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Journal of Applied Crystallography

Emre Brookes, Patrice Vachette, Mattia Rocco, Javier Pérez
Size-exclusion chromatography coupled with SAXS (small-angle X-ray scattering), often performed using a flow-through capillary, should allow direct collection of monodisperse sample data. However, capillary fouling issues and non-baseline-resolved peaks can hamper its efficacy. The UltraScan solution modeler (US-SOMO) HPLC-SAXS (high-performance liquid chromatography coupled with SAXS) module provides a comprehensive framework to analyze such data, starting with a simple linear baseline correction and symmetrical Gaussian decomposition tools [Brookes, Pérez, Cardinali, Profumo, Vachette & Rocco (2013 ▸)...
October 1, 2016: Journal of Applied Crystallography
Gerhard Fritz-Popovski, Roland Morak, Parvin Sharifi, Heinz Amenitsch, Oskar Paris
Mesoporous silica films templated by pluronic P123 were prepared using spin and dip coating. The ordered cylindrical structure within the films deforms due to shrinkage during calcination. Grazing-incidence small-angle X-ray scattering (GISAXS) measurements reveal that both the unit cell and the cross section of the pores decrease in size, mainly normal to the surface of the substrate, leading to elliptical cross sections of the pores with axis ratios of about 1:2. Water take-up by the pores upon changing the relative humidity can be monitored quantitatively by the shift in the critical angle of X-ray reflection as seen by the Yoneda peak...
October 1, 2016: Journal of Applied Crystallography
Marko Karlušić, Sigrid Bernstorff, Zdravko Siketić, Branko Šantić, Ivančica Bogdanović-Radović, Milko Jakšić, Marika Schleberger, Maja Buljan
Nanostructuring of surfaces and two-dimensional materials using swift heavy ions offers some unique possibilities owing to the deposition of a large amount of energy localized within a nanoscale volume surrounding the ion trajectory. To fully exploit this feature, the morphology of nanostructures formed after ion impact has to be known in detail. In the present work the response of a rutile TiO2 (001) surface to grazing-incidence swift heavy ion irradiation is investigated. Surface ion tracks with the well known intermittent inner structure were successfully produced using 23 MeV I ions...
October 1, 2016: Journal of Applied Crystallography
Yojiro Oba, Satoshi Morooka, Kazuki Ohishi, Nobuhiro Sato, Rintaro Inoue, Nozomu Adachi, Jun-Ichi Suzuki, Toshihiro Tsuchiyama, Elliot Paul Gilbert, Masaaki Sugiyama
Pulsed neutron sources enable the simultaneous measurement of small-angle neutron scattering (SANS) and Bragg edge transmission. This simultaneous measurement is useful for microstructural characterization in steel. Since most steels are ferromagnetic, magnetic scattering contributions should be considered in both SANS and Bragg edge transmission analyses. An expression for the magnetic scattering contribution to Bragg edge transmission analysis has been derived. The analysis using this expression was applied to Cu steel...
October 1, 2016: Journal of Applied Crystallography
G M Hansford
A powder X-ray diffraction (XRD) method to enhance the signal of a specific crystalline phase within a mixture is presented for the first time. Specificity to the targeted phase relies on finding coincidences in the ratios of crystal d spacings and the ratios of elemental characteristic X-ray energies. Such coincidences can be exploited so that the two crystal planes diffract through the same scattering angle at two different X-ray energies. An energy-resolving detector placed at the appropriate scattering angle will detect a significantly enhanced signal at these energies if the target mineral or phase is present in the sample...
October 1, 2016: Journal of Applied Crystallography
Tikhon Vergentev, Iurii Bronwald, Dmitry Chernyshov, Semen Gorfman, Stephanie H M Ryding, Paul Thompson, Robert J Cernik
Synchrotron X-rays on the Swiss Norwegian Beamline and BM28 (XMaS) at the ESRF have been used to record the diffraction response of the PMN-PT relaxor piezoelectric 67% Pb(Mg1/3Nb2/3)O3-33% PbTiO3 as a function of externally applied electric field. A DC field in the range 0-18 kV cm(-1) was applied along the [001] pseudo-cubic direction using a specially designed sample cell for in situ single-crystal diffraction experiments. The cell allowed data to be collected on a Pilatus 2M area detector in a large volume of reciprocal space using transmission geometry...
