| 1. |
- Adlmann, Franz A., et al.
(författare)
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Towards neutron scattering experiments with sub-millisecond time resolution
- 2015
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Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 48, s. 220-226
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Tidskriftsartikel (refereegranskat)abstract
- Neutron scattering techniques offer several unique opportunities in materials research. However, most neutron scattering experiments suffer from the limited flux available at current facilities. This limitation becomes even more severe if time-resolved or kinetic experiments are performed. A new method has been developed which overcomes these limitations when a reversible process is studied, without any compromise on resolution or beam intensity. It is demonstrated that, by recording in absolute time the neutron detector events linked to an excitation, information can be resolved on sub-millisecond timescales. Specifically, the concept of the method is demonstrated by neutron reflectivity measurements in time-of-flight mode at the Liquids Reflectometer located at the Spallation Neutron Source, Oak Ridge National Laboratory, Tennessee, USA, combined with in situ rheometry. The opportunities and limitations of this new technique are evaluated by investigations of a micellar polymer solution offering excellent scattering contrast combined with high sensitivity to shear.
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| 2. |
- Adlmann, Franz A., et al.
(författare)
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Överlåtaren : a fast way to transfer and orthogonalize two-dimensional off-specular reflectivity data
- 2016
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Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 49, s. 2091-2099
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Tidskriftsartikel (refereegranskat)abstract
- Reflectivity measurements offer unique opportunities for the study of surfaces and interfaces, and specular reflectometry has become a standard tool in materials science to resolve structures normal to the surface of a thin film. Off-specular scattering, which probes lateral structures, is more difficult to analyse, because the Fourier space being probed is highly anisotropic and the scattering pattern is truncated by the interface. As a result, scattering patterns collected with (especially time-of-flight) neutron reflectometers are difficult to transform into reciprocal space for comparison with model calculations. A program package is presented for a generic two-dimensional transformation of reflectometry data into q space and back. The data are represented on an orthogonal grid, allowing cuts along directions relevant for theoretical modelling. This treatment includes background subtraction as well as a full characterization of the resolution function. The method is optimized for computational performance using repeatable operations and standardized instrument settings.
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| 3. |
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| 4. |
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| 5. |
- Altomare, Angela, et al.
(författare)
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Advances in powder pattern indexing: N-TREOR09
- 2009
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Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 42, s. 768-775
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Tidskriftsartikel (refereegranskat)abstract
- Powder pattern indexing can still be a challenge, despite the great recent advances in theoretical approaches, computer speed and experimental devices. More plausible unit cells, belonging to different crystal systems, are frequently found by the indexing programs, and recognition of the correct one may not be trivial. The task is, however, of extreme importance: in case of failure a lot of effort and computing time may be wasted. The classical figures of merit for estimating the unit-cell reliability {i.e.M20 [de Wolff (1968). J. Appl. Cryst.1, 108–113] and FN [Smith & Snyder (1979). J. Appl. Cryst.12, 60–65]} sometimes fail. For this reason, a new figure of merit has been introduced in N-TREOR09, the updated version of the indexing package N-TREOR [Altomare, Giacovazzo, Guagliardi, Moliterni, Rizzi & Werner (2000). J. Appl. Cryst. 33, 1180–1186], combining the information supplied by M20 with additional parameters such as the number of unindexed lines, the degree of overlap in the pattern (the so-called number of statistically independent observations), the symmetry deriving from the automatic evaluation of the extinction group, and the agreement between the calculated and observed profiles. The use of the new parameters requires a dramatic modification of the procedures used worldwide: in the approach presented here, extinction symbol and unit-cell determination are simultaneously estimated. N-TREOR09 benefits also from an improved indexing procedure in the triclinic system and has been integrated into EXPO2009, the updated version of EXPO2004 [Altomare, Caliandro, Camalli, Cuocci, Giacovazzo, Moliterni & Rizzi (2004). J. Appl. Cryst. 37, 1025–1028]. The application of the new procedure to a large set of test structures is described.
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| 6. |
- Aslandukov, Andrey, et al.
(författare)
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Domain Auto Finder (DAFi) program : the analysis of single-crystal X-ray diffraction data from polycrystalline samples
- 2022
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Ingår i: Journal of applied crystallography. - : Wiley-Blackwell Publishing Ltd.. - 0021-8898 .- 1600-5767. ; 55, s. 1383-1391
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Tidskriftsartikel (refereegranskat)abstract
- This paper presents the Domain Auto Finder (DAFi) program and its application to the analysis of single-crystal X-ray diffraction (SC-XRD) data from multiphase mixtures of microcrystalline solids and powders. Superposition of numerous reflections originating from a large number of single-crystal domains of the same and/or different (especially unknown) phases usually precludes the sorting of reflections coming from individual domains, making their automatic indexing impossible. The DAFi algorithm is designed to quickly find subsets of reflections from individual domains in a whole set of SC-XRD data. Further indexing of all found subsets can be easily performed using widely accessible crystallographic packages. As the algorithm neither requires a priori crystallographic information nor is limited by the number of phases or individual domains, DAFi is powerful software to be used for studies of multiphase polycrystalline and microcrystalline (powder) materials. The algorithm is validated by testing on X-ray diffraction data sets obtained from real samples: a multi-mineral basalt rock at ambient conditions and products of the chemical reaction of yttrium and nitrogen in a laser-heated diamond anvil cell at 50 GPa. The high performance of the DAFi algorithm means it can be used for processing SC-XRD data online during experiments at synchrotron facilities.
