the crystal field parameters for a series of phthalocyanine and porphyrins dyes are systematically determined using density functional calculations and atomic multiplet calculations with polarization-dependent X-ray absorption spectra. The polarization dependence of the spectra provides information on orbital symmetries which ensures the determination of the crystal field parameters is unique. A uniform downward scaling of the calculated crystal field parameters by 5-30% is found to be necessary to best fit the spectra. This work is a part of the ongoing effort to design and test new solar cell dyes. Replacing the rare metal Ru with abundant metals like Fe would be a significant advance for dye-sensitized solar cells. Understanding the effects of changing the metal centers in these dyes in terms of optical absorption, charge transfer, and electronic

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.

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.

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).

X-ray, UV and optical analysis of supergiants: ɛ Ori

NASA Astrophysics Data System (ADS)

Puebla, Raul E.; Hillier, D. John; Zsargó, Janos; Cohen, David H.; Leutenegger, Maurice A.

2016-03-01

We present a multi-wavelength (X-ray to optical) analysis, based on non-local thermodynamic equilibrium photospheric+wind models, of the B0 Ia-supergiant: ɛ Ori. The aim is to test the consistency of physical parameters, such as the mass-loss rate and CNO abundances, derived from different spectral bands. The derived mass-loss rate is {dot {M}} / {√{f_{∞}}} {˜} 1.6 × 10-6 M⊙ yr-1 where f∞ is the volume filling factor. However, the S IV λλ1062,1073 profiles are too strong in the models; to fit the observed profiles it is necessary to use f∞ <0.01. This value is a factor of 5 to 10 lower than inferred from other diagnostics, and implies {dot{M}} ≲ 1 × 10^{-7} M⊙ yr-1. The discrepancy could be related to porosity-vorosity effects or a problem with the ionization of sulphur in the wind. To fit the UV profiles of N V and O VI it was necessary to include emission from an interclump medium with a density contrast (ρcl/ρICM) of ˜100. X-ray emission in H/He like and Fe L lines was modelled using four plasma components located within the wind. We derive plasma temperatures from 1 × 106 to 7 × 106 K, with lower temperatures starting in the outer regions (R0 ˜ 3-6 R*), and a hot component starting closer to the star (R0 ≲ 2.9 R*). From X-ray line profiles we infer {dot{M}} < 4.9 × 10-7 M⊙ yr-1. The X-ray spectrum (≥0.1 kev) yields an X-ray luminosity LX ˜ 2.0 × 10-7Lbol, consistent with the superion line profiles. X-ray abundances are in agreement with those derived from the UV and optical analysis: ɛ Ori is slightly enhanced in nitrogen and depleted in carbon and oxygen, evidence for CNO processed material.

3D-analysis of plant microstructures: advantages and limitations of synchrotron X-ray microtomography

NASA Astrophysics Data System (ADS)

Matsushima, U.; Graf, W.; Zabler, S.; Manke, I.; Dawson, M.; Choinka, G.; Hilger, A.; Herppich, W. B.

2013-01-01

Synchrotron X-ray computer microtomography was used to analyze the microstructure of rose peduncles. Samples from three rose cultivars, differing in anatomy, were scanned to study the relation between tissue structure and peduncles mechanical strength. Additionally, chlorophyll fluorescence imaging and conventional light microscopy was applied to quantify possible irradiation-induced damage to plant physiology and tissue structure. The spatial resolution of synchrotron X-ray computer microtomography was sufficiently high to investigate the complex tissues of intact rose peduncles without the necessity of any preparation. However, synchrotron X-radiation induces two different types of damage on irradiated tissues. First, within a few hours after first X-ray exposure, there is a direct physical destruction of cell walls. In addition, a slow and delayed destruction of chlorophyll and, consequently, of photosynthetic activity occurred within hours/ days after the exposure. The results indicate that synchrotron X-ray computer microtomography is well suited for three-dimensional visualization of the microstructure of rose peduncles. However, in its current technique, synchrotron X-ray computer microtomography is not really non-destructive but induce tissue damage. Hence, this technique needs further optimization before it can be applied for time-series investigations of living plant materials

Analysis of photographic X-ray images. [S-054 telescope on Skylab

NASA Technical Reports Server (NTRS)

Krieger, A. S.

