| 1. |
- Barty, Anton, et al.
(författare)
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Cheetah : software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data
- 2014
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Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 47, s. 1118-1131
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Tidskriftsartikel (refereegranskat)abstract
- The emerging technique of serial X-ray diffraction, in which diffraction data are collected from samples flowing across a pulsed X-ray source at repetition rates of 100 Hz or higher, has necessitated the development of new software in order to handle the large data volumes produced. Sorting of data according to different criteria and rapid filtering of events to retain only diffraction patterns of interest results in significant reductions in data volume, thereby simplifying subsequent data analysis and management tasks. Meanwhile the generation of reduced data in the form of virtual powder patterns, radial stacks, histograms and other meta data creates data set summaries for analysis and overall experiment evaluation. Rapid data reduction early in the analysis pipeline is proving to be an essential first step in serial imaging experiments, prompting the authors to make the tool described in this article available to the general community. Originally developed for experiments at X-ray free-electron lasers, the software is based on a modular facility-independent library to promote portability between different experiments and is available under version 3 or later of the GNU General Public License.
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| 2. |
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| 3. |
- Inge, A. Ken, et al.
(författare)
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Solving complex open-framework structures from X-ray powder diffraction by direct-space methods using composite building units
- 2013
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Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 46, s. 1094-1104
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Tidskriftsartikel (refereegranskat)abstract
- The crystal structure of a novel open-framework gallogermanate, SU-66 {|(C6H18N2)(18)(H2O)(32)|[Ga4.8Ge87.2O208]}, has been solved from laboratory X-ray powder diffraction (XPD) data by using a direct-space structure solution algorithm and local structural information obtained from infrared (IR) spectroscopy. IR studies on 18 known germanates revealed that the bands in their IR spectra were characteristic of the different composite building units (CBUs) present in the structures. By comparing the bands corresponding to Ge-O vibrations in the IR spectra of SU-66 with those of the 18 known structures with different CBUs, the CBU of SU-66 could be identified empirically as the Ge-10(O,OH)(27) cluster (Ge-10). The unit cell and space group (extinction symbol P--a; a = 14.963, b = 31.593, c = 18.759 angstrom) were determined initially from the XPD pattern and then confirmed by selected-area electron diffraction. The structure of SU-66 was solved from the XPD data using parallel tempering as implemented in FOX [Favre-Nicolin & Cerny (2002). J. Appl. Cryst. 35, 734-743] by assuming P2(1)ma symmetry and two Ge-10 clusters in the asymmetric unit. Rietveld refinement of the resulting structure using synchrotron XPD data showed the framework structure to be correct and the space group to be Pmma. The framework has extra-large (26-ring) onedimensional channels and a very low framework density of 10.1 Ge/Ga atoms per 1000 angstrom(3). SU-66, with 55 framework atoms in the asymmetric unit, is one of the more complicated framework structures solved from XPD data. Indeed, 98% of the reflections were overlapping in the XPD pattern used for structure solution. Tests on other open-framework germanates (SU-62, SU-65, SU-74, PKU-12 and ITQ-37) for which the XPD data, unit cell, space group and IR spectra were available proved to be equally successful. In a more complex case (SU-72) the combination of FOX and powder charge flipping was required for structure solution.
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| 4. |
- Maia, Filipe R. N. C., et al.
(författare)
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Hawk : the image reconstruction package for coherent X-ray diffractive imaging
- 2010
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Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 43:6, s. 1535-1539
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The past few years have seen a tremendous growth in the field of coherent X-ray diffractive imaging, in large part due to X-ray free-electron lasers which provide a peak brilliance billions of times higher than that of synchrotrons. However, this rapid development in terms of hardware has not been matched on the software side. The release of Hawk is intended to close this gap. To the authors knowledge Hawk is the first publicly available and fully open source software program for reconstructing images from continuous diffraction patterns. The software handles all steps leading from a raw diffraction pattern to a reconstructed two-dimensional image including geometry determination, background correction, masking and phasing. It also includes preliminary three-dimensional support and support for graphics processing units using the Compute Unified Device Architecture, which speeds up processing by orders of magnitude compared to a single central processing unit. Hawk implements numerous algorithms and is easily extended. This, in combination with its open-source licence, provides a platform for other groups to test, develop and distribute their own algorithms.
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| 5. |
- Masiello, Fabio, et al.