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| 7. |
- 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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| 8. |
- Beck, Christian, et al.
(författare)
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Accessing self-diffusion on nanosecond time and nanometre length scales with minute kinetic resolution
- 2024
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Ingår i: Journal of Applied Crystallography. - : International Union of Crystallography (IUCr). - 0021-8898 .- 1600-5767. ; 57:Pt 4, s. 912-924
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Tidskriftsartikel (refereegranskat)abstract
- Neutron spectroscopy uniquely and non-destructively accesses diffusive dynamics in soft and biological matter, including for instance proteins in hydrated powders or in solution, and more generally dynamic properties of condensed matter on the molecular level. Given the limited neutron flux resulting in long counting times, it is important to optimize data acquisition for the specific question, in particular for time-resolved (kinetic) studies. The required acquisition time was recently significantly reduced by measurements of discrete energy transfers rather than quasi-continuous neutron scattering spectra on neutron backscattering spectrometers. Besides this reduction in acquisition times, smaller amounts of samples can be measured with better statistics, and most importantly, kinetically changing samples, such as aggregating or crystallizing samples, can be followed. However, given the small number of discrete energy transfers probed in this mode, established analysis frameworks for full spectra can break down. Presented here are new approaches to analyze measurements of diffusive dynamics recorded within fixed windows in energy transfer, and these are compared with the analysis of full spectra. The new approaches are tested by both modeled scattering functions and a comparative analysis of fixed energy window data and full spectra on well understood reference samples. This new approach can be employed successfully for kinetic studies of the dynamics focusing on the short-time apparent center-of-mass diffusion.
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| 9. |
- Bellisario, Alfredo, et al.
(författare)
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Noise reduction and mask removal neural network for X-ray single-particle imaging
- 2022
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Ingår i: Journal of applied crystallography. - : International Union of Crystallography (IUCr). - 0021-8898 .- 1600-5767. ; 55, s. 122-132
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Tidskriftsartikel (refereegranskat)abstract
- Free-electron lasers could enable X-ray imaging of single biological macro-molecules and the study of protein dynamics, paving the way for a powerful new imaging tool in structural biology, but a low signal-to-noise ratio and missing regions in the detectors, colloquially termed 'masks', affect data collection and hamper real-time evaluation of experimental data. In this article, the challenges posed by noise and masks are tackled by introducing a neural network pipeline that aims to restore diffraction intensities. For training and testing of the model, a data set of diffraction patterns was simulated from 10 900 different proteins with molecular weights within the range of 10-100 kDa and collected at a photon energy of 8 keV. The method is compared with a simple low-pass filtering algorithm based on autocorrelation constraints. The results show an improvement in the mean-squared error of roughly two orders of magnitude in the presence of masks compared with the noisy data. The algorithm was also tested at increasing mask width, leading to the conclusion that demasking can achieve good results when the mask is smaller than half of the central speckle of the pattern. The results highlight the competitiveness of this model for data processing and the feasibility of restoring diffraction intensities from unknown structures in real time using deep learning methods. Finally, an example is shown of this preprocessing making orientation recovery more reliable, especially for data sets containing very few patterns, using the expansion-maximization-compression algorithm.
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| 10. |
- Bender, Philipp, et al.
(författare)
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Shape-induced superstructure formation in concentrated ferrofluids under applied magnetic fields
- 2022
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Ingår i: Journal of applied crystallography. - : INT UNION CRYSTALLOGRAPHY. - 0021-8898 .- 1600-5767. ; 55:6, s. 1613-1621
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Tidskriftsartikel (refereegranskat)abstract
- The field-induced ordering of concentrated ferrofluids based on spherical and cuboidal maghemite nanoparticles is studied using small-angle neutron scattering, revealing a qualitative effect of the faceted shape on the interparticle interactions as shown in the structure factor and correlation lengths. Whereas a spatially disordered hard-sphere interaction potential with a short correlation length is found for similar to 9 nm spherical nanoparticles, nanocubes of a comparable particle size exhibit a more pronounced interparticle interaction and the formation of linear arrangements. Analysis of the anisotropic two-dimensional pair distance correlation function gives insight into the real-space arrangement of the nanoparticles. On the basis of the short interparticle distances found here, oriented attachment, i.e. a face-to-face arrangement of the nanocubes, is likely. The unusual field dependence of the interparticle correlations suggests a field-induced structural rearrangement.
