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Journal of Applied Crystallography

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https://www.readbyqxmd.com/read/28808439/saxs4coll-an-integrated-software-tool-for-analysing-fibrous-collagen-based-tissues
#1
Ahmed Abass, James S Bell, Martin T Spang, Sally Hayes, Keith M Meek, Craig Boote
This article provides an overview of a new integrated software tool for reduction and analysis of small-angle X-ray scattering (SAXS) data from fibrous collagen tissues, with some wider applicability to other cylindrically symmetric scattering systems. SAXS4COLL combines interactive features for data pre-processing, bespoke background subtraction, semi-automated peak detection and calibration. Both equatorial and meridional SAXS peak parameters can be measured, and the former can be deconstructed into cylinder and lattice contributions...
August 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28808438/atsas-2-8-a-comprehensive-data-analysis-suite-for-small-angle-scattering-from-macromolecular-solutions
#2
D Franke, M V Petoukhov, P V Konarev, A Panjkovich, A Tuukkanen, H D T Mertens, A G Kikhney, N R Hajizadeh, J M Franklin, C M Jeffries, D I Svergun
ATSAS is a comprehensive software suite for the analysis of small-angle scattering data from dilute solutions of biological macromolecules or nanoparticles. It contains applications for primary data processing and assessment, ab initio bead modelling, and model validation, as well as methods for the analysis of flexibility and mixtures. In addition, approaches are supported that utilize information from X-ray crystallography, nuclear magnetic resonance spectroscopy or atomistic homology modelling to construct hybrid models based on the scattering data...
August 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28808437/how-to-assign-a-3%C3%A2-%C3%A2-1-dimensional-superspace-group-to-an-incommensurately-modulated-biological-macromolecular-crystal
#3
Jason Porta, Jeff Lovelace, Gloria E O Borgstahl
Periodic crystal diffraction is described using a three-dimensional (3D) unit cell and 3D space-group symmetry. Incommensurately modulated crystals are a subset of aperiodic crystals that need four to six dimensions to describe the observed diffraction pattern, and they have characteristic satellite reflections that are offset from the main reflections. These satellites have a non-integral relationship to the primary lattice and require q vectors for processing. Incommensurately modulated biological macromolecular crystals have been frequently observed but so far have not been solved...
August 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28808436/ewald-an-extended-wide-angle-laue-diffractometer-for-the-second-target-station-of-the-spallation-neutron-source
#4
Leighton Coates, Lee Robertson
Visualizing hydrogen atoms in biological materials is one of the biggest remaining challenges in biophysical analysis. While X-ray techniques have unrivaled capacity for high-throughput structure determination, neutron diffraction is uniquely sensitive to hydrogen atom positions in crystals of biological materials and can provide a more complete picture of the atomic and electronic structures of biological macromolecules. This information can be essential in providing predictive understanding and engineering control of key biological processes, for example, in catalysis, ligand binding and light harvesting, and to guide bioengineering of enzymes and drug design...
August 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28808435/double-cone-of-eigendirections-in-optically-active-ethylenediammonium-selenate-crystals
#5
Alexander T Martin, Shane M Nichols, Sichao Li, Melissa Tan, Bart Kahr
Circular birefringence (CB) is generally responsible for only a small perturbation to the state of light polarization in crystals that also exhibit linear birefringence (LB). As such, the magnetoelectric tensor of gyration, which gives rise to CB and optical activity, is less well determined than the electric permittivity tensor in optical models of the Mueller matrix. To visualize the effect of the magnetoelectric tensor on polarimetric measurements, reported here are experimental mappings of the Mueller matrix and of the CB in a new chiral crystal with accidental null LB at an accessible optical frequency...
August 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28808434/continuous-diffraction-of-molecules-and-disordered-molecular-crystals
#6
Henry N Chapman, Oleksandr M Yefanov, Kartik Ayyer, Thomas A White, Anton Barty, Andrew Morgan, Valerio Mariani, Dominik Oberthuer, Kanupriya Pande
The intensities of far-field diffraction patterns of orientationally aligned molecules obey Wilson statistics, whether those molecules are in isolation (giving rise to a continuous diffraction pattern) or arranged in a crystal (giving rise to Bragg peaks). Ensembles of molecules in several orientations, but uncorrelated in position, give rise to the incoherent sum of the diffraction from those objects, modifying the statistics in a similar way as crystal twinning modifies the distribution of Bragg intensities...
August 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28808433/felix-an-algorithm-for-indexing-multiple-crystallites-in-x-ray-free-electron-laser-snapshot-diffraction-images
#7
Kenneth R Beyerlein, Thomas A White, Oleksandr Yefanov, Cornelius Gati, Ivan G Kazantsev, Nicolai Fog-Gade Nielsen, Peter M Larsen, Henry N Chapman, Søren Schmidt
A novel algorithm for indexing multiple crystals in snapshot X-ray diffraction images, especially suited for serial crystallography data, is presented. The algorithm, FELIX, utilizes a generalized parametrization of the Rodrigues-Frank space, in which all crystal systems can be represented without singularities. The new algorithm is shown to be capable of indexing more than ten crystals per image in simulations of cubic, tetragonal and monoclinic crystal diffraction patterns. It is also used to index an experimental serial crystallography dataset from lysozyme microcrystals...
