Journal of Applied Crystallography
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Journal of Applied Crystallography covers a wide range of crystallographic topics from the viewpoints of both techniques and theory. The journal presents articles on the application of crystallographic techniques and on the related apparatus and computer software. For many years, Journal of Applied Crystallography has been the main vehicle for the publication of small-angle scattering articles and powder diffraction techniques. The journal is the primary place where crystallographic computer program information is published.enCopyright (c) 2022 International Union of Crystallography2022-01-10International Union of CrystallographyInternational Union of Crystallographyhttp://journals.iucr.orgurn:issn:1600-5767Journal of Applied Crystallography covers a wide range of crystallographic topics from the viewpoints of both techniques and theory. The journal presents articles on the application of crystallographic techniques and on the related apparatus and computer software. For many years, Journal of Applied Crystallography has been the main vehicle for the publication of small-angle scattering articles and powder diffraction techniques. The journal is the primary place where crystallographic computer program information is published.text/htmlJournal of Applied Crystallography, Volume 55, Part 1, 2022textweekly62002-02-01T00:00+00:001552022-01-10Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallography1urn:issn:1600-5767med@iucr.orgJanuary 20222022-01-10Journal of Applied Crystallographyhttp://journals.iucr.org/logos/rss10j.gif
//journals.iucr.org/j/issues/2022/01/00/index.html
Still imageCo-flow injection for serial crystallography at X-ray free-electron lasers
http://scripts.iucr.org/cgi-bin/paper?te5082
Serial femtosecond crystallography (SFX) is a powerful technique that exploits X-ray free-electron lasers to determine the structure of macromolecules at room temperature. Despite the impressive exposition of structural details with this novel crystallographic approach, the methods currently available to introduce crystals into the path of the X-ray beam sometimes exhibit serious drawbacks. Samples requiring liquid injection of crystal slurries consume large quantities of crystals (at times up to a gram of protein per data set), may not be compatible with vacuum configurations on beamlines or provide a high background due to additional sheathing liquids present during the injection. Proposed and characterized here is the use of an immiscible inert oil phase to supplement the flow of sample in a hybrid microfluidic 3D-printed co-flow device. Co-flow generation is reported with sample and oil phases flowing in parallel, resulting in stable injection conditions for two different resin materials experimentally. A numerical model is presented that adequately predicts these flow-rate conditions. The co-flow generating devices reduce crystal clogging effects, have the potential to conserve protein crystal samples up to 95% and will allow degradation-free light-induced time-resolved SFX.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Doppler, D.Rabbani, M.T.Letrun, R.Cruz Villarreal, J.Kim, D.H.Gandhi, S.Egatz-Gomez, A.Sonker, M.Chen, J.Koua, F.H.M.Yang, J.Youssef, M.Mazalova, V.Bajt, S.Shelby, M.L.Coleman, M.A.Wiedorn, M.O.Knoska, J.Schön, S.Sato, T.Hunter, M.S.Hosseinizadeh, A.Kuptiz, C.Nazari, R.Alvarez, R.C.Karpos, K.Zaare, S.Dobson, Z.Discianno, E.Zhang, S.Zook, J.D.Bielecki, J.de Wijn, R.Round, A.R.Vagovic, P.Kloos, M.Vakili, M.Ketawala, G.K.Stander, N.E.Olson, T.L.Morin, K.Mondal, J.Nguyen, J.Meza-Aguilar, J.D.Kodis, G.Vaiana, S.Martin-Garcia, J.M.Mariani, V.Schwander, P.Schmidt, M.Messerschmidt, M.Ourmazd, A.Zatsepin, N.Weierstall, U.Bruce, B.D.Mancuso, A.P.Grant, T.Barty, A.Chapman, H.N.Frank, M.Fromme, R.Spence, J.C.H.Botha, S.Fromme, P.Kirian, R.A.Ros, A.2022-02-01doi:10.1107/S1600576721011079International Union of CrystallographyThe development and characterization are described of a co-flow injector for liquid-jet crystal delivery applied for serial crystallography with X-ray free-electron lasers.ENmicrofluidic devicesserial crystallography3D printingX-ray free-electron lasersXFELsviscous mediasample consumptionSerial femtosecond crystallography (SFX) is a powerful technique that exploits X-ray free-electron lasers to determine the structure of macromolecules at room temperature. Despite the impressive exposition of structural details with this novel crystallographic approach, the methods currently available to introduce crystals into the path of the X-ray beam sometimes exhibit serious drawbacks. Samples requiring liquid injection of crystal slurries consume large quantities of crystals (at times up to a