1977-01-01

Some techniques used to extract quantitative data from the information contained in photographic images produced by grazing incidence soft X-ray optical systems are described. The discussion is focussed on the analysis of the data returned by the S-054 X-Ray Spectrographic Telescope Experiment on Skylab. The parameters of the instrument and the procedures used for its calibration are described. The technique used to convert photographic density to focal plane X-ray irradiance is outlined. The deconvolution of the telescope point response function from the image data is discussed. Methods of estimating the temperature, pressure, and number density of coronal plasmas are outlined.

Quantitative analysis of crystalline pharmaceuticals in tablets by pattern-fitting procedure using X-ray diffraction pattern.

PubMed

Takehira, Rieko; Momose, Yasunori; Yamamura, Shigeo

2010-10-15

A pattern-fitting procedure using an X-ray diffraction pattern was applied to the quantitative analysis of binary system of crystalline pharmaceuticals in tablets. Orthorhombic crystals of isoniazid (INH) and mannitol (MAN) were used for the analysis. Tablets were prepared under various compression pressures using a direct compression method with various compositions of INH and MAN. Assuming that X-ray diffraction pattern of INH-MAN system consists of diffraction intensities from respective crystals, observed diffraction intensities were fitted to analytic expression based on X-ray diffraction theory and separated into two intensities from INH and MAN crystals by a nonlinear least-squares procedure. After separation, the contents of INH were determined by using the optimized normalization constants for INH and MAN. The correction parameter including all the factors that are beyond experimental control was required for quantitative analysis without calibration curve. The pattern-fitting procedure made it possible to determine crystalline phases in the range of 10-90% (w/w) of the INH contents. Further, certain characteristics of the crystals in the tablets, such as the preferred orientation, size of crystallite, and lattice disorder were determined simultaneously. This method can be adopted to analyze compounds whose crystal structures are known. It is a potentially powerful tool for the quantitative phase analysis and characterization of crystals in tablets and powders using X-ray diffraction patterns. Copyright 2010 Elsevier B.V. All rights reserved.

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

Recent Advances and Applications in Synchrotron X-Ray Protein Footprinting for Protein Structure and Dynamics Elucidation.

PubMed

Gupta, Sayan; Feng, Jun; Chance, Mark; Ralston, Corie

2016-01-01

Synchrotron X-ray Footprinting is a powerful in situ hydroxyl radical labeling method for analysis of protein structure, interactions, folding and conformation change in solution. In this method, water is ionized by high flux density broad band synchrotron X-rays to produce a steady-state concentration of hydroxyl radicals, which then react with solvent accessible side-chains. The resulting stable modification products are analyzed by liquid chromatography coupled to mass spectrometry. A comparative reactivity rate between known and unknown states of a protein provides local as well as global information on structural changes, which is then used to develop structural models for protein function and dynamics. In this review we describe the XF-MS method, its unique capabilities and its recent technical advances at the Advanced Light Source. We provide a comparison of other hydroxyl radical and mass spectrometry based methods with XFMS. We also discuss some of the latest developments in its usage for studying bound water, transmembrane proteins and photosynthetic protein components, and the synergy of the method with other synchrotron based structural biology methods.

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.

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

PROS: An IRAF based system for analysis of x ray data

NASA Technical Reports Server (NTRS)

Conroy, M. A.; Deponte, J.; Moran, J. F.; Orszak, J. S.; Roberts, W. P.; Schmidt, D.

1992-01-01

PROS is an IRAF based software package for the reduction and analysis of x-ray data. The use of a standard, portable, integrated environment provides for both multi-frequency and multi-mission analysis. The analysis of x-ray data differs from optical analysis due to the nature of the x-ray data and its acquisition during constantly varying conditions. The scarcity of data, the low signal-to-noise ratio and the large gaps in exposure time make data screening and masking an important part of the analysis. PROS was developed to support the analysis of data from the ROSAT and Einstein missions but many of the tasks have been used on data from other missions. IRAF/PROS provides a complete end-to-end system for x-ray data analysis: (1) a set of tools for importing and exporting data via FITS format -- in particular, IRAF provides a specialized event-list format, QPOE, that is compatible with its IMAGE (2-D array) format; (2) a powerful set of IRAF system capabilities for both temporal and spatial event filtering; (3) full set of imaging and graphics tasks; (4) specialized packages for scientific analysis such as spatial, spectral and timing analysis -- these consist of both general and mission specific tasks; and (5) complete system support including ftp and magnetic tape releases, electronic and conventional mail hotline support, electronic mail distribution of solutions to frequently asked questions and current known bugs. We will discuss the philosophy, architecture and development environment used by PROS to generate a portable, multimission software environment. PROS is available on all platforms that support IRAF, including Sun/Unix, VAX/VMS, HP, and Decstations. It is available on request at no charge.