August 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28808432/grazing-incidence-small-angle-neutron-scattering-from-structures-below-an-interface
#8
Shirin Nouhi, Maja S Hellsing, Vassilios Kapaklis, Adrian R Rennie
Changes of scattering are observed as the grazing angle of incidence of an incoming beam increases and probes different depths in samples. A model has been developed to describe the observed intensity in grazing-incidence small-angle neutron scattering (GISANS) experiments. This includes the significant effects of instrument resolution, the sample transmission, which depends on both absorption and scattering, and the sample structure. The calculations are tested with self-organized structures of two colloidal samples with different size particles that were measured on two different instruments...
August 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28808431/reconstructing-three-dimensional-protein-crystal-intensities-from-sparse-unoriented-two-axis-x-ray-diffraction-patterns
#9
Ti-Yen Lan, Jennifer L Wierman, Mark W Tate, Hugh T Philipp, Veit Elser, Sol M Gruner
Recently, there has been a growing interest in adapting serial microcrystallography (SMX) experiments to existing storage ring (SR) sources. For very small crystals, however, radiation damage occurs before sufficient numbers of photons are diffracted to determine the orientation of the crystal. The challenge is to merge data from a large number of such 'sparse' frames in order to measure the full reciprocal space intensity. To simulate sparse frames, a dataset was collected from a large lysozyme crystal illuminated by a dim X-ray source...
August 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28656043/processing-two-dimensional-x-ray-diffraction-and-small-angle-scattering-data-in-dawn-2
#10
J Filik, A W Ashton, P C Y Chang, P A Chater, S J Day, M Drakopoulos, M W Gerring, M L Hart, O V Magdysyuk, S Michalik, A Smith, C C Tang, N J Terrill, M T Wharmby, H Wilhelm
A software package for the calibration and processing of powder X-ray diffraction and small-angle X-ray scattering data is presented. It provides a multitude of data processing and visualization tools as well as a command-line scripting interface for on-the-fly processing and the incorporation of complex data treatment tasks. Customizable processing chains permit the execution of many data processing steps to convert a single image or a batch of raw two-dimensional data into meaningful data and one-dimensional diffractograms...
June 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28656042/single-shot-full-strain-tensor-determination-with-microbeam-x-ray-laue-diffraction-and-a-two-dimensional-energy-dispersive-detector
#11
A Abboud, C Kirchlechner, J Keckes, T Conka Nurdan, S Send, J S Micha, O Ulrich, R Hartmann, L Strüder, U Pietsch
The full strain and stress tensor determination in a triaxially stressed single crystal using X-ray diffraction requires a series of lattice spacing measurements at different crystal orientations. This can be achieved using a tunable X-ray source. This article reports on a novel experimental procedure for single-shot full strain tensor determination using polychromatic synchrotron radiation with an energy range from 5 to 23 keV. Microbeam X-ray Laue diffraction patterns were collected from a copper micro-bending beam along the central axis (centroid of the cross section)...
June 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28656041/instrumental-resolution-as-a-function-of-scattering-angle-and-wavelength-as-exemplified-for-the-powgen-instrument
#12
Philipp Jacobs, Andreas Houben, Werner Schweika, Andrei L Tchougréeff, Richard Dronskowski
The method of angular- and wavelength-dispersive (e.g. two-dimensional) Rietveld refinement is a new and emerging tool for the analysis of neutron diffraction data measured at time-of-flight instruments with large area detectors. Following the approach for one-dimensional refinements (using either scattering angle or time of flight), the first step at each beam time cycle is the calibration of the instrument including the determination of instrumental contributions to the peak shape variation to be expected for diffraction patterns measured by the users...
June 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28656040/the-origin-of-striation-in-the-metastable-%C3%AE-phase-of-titanium-alloys-observed-by-transmission-electron-microscopy
#13
Jiangkun Fan, Jinshan Li, Yudong Zhang, Hongchao Kou, Jaafar Ghanbaja, Weimin Gan, Lionel Germain, Claude Esling
For the β phase of Ti-5553-type metastable β-Ti alloys, striations in transmission electron microscopy (TEM) bright- and dark-field images have been frequently observed but their origin has not been sufficiently investigated. In the present work, this phenomenon is studied in depth from the macroscopic scale by neutron diffraction to the atomic scale by high-resolution TEM. The results reveal that the β phase contains homogeneously distributed modulated structures, intermediate between that of the β phase (cubic) and that of the α phase or the ω phase (hexagonal), giving rise to the appearance of additional diffraction spots at 1/2, 1/3 and 2/3 β diffraction positions...