gram of protein per data set), may not be compatible with vacuum configurations on beamlines or provide a high background due to additional sheathing liquids present during the injection. Proposed and characterized here is the use of an immiscible inert oil phase to supplement the flow of sample in a hybrid microfluidic 3D-printed co-flow device. Co-flow generation is reported with sample and oil phases flowing in parallel, resulting in stable injection conditions for two different resin materials experimentally. A numerical model is presented that adequately predicts these flow-rate conditions. The co-flow generating devices reduce crystal clogging effects, have the potential to conserve protein crystal samples up to 95% and will allow degradation-free light-induced time-resolved SFX.text/htmlCo-flow injection for serial crystallography at X-ray free-electron laserstext1552022-02-01Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Optimized signal deduction procedure for the MIEZE spectroscopy technique
http://scripts.iucr.org/cgi-bin/paper?in5058
A method is reported to determine the phase and amplitude of sinusoidally modulated event rates, binned into four bins per oscillation, based on data generated at the resonant neutron spin-echo spectrometer RESEDA at FRM-II. The presented algorithm relies on a reconstruction of the unknown parameters. It omits a calculation-intensive fitting procedure and avoids contrast reduction due to averaging effects. It allows the current data acquisition bottleneck at RESEDA to be relaxed by a factor of four and thus increases the potential time resolution of the detector by the same factor. The approach is explained in detail and compared with the established fitting procedures of time series having four and 16 time bins per oscillation. In addition the empirical estimates of the errors of the three methods are presented and compared with each other. The reconstruction is shown to be unbiased, asymptotic and efficient for estimating the phase. Reconstructing the contrast increases the error bars by roughly 10% as compared with fitting 16 time-binned oscillations. Finally, the paper gives heuristic, analytical equations to estimate the error for phase and contrast as a function of their initial values and counting statistics.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Jochum, J.K.Spitz, L.Franz, C.Wendl, A.Leiner, J.C.Pfleiderer, C.Soltwedel, O.2022-02-01doi:10.1107/S1600576721011936International Union of CrystallographyA method is reported to determine the phase and amplitude of sinusoidally modulated event rates, binned into four bins per oscillation, based on data generated at the resonant neutron spin-echo spectrometer RESEDA at FRM-II.ENneutron spectroscopyneutron resonance spin-echoMIEZEerror estimationA method is reported to determine the phase and amplitude of sinusoidally modulated event rates, binned into four bins per oscillation, based on data generated at the resonant neutron spin-echo spectrometer RESEDA at FRM-II. The presented algorithm relies on a reconstruction of the unknown parameters. It omits a calculation-intensive fitting procedure and avoids contrast reduction due to averaging effects. It allows the current data acquisition bottleneck at RESEDA to be relaxed by a factor of four and thus increases the potential time resolution of the detector by the same factor. The approach is explained in detail and compared with the established fitting procedures of time series having four and 16 time bins per oscillation. In addition the empirical estimates of the errors of the three methods are presented and compared with each other. The reconstruction is shown to be unbiased, asymptotic and efficient for estimating the phase. Reconstructing the contrast increases the error bars by roughly 10% as compared with fitting 16 time-binned oscillations. Finally, the paper gives heuristic, analytical equations to estimate the error for phase and contrast as a function of their initial values and counting statistics.text/htmlOptimized signal deduction procedure for the MIEZE spectroscopy techniquetext1552022-02-01Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Three-dimensional grain resolved strain mapping using laboratory X-ray diffraction contrast tomography: theoretical analysis
http://scripts.iucr.org/cgi-bin/paper?nb5305