Serial femtosecond X-ray diffraction of enveloped virus microcrystals

DOE PAGES

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

2015-08-20

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

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)

First use of portable system coupling X-ray diffraction and X-ray fluorescence for in-situ analysis of prehistoric rock art.

PubMed

Beck, L; Rousselière, H; Castaing, J; Duran, A; Lebon, M; Moignard, B; Plassard, F

2014-11-01

Study of prehistoric art is playing a major role in the knowledge of human evolution. Many scientific methods are involved in this investigation including chemical analysis of pigments present on artefacts or applied to cave walls. In the past decades, the characterization of coloured materials was carried on by taking small samples. This procedure had two main disadvantages: slight but existing damage of the paintings and limitation of the number of samples. Thanks to the advanced development of portable systems, in-situ analysis of pigment in cave can be now undertaken without fear for this fragile Cultural Heritage. For the first time, a portable system combining XRD and XRF was used in an underground and archaeological environment for prehistoric rock art studies. In-situ non-destructive analysis of black prehistoric drawings and determination of their composition and crystalline structure were successfully carried out. Original results on pigments used 13,000 years ago in the cave of Rouffignac (France) were obtained showing the use of two main manganese oxides: pyrolusite and romanechite. The capabilities of the portable XRD-XRF system have been demonstrated for the characterization of pigments as well as for the analysis of rock in a cave environment. This first in-situ experiment combining X-ray diffraction and X-ray fluorescence open up new horizons and can fundamentally change our approach of rock art studies. Copyright © 2014 Elsevier B.V. All rights reserved.

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.

X-ray vision of fuel sprays.

PubMed

Wang, Jin

2005-03-01

With brilliant synchrotron X-ray sources, microsecond time-resolved synchrotron X-ray radiography and tomography have been used to elucidate the detailed three-dimensional structure and dynamics of high-pressure high-speed fuel sprays in the near-nozzle region. The measurement allows quantitative determination of the fuel distribution in the optically impenetrable region owing to the multiple scattering of visible light by small atomized fuel droplets surrounding the jet. X-radiographs of the jet-induced shock waves prove that the fuel jets become supersonic under appropriate injection conditions and that the quantitative analysis of the thermodynamic properties of the shock waves can also be derived from the most direct measurement. In other situations where extremely axial-asymmetric sprays are encountered, mass deconvolution and cross-sectional fuel distribution models can be computed based on the monochromatic and time-resolved X-radiographic images collected from various rotational orientations of the sprays. Such quantitative analysis reveals the never-before-reported characteristics and most detailed near-nozzle mass distribution of highly transient fuel sprays.

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.

Sensitivity and Limitations of Structures from X-ray and Neutron-Based Diffraction Analyses of Transition Metal Oxide Lithium-Battery Electrodes

DOE PAGES

Liu, Hao; Liu, Haodong; Lapidus, Saul H.; ...

2017-06-21

Lithium transition metal oxides are an important class of electrode materials for lithium-ion batteries. Binary or ternary (transition) metal doping brings about new opportunities to improve the electrode’s performance and often leads to more complex stoichiometries and atomic structures than the archetypal LiCoO 2. Rietveld structural analyses of X-ray and neutron diffraction data is a widely-used approach for structural characterization of crystalline materials. But, different structural models and refinement approaches can lead to differing results, and some parameters can be difficult to quantify due to the inherent limitations of the data. Here, through the example of LiNi 0.8Co 0.15Al 0.05Omore » 2 (NCA), we demonstrated the sensitivity of various structural parameters in Rietveld structural analysis to different refinement approaches and structural models, and proposed an approach to reduce refinement uncertainties due to the inexact X-ray scattering factors of the constituent atoms within the lattice. Furthermore, this refinement approach was implemented for electrochemically-cycled NCA samples and yielded accurate structural parameters using only X-ray diffraction data. The present work provides the best practices for performing structural refinement of lithium transition metal oxides.« less

Sensitivity and Limitations of Structures from X-ray and Neutron-Based Diffraction Analyses of Transition Metal Oxide Lithium-Battery Electrodes

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

Liu, Hao; Liu, Haodong; Lapidus, Saul H.