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| 11. |
- Bengtsson, Viktor E. G., 1989-, et al.
(författare)
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Scipion-ED : a graphical user interface for batch processing and analysis of 3D ED/MicroED data
- 2022
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Ingår i: Journal of applied crystallography. - : International Union of Crystallography (IUCr). - 0021-8898 .- 1600-5767. ; 55:3, s. 638-646
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Tidskriftsartikel (refereegranskat)abstract
- Three-dimensional electron diffraction (3D ED)/microcrystal electron diffraction (MicroED) techniques are gaining in popularity. However, the data processing often does not fit existing graphical user interface software, instead requiring the use of the terminal or scripting. Scipion-ED, described in this article, provides a graphical user interface and extendable framework for processing of 3D ED/MicroED data. An illustrative project is described, in which multiple 3D ED/MicroED data sets collected on tetragonal lysozyme were processed with DIALS through the Scipion-ED interface. The ability to resolve unmodelled features in the electrostatic potential map was compared between three strategies for merging data sets.
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| 12. |
- Bergenholtz, Johan, 1964, et al.
(författare)
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Analysis of small-angle X-ray scattering data in the presence of significant instrumental smearing
- 2016
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Ingår i: Journal of Applied Crystallography. - 0021-8898 .- 1600-5767. ; 49, s. 47-54
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Tidskriftsartikel (refereegranskat)abstract
- A laboratory-scale small-angle X-ray scattering instrument with pinhole collimation has been used to assess smearing effects due to instrumental resolution. A new, numerically efficient method to smear ideal model intensities is developed and presented. It allows for directly using measured profiles of isotropic but otherwise arbitrary beams in smearing calculations. Samples of low-polydispersity polymer spheres have been used to show that scattering data can in this way be quantitatively modeled even when there is substantial distortion due to instrumental resolution.
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| 13. |
- Bergfors, Terese, et al.
(författare)
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Screening cells for crystals : a synergistic approach
- 2020
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Ingår i: Journal of applied crystallography. - : International Union of Crystallography (IUCr). - 0021-8898 .- 1600-5767. ; 53, s. 1414-1415
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 14. |
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| 15. |
- Björck, Matts, et al.
(författare)
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GenX : an extensible X-ray reflectivity refinement program utilizing differential evolution
- 2007
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Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 40:6, s. 1174-1178
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Tidskriftsartikel (refereegranskat)abstract
- GenX is a versatile program using the differential evolution algorithm for fitting X-ray and neutron reflectivity data. It utilizes the Parratt recursion formula for simulating specular reflectivity. The program is easily extensible, allowing users to incorporate their own models into the program. This can be useful for fitting data from other scattering experiments, or for any other minimization problem which has a large number of input parameters and/or contains many local minima, where the differential evolution algorithm is suitable. In addition, GenX manages to fit an arbitrary number of data sets simultaneously. The program is released under the GNU General Public License.
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| 16. |
- Cerenius, Y., et al.
(författare)
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Preliminary tests on the use of an acoustic levitator for liquid X-ray diffraction experiments
- 2003
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Ingår i: Journal of applied crystallography. - : International Union of Crystallography (IUCr). - 0021-8898 .- 1600-5767. ; 36, s. 163-164
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Tidskriftsartikel (refereegranskat)abstract
- Some preliminary tests at the crystallography beamline I711 at the MAX II synchrotron in Lund, Sweden, have shown that it is possible to use acoustical levitation to keep a droplet of liquid and solid (powder) samples in an X-ray beam for a sufficient time for collection of the X-ray diffraction pattern.
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| 17. |
- Cichocka, Magdalena O., et al.
(författare)
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High-throughput continuous rotation electron diffraction data acquisition via software automation
- 2018
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Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 51:6, s. 1652-1661
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Tidskriftsartikel (refereegranskat)abstract
- Single-crystal electron diffraction (SCED) is emerging as an effective technique to determine and refine the structures of unknown nano-sized crystals. In this work, the implementation of the continuous rotation electron diffraction (cRED) method for high-throughput data collection is described. This is achieved through dedicated software that controls the transmission electron microscope and the camera. Crystal tracking can be performed by defocusing every nth diffraction pattern while the crystal rotates, which addresses the problem of the crystal moving out of view of the selected area aperture during rotation. This has greatly increased the number of successful experiments with larger rotation ranges and turned cRED data collection into a high-throughput method. The experimental parameters are logged, and input files for data processing software are written automatically. This reduces the risk of human error, and makes data collection more reproducible and accessible for novice and irregular users. In addition, it is demonstrated how data from the recently developed serial electron diffraction technique can be used to supplement the cRED data collection by automatic screening for suitable crystals using a deep convolutional neural network that can identify promising crystals through the corresponding diffraction data. The screening routine and cRED data collection are demonstrated using a sample of the zeolite mordenite, and the quality of the cRED data is assessed on the basis of the refined crystal structure.