Laboratory diffraction contrast tomography (LabDCT) is a recently developed technique to map crystallographic orientations of polycrystalline samples in three dimensions non-destructively using a laboratory X-ray source. In this work, a new theoretical procedure, named LabXRS, expanding LabDCT to include mapping of the deviatoric strain tensors on the grain scale, is proposed and validated using simulated data. For the validation, the geometries investigated include a typical near-field LabDCT setup utilizing Laue focusing with equal source-to-sample and sample-to-detector distances of 14 mm, a magnified setup where the sample-to-detector distance is increased to 200 mm, a far-field Laue focusing setup where the source-to-sample distance is also increased to 200 mm, and a near-field setup with a source-to-sample distance of 200 mm. The strain resolution is found to be in the range of 1–5 × 10−4, depending on the geometry of the experiment. The effects of other experimental parameters, including pixel binning, number of projections and imaging noise, as well as microstructural parameters, including grain position, grain size and grain orientation, on the strain resolution are examined. The dependencies of these parameters, as well as the implications for practical experiments, are discussed.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Lindkvist, A.Zhang, Y.2022-02-01doi:10.1107/S1600576721011274International Union of CrystallographyA novel method enabling 3D non-destructive strain mapping on the grain scale using laboratory X-ray diffraction contrast tomography is presented and validated using simulated data.ENstrainstresslaboratory diffraction contrast tomography (LabDCT)three-dimensional mappinglaboratory X-ray strain mapping (LabXRS)Laboratory diffraction contrast tomography (LabDCT) is a recently developed technique to map crystallographic orientations of polycrystalline samples in three dimensions non-destructively using a laboratory X-ray source. In this work, a new theoretical procedure, named LabXRS, expanding LabDCT to include mapping of the deviatoric strain tensors on the grain scale, is proposed and validated using simulated data. For the validation, the geometries investigated include a typical near-field LabDCT setup utilizing Laue focusing with equal source-to-sample and sample-to-detector distances of 14 mm, a magnified setup where the sample-to-detector distance is increased to 200 mm, a far-field Laue focusing setup where the source-to-sample distance is also increased to 200 mm, and a near-field setup with a source-to-sample distance of 200 mm. The strain resolution is found to be in the range of 1–5 × 10−4, depending on the geometry of the experiment. The effects of other experimental parameters, including pixel binning, number of projections and imaging noise, as well as microstructural parameters, including grain position, grain size and grain orientation, on the strain resolution are examined. The dependencies of these parameters, as well as the implications for practical experiments, are discussed.text/htmlThree-dimensional grain resolved strain mapping using laboratory X-ray diffraction contrast tomography: theoretical analysistext1552022-02-01Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Effective structural unit analysis in hexagonal close-packed alloys – reconstruction of parent β microstructures and crystal orientation post-processing analysis
http://scripts.iucr.org/cgi-bin/paper?nb5301
Materials with an allotropic phase transformation can form microstructures where grains have orientation relationships determined by the transformation history. These microstructures influence the final material properties. In zirconium alloys, there is a solid-state body-centred cubic (b.c.c.) to hexagonal close-packed (h.c.p.) phase transformation, where the crystal orientations of the h.c.p. phase can be related to the parent b.c.c. structure via the Burgers orientation relationship (BOR). In the present work, a reconstruction code, developed for steels and which uses a Markov chain clustering algorithm to analyse electron backscatter diffraction maps, is adapted and applied to the h.c.p./b.c.c. BOR. This algorithm is released as open-source code (via github, as ParentBOR). The algorithm enables new post-processing of the original and reconstructed data sets to analyse the variants of the h.c.p. α phase that are present and understand shared crystal planes and shared lattice directions within each parent β grain; it is anticipated that this will assist in understanding the transformation-related deformation properties of the final microstructure. Finally, the ParentBOR code is compared with recently released reconstruction codes implemented in MTEX to reveal differences and similarities in how the microstructure is described.