(författare)
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Investigation by coherent X-ray section topography of ferroelectric domain behaviour as a function of temperature in periodically poled Rb:KTP
- 2011
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Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 44, s. 462-466
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Tidskriftsartikel (refereegranskat)abstract
- The behaviour of ferroelectric domains at high temperatures near the Curie temperature in a periodically poled rubidium-doped potassium titanyl phosphate crystal (Rb:KTP) has been studied by Bragg-Fresnel X-ray diffraction imaging in situ using a compact coherence-preserving furnace. The development and partial disappearance of the inverted domain structure as the temperature increases has been successfully modelled, and is explained by invoking a built-in electric field produced under heating in a low vacuum by out-diffusion of atoms from the sample.
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| 6. |
- Niebling, Stephan, et al.
(författare)
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MARTINI bead form factors for the analysis of time-resolved X-ray scattering of proteins
- 2014
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Ingår i: Journal of Applied Crystallography. - 0021-8898 .- 1600-5767. ; 47:4, s. 1190-1198
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Tidskriftsartikel (refereegranskat)abstract
- Time-resolved small- and wide-angle X-ray scattering (SAXS and WAXS) methods probe the structural dynamics of proteins in solution. Although technologically advanced, these methods are in many cases limited by data interpretation. The calculation of X-ray scattering profiles is computationally demanding and poses a bottleneck for all SAXS/WAXS-assisted structural refinement and, in particular, for the analysis of time-resolved data. A way of speeding up these calculations is to represent biomolecules as collections of coarse-grained scatterers. Here, such coarse-graining schemes are presented and discussed and their accuracies examined. It is demonstrated that scattering factors coincident with the popular MARTINI coarse-graining scheme produce reliable difference scattering in the range 0 < q < 0.75 Å-1. The findings are promising for future attempts at X-ray scattering data analysis, and may help to bridge the gap between time-resolved experiments and their interpretation.
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| 7. |
- Paul, Amitesh, et al.
(författare)
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Structural, electronic and magnetic properties of YMnO3/La0.7Sr0.3MnO3 heterostructures
- 2014
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Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 47, s. 1054-1064
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Tidskriftsartikel (refereegranskat)abstract
- Heterostructures with competing magnetic interactions are often exploited for their tailored new functionalities. Exchange bias is one such outcome of interfacial coupling across ferromagnetic-antiferromagnetic, multiferroic-ferromagnetic, two antiferromagnetic, or antiferromagnetic and paramagnetic interfaces. Apart from the usual horizontal shift of the hysteresis loop (exchange bias shift), a small 'vertical shift' of the hysteresis loops along the magnetization axis has also been seen, but it was always relatively small. Recently, an unusually large 'vertical shift' in epitaxial bilayer heterostructures comprising ferromagnetic La0.7Sr0.3MnO3 and multiferroic orthorhombic YMnO3 layers was reported. Here, using polarized neutron reflectometry, the magnetic proximity effect in such bilayers has been investigated. A detailed magnetic depth profile at the interface, elucidating the intrinsic nature of the vertical shift in such heterostructures, is reported. Further corroboration of this observation has been made by means of first-principles calculations, and the structural and electronic properties of YMnO3/La0.7Sr0.3MnO3 heterostructures are studied. Although in the bulk, the ground state of YMnO3 is an E-type antiferromagnet, the YMnO3/La0.7Sr0.3MnO3 heterostructure stabilizes the ferromagnetic phase in YMnO3 in the interface region. It is found that, in the hypothetical ferromagnetic phase of bulk YMnO3, the polarization is suppressed, and owing to a large difference between the lattice constants in the ab plane a strong magnetocrystalline anisotropy is present. This anisotropy produces a high coercivity of the unusual ferromagnetic YMnO3 phase at the interface, which is responsible for the large vertical shift observed in experiment. (C) 2014 International Union of Crystallography
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| 8. |
- Piegsa, F. M., et al.
(författare)
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Polarized neutron Laue diffraction on a crystal containing dynamically polarized proton spins
- 2013
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Ingår i: Journal of Applied Crystallography. - 1600-5767 .- 0021-8898. ; 46:1, s. 30-34
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Tidskriftsartikel (refereegranskat)abstract
- A polarized neutron Laue diffraction experiment on a single crystal of neodymium-doped lanthanum magnesium nitrate hydrate containing polarized proton spins is reported. By using dynamic nuclear polarization to polarize the proton spins, it is demonstrated that the intensities of the Bragg peaks can be enhanced or diminished significantly, whilst the incoherent background, due to proton spin disorder, is reduced. It follows that the method offers unique possibilities to tune continuously the contrast of the Bragg reflections and thereby represents a new tool for increasing substantially the signal-to-noise ratio in neutron diffraction patterns of hydrogenous matter.
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| 9. |
- Rennie, Adrian R., et al.
