| 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. |
- Andersen, Ken Holst, et al.
(författare)
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Optimization of moderators and beam extraction at the ESS
- 2018
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Ingår i: Journal of Applied Crystallography. - 0021-8898. ; 51:2, s. 264-281
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Tidskriftsartikel (refereegranskat)abstract
- A global approach coupling the moderator to the beam extraction system has been applied for the design optimization of the thermal and cold moderators of the European Spallation Source (ESS), which will be the brightest neutron source in the world for condensed-matter studies. The design is based on the recently developed high-brightness low-dimensional moderator concepts. Para-hydrogen is used for the cold neutron source, while thermal neutrons are provided by moderation in water. The overall moderation configuration was chosen in order to satisfy a range of requirements on bispectral extraction, beamport configuration and instrument performance. All instruments are served by a single moderator assembly above the target, arranged in a 'butterfly' geometry with a height of 3 cm. This was determined to be the optimal height for trade-off between high brightness and efficient guide illumination, by analysis of the performance of 23 instruments, based on the reference suite of the ESS Technical Design Report. The concept of 'brilliance transfer' is introduced to quantify the performance of the neutron optical system from the source to the sample. The target monolith incorporates a grid of 42 neutron beamports with an average separation of 6°, allowing a free choice between cold and thermal neutron sources at all instrument positions. With the large number of beamports and the space below the target available for future moderators, ample opportunities are available for future upgrades.
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| 7. |
- 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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| 8. |
- 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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| 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. |
- Berg, H, et al.
(författare)
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Structural aspects of lithium insertion in transition metal oxide electrodes
- 1998
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Ingår i: JOURNAL OF APPLIED CRYSTALLOGRAPHY. - 0021-8898. ; 31, s. 103-105
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Tidskriftsartikel (refereegranskat)abstract
- There is a considerable lack of detailed information on the structure of lithiated phases of popular-consensus positive electrode materials for lithium/polymer and lithium-ion/polymer batteries. Having illustrated this phenomenon for the specific cases o
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| 13. |
- 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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| 14. |
- 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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| 15. |
- Bergstrom, Örjan, et al.
(författare)
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A neutron diffraction cell for studying lithium-insertion processes in electrode materials
- 1998
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Ingår i: JOURNAL OF APPLIED CRYSTALLOGRAPHY. - 0021-8898. ; 31, s. 823-825
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- An electrochemical cell has been constructed for in situ neutron diffraction studies of lithium-insertion/extraction processes in electrode materials for Li-ion batteries. Its key components are a Pyrex tube, gold plated on its inside, which functions as
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| 16. |
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| 17. |
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| 18. |
- 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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| 19. |
- Borlado, CR, et al.
(författare)
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Monte Carlo simulation of a reactor-based neutron strain scanning diffractometer
- 2001
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Ingår i: JOURNAL OF APPLIED CRYSTALLOGRAPHY. - : MUNKSGAARD INT PUBL LTD. - 0021-8898. ; 34, s. 613-624
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Tidskriftsartikel (refereegranskat)abstract
- A Monte Carlo code for the simulation of neutron strain scanning experiments on a reactor-based two-axis diffractometer is described. In order to validate this code, several experiments have been performed. A comparison is made between experimental and si
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| 20. |
- Carlson, Stefan
(författare)
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High-pressure studies of the cubic to rhombohedral transformation in NbO2F
- 2000
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Ingår i: Journal of Applied Crystallography. - 0021-8898. ; 33:4, s. 1175-1176
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Tidskriftsartikel (refereegranskat)abstract
- The Pm3̄m to R3̄c high-pressure transition of NbO2F has been studied in detail using diamond anvil cells and synchrotron X-ray radiation. The transition starts at 0.28 GPa and is complete at 0.65 GPa. The bulk modulus for the cubic phase became 24.8 (11) GPa, which is roughly two times higher than for the rhombohedral phase.
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| 21. |
- 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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| 22. |
- Chayanun, Lert, et al.