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Birch, R.Britton, T.B.2022-02-01doi:10.1107/S1600576721011584International Union of CrystallographyA method is presented to reconstruct the parent body-centred cubic microstructure from the child hexagonal close-packed microstructure in zirconium alloys. This is used to provide post-processing of the microstructure to understand structural units in the material.ENelectron backscatter diffractionmicrostructureorientation relationshipsreconstructionMaterials with an allotropic phase transformation can form microstructures where grains have orientation relationships determined by the transformation history. These microstructures influence the final material properties. In zirconium alloys, there is a solid-state body-centred cubic (b.c.c.) to hexagonal close-packed (h.c.p.) phase transformation, where the crystal orientations of the h.c.p. phase can be related to the parent b.c.c. structure via the Burgers orientation relationship (BOR). In the present work, a reconstruction code, developed for steels and which uses a Markov chain clustering algorithm to analyse electron backscatter diffraction maps, is adapted and applied to the h.c.p./b.c.c. BOR. This algorithm is released as open-source code (via github, as ParentBOR). The algorithm enables new post-processing of the original and reconstructed data sets to analyse the variants of the h.c.p. α phase that are present and understand shared crystal planes and shared lattice directions within each parent β grain; it is anticipated that this will assist in understanding the transformation-related deformation properties of the final microstructure. Finally, the ParentBOR code is compared with recently released reconstruction codes implemented in MTEX to reveal differences and similarities in how the microstructure is described.text/htmlEffective structural unit analysis in hexagonal close-packed alloys – reconstruction of parent β microstructures and crystal orientation post-processing analysistext1552022-02-01Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Quantitative phase analysis and microstructural characterization of urinary tract calculi with X-ray diffraction Rietveld analysis on a Caribbean island
http://scripts.iucr.org/cgi-bin/paper?jo5072
In the twin-island state of Trinidad and Tobago, urinary stone analysis is not routinely performed. This study investigates, via powder X-ray diffraction, 52 urinary tract calculi collected from hospitals in Trinidad. Of these, 46 stones were analysed with Rietveld refinement for quantitative analysis and materials characterization. Refined unit-cell, microstructural and weight fraction parameters were obtained, with the last being used for stone classification. The results revealed seven distinct mineralogical phases of varying frequency: calcium oxalate monohydrate (COM, 58%), calcium oxalate dihydrate (COD, 23%), carbonated apatite (APA, 48%), brushite (BRU, 6%), struvite (STR, 42%), uric acid (UA, 23%) and ammonium acid urate (AAU, 19%). The average refined crystallite sizes were 1352 ± 90 Å (COM), 1921 ± 285 Å (COD), 83 ± 5 Å (APA), 1172 ± 9 Å (BRU), 1843 ± 138 Å (STR), 981 ± 87 Å (UA) and 292 ± 83 Å (AAU). Subsequently, 36.5% of stones were categorized as phosphates, 34.6% as oxalates, 13.5% as uric acid/urates and 15.4% as mixed compositions. The study findings highlight the importance of stone analysis as a necessary step towards disease management of local patients, and endorse the application of Rietveld refinement as a natural extension to diffraction-based kidney stone investigations.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Greasley, J.Goolcharan, S.Andrews, R.2022-02-01doi:10.1107/S1600576721011602International Union of CrystallographyPowder X-ray diffraction with Rietveld analysis was used for quantitative assessment and characterization of the crystalline composition of urinary tract calculi. Refined unit-cell parameters and crystallite size data for crystalline phases were generated.ENkidney stone analysisX-ray diffractionquantitative Rietveld analysiskidney stone compositionurolithiasisIn the twin-island state of Trinidad and Tobago, urinary stone analysis is not routinely performed. This study investigates, via powder X-ray diffraction, 52 urinary tract calculi collected from hospitals in Trinidad. Of these, 46 stones were analysed with Rietveld refinement for quantitative analysis and materials characterization. Refined unit-cell, microstructural and weight fraction parameters were obtained, with the last being used for stone classification. The results revealed seven distinct mineralogical phases of varying frequency: calcium oxalate monohydrate (COM, 58%), calcium oxalate dihydrate (COD, 23%), carbonated apatite (APA, 48%), brushite (BRU, 6%), struvite (STR, 42%), uric acid (UA, 23%) and ammonium acid urate (AAU, 19%). The average refined crystallite sizes were 1352 ± 90 Å (COM), 1921 ± 285 Å (COD), 83 ± 5 Å (APA), 1172 ± 9 Å (BRU), 1843 ± 138 Å (STR), 981 ± 87 Å (UA) and 292 ± 83 Å (AAU). Subsequently, 36.5% of stones were categorized as phosphates, 34.6% as oxalates, 13.5% as uric acid/urates and 15.4% as mixed compositions. The study findings highlight the importance of stone analysis as a necessary step towards disease management of local patients, and endorse the application of Rietveld refinement as a natural extension to diffraction-based kidney stone investigations.text/htmlQuantitative phase analysis and microstructural characterization of urinary tract calculi with X-ray diffraction Rietveld analysis on a Caribbean islandtext1552022-02-01Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Low-background neutron reflectometry from solid/liquid interfaces