Lithium transition metal oxides are an important class of electrode materials for lithium-ion batteries. Binary or ternary (transition) metal doping brings about new opportunities to improve the electrode’s performance and often leads to more complex stoichiometries and atomic structures than the archetypal LiCoO 2. Rietveld structural analyses of X-ray and neutron diffraction data is a widely-used approach for structural characterization of crystalline materials. But, different structural models and refinement approaches can lead to differing results, and some parameters can be difficult to quantify due to the inherent limitations of the data. Here, through the example of LiNi 0.8Co 0.15Al 0.05Omore » 2 (NCA), we demonstrated the sensitivity of various structural parameters in Rietveld structural analysis to different refinement approaches and structural models, and proposed an approach to reduce refinement uncertainties due to the inexact X-ray scattering factors of the constituent atoms within the lattice. Furthermore, this refinement approach was implemented for electrochemically-cycled NCA samples and yielded accurate structural parameters using only X-ray diffraction data. The present work provides the best practices for performing structural refinement of lithium transition metal oxides.« less

Structure Evolution of BaTiO3 on Co Doping: X-ray diffraction and Raman study

NASA Astrophysics Data System (ADS)

Mansuri, Amantulla; Mishra, Ashutosh

2016-10-01

In the present study, we have synthesize polycrystalline samples of BaTi1-xCoxO3 (x = 0, 0.05 and 0.1) with standard solid state reaction technique. The obtained samples are characterized by X-ray diffraction (XRD) and Raman spectroscopy. The detail structural analysis has been performed by Rietveld refinement using Fullprof program. The structural analysis reveal the samples are chemical pure and crystallize in tetragonal phase with space group Pm3m. We observe an increase in lattice parameters which results due to substitution of Co2+ with large ionic radii (0.9) for smaller ionic radii (0.6) Ti4+. Moreover peak at 45.5° shift to 45° on Co doping, which is due to structure phase transition from tetragonal to cubic. Raman study infers that the intensity of characteristic peaks decreases and linewidth increases with Co doping. The bands linked with the tetragonal structure (307 cm1) decreased due to the tetragonal-towards-cubic phase transition with Co doping. Our structural study reveals the expansion of BTO unit cell and tetragonal-to-cubic phase transformation takes place, results from different characterization techniques are conclusive and show structural evolution with Co doping.

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

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

Correlative analysis of hard and soft x ray observations of solar flares

NASA Technical Reports Server (NTRS)

Zarro, Dominic M.

1994-01-01

We have developed a promising new technique for jointly analyzing BATSE hard X-ray observations of solar flares with simultaneous soft X-ray observations. The technique is based upon a model in which electric currents and associated electric fields are responsible for the respective heating and particle acceleration that occur in solar flares. A useful by-product of this technique is the strength and evolution of the coronal electric field. The latter permits one to derive important flare parameters such as the current density, the number of current filaments composing the loop, and ultimately the hard X-ray spectrum produced by the runaway electrons. We are continuing to explore the technique by applying it to additional flares for which we have joint BATSE/Yohkoh observations. A central assumption of our analysis is the constant of proportionality alpha relating the hard X-ray flux above 50 keV and the rate of electron acceleration. For a thick-target model of hard X-ray production, it can be shown that cv is in fact related to the spectral index and low-energy cutoff of precipitating electrons. The next step in our analysis is to place observational constraints on the latter parameters using the joint BATSE/Yohkoh data.

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

Synchrotron X-Ray Diffraction Study of Structure and Growth of Adsorbed Layers

NASA Astrophysics Data System (ADS)