(författare)
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Learning about SANS instruments and data reduction from round robin measurements on samples of polystyrene latex
- 2013
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Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 46:5, s. 1289-1297
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Tidskriftsartikel (refereegranskat)abstract
- Measurements of a well-characterized `standard' sample can verify the performance of an instrument. Typically, small-angle neutron scattering instruments are used to investigate a wide range of samples and may often be used in a number of configurations. Appropriate `standard' samples are useful to test different aspects of the performance of hardware as well as that of the data reduction and analysis software. Measurements on a number of instruments with different intrinsic characteristics and designs in a round robin can not only better characterize the performance for a wider range of conditions but also, perhaps more importantly, reveal the limits of the current state of the art of small-angle scattering. The exercise, followed by detailed analysis, tests the limits of current understanding as well as uncovering often forgotten assumptions, simplifications and approximations that underpin the current practice of the technique. This paper describes measurements of polystyrene latex, radius 720 Å, with a number of instruments. Scattering from monodisperse, uniform spherical particles is simple to calculate and displays sharp minima. Such data test the calibrations of intensity, wavelength and resolution as well as the detector response. Smoothing due to resolution, multiple scattering and polydispersity has been determined. Sources of uncertainty are often related to systematic deviations and calibrations rather than random counting errors. The study has prompted development of software to treat modest multiple scattering and to better model the instrument resolution. These measurements also allow checks of data reduction algorithms and have identified how they can be improved. The reproducibility and the reliability of instruments and the accuracy of parameters derived from the data are described.
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| 10. |
- Singh, Devinder, et al.
(författare)
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A complex pseudo-decagonal quasicrystal approximant, Al-37(Co,Ni)(15.5), solved by rotation electron diffraction
- 2014
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Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 47:1, s. 215-221
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Tidskriftsartikel (refereegranskat)abstract
- Electron diffraction is a complementary technique to single-crystal X-ray diffraction and powder X-ray diffraction for structure solution of unknown crystals. Crystals too small to be studied by single-crystal X-ray diffraction or too complex to be solved by powder X-ray diffraction can be studied by electron diffraction. The main drawbacks of electron diffraction have been the difficulties in collecting complete three-dimensional electron diffraction data by conventional electron diffraction methods and the very time-consuming data collection. In addition, the intensities of electron diffraction suffer from dynamical scattering. Recently, a new electron diffraction method, rotation electron diffraction (RED), was developed, which can overcome the drawbacks and reduce dynamical effects. A complete three-dimensional electron diffraction data set can be collected from a sub-micrometre-sized single crystal in less than 2 h. Here the RED method is applied for ab initio structure determination of an unknown complex intermetallic phase, the pseudo-decagonal (PD) quasicrystal approximant Al-37.0(Co,Ni)(15.5), denoted as PD2. RED shows that the crystal is F-centered, with a = 46.4, b = 64.6, c = 8.2 angstrom. However, as with other approximants in the PD series, the reflections with odd l indices are much weaker than those with l even, so it was decided to first solve the PD2 structure in the smaller, primitive unit cell. The basic structure of PD2 with unit-cell parameters a = 23.2, b = 32.3, c = 4.1 angstrom and space group Pnmm has been solved in the present study. The structure with c = 8.2 angstrom will be taken up in the near future. The basic structure contains 55 unique atoms (17 Co/Ni and 38 Al) and is one of the most complex structures solved by electron diffraction. PD2 is built of characteristic 2 nm wheel clusters with fivefold rotational symmetry, which agrees with results from high-resolution electron microscopy images. Simulated electron diffraction patterns for the structure model are in good agreement with the experimental electron diffraction patterns obtained by RED.
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| 11. |
- Wan, Wei, et al.
(författare)
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Three-dimensional rotation electron diffraction : software RED for automated data collection and data processing
- 2013
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Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 46, s. 1863-1873
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Tidskriftsartikel (refereegranskat)abstract
- Implementation of a computer program package for automated collection and processing of rotation electron diffraction (RED) data is described. The software package contains two computer programs: RED data collection and RED data processing. The RED data collection program controls the transmission electron microscope and the camera. Electron beam tilts at a fine step (0.05-0.20 degrees) are combined with goniometer tilts at a coarse step (2.0-3.0 degrees) around a common tilt axis, which allows a fine relative tilt to be achieved between the electron beam and the crystal in a large tilt range. An electron diffraction (ED) frame is collected at each combination of beam tilt and goniometer tilt. The RED data processing program processes three-dimensional ED data generated by the RED data collection program or by other approaches. It includes shift correction of the ED frames, peak hunting for diffraction spots in individual ED frames and identification of these diffraction spots as reflections in three dimensions. Unit-cell parameters are determined from the positions of reflections in three-dimensional reciprocal space. All reflections are indexed, and finally a list with hkl indices and intensities is output. The data processing program also includes a visualizer to view and analyse three-dimensional reciprocal lattices reconstructed from the ED frames. Details of the implementation are described. Data collection and data processing with the software RED are demonstrated using a calcined zeolite sample, silicalite-1. The structure of the calcined silicalite-1, with 72 unique atoms, could be solved from the RED data by routine direct methods.