http://scripts.iucr.org/cgi-bin/paper?ge5108
Liquid cells are an increasingly common sample environment for neutron reflectometry experiments and are critical for measuring the properties of materials at solid/liquid interfaces. Background scattering determines the maximum useful scattering vector, and hence the spatial resolution, of the neutron reflectometry measurement. The primary sources of background are the liquid in the cell reservoir and the materials forming the liquid cell itself. Thus, characterization and mitigation of these background sources are necessary for improvements in the signal-to-background ratio and resolution of neutron reflectometry measurements employing liquid cells. Single-crystal silicon is a common material used for liquid cells due to its low incoherent scattering cross section for neutrons, and the path lengths of the neutron beam through silicon can be several centimetres in modern cell designs. Here, a liquid cell is constructed with a sub-50 µm thick liquid reservoir encased in single-crystal silicon. It is shown that, at high scattering vectors, inelastic scattering from silicon represents a significant portion of the scattering background and is, moreover, structured, confounding efforts to correct for it by established background subtraction techniques. A significant improvement in the measurement quality is achieved using energy-analyzed detection. Energy-analyzed detection reduces the scattering background from silicon by nearly an order of magnitude, and from fluids such as air and liquids by smaller but significant factors. Combining thin liquid reservoirs with energy-analyzed detection and the high flux of the CANDOR polychromatic reflectometer at the NIST Center for Neutron Research, a background-subtracted neutron reflectivity smaller than 10−8 from a liquid cell sample is reported.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Hoogerheide, D.P.Dura, J.A.Maranville, B.B.Majkrzak, C.F.2022-02-01doi:10.1107/S1600576721011924International Union of CrystallographyA liquid cell design with low inelastic and incoherent elastic neutron scattering background is realized. Using this cell design with the new high-flux CANDOR neutron reflectometer, practical measurement of the neutron reflectivity from a thin film bathed by a fluid reservoir at the 10−8 level is demonstrated.ENneutron reflectometryinelastic scatteringbackground subtractionliquid cellsmeasurement resolutionenergy analysissingle-crystal siliconLiquid cells are an increasingly common sample environment for neutron reflectometry experiments and are critical for measuring the properties of materials at solid/liquid interfaces. Background scattering determines the maximum useful scattering vector, and hence the spatial resolution, of the neutron reflectometry measurement. The primary sources of background are the liquid in the cell reservoir and the materials forming the liquid cell itself. Thus, characterization and mitigation of these background sources are necessary for improvements in the signal-to-background ratio and resolution of neutron reflectometry measurements employing liquid cells. Single-crystal silicon is a common material used for liquid cells due to its low incoherent scattering cross section for neutrons, and the path lengths of the neutron beam through silicon can be several centimetres in modern cell designs. Here, a liquid cell is constructed with a sub-50 µm thick liquid reservoir encased in single-crystal silicon. It is shown that, at high scattering vectors, inelastic scattering from silicon represents a significant portion of the scattering background and is, moreover, structured, confounding efforts to correct for it by established background subtraction techniques. A significant improvement in the measurement quality is achieved using energy-analyzed detection. Energy-analyzed detection reduces the scattering background from silicon by nearly an order of magnitude, and from fluids such as air and liquids by smaller but significant factors. Combining thin liquid reservoirs with energy-analyzed detection and the high flux of the CANDOR polychromatic reflectometer at the NIST Center for Neutron Research, a background-subtracted neutron reflectivity smaller than 10−8 from a liquid cell sample is reported.text/htmlLow-background neutron reflectometry from solid/liquid interfacestext1552022-02-01Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00A double-walled sapphire single-crystal gas-pressure cell (type III) for in situ neutron diffraction