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| 18. |
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| 19. |
- Dawe, Louise N., et al.
(författare)
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Teaching and Education highlighted
- 2022
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Ingår i: Journal of applied crystallography. - : International Union of Crystallography (IUCr). - 0021-8898 .- 1600-5767. ; 55, s. 215-217
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 20. |
- Droulias, Sotirios A., et al.
(författare)
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Limitations of the kinematic approximation in neutron reflectivity measurements for the analysis of bilayers
- 2018
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Ingår i: Journal of applied crystallography. - : INT UNION CRYSTALLOGRAPHY. - 0021-8898 .- 1600-5767. ; 51, s. 1556-1563
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Tidskriftsartikel (refereegranskat)abstract
- The limitations of a phenomenological fitting approach compared to simulations of the optical model including reflection and refraction at all interfaces are demonstrated using the example of hydrogen loading in ultra-thin vanadium layers. Fe/V superlattices are loaded with deuterium and the lattice expansion and deuterium concentration are extracted from neutron reflectivity data. A noticeable difference is found between the extraction of concentrations and bilayer thicknesses directly from the superlattice peaks and fits of the density profile using the Parratt formalism. The results underline the importance of carefully considering the limitations of phenomenological approaches, in order to obtain robust results. The limitations of the kinematic approximation for the analysis are discussed in detail.
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| 21. |
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| 22. |
- Glavic, Artur, et al.
(författare)
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GenX 3 : the latest generation of an established tool
- 2022
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Ingår i: Journal of applied crystallography. - : International Union of Crystallography (IUCr). - 0021-8898 .- 1600-5767. ; 55, s. 1063-1071
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Tidskriftsartikel (refereegranskat)abstract
- Since its publication more than 15 years ago the GenX software has been continuously developed and has established itself as a standard package for analyzing X-ray and neutron reflectometry data. The evolution of the software during the last two major revisions is reported here. This includes a simplified model builder for beginners, simple samples, additional sample models, statistical error analysis and the use of just-in-time compilation modules for the reflectometry kernel to achieve higher performance. In addition, the influence of experimental errors on the reflectivity curve is discussed, and new features are described that allow the user to include these in the error statistics to improve the fitting and uncertainty estimation.
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| 23. |
- Gruene, Tim, et al.
(författare)
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CELLOPT : improved unit-cell parameters for electron diffraction data of small-molecule crystals
- 2022
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Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 55, s. 647-655
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Tidskriftsartikel (refereegranskat)abstract
- Electron diffraction enables structure determination of organic small molecules using crystals that are too small for conventional X-ray crystallography. However, because of uncertainties in the experimental parameters, notably the detector distance, the unit-cell parameters and the geometry of the structural models are typically less accurate and precise compared with results obtained by X-ray diffraction. Here, an iterative procedure to optimize the unit-cell parameters obtained from electron diffraction using idealized restraints is proposed. The cell optimization routine has been implemented as part of the structure refinement, and a gradual improvement in lattice parameters and data quality is demonstrated. It is shown that cell optimization, optionally combined with geometrical corrections for any apparent detector distortions, benefits refinement of electron diffraction data in small-molecule crystallography and leads to more accurate structural models.
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| 24. |
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| 25. |
- Han, Huijong, et al.
(författare)
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The XBI BioLab for life science experiments at the European XFEL
- 2021
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Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 54, s. 7-21
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Tidskriftsartikel (refereegranskat)abstract
- The science of X-ray free-electron lasers (XFELs) critically depends on the performance of the X-ray laser and on the quality of the samples placed into the X-ray beam. The stability of biological samples is limited and key biomolecular transformations occur on short timescales. Experiments in biology require a support laboratory in the immediate vicinity of the beamlines. The XBI BioLab of the European XFEL (XBI denotes XFEL Biology Infrastructure) is an integrated user facility connected to the beamlines for supporting a wide range of biological experiments. The laboratory was financed and built by a collaboration between the European XFEL and the XBI User Consortium, whose members come from Finland, Germany, the Slovak Republic, Sweden and the USA, with observers from Denmark and the Russian Federation. Arranged around a central wet laboratory, the XBI BioLab provides facilities for sample preparation and scoring, laboratories for growing prokaryotic and eukaryotic cells, a Bio Safety Level 2 laboratory, sample purification and characterization facilities, a crystallization laboratory, an anaerobic laboratory, an aerosol laboratory, a vacuum laboratory for injector tests, and laboratories for optical microscopy, atomic force microscopy and electron microscopy. Here, an overview of the XBI facility is given and some of the results of the first user experiments are highlighted.
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| 26. |
- Hantke, Max F., et al.