(författare)
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Optical demonstration of crystallography and reciprocal space using laser diffraction from Au microdisc arrays
- 2022
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Ingår i: Journal of Applied Crystallography. - 0021-8898. ; 55, s. 168-171
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Tidskriftsartikel (refereegranskat)abstract
- Crystallography is an invaluable tool in materials science, solid state physics and protein science. Understanding crystallography requires grasping the powerful but abstract concept of reciprocal space. Here a simple but insightful experiment using a laser pointer and Au microdisc arrays to explore and illustrate Bragg diffraction and reciprocal space is demonstrated. The Au microdisc arrays were manufactured using standard semiconductor fabrication techniques. The flexibility of the array design allows the demonstration of basic concepts such as lattice and atomic form factor, but also more advanced ones such as quasicrystal and shape function.
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| 23. |
- 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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| 24. |
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| 25. |
- 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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| 26. |
- 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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| 27. |
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| 28. |
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| 29. |
- Ghazal, Aghiad, et al.
(författare)
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Direct monitoring of calcium-triggered phase transitions in cubosomes using small-angle X-ray scattering combined with microfluidics
- 2016
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Ingår i: Journal of Applied Crystallography. - 0021-8898. ; 49:6, s. 2005-2014
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Tidskriftsartikel (refereegranskat)abstract
- This article introduces a simple microfluidic device that can be combined with synchrotron small-angle X-ray scattering (SAXS) for monitoring dynamic structural transitions. The microfluidic device is a thiol-ene-based system equipped with 125 μm-thick polystyrene windows, which are suitable for X-ray experiments. The device was prepared by soft lithography using elastomeric molds followed by a simple UV-initiated curing step to polymerize the chip material and simultaneously seal the device with the polystyrene windows. The microfluidic device was successfully used to explore the dynamics of the structural transitions of phytantriol/dioleoylphosphatidylglycerol-based cubosomes on exposure to a buffer containing calcium ions. The resulting SAXS data were resolved in the time frame between 0.5 and 5.5 s, and a calcium-triggered structural transition from an internal inverted-type cubic phase of symmetry Im3m to an internal inverted-type cubic phase of symmetry Pn3m was detected. The combination of microfluidics with X-ray techniques opens the door to the investigation of early dynamic structural transitions, which is not possible with conventional techniques such as glass flow cells. The combination of microfluidics with X-ray techniques can be used for investigating protein unfolding, for monitoring the formation of nanoparticles in real time, and for other biomedical and pharmaceutical investigations. A combination of microfluidics with X-ray techniques has been used to perform dynamic structural studies on nanoparticulate formulations.
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| 30. |
- Ghosh, Swagatha, et al.
(författare)
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A simple goniometer-compatible flow cell for serial synchrotron X-ray crystallography
- 2023
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Ingår i: Journal of Applied Crystallography. - 0021-8898. ; 56:Pt 2, s. 449-460
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Tidskriftsartikel (refereegranskat)abstract
- Serial femtosecond crystallography was initially developed for room-temperature X-ray diffraction studies of macromolecules at X-ray free electron lasers. When combined with tools that initiate biological reactions within microcrystals, time-resolved serial crystallography allows the study of structural changes that occur during an enzyme catalytic reaction. Serial synchrotron X-ray crystallography (SSX), which extends serial crystallography methods to synchrotron radiation sources, is expanding the scientific community using serial diffraction methods. This report presents a simple flow cell that can be used to deliver microcrystals across an X-ray beam during SSX studies. This device consists of an X-ray transparent glass capillary mounted on a goniometer-compatible 3D-printed support and is connected to a syringe pump via lightweight tubing. This flow cell is easily mounted and aligned, and it is disposable so can be rapidly replaced when blocked. This system was demonstrated by collecting SSX data at MAX IV Laboratory from microcrystals of the integral membrane protein cytochrome c oxidase from Thermus thermophilus, from which an X-ray structure was determined to 2.12 Å resolution. This simple SSX platform may help to lower entry barriers for non-expert users of SSX.
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| 31. |
- 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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| 32. |
- 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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| 33. |
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| 34. |
- Hammarberg, Susanna, et al.