October 1, 2016: Journal of Applied Crystallography
Na Li, Xiuhong Li, Yuzhu Wang, Guangfeng Liu, Ping Zhou, Hongjin Wu, Chunxia Hong, Fenggang Bian, Rongguang Zhang
The beamline BL19U2 is located in the Shanghai Synchrotron Radiation Facility (SSRF) and is its first beamline dedicated to biological material small-angle X-ray scattering (BioSAXS). The electrons come from an undulator which can provide high brilliance for the BL19U2 end stations. A double flat silicon crystal (111) monochromator is used in BL19U2, with a tunable monochromatic photon energy ranging from 7 to 15 keV. To meet the rapidly growing demands of crystallographers, biochemists and structural biologists, the BioSAXS beamline allows manual and automatic sample loading/unloading...
October 1, 2016: Journal of Applied Crystallography
Fumitoshi Kaneko, Naoki Seto, Shuma Sato, Aurel Radulescu, Maria Maddalena Schiavone, Jürgen Allgaier, Koichi Ute
Syndiotactic polystyrene (sPS) is a crystalline polymer which has a unique property; it is able to form cocrystals with a wide range of chemical compounds, in which the guest molecules are confined in the vacancies of the host sPS crystalline region. Recently, it has been found that even polyethylene glycol oligomers with a molecular weight of more than several hundreds can be introduced into the sPS crystalline region. It is quite important to know how such a long-chain molecule is stored in the host sPS lattice...
October 1, 2016: Journal of Applied Crystallography
Christopher D Putnam
The Guinier region in small-angle X-ray scattering (SAXS) defines the radius of gyration, Rg, and the forward scattering intensity, I(0). In Guinier peak analysis (GPA), the plot of qI(q) versus q(2) transforms the Guinier region into a characteristic peak for visual and automated inspection of data. Deviations of the peak position from the theoretical position in dimensionless GPA plots can suggest parameter errors, problematic low-resolution data, some kinds of intermolecular interactions or elongated scatters...
October 1, 2016: Journal of Applied Crystallography
Max F Hantke, Tomas Ekeberg, Filipe R N C Maia
Flash X-ray imaging has the potential to determine structures down to molecular resolution without the need for crystallization. The ability to accurately predict the diffraction signal and to identify the optimal experimental configuration within the limits of the instrument is important for successful data collection. This article introduces Condor, an open-source simulation tool to predict X-ray far-field scattering amplitudes of isolated particles for customized experimental designs and samples, which the user defines by an atomic or a refractive index model...
August 1, 2016: Journal of Applied Crystallography
Liubov Samoylova, Alexey Buzmakov, Oleg Chubar, Harald Sinn
This article describes the WavePropaGator (WPG) package, a new interactive software framework for coherent and partially coherent X-ray wavefront propagation simulations. The package has been developed at European XFEL for users at the existing and emerging free-electron laser (FEL) facilities, as well as at the third-generation synchrotron sources and future diffraction-limited storage rings. The WPG addresses the needs of beamline scientists and user groups to facilitate the design, optimization and improvement of X-ray optics to meet their experimental requirements...
August 1, 2016: Journal of Applied Crystallography
Lutz Foucar
CASS [Foucar et al. (2012). Comput. Phys. Commun. 183, 2207-2213] is a well established software suite for experiments performed at any sort of light source. It is based on a modular design and can easily be adapted for use at free-electron laser (FEL) experiments that have a biological focus. This article will list all the additional functionality and enhancements of CASS for use with FEL experiments that have been introduced since the first publication. The article will also highlight some advanced experiments with biological aspects that have been performed...
August 1, 2016: Journal of Applied Crystallography
Kartik Ayyer, Ti-Yen Lan, Veit Elser, N Duane Loh
Single-particle imaging (SPI) with X-ray free-electron lasers has the potential to change fundamentally how biomacromolecules are imaged. The structure would be derived from millions of diffraction patterns, each from a different copy of the macromolecule before it is torn apart by radiation damage. The challenges posed by the resultant data stream are staggering: millions of incomplete, noisy and un-oriented patterns have to be computationally assembled into a three-dimensional intensity map and then phase reconstructed...