Dai, Pengcheng

Synchrotron x-ray diffraction and scanning-tunneling -microscopy (STM) experiments reveal a new commensurate monolayer structure of 10CB (decylcyanobiphenyl) molecules adsorbed on the (0001) graphite surface. Our results are consistent with two generic structures for nCB monolayers on surfaces of hexagonal symmetry. The monolayer d spacing of the new phase inferred by STM is 10% layer than that obtained by x-ray diffraction on the same sample. We suggest that part of this discrepancy results from a systematic error introduced in calibration of the STM length scale against the graphite substrate. For multilayer nCB films, we find that a polycrystalline structure is formed and most of the adsorbed molecules are aligned with their long axis perpendicular to the graphite surface. Synchrotron x-ray scattering has been used to investigate the structure and growth of xenon physisorbed on the Ag(111) surface using a specially designed ultra -high vacuum (UHV) chamber. For growth under quasi-equilibrium conditions, the bulk Xe-Xe spacing is reached at monolayer completion and solid films of thickness >= 220 A are observed in which an 'ABC' stacking sequence predominates. Under kinetic growth conditions, intensity oscillations at the Xe anti-Bragg position of the specular rod are observed as a function of time, indicating layer -by-layer growth. Analysis of the specular reflectivity at different coverages yields the fractional layer occupancies and the spacing between the Ag(111) surface and first Xe layer. We have conducted a series of low-energy electron diffraction (LEED) 'kinetic isotherm' experiments on both xenon and hexane rm(C_6H_{14 }) films adsorbed on the Ag(111) surface. Our preliminary results show that under the pressure and temperature range accessible to the experiments, all of the Xe kinetic isotherms fall on a universal curve which is concave upward. However, the hexane kinetic isotherms have a qualitatively different shape (S-like) at the higher

Rapid soft X-ray fluctuations in solar flares observed with the X-ray polychromator

NASA Technical Reports Server (NTRS)

Zarro, D. M.; Saba, J. L. R.; Strong, K. T.

1986-01-01

Three flares observed by the Soft X-Ray Polychromator on the Solar Maximum Mission were studied. Flare light curves from the Flat Crystal Spectrometer and Bent Crystal Spectrometer were examined for rapid signal variations. Each flare was characterized by an initial fast (less than 1 min) burst, observed by the Hard X-Ray Burst Spectrometer (HXRBS), followed by softer gradual X-ray emission lasting several minutes. From an autocorrelation function analysis, evidence was found for quasi-periodic fluctuations with rise and decay times of 10 s in the Ca XIX and Fe XXV light curves. These variations were of small amplitude (less than 20%), often coincided with hard X-ray emissions, and were prominent during the onset of the gradual phase after the initial hard X-ray burst. It is speculated that these fluctuations were caused by repeated energy injections in a coronal loop that had already been heated and filled with dense plasma associated with the initial hard X-ray burst.

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.

Combining theory and experiment for X-ray absorption spectroscopy and resonant X-ray scattering characterization of polymers

DOE PAGES

Su, Gregory M.; Cordova, Isvar A.; Brady, Michael A.; ...

2016-07-04

We present that an improved understanding of fundamental chemistry, electronic structure, morphology, and dynamics in polymers and soft materials requires advanced characterization techniques that are amenable to in situ and operando studies. Soft X-ray methods are especially useful in their ability to non-destructively provide information on specific materials or chemical moieties. Analysis of these experiments, which can be very dependent on X-ray energy and polarization, can quickly become complex. Complementary modeling and predictive capabilities are required to properly probe these critical features. Here, we present relevant background on this emerging suite of techniques. Finally, we focus on how the combinationmore » of theory and experiment has been applied and can be further developed to drive our understanding of how these methods probe relevant chemistry, structure, and dynamics in soft materials.« less

The Prompt-afterglow Connection in Gamma-ray Bursts: a Comprehensive Statistical Analysis of Swift X-ray Light-curves

NASA Technical Reports Server (NTRS)

Margutti, R.; Zaninoni, E.; Bernardini, M. G.; Chincarini, G.; Pasotti, F.; Guidorzi, C.; Angelini, Lorella; Burrows, D. N.; Capalbi, M.; Evans, P. A.;

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.

NMR and X-ray structural characterization and conformational aspects of fluorinated (5Z)-3-benzil-5-arylidenofuran-2(5H)-ones

NASA Astrophysics Data System (ADS)

Teixeira, R. R.; Barbosa, L. C. A.; Kabeshov, M. A.; Maltha, C. R. A.; Corrêa, R. S.; Doriguetto, A. C.

2014-10-01

Herein we describe structural insights of (5Z)-3-benzyl-5-(2-fluorobenzylidene)furan-2(5H)-one (6) and (5Z)-3-benzyl-5-(pentafluorobenzylidene)furan-2(5H)-one (7), γ-alkylidenebutenolides analogues of the natural products nostoclides. Their structures were investigated by NMR spectroscopy and X-ray crystallography. The stereochemistry of the exocyclic double bond of these fluorinated compounds was determined to be Z by NMR analysis and confirmed by X-ray data. Compounds 6 and 7 crystallized in the monoclinic crystal system P21/c group. A comparison between structural features of (6) and (7) and nostoclide derivatives previously published by us is described.