(författare)
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Condor : a simulation tool for flash X-ray imaging
- 2016
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Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 49, s. 1356-1362
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Forskningsöversikt (refereegranskat)abstract
- 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. The software enables researchers to test whether their envisaged imaging experiment is feasible, and to optimize critical parameters for reaching the best possible result. It also aims to support researchers who intend to create or advance reconstruction algorithms by simulating realistic test data. Condor is designed to be easy to use and can be either installed as a Python package or used from its web interface (http://lmb.icm.uu.se/condor). X-ray free-electron lasers have high running costs and beam time at these facilities is precious. Data quality can be substantially improved by using simulations to guide the experimental design and simplify data analysis.
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| 27. |
- Hoang-Minh, Thao, et al.
(författare)
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Use of TEM-EDX for structural formula identification of clay minerals : a case study of Di Linh bentonite, Vietnam
- 2019
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Ingår i: Journal of applied crystallography. - : International Union of Crystallography (IUCr). - 0021-8898 .- 1600-5767. ; 52:1, s. 133-147
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Tidskriftsartikel (refereegranskat)abstract
- Transmission electron microscopy linked with energy-dispersive X-ray spectroscopy (TEM-EDX) was applied to characterize mineralogical signals ofweathering processes in the Di Linh bentonite deposit (Vietnam) and to visualize the effects of Na activation on the smectitic phases. Modelling of X ray diffraction patterns (oriented mount) was applied in order to refine the computed structural formula. X-ray diffraction, X-ray fluorescence and Fouriertransform infrared spectroscopy (FT-IR) methods were also applied to verify the TEM-EDX results. An Excel-based routine has been developed in this research to allow fast computation of structural formulae and classification of the investigated clay particles. This routine supports the acquirement of 100 300 TEM-EDX analyses as a representative set of individual particles for each sample. The Excel-based routine involves end members of different clay mineral groups and interstratifications with two or three members (e.g. illite smectite interstratifications – IS-ml; dioctahedral vermiculite–smectite interstratifications – diVS-ml; and kaolinite–montmorillonite–dioctahedral vermiculite interstratifications – KSV-ml). The routine is now freely available. According to the identification procedure, the <2 mm fraction of the Di Linh bentonite (Vietnam) is composed mainly of K- and charge-deficient illite smectite interstratifications (or diVS-ml): montmorillonite-rich randomly ordered (R0) type and illite-rich regularly ordered (R1) type. Additionally, Fe-poor KSV-ml was identified.Industrial Na activation of the Di Linh bentonite resulted in an increase of theR1 diVS-ml portion and dissolution of a large part of the smectite-rich phases.The TEM-EDX approach also gave analytical proof of a sedimentary processfor Di Linh smectite. The parent muscovite was altered in two different environments: (i) K-leaching and layer-wise alteration into kaolinite (weathering), and (ii) further edge-controlled alteration of mica into lath-like montmorillonite particles associated with a dissolution of kaolinite layers from the former kaolinite–mica intergrowths by heat impact (basalt flow).
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| 28. |
- 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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| 29. |
- Joosten, Robbie P., et al.
(författare)
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PDB_REDO : automated re-refinement of X-ray structure models in the PDB
- 2009
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Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 42, s. 376-384
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Tidskriftsartikel (refereegranskat)abstract
- Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X-ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour.
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| 30. |
- Karppinen, Markku
(författare)
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Net atomic charges, electric moments, and sign and magnitude of optical rotatory power in alpha-TeO2 at 296K
- 2020
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Ingår i: Journal of applied crystallography. - : INT UNION CRYSTALLOGRAPHY. - 0021-8898 .- 1600-5767. ; 53, s. 1252-1256
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Tidskriftsartikel (refereegranskat)abstract
- Optical activity is determined from a point charge model in one enantiomorph of a chiral and semiconducting alpha-TeO2 crystal. Net atomic charges of Te and O atoms are iterated and electric moments derived. Second electric moments in the principal axis directions are calculated and their ratio is fitted by comparison with the corresponding ratio of the optical refraction indices. The components of the axial vectors are calculated and converted to the gyration tensor components. The optical rotatory power in the positive direction of the optic axis is determined, and the sense of optical rotation is defined from transformations of polar vectors of first rank of the TeO2 groups and visually confirmed in both enantiomorphs.
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| 31. |
- Li, C., et al.