http://scripts.iucr.org/cgi-bin/paper?tu5015
In situ neutron diffraction is an important characterization technique for the investigation of many functional materials, e.g. for hydrogen uptake and release in hydrogen storage materials. A new sapphire single-crystal gas-pressure cell for elastic neutron scattering has been developed and evaluated; it allows conditions of 298 K and 9.5 MPa hydrogen pressure and 1110 K at ambient pressure. The pressure vessel consists of a sapphire single-crystal tube of 35 mm radius and a sapphire single-crystal crucible as sample holder. Heating is realized by two 100 W diode lasers. It is optimized for the D20 diffractometer, ILL, Grenoble, France, and requires the use of a radial oscillating collimator. Its advantages over earlier sapphire single-crystal gas-pressure cells are higher maximum temperatures and lower background at low and high diffraction angles. The deuterium uptake in palladium was followed in situ for validation, proving the potential of the type-III gas-pressure cell for in situ neutron diffraction on solid–gas reactions.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Finger, R.Hansen, T.C.Kohlmann, H.2022-02-01doi:10.1107/S1600576721012048International Union of CrystallographyA new sapphire single-crystal gas-pressure cell for elastic neutron scattering to study solid–gas reactions is presented and evaluated; it allows conditions of 298 K and 9.5 MPa hydrogen pressure and 1110 K at ambient pressure.ENneutron diffractionhydrogenationneutron instrumentationsolid–gasmetal hydridessapphirepowder diffractionIn situ neutron diffraction is an important characterization technique for the investigation of many functional materials, e.g. for hydrogen uptake and release in hydrogen storage materials. A new sapphire single-crystal gas-pressure cell for elastic neutron scattering has been developed and evaluated; it allows conditions of 298 K and 9.5 MPa hydrogen pressure and 1110 K at ambient pressure. The pressure vessel consists of a sapphire single-crystal tube of 35 mm radius and a sapphire single-crystal crucible as sample holder. Heating is realized by two 100 W diode lasers. It is optimized for the D20 diffractometer, ILL, Grenoble, France, and requires the use of a radial oscillating collimator. Its advantages over earlier sapphire single-crystal gas-pressure cells are higher maximum temperatures and lower background at low and high diffraction angles. The deuterium uptake in palladium was followed in situ for validation, proving the potential of the type-III gas-pressure cell for in situ neutron diffraction on solid–gas reactions.text/htmlA double-walled sapphire single-crystal gas-pressure cell (type III) for in situ neutron diffractiontext1552022-02-01Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Structure solution of the Al69.2Cu20Cr10.8 ϕ phase
http://scripts.iucr.org/cgi-bin/paper?tu5013
The stable ϕ phase that forms below ∼923 K around the Al69.2Cu20.0Cr10.8 composition was found to be hexagonal [P63, a = 11.045 (2), c = 12.688 (2) Å] and isostructural to the earlier reported Al6.2Cu2Re X phase [Samuha, Grushko & Meshi (2016). J. Alloys Compd. 670, 18–24]. Using the structural model of the latter, a successful Rietveld refinement of the XRD data for Al69.5Cu20.0Cr10.5 was performed. Both ϕ and X were found to be structurally related to the Al72.6Cu11.0Cr16.4 ζ phase [P63/m, a = 17.714, c = 12.591 Å; Sugiyama, Saito & Hiraga (2002). J. Alloys Compd. 342, 148–152], with a close lattice parameter c and a τ-times-larger lattice parameter a (τ is the golden mean). The structural relationship between ζ and ϕ was established on the basis of the similarity of their layered structures and common features. Additionally, the strong-reflections approach was successfully applied for the modeling of the ϕ phase based on the structural model of the ζ phase. The latter and the experimental structural model (retrieved following Rietveld refinement) were found to be essentially identical.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Samuha, S.Tamari, R.Grushko, B.Meshi, L.2022-02-01doi:10.1107/S1600576721011961International Union of CrystallographyThe atomic model of a new ϕ phase of Au–Cu–Cr was determined using powder X-ray diffraction and verified by similarity to the known ζ phase. The similarity was assessed using a `strong-reflections approach' based on analysis of electron diffraction patterns.ENintermetallicsRietveld refinementstrong-reflections approachelectron crystallographystructure predictionThe stable ϕ phase that forms below ∼923 K around the Al69.2Cu20.0Cr10.8 composition was found to be hexagonal [P63, a = 11.045 (2), c = 12.688 (2) Å] and isostructural to the earlier reported Al6.2Cu2Re X phase [Samuha, Grushko & Meshi (2016). J. Alloys Compd. 