August 1, 2016: Journal of Applied Crystallography
T Sibillano, L De Caro, F Scattarella, G Scarcelli, D Siliqi, D Altamura, M Liebi, M Ladisa, O Bunk, C Giannini
Bovine cornea was studied with scanning small-angle X-ray scattering (SAXS) microscopy, by using both synchrotron radiation and a microfocus laboratory source. A combination of statistical (adaptive binning and canonical correlation analysis) and crystallographic (pair distribution function analysis) approaches allowed inspection of the collagen lateral packing of the supramolecular structure. Results reveal (i) a decrease of the interfibrillar distance and of the shell thickness around the fibrils from the periphery to the center of the cornea, (ii) a uniform fibril diameter across the explored area, and (iii) a distorted quasi-hexagonal arrangement of the collagen fibrils...
August 1, 2016: Journal of Applied Crystallography
John P Sutter, Roberto Boada, Daniel T Bowron, Sergey A Stepanov, Sofía Díaz-Moreno
EXAFS studies on dilute samples are usually carried out by collecting the fluorescence yield using a large-area multi-element detector. This method is susceptible to the 'glitches' produced by all single-crystal monochromators. Glitches are sharp dips or spikes in the diffracted intensity at specific crystal orientations. If incorrectly compensated, they degrade the spectroscopic data. Normalization of the fluorescence signal by the incident flux alone is sometimes insufficient to compensate for the glitches...
August 1, 2016: Journal of Applied Crystallography
Anton S Tremsin, Supriyo Ganguly, Sonia M Meco, Goncalo R Pardal, Takenao Shinohara, W Bruce Feller
A nondestructive study of the internal structure and compositional gradient of dissimilar metal-alloy welds through energy-resolved neutron imaging is described in this paper. The ability of neutrons to penetrate thick metal objects (up to several cm) provides a unique possibility to examine samples which are opaque to other conventional techniques. The presence of Bragg edges in the measured neutron transmission spectra can be used to characterize the internal residual strain within the samples and some microstructural features, e...
August 1, 2016: Journal of Applied Crystallography
Brian B Maranville, Brian J Kirby, Alexander J Grutter, Paul A Kienzle, Charles F Majkrzak, Yaohua Liu, Cindi L Dennis
The presence of a large applied magnetic field removes the degeneracy of the vacuum energy states for spin-up and spin-down neutrons. For polarized neutron reflectometry, this must be included in the reference potential energy of the Schrödinger equation that is used to calculate the expected scattering from a magnetic layered structure. For samples with magnetization that is purely parallel or antiparallel to the applied field which defines the quantization axis, there is no mixing of the spin states (no spin-flip scattering) and so this additional potential is constant throughout the scattering region...
August 1, 2016: Journal of Applied Crystallography
Huanwang Yang, Ezra Peisach, John D Westbrook, Jasmine Young, Helen M Berman, Stephen K Burley
Since 2008, X-ray structure depositions to the Protein Data Bank archive (PDB) have required submission of experimental data in the form of structure factor files. RCSB PDB has developed the program DCC to allow worldwide PDB (wwPDB; biocurators, using a single command-line program, to invoke a number of third-party software packages to compare the model file with the experimental data. DCC functionality includes structure factor validation, electron-density map generation and slicing, local electron-density analysis, and residual B factor analysis...
June 1, 2016: Journal of Applied Crystallography
Valerio Mariani, Andrew Morgan, Chun Hong Yoon, Thomas J Lane, Thomas A White, Christopher O'Grady, Manuela Kuhn, Steve Aplin, Jason Koglin, Anton Barty, Henry N Chapman
This article describes a free and open-source data analysis utility designed for fast online feedback during serial X-ray diffraction and scattering experiments: OnDA (online data analysis). Three complete real-time monitors for common types of serial X-ray imaging experiments are presented. These monitors are capable of providing the essential information required for quick decision making in the face of extreme rates of data collection. In addition, a set of modules, functions and algorithms that allow developers to modify the provided monitors or develop new ones are provided...
June 1, 2016: Journal of Applied Crystallography
Helen Mary Ginn, Gwyndaf Evans, Nicholas K Sauter, David Ian Stuart
As serial femtosecond crystallography expands towards a variety of delivery methods, including chip-based methods, and smaller collected data sets, the requirement to optimize the data analysis to produce maximum structure quality is becoming increasingly pressing. Here cppxfel, a software package primarily written in C++, which showcases several data analysis techniques, is released. This software package presently indexes images using DIALS (diffraction integration for advanced light sources) and performs an initial orientation matrix refinement, followed by post-refinement of individual images against a reference data set...
June 1, 2016: Journal of Applied Crystallography
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