(författare)
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A synchrotron X-ray diffraction deconvolution method for the measurement of residual stress in thermal barrier coatings as a function of depth
- 2016
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Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 49:Pt 6, s. 1904-1911
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Tidskriftsartikel (refereegranskat)abstract
- The average residual stress distribution as a function of depth in an air plasma-sprayed yttria stabilized zirconia top coat used in thermal barrier coating (TBC) systems was measured using synchrotron radiation X-ray diffraction in reflection geometry on station I15 at Diamond Light Source, UK, employing a series of incidence angles. The stress values were calculated from data deconvoluted from diffraction patterns collected at increasing depths. The stress was found to be compressive through the thickness of the TBC and a fluctuation in the trend of the stress profile was indicated in some samples. Typically this fluctuation was observed to increase from the surface to the middle of the coating, decrease a little and then increase again towards the interface. The stress at the interface region was observed to be around 300 MPa, which agrees well with the reported values. The trend of the observed residual stress was found to be related to the crack distribution in the samples, in particular a large crack propagating from the middle of the coating. The method shows promise for the development of a nondestructive test for as-manufactured samples.
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| 32. |
- Lovelace, Jeffrey J., et al.
(författare)
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Protein crystals can be incommensurately modulated
- 2008
-
Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 41, s. 600-605
-
Tidskriftsartikel (refereegranskat)abstract
- For a normal periodic crystal, the X-ray diffraction pattern can be described by an orientation matrix and a set of three integers that indicate the reciprocal lattice points. Those integers determine the spacing along the reciprocal lattice directions. In aperiodic crystals, the diffraction pattern is modulated and the standard periodic main reflections are surrounded by satellite reflections. The successful indexing and refinement of the main unit cell and q vector using TWINSOLVE, developed by Svensson [(2003). Lund University, Sweden], are reported here for an incommensurately modulated, aperiodic crystal of a profilin: actin complex. The indexing showed that the modulation is along the b direction in the crystal, which corresponds to an 'actin ribbon' formed by the crystal lattice. Interestingly, the transition to the aperiodic state was shown to be reversible and the diffraction pattern returned to the periodic state during data collection. It is likely that the protein underwent a conformational change that affected the neighbouring profilin: actin molecules in such a way as to produce the observed modulation in the diffraction pattern. Future work will aim to trap the incommensurately modulated crystal state, for example using cryocooling or chemical crosslinking, thus allowing complete X-ray data to be collected.
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| 33. |
- Maia, Filipe R. N. C., et al.
(författare)
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CCP-FEL : a collection of computer programs for free-electron laser research
- 2016
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Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 49, s. 1117-1120
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The latest virtual special issue of Journal of Applied Crystallography (http://journals.iucr.org/special_issues/2016/ccpfel) collects software for free-electron laser research and presents tools for a range of topics such as simulation of experiments, online monitoring of data collection, selection of hits, diagnostics of data quality, data management, data analysis and structure determination for both nanocrystallography and single-particle diffractive imaging. This article provides an introduction to the special issue.
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| 34. |
- Maia, Filipe R. N. C., et al.
(författare)
-
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
-
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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| 35. |
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| 36. |
- Marchesini, Stefano, et al.
(författare)
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SHARP : a distributed GPU-based ptychographic solver
- 2016
-
Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 49, s. 1245-1252
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Tidskriftsartikel (refereegranskat)abstract
- Ever brighter light sources, fast parallel detectors and advances in phase retrieval methods have made ptychography a practical and popular imaging technique. Compared to previous techniques, ptychography provides superior robustness and resolution at the expense of more advanced and time-consuming data analysis. By taking advantage of massively parallel architectures, high-throughput processing can expedite this analysis and provide microscopists with immediate feedback. These advances allow real-time imaging at wavelength-limited resolution, coupled with a large field of view. This article describes a set of algorithmic and computational methodologies used at the Advanced Light Source and US Department of Energy light sources. These are packaged as a CUDA-based software environment named SHARP (http://camera.lbl.gov/sharp), aimed at providing state-of-the-art high-throughput ptychography reconstructions for the coming era of diffraction-limited light sources.
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| 37. |
- Martel, Anne, et al.
(författare)
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Upgraded D22 SEC-SANS setup dedicated to the biology community
- 2023
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Ingår i: Journal of applied crystallography. - : INT UNION CRYSTALLOGRAPHY. - 0021-8898 .- 1600-5767. ; 56, s. 994-1001
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Tidskriftsartikel (refereegranskat)abstract
- Described here is the current status of the upgraded in situ size-exclusion chromatography (SEC) system implemented with the D22 small-angle neutron scattering (SANS) instrument at the Institut Laue-Langevin. Since its initial proof of principle in 2016, this SEC-SANS arrangement has been continuously requested by the user community, leading to the design of an upgraded version. A detailed description of the setup and its control is provided, and a few examples of protein structural investigations are presented, which will highlight the various possibilities and limitations of the setup to optimize experimental success.
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| 38. |
- 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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| 39. |
- Mühlig, Kerstin, et al.