(författare)
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Fast nanoscale imaging of strain in a multi-segment heterostructured nanowire with 2D Bragg ptychography
- 2024
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Ingår i: Journal of Applied Crystallography. - 0021-8898. ; 57, s. 60-70
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Tidskriftsartikel (refereegranskat)abstract
- Developing semiconductor devices requires a fast and reliable source of strain information with high spatial resolution and strain sensitivity. This work investigates the strain in an axially heterostructured 180 nm-diameter GaInP nanowire with InP segments of varying lengths down to 9 nm, simultaneously probing both materials. Scanning X-ray diffraction (XRD) is compared with Bragg projection ptychography (BPP), a fast single-projection method. BPP offers a sufficient spatial resolution to reveal fine details within the largest segments, unlike scanning XRD. The spatial resolution affects the quantitative accuracy of the strain maps, where BPP shows much-improved agreement with an elastic 3D finite element model compared with scanning XRD. The sensitivity of BPP to small deviations from the Bragg condition is systematically investigated. The experimental confirmation of the model suggests that the large lattice mismatch of 1.52% is accommodated without defects.
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| 35. |
- 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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| 36. |
- 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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| 37. |
- Harlow, Gary S., et al.
(författare)
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HAT : a high-energy surface X-ray diffraction analysis toolkit
- 2023
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Ingår i: Journal of Applied Crystallography. - 0021-8898. ; 56, s. 312-321
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Tidskriftsartikel (refereegranskat)abstract
- This work introduces the high-energy surface X-ray diffraction analysis toolkit (HAT), an open-source cross-platform software package written in Python to allow the extraction and processing of high-energy surface X-ray diffraction (HESXRD) data sets. Thousands of large-area detector images are collected in a single HESXRD scan, corresponding to billions of pixels and hence reciprocal space positions. HAT is an optimized reciprocal space binner that implements a graphical user interface to allow the easy and interactive exploration of HESXRD data sets. Regions of reciprocal space can be selected with movable and resizable masks in multiple views and are projected onto different axes to allow the creation of reciprocal space maps and the extraction of crystal truncation rods. Current and future versions of HAT can be downloaded and used free of charge.
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| 38. |
- Henningsson, N. Axel, et al.
(författare)
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Reconstructing intragranular strain fields in polycrystalline materials from scanning 3DXRD data
- 2020
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Ingår i: Journal of Applied Crystallography. - 0021-8898. ; 53, s. 314-325
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Tidskriftsartikel (refereegranskat)abstract
- Two methods for reconstructing intragranular strain fields are developed for scanning three-dimensional X-ray diffraction (3DXRD). The methods are compared with a third approach where voxels are reconstructed independently of their neighbours [Hayashi, Setoyama & Seno (2017). Mater. Sci. Forum, 905, 157-164]. The 3D strain field of a tin grain, located within a sample of approximately 70 grains, is analysed and compared across reconstruction methods. Implicit assumptions of sub-problem independence, made in the independent voxel reconstruction method, are demonstrated to introduce bias and reduce reconstruction accuracy. It is verified that the two proposed methods remedy these problems by taking the spatial properties of the inverse problem into account. Improvements in reconstruction quality achieved by the two proposed methods are further supported by reconstructions using synthetic diffraction data.
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| 39. |
- 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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| 40. |
- 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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| 41. |
- Jacobs, Philipp, et al.
(författare)
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Instrumental resolution as a function of scattering angle and wavelength as exemplified for the POWGEN instrument
- 2017
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Ingår i: Journal of Applied Crystallography. - 0021-8898. ; 50:3, s. 866-875
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Tidskriftsartikel (refereegranskat)abstract
- 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. The aim of this work is to provide the users with calibration files and - for the later Rietveld refinement of the measured data - with an instrumental resolution file (IRF). This article will elaborate on the necessary steps to generate such an IRF for the angular- and wavelength-dispersive case, exemplified for the POWGEN instrument. A dataset measured on a standard diamond sample is used to extract the profile function in the two-dimensional case. It is found that the variation of reflection width with 2gθ and λ can be expressed by the standard equation used for evaluating the instrumental resolution, which yields a substantially more fundamental approach to the parameterization of the instrumental contribution to the peak shape. Geometrical considerations of the POWGEN instrument and sample effects lead to values for Δgθ, Δt and ΔL that yield a very good match to the extracted FWHM values. In a final step the refinement results are compared with the one-dimensional, i.e. diffraction-focused, case.A fundamental description of the instrument resolution file is elaborated for the angular- and wavelength-dispersive cases of Rietveld refinement, exemplified for the POWGEN instrument. It is shown how to refine the necessary profile function parameters from a dataset measured on a diamond reference sample. The analysis is performed in a two-dimensional refinement space based on the convenient variables d and d?.