June 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28656039/an-in-situ-usaxs-saxs-waxs-study-of-precipitate-size-distribution-evolution-in-a-model-ni-based-alloy
#14
Ross N Andrews, Joseph Serio, Govindarajan Muralidharan, Jan Ilavsky
Intermetallic γ' precipitates typically strengthen nickel-based superalloys. The shape, size and spatial distribution of strengthening precipitates critically influence alloy strength, while their temporal evolution characteristics determine the high-temperature alloy stability. Combined ultra-small-, small- and wide-angle X-ray scattering (USAXS-SAXS-WAXS) analysis can be used to evaluate the temporal evolution of an alloy's precipitate size distribution (PSD) and phase structure during in situ heat treatment...
June 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28656038/x-ray-topography-of-subsurface-crystal-layers
#15
Zbigniew Swiatek, Igor Fodchuk, Ruslan Zaplitnyy
New capabilities of the Berg-Barrett topographic method are demonstrated using a skew-asymmetric X-ray diffraction scheme for investigating structural changes near the surface of semiconductor materials. Specifying the X-ray extinction depth, the details of defects and strains are revealed with high resolution. Consequently, analysis of structural distortion of layers near the surface after various types of surface processing becomes more complete.
June 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28656037/structure-diagnostics-of-heterostructures-and-multi-layered-systems-by-x-ray-multiple-diffraction
#16
Mariana Borcha, Igor Fodchuk, Mykola Solodkyi, Marina Baidakova
This article presents the results of research on multi-layered heterostructures by a modified calculation technique of multiple X-ray diffraction. The Al x In1-x Sb heterostructure and a Zn(Mn)Se/GaAs(001) multi-layered system were used as models to specify conditions for cases of coincidental coplanar three-beam or coincidental noncoplanar four-beam X-ray diffraction. These conditions provide the means for a high-precision determination of lattice parameters and strain anisotropy in layers.
June 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28656036/interface-sensitive-imaging-by-an-image-reconstruction-aided-x-ray-reflectivity-technique
#17
Jinxing Jiang, Keiichi Hirano, Kenji Sakurai
Recently, the authors have succeeded in realizing X-ray reflectivity imaging of heterogeneous ultrathin films at specific wavevector transfers by applying a wide parallel beam and an area detector. By combining in-plane angle and grazing-incidence angle scans, it is possible to reconstruct a series of interface-sensitive X-ray reflectivity images at different grazing-incidence angles (proportional to wavevector transfers). The physical meaning of a reconstructed X-ray reflectivity image at a specific wavevector transfer is the two-dimensional reflectivity distribution of the sample...
June 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28656035/reconstruction-of-the-near-field-distribution-in-an-x-ray-waveguide-array
#18
Qi Zhong, Lars Melchior, Jichang Peng, Qiushi Huang, Zhanshan Wang, Tim Salditt
Iterative phase retrieval has been used to reconstruct the near-field distribution behind tailored X-ray waveguide arrays, by inversion of the measured far-field pattern recorded under fully coherent conditions. It is thereby shown that multi-waveguide interference can be exploited to control the near-field distribution behind the waveguide exit. This can, for example, serve to create a secondary quasi-focal spot outside the waveguide structure. For this proof of concept, an array of seven planar Ni/C waveguides are used, with precisely varied guiding layer thickness and cladding layer thickness, as fabricated by high-precision magnetron sputtering systems...
June 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28656034/x-ray-dynamical-diffraction-in-amino-acid-crystals-a-step-towards-improving-structural-resolution-of-biological-molecules-via-physical-phase-measurements
#19
Sérgio L Morelhão, Cláudio M R Remédios, Guilherme A Calligaris, Gareth Nisbet
In this work, experimental and data analysis procedures were developed and applied for studying amino acid crystals by means of X-ray phase measurements. The results clearly demonstrated the sensitivity of invariant triplet phases to electronic charge distribution in d-alanine crystals, providing useful information for molecular dynamics studies of intermolecular forces. The feasibility of using phase measurements to investigate radiation damage mechanisms is also discussed on experimental and theoretical grounds...
June 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28656033/incorporation-of-interfacial-roughness-into-recursion-matrix-formalism-of-dynamical-x-ray-diffraction-in-multilayers-and-superlattices
#20
Ihar Lobach, Andrei Benediktovitch, Alexander Ulyanenkov
Diffraction in multilayers in the presence of interfacial roughness is studied theoretically, the roughness being considered as a transition layer. Exact (within the framework of the two-beam dynamical diffraction theory) differential equations for field amplitudes in a crystalline structure with varying properties along its surface normal are obtained. An iterative scheme for approximate solution of the equations is developed. The presented approach to interfacial roughness is incorporated into the recursion matrix formalism in a way that obviates possible numerical problems...
June 1, 2017: Journal of Applied Crystallography
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