(författare)
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Nanometre-sized droplets from a gas dynamic virtual nozzle
- 2019
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Ingår i: Journal of Applied Crystallography. - : INT UNION CRYSTALLOGRAPHY. - 1600-5767 .- 0021-8898. ; 52, s. 800-808
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Tidskriftsartikel (refereegranskat)abstract
- This paper reports on improved techniques to create and characterize nanometre-sized droplets from dilute aqueous solutions by using a gas dynamic virtual nozzle (GDVN). It describes a method to measure the size distribution of uncharged droplets, using an environmental scanning electron microscope, and provides theoretical models for the droplet sizes created. The results show that droplet sizes can be tuned by adjusting the gas and liquid flow rates in the GDVN, and at the lowest liquid flow rates, the size of the water droplets peaks at about 120 nm. This droplet size is similar to droplet sizes produced by electrospray ionization but requires neither electrolytes nor charging of the solution. The results presented here identify a new operational regime for GDVNs and show that predictable droplet sizes, comparable to those obtained by electrospray ionization, can be produced by purely mechanical means in GDVNs.
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| 40. |
- Nawaz, S., et al.
(författare)
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Explainable machine learning for diffraction patterns
- 2023
-
Ingår i: Journal of applied crystallography. - : International Union of Crystallography (IUCr). - 0021-8898 .- 1600-5767. ; 56:5, s. 1494-1504
-
Tidskriftsartikel (refereegranskat)abstract
- Serial crystallography experiments at X-ray free-electron laser facilities produce massive amounts of data but only a fraction of these data are useful for downstream analysis. Thus, it is essential to differentiate between acceptable and unacceptable data, generally known as 'hit' and 'miss', respectively. Image classification methods from artificial intelligence, or more specifically convolutional neural networks (CNNs), classify the data into hit and miss categories in order to achieve data reduction. The quantitative performance established in previous work indicates that CNNs successfully classify serial crystallography data into desired categories [Ke, Brewster, Yu, Ushizima, Yang & Sauter (2018). J. Synchrotron Rad. 25, 655-670], but no qualitative evidence on the internal workings of these networks has been provided. For example, there are no visualization methods that highlight the features contributing to a specific prediction while classifying data in serial crystallography experiments. Therefore, existing deep learning methods, including CNNs classifying serial crystallography data, are like a 'black box'. To this end, presented here is a qualitative study to unpack the internal workings of CNNs with the aim of visualizing information in the fundamental blocks of a standard network with serial crystallography data. The region(s) or part(s) of an image that mostly contribute to a hit or miss prediction are visualized.
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| 41. |
- 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
-
Ingår i: Journal of Applied Crystallography. - 0021-8898 .- 1600-5767. ; 47:4, s. 1190-1198
-
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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| 42. |
- Norberg, Stefan, 1972, et al.
(författare)
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Bond valence sum: a new soft chemical constraint for RMCProfile
- 2009
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Ingår i: Journal of Applied Crystallography. - 1600-5767 .- 0021-8898. ; 42:2, s. 179-184
-
Tidskriftsartikel (refereegranskat)abstract
- The implementation of a new soft chemical constraint for the reverse Monte Carlo (RMC) program RMCProfile, based on bond valence sum (BVS) calculations, is described and its advantages for the analysis of 'total scattering' diffraction data collected from disordered crystalline systems discussed. The inclusion of the BVS formalism proves particularly valuable in the early stages of the RMC fitting procedure, by avoiding the formation of regions containing chemically unreasonable local configurations which can become frozen in. Furthermore, this approach provides the fitting procedure with additional chemical information to differentiate between cation species that share the same crystallographic sites within the averaged unit cell and possess similar neutron scattering lengths. These issues are illustrated using total neutron scattering data collected at room temperature on the oxide-ion conductor Zr2Y2O7 and the nonlinear optical material KTiOPO4.
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| 43. |
- Nouhi, Shirin, et al.
(författare)
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Grazing-Incidence Small Angle Neutron Scattering from Structures below an Interface
- 2017
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Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 50:4, s. 1066-1074
-
Tidskriftsartikel (refereegranskat)abstract
- 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, as well as the sample structure. The calculations are tested with self-organised structures of two colloidal samples with different size particles that were measured on two different instruments. The model allows calculations for various instruments with defined resolution and can be used to design future improved experiments. The possibilities and limits of GISANS for different studies are discussed using the model calculations.
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| 44. |
- Olsson, Anders, et al.
(författare)
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Boron carbide composite apertures for small-angle neutron scattering made by three-dimensional printing
- 2016
-
Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 49:2, s. 696-699
-
Tidskriftsartikel (refereegranskat)abstract
- Apertures for small-angle neutron scattering prepared from a boron carbide/polymer composite have been made by three-dimensional printing using fused filament fabrication. Use of enriched (B4C)-B-10 gives higher absorption and much lower parasitic scattering than natural B4C. The simple fabrication, the capability to replace toxic and environmentally hazardous materials such as cadmium, and the possibility to diminish the secondary background of gamma-radiation are attractive features of use of these materials. Complex shapes, apart from apertures, can be fabricated readily with this composite, for example, to make shielding for instrument components and masks used to calibrate detectors.
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| 45. |
- Paul, Amitesh, et al.