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| 42. |
- 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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| 43. |
- Kahnt, Maik, et al.
(författare)
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First ptychographic X-ray computed tomography experiment on the NanoMAX beamline
- 2020
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Ingår i: Journal of Applied Crystallography. - 0021-8898. ; 53, s. 1444-1451
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Tidskriftsartikel (refereegranskat)abstract
- Ptychographic X-ray computed tomography is a quantitative three-dimensional imaging technique offered to users of multiple synchrotron radiation sources. Its dependence on the coherent fraction of the available X-ray beam makes it perfectly suited to diffraction-limited storage rings. Although MAX IV is the first, and so far only, operating fourth-generation synchrotron light source, none of its experimental stations is currently set up to offer this technique to its users. The first ptychographic X-ray computed tomography experiment has therefore been performed on the NanoMAX beamline. From the results, information was gained about the current limitations of the experimental setup and where attention should be focused for improvement. The extracted parameters in terms of scanning speed, size of the imaged volume and achieved resolutions should provide a baseline for future users designing nano-Tomography experiments on the NanoMAX beamline.
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| 44. |
- Karppinen, Markku
(författare)
-
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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| 45. |
- Krogh Andersen, A.M., et al.
(författare)
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High-pressure properties of TiP2O7, ZrP2O7 and ZrV2O7
- 2001
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Ingår i: Journal of Applied Crystallography. - : Wiley. - 0021-8898. ; 34:1, s. 7-12
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Tidskriftsartikel (refereegranskat)abstract
- High-pressure synchrotron X-ray powder diffraction studies of TiP2O7, ZrP2O7 and ZrV2O7 have been performed. The ZrV2O7 structure undergoes a reversible transition at 1.38–1.58 GPa from cubic α- to pseudo-tetragonal β-ZrV2O7 that displays an orthorhombic 2 × 3 × 3 supercell. At pressures above 4 GPa, ZrV2O7 becomes irreversibly X-ray amorphous. No such transformations are observed for TiP2O7 and ZrP2O7, which compress smoothly up to the highest investigated pressures (40.3 and 20.5 GPa, respectively). These differences in high-pressure properties are discussed in terms of the negative thermal expansion of ZrV2O7. The bulk moduli at ambient pressure (B0) for TiP2O7, ZrP2O7, α-ZrV2O7 and β-ZrV2O7 were estimated to be 42 (3), 39 (1), 17.0 (7) and 20.8 (10) GPa, respectively.
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| 46. |
- 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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| 47. |
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| 48. |
- Lovelace, Jeffrey J., et al.
(författare)
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Protein crystals can be incommensurately modulated
- 2008
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Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 41, s. 600-605
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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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| 49. |
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| 50. |
- Maia, Filipe, et al.
(författare)
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Interactive visualization of electron density slices
- 2005
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Ingår i: J. Appl. Cryst.. - 0021-8898. ; 38, s. 563-565
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Tidskriftsartikel (populärvet., debatt m.m.)abstract
- A new tool has been developed to aid in the visualization of electron density in crystals or from quantum chemistry calculations. It displays the fine details of the electron density on a plane and the three-dimensional model of the molecule at the same time. The program enables the user to examine the details of weak or irregular features. Such features frequently occur in low-resolution maps, where they determine the correct tracing of a protein backbone. In high-resolution maps, solvent regions are difficult or impossible to observe using isosurfaces. The tool has been integrated into an existing molecular visualization package (PyMol) making it possible to observe and interact both with a structure model and the electron density slices freely, simultaneously and independently. This visualization model fills a gap in the visualization methods available to crystallographers and others who work with electron density maps.
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