Lead foil in dental X-ray film: Backscattering rejection or image intensifier?

NASA Astrophysics Data System (ADS)

Hönnicke, M. G.; Delben, G. J.; Godoi, W. C.; Swinka-Filho, V.

2014-11-01

Dental X-ray films are still largely used due to sterilization issues, simplicity and, mainly, economic reasons. These films almost always are double coated (double emulsion) and have a lead foil in contact with the film for X-ray backscattering rejection. Herein we explore the use of the lead foil as an image intensifier. In these studies, spatial resolution was investigated when images were acquired on the dental X-ray films with and without the lead foil. Also, the lead foil was subjected to atomic analysis (fluorescent measurements) and structure analysis (X-ray diffraction). We determined that the use of the lead foil reduces the exposure time, however, does not affect the spatial resolution on the acquired images. This suggests that the fluorescent radiation spread is smaller than the grain sizes of the dental X-ray films.

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

NASA Astrophysics Data System (ADS)

Rohringer, Nina

2015-05-01

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

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.

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.

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

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

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

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.

Synthesis, high-resolution NMR spectroscopic analysis, and single-crystal X-ray diffraction of isoxazoline tetracycles.

PubMed

Fascio, Mirta L; Alvarez-Larena, Angel; D'Accorso, Norma B

2002-11-29

Three isoxazoline tetracycles were obtained enantiomerically pure by intramolecular 1,3-dipolar cycloaddition. The characterization of the new compounds was performed by high-resolution 1H and 13C NMR spectroscopy. The relative configuration of the new chiral centers was determined by NOESY experiments and confirmed by single-crystal X-ray structural analysis.

Image enhancement for on-site X-ray nondestructive inspection of reinforced concrete structures.

PubMed

Pei, Cuixiang; Wu, Wenjing; Ueaska, Mitsuru

2016-11-22

The use of portable and high-energy X-ray system can provide a very promising approach for on-site nondestructive inspection of inner steel reinforcement of concrete structures. However, the noise properties and contrast of the radiographic images for thick concrete structures do often not meet the demands. To enhance the images, we present a simple and effective method for noise reduction based on a combined curvelet-wavelet transform and local contrast enhancement based on neighborhood operation. To investigate the performance of this method for our X-ray system, we have performed several experiments with using simulated and experimental data. With comparing to other traditional methods, it shows that the proposed image enhancement method has a better performance and can significantly improve the inspection performance for reinforced concrete structures.

Bayesian Multiscale Analysis of X-Ray Jet Features in High Redshift Quasars

NASA Astrophysics Data System (ADS)

McKeough, Kathryn; Siemiginowska, A.; Kashyap, V.; Stein, N.

2014-01-01

X-ray emission of powerful quasar jets may be a result of the inverse Compton (IC) process in which the Cosmic Microwave Background (CMB) photons gain energy by interactions with the jet’s relativistic electrons. However, there is no definite evidence that IC/CMB process is responsible for the observed X-ray emission of large scale jets. A step toward understanding the X-ray emission process is to study the Radio and X-ray morphologies of the jet. We implement a sophisticated Bayesian image analysis program, Low-count Image Reconstruction and Analysis (LIRA) (Esch et al. 2004; Conners & van Dyk 2007), to analyze jet features in 11 Chandra images of high redshift quasars (z ~ 2 - 4.8). Out of the 36 regions where knots are visible in the radio jets, nine showed detectable X-ray emission. We measured the ratios of the X-ray and radio luminosities of the detected features and found that they are consistent with the CMB radiation relationship. We derived a range of the bulk lorentz factor (Γ) for detected jet features under the CMB jet emission model. There is no discernible trend of Γ with redshift within the sample. The efficiency of the X-ray emission between the detected jet feature and the corresponding quasar also shows no correlation with redshift. This work is supported in part by the National Science Foundation REU and the Department of Defense ASSURE programs under NSF Grant no.1262851 and by the Smithsonian Institution, and by NASA Contract NAS8-39073 to the Chandra X-ray Center (CXC). This research has made use of data obtained from the Chandra Data Archive and Chandra Source Catalog, and software provided by the CXC in the application packages CIAO, ChIPS, and Sherpa. We thank Teddy Cheung for providing the VLA radio images. Connors, A., & van Dyk, D. A. 2007, Statistical Challenges in Modern Astronomy IV, 371, 101 Esch, D. N., Connors, A., Karovska, M., & van Dyk, D. A. 2004, ApJ, 610, 1213