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| 12. |
- Witala, Monika, 1986, et al.
(författare)
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In situ small-angle X-ray scattering characterization of X-ray-induced local heating
- 2014
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Ingår i: Journal of Applied Crystallography. - 0021-8898 .- 1600-5767. ; 47:6, s. 2078-2080
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Tidskriftsartikel (refereegranskat)abstract
- It is shown that small-angle X-ray scattering from binary liquid mixtures close to the critical point of demixing can be used for in situ characterization of beam- induced heating of liquid samples. For demonstration purposes, the proposed approach is applied on a well studied critical mixture of water and 2,6-lutidine. Given a typical incident X-ray flux at a third-generation synchrotron light source and using a 1.5 mm-diameter glass capillary as sample container, a beam-induced local temperature increase of 0.45 +- 0.10 K is observed.
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| 13. |
- Wolff, Max, et al.
(författare)
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Combined neutron reflectometry and rheology
- 2013
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Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 46:Part 6, s. 1729-1733
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Tidskriftsartikel (refereegranskat)abstract
- Neutron reflectometry has been combined with rheology in order to investigate the solid boundary of liquids and polymers under shear deformation. This approach allows one to apply a controlled stress to a material while resolving the structural arrangements on the sub-nanometre length scale with neutron reflectivity, off-specular scattering and small-angle scattering at the same time. The specularly reflected neutron intensity of a 20% by weight solution of Pluronic F127 in deuterated water in contact with an octadecyl trichlorosilane-covered and a piranha-treated silicon wafer is evaluated. A pronounced difference is found in the structure formed by the polymer micelles at the two surfaces, which is explained by the difference in the affinity of the micellar shell to the solid interfaces. Under deformation, the near interface structure changes at deformations of about 2, 30 and 900%. The structural changes are correlated with changes in the storage and loss modulus of the polymer solution, revealing a transition from more solid to more liquid like properties.
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| 14. |
- Wolff, Max, et al.
(författare)
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Depth-resolved grazing-incidence time-of-flight neutron scattering from a solid-liquid interface
- 2014
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Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 47, s. 130-135
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Tidskriftsartikel (refereegranskat)abstract
- Small-angle scattering in grazing-incidence beam geometry has been applied on a time-of-flight neutron instrument to investigate a solid-liquid boundary. Owing to the broad wavelength distribution provided for a specific incident beam angle, the penetration depth of the neutron beam is varied over a wide range in a single measurement. The near surface structures of block copolymer micelles close to silicon substrates with distinct surface energies are resolved. It is observed that the very near surface structure strongly depends on the surface coating, whereas further away from the surface, bulk-like ordering is found.
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| 15. |
- Yun, Yifeng, et al.
(författare)
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Phase identification and structure determination from multiphasic crystalline powder samples by rotation electron diffraction
- 2014
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Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 47, s. 2048-2054
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Tidskriftsartikel (refereegranskat)abstract
- Phase identification and structure characterization are important in synthetic and materials science. It is difficult to characterize the individual phases from multiphase crystalline powder samples, especially if some of the phases are unknown. This problem can be solved by combining rotation electron diffraction (RED) and powder X-ray diffraction (PXRD). Four phases were identified on the same transmission electron microscopy grid from a multiphase sample in the Ni-Se-O-Cl system, and their structures were solved from the RED data. Phase 1 (NiSeO3) was found in the Inorganic Crystal Structure Database using the information from RED. Phase 2 (Ni3Se4O10Cl2) is an unknown compound, but it is isostructural to Co3Se4O10Cl2, which was recently solved by single-crystal X-ray diffraction. Phase 3 (Ni5Se6O16Cl4H2) and Phase 4 (Ni5Se4O12Cl2) are new compounds. The fact that there are at least four different compounds in the as-synthesized material explains why the phase identification and structure determination could not be done by PXRD alone. The RED method makes phase identification from such multiphase powder samples much easier than would be the case using powder X-ray diffraction. The RED method also makes structure determination of submicrometre-sized crystals from multiphase samples possible.
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