(författare)
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Structural, electronic and magnetic properties of YMnO3/La0.7Sr0.3MnO3 heterostructures
- 2014
-
Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 47, s. 1054-1064
-
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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| 46. |
- Persson, Rasmus, 1985, et al.
(författare)
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Efficient computation of the scattering intensity from systems of nonspherical particles
- 2016
-
Ingår i: Journal of Applied Crystallography. - 0021-8898 .- 1600-5767. ; 49:5, s. 1524-1531
-
Tidskriftsartikel (refereegranskat)abstract
- The analysis of the angle dependence of the elastic scattering of radiation from a sample is an efficient and non-invasive technique that is used in fundamental science, in medicine and in technical quality control in industry. Precise information on the shape, size, polydispersity and interactions of a colloidal sample is readily obtained provided an underlying scattering model, i.e. form and structure factors, can be computed for the sample. Here, a numerical method that can efficiently compute the form factor amplitude (and thus the scattering intensity) of nonspherical scatterers through an importance sampling algorithm of the Fourier integral of the scattering density is presented. Using the precomputed form factor amplitudes, the calculation of the scattering intensity at any particle concentration then scales linearly with the particle number and linearly with the number of q points for its evaluation. This is illustrated by an example calculation of the scattering by concentrated suspensions of ellipsoidal Janus particles and the numerical accuracy for the computed form factor amplitudes is compared with analytical benchmarks.
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| 47. |
- Piegsa, F. M., et al.
(författare)
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Polarized neutron Laue diffraction on a crystal containing dynamically polarized proton spins
- 2013
-
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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| 48. |
- Polovinkin, Vitaly, et al.
(författare)
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Demonstration of electron diffraction from membrane protein crystals grown in a lipidic mesophase after lamella preparation by focused ion beam milling at cryogenic temperatures
- 2020
-
Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 53, s. 1416-1424
-
Tidskriftsartikel (refereegranskat)abstract
- Electron crystallography of sub-micrometre-sized 3D protein crystals has emerged recently as a valuable field of structural biology. In meso crystallization methods, utilizing lipidic mesophases, particularly lipidic cubic phases (LCPs), can produce high-quality 3D crystals of membrane proteins (MPs). A major step towards realizing 3D electron crystallography of MP crystals, grown in meso, is to demonstrate electron diffraction from such crystals. The first task is to remove the viscous and sticky lipidic matrix that surrounds the crystals without damaging the crystals. Additionally, the crystals have to be thin enough to let electrons traverse them without significant multiple scattering. In the present work, the concept that focused ion beam milling at cryogenic temperatures (cryo-FIB milling) can be used to remove excess host lipidic mesophase matrix is experimentally verified, and then the crystals are thinned to a thickness suitable for electron diffraction. In this study, bacteriorhodopsin (BR) crystals grown in a lipidic cubic mesophase of monoolein were used as a model system. LCP from a part of a hexagon-shaped plate-like BR crystal (∼10 µm in thickness and ∼70 µm in the longest dimension), which was flash-frozen in liquid nitrogen, was milled away with a gallium FIB under cryogenic conditions, and a part of the crystal itself was thinned into a ∼210 nm-thick lamella with the ion beam. The frozen sample was then transferred into an electron cryo-microscope, and a nanovolume of ∼1400 × 1400 × 210 nm of the BR lamella was exposed to 200 kV electrons at a fluence of ∼0.06 e Å−2. The resulting electron diffraction peaks were detected beyond 2.7 Å resolution (with an average peak height to background ratio of >2) by a CMOS-based Ceta 16M camera. The results demonstrate that cryo-FIB milling produces high-quality lamellae from crystals grown in lipidic mesophases and pave the way for 3D electron crystallography on crystals grown or embedded in highly viscous media.
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| 49. |
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| 50. |
- Rahmani, V., et al.
(författare)
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Data reduction for X-ray serial crystallography using machine learning
- 2023
-
Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 56, s. 200-213
-
Tidskriftsartikel (refereegranskat)abstract
- Serial crystallography experiments produce massive amounts of experimental data. Yet in spite of these large-scale data sets, only a small percentage of the data are useful for downstream analysis. Thus, it is essential to differentiate reliably between acceptable data (hits) and unacceptable data (misses). To this end, a novel pipeline is proposed to categorize the data, which extracts features from the images, summarizes these features with the 'bag of visual words' method and then classifies the images using machine learning. In addition, a novel study of various feature extractors and machine learning classifiers is presented, with the aim of finding the best feature extractor and machine learning classifier for serial crystallography data. The study reveals that the oriented FAST and rotated BRIEF (ORB) feature extractor with a multilayer perceptron classifier gives the best results. Finally, the ORB feature extractor with multilayer perceptron is evaluated on various data sets including both synthetic and experimental data, demonstrating superior performance compared with other feature extractors and classifiers.
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