Femtosecond X-ray protein nanocrystallography

PubMed Central

Chapman, Henry N.; Fromme, Petra; Barty, Anton; White, Thomas A.; Kirian, Richard A.; Aquila, Andrew; Hunter, Mark S.; Schulz, Joachim; DePonte, Daniel P.; Weierstall, Uwe; Doak, R. Bruce; Maia, Filipe R. N. C.; Martin, Andrew V.; Schlichting, Ilme; Lomb, Lukas; Coppola, Nicola; Shoeman, Robert L.; Epp, Sascha W.; Hartmann, Robert; Rolles, Daniel; Rudenko, Artem; Foucar, Lutz; Kimmel, Nils; Weidenspointner, Georg; Holl, Peter; Liang, Mengning; Barthelmess, Miriam; Caleman, Carl; Boutet, Sébastien; Bogan, Michael J.; Krzywinski, Jacek; Bostedt, Christoph; Bajt, Saša; Gumprecht, Lars; Rudek, Benedikt; Erk, Benjamin; Schmidt, Carlo; Hömke, André; Reich, Christian; Pietschner, Daniel; Strüder, Lothar; Hauser, Günter; Gorke, Hubert; Ullrich, Joachim; Herrmann, Sven; Schaller, Gerhard; Schopper, Florian; Soltau, Heike; Kühnel, Kai-Uwe; Messerschmidt, Marc; Bozek, John D.; Hau-Riege, Stefan P.; Frank, Matthias; Hampton, Christina Y.; Sierra, Raymond G.; Starodub, Dmitri; Williams, Garth J.; Hajdu, Janos; Timneanu, Nicusor; Seibert, M. Marvin; Andreasson, Jakob; Rocker, Andrea; Jönsson, Olof; Svenda, Martin; Stern, Stephan; Nass, Karol; Andritschke, Robert; Schröter, Claus-Dieter; Krasniqi, Faton; Bott, Mario; Schmidt, Kevin E.; Wang, Xiaoyu; Grotjohann, Ingo; Holton, James M.; Barends, Thomas R. M.; Neutze, Richard; Marchesini, Stefano; Fromme, Raimund; Schorb, Sebastian; Rupp, Daniela; Adolph, Marcus; Gorkhover, Tais; Andersson, Inger; Hirsemann, Helmut; Potdevin, Guillaume; Graafsma, Heinz; Nilsson, Björn; Spence, John C. H.

2012-01-01

X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded1-3. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction ‘snapshots’ are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source4. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes5. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (~200 nm to 2 μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes6. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage. PMID:21293373

Femtosecond X-ray protein nanocrystallography.

PubMed

Chapman, Henry N; Fromme, Petra; Barty, Anton; White, Thomas A; Kirian, Richard A; Aquila, Andrew; Hunter, Mark S; Schulz, Joachim; DePonte, Daniel P; Weierstall, Uwe; Doak, R Bruce; Maia, Filipe R N C; Martin, Andrew V; Schlichting, Ilme; Lomb, Lukas; Coppola, Nicola; Shoeman, Robert L; Epp, Sascha W; Hartmann, Robert; Rolles, Daniel; Rudenko, Artem; Foucar, Lutz; Kimmel, Nils; Weidenspointner, Georg; Holl, Peter; Liang, Mengning; Barthelmess, Miriam; Caleman, Carl; Boutet, Sébastien; Bogan, Michael J; Krzywinski, Jacek; Bostedt, Christoph; Bajt, Saša; Gumprecht, Lars; Rudek, Benedikt; Erk, Benjamin; Schmidt, Carlo; Hömke, André; Reich, Christian; Pietschner, Daniel; Strüder, Lothar; Hauser, Günter; Gorke, Hubert; Ullrich, Joachim; Herrmann, Sven; Schaller, Gerhard; Schopper, Florian; Soltau, Heike; Kühnel, Kai-Uwe; Messerschmidt, Marc; Bozek, John D; Hau-Riege, Stefan P; Frank, Matthias; Hampton, Christina Y; Sierra, Raymond G; Starodub, Dmitri; Williams, Garth J; Hajdu, Janos; Timneanu, Nicusor; Seibert, M Marvin; Andreasson, Jakob; Rocker, Andrea; Jönsson, Olof; Svenda, Martin; Stern, Stephan; Nass, Karol; Andritschke, Robert; Schröter, Claus-Dieter; Krasniqi, Faton; Bott, Mario; Schmidt, Kevin E; Wang, Xiaoyu; Grotjohann, Ingo; Holton, James M; Barends, Thomas R M; Neutze, Richard; Marchesini, Stefano; Fromme, Raimund; Schorb, Sebastian; Rupp, Daniela; Adolph, Marcus; Gorkhover, Tais; Andersson, Inger; Hirsemann, Helmut; Potdevin, Guillaume; Graafsma, Heinz; Nilsson, Björn; Spence, John C H

2011-02-03

X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction 'snapshots' are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (∼200 nm to 2 μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.

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

PubMed

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

2015-09-21

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

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

NASA Astrophysics Data System (ADS)

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

2015-09-01

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

Investigating biofilm structure using x-ray microtomography and gratings-based phase contrast

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

Miller, Erin A.; Xiao, Xianghui; Miller, Micah D.

2012-10-17

Direct examination of natural and engineered environments has revealed that the majority of microorganisms in these systems live in structured communities termed biofilms. To gain a better understanding for how biofilms function and interact with their local environment, fundamental capabilities for enhanced visualization, compositional analysis, and functional characterization of biofilms are needed. For pore-scale and community-scale analysis (100’s of nm to 10’s of microns), a variety of surface tools are available. However, understanding biofilm structure in complex three-dimensional (3-D) environments is considerably more difficult. X-ray microtomography can reveal a biofilm’s internal structure, but the obtaining sufficient contrast to image low-Zmore » biological material against a higher-Z substrate makes detecting biofilms difficult. Here we present results imaging Shewanella oneidensis biofilms on a Hollow-fiber Membrane Biofilm Reactor (HfMBR), using the x-ray microtomography system at sector 2-BM of the Advanced Photon Source (APS), at energies ranging from 13-15.4 keV and pixel sizes of 0.7 and 1.3 μm/pixel. We examine the use of osmium (Os) as a contrast agent to enhance biofilm visibility and demonstrate that staining improves imaging of hydrated biofilms. We also present results using a Talbot interferometer to provide phase and scatter contrast information in addition to absorption. Talbot interferometry allows imaging of unstained hydrated biofilms with phase contrast, while absorption contrast primarily highlights edges and scatter contrast provides little information. However, the gratings used here limit the spatial resolution to no finer than 2 μm, which hinders the ability to detect small features. Future studies at higher resolution or higher Talbot order for greater sensitivity to density variations may improve imaging.« less

X-ray induced chemical reaction revealed by in-situ X-ray diffraction and scanning X-ray microscopy in 15 nm resolution (Conference Presentation)

NASA Astrophysics Data System (ADS)

Ge, Mingyuan; Liu, Wenjun; Bock, David; De Andrade, Vincent; Yan, Hanfei; Huang, Xiaojing; Marschilok, Amy; Takeuchi, Esther; Xin, Huolin; Chu, Yong S.

2016-09-01

The detection sensitivity of synchrotron-based X-ray techniques has been largely improved due to the ever increasing source brightness, which have significantly advanced ex-situ and in-situ research for energy materials, such as lithium-ion batteries. However, the strong beam-matter interaction arisen from the high beam flux can significantly modify the material structure. The parasitic beam-induced effect inevitably interferes with the intrinsic material property, which brings difficulties in interpreting experimental results, and therefore requires comprehensive evaluation. Here we present a quantitative in-situ study of the beam-effect on one electrode material Ag2VO2PO4 using four different X-ray probes with different radiation dose rate. The material system we reported exhibits interesting and reversible radiation-induced thermal and chemical reactions, which was further evaluated under electron microscopy to illustrate the underlying mechanism. The work we presented here will provide a guideline in using synchrotron X-rays to distinguish the materials' intrinsic behavior from extrinsic structure changed induced by X-rays, especially in the case of in-situ and operando study where the materials are under external field of either temperature or electric field.

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.

X-Ray Crystal Structure of Bone Marrow Kinase in the X Chromosome: A Tec Family Kinase