670, 18–24]. Using the structural model of the latter, a successful Rietveld refinement of the XRD data for Al69.5Cu20.0Cr10.5 was performed. Both ϕ and X were found to be structurally related to the Al72.6Cu11.0Cr16.4 ζ phase [P63/m, a = 17.714, c = 12.591 Å; Sugiyama, Saito & Hiraga (2002). J. Alloys Compd. 342, 148–152], with a close lattice parameter c and a τ-times-larger lattice parameter a (τ is the golden mean). The structural relationship between ζ and ϕ was established on the basis of the similarity of their layered structures and common features. Additionally, the strong-reflections approach was successfully applied for the modeling of the ϕ phase based on the structural model of the ζ phase. The latter and the experimental structural model (retrieved following Rietveld refinement) were found to be essentially identical.text/htmlStructure solution of the Al69.2Cu20Cr10.8 ϕ phasetext1552022-02-01Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographyresearch papers002121302Tangible symmetry elements and space-group models to guide from molecular to solid-state composition
http://scripts.iucr.org/cgi-bin/paper?gj5276
The ability to imagine symmetry and the spatial arrangement of atoms and molecules is crucial in chemistry in general. Teaching and understanding crystallography and the composition of the solid state therefore require understanding of symmetry elements and their relationships. To foster the student's spatial imagination, models representing a range of concepts from individual rotation axes to complete space groups have been designed and built. These models are robust and large enough to be presented and operated in a lecture hall, and they enable students to translate conventional 2D notations into 3D objects and vice versa. Tackling them hands-on means understanding them.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Graw, N.Stalke, D.2022-02-01doi:10.1107/S1600576721012218International Union of CrystallographyLarge and robust models of the most abundant space groups and symmetry elements are presented as an aid to visualization. In this way, space-group symmetry can be introduced to any audience in a readily understandable manner.ENspace groupseducationsymmetry elementsThe ability to imagine symmetry and the spatial arrangement of atoms and molecules is crucial in chemistry in general. Teaching and understanding crystallography and the composition of the solid state therefore require understanding of symmetry elements and their relationships. To foster the student's spatial imagination, models representing a range of concepts from individual rotation axes to complete space groups have been designed and built. These models are robust and large enough to be presented and operated in a lecture hall, and they enable students to translate conventional 2D notations into 3D objects and vice versa. Tackling them hands-on means understanding them.text/htmlTangible symmetry elements and space-group models to guide from molecular to solid-state compositiontext1552022-02-01Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographyteaching and education00CRISTAL-ITE: a single-crystal X-ray diffractometer scale model for scientific dissemination
http://scripts.iucr.org/cgi-bin/paper?oc5015
This article presents the design and manufacture of an automated scale model of a four-circle single-crystal X-ray diffractometer that can be used for scientific dissemination. The purpose of this device is to reach out to the wider public and students to introduce them in an entertaining way to one of the laboratory apparatuses to which they do not usually have access, to talk to them about crystallography in the broadest sense, to develop concepts in various fields of science and technology, and to initiate interest and discussions. The main technical aspects of the project are described, with the expectation that such an approach could be useful to anyone involved in scientific dissemination and could be developed for other laboratory equipment and other disciplines. This kind of device can also be the subject of scientific and technological projects in close collaboration with educational institutions.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Giorgi, M.Berchadsky, Y.2022-02-01doi:10.1107/S160057672101253XInternational Union of CrystallographyThe design and manufacture of an automated scale model of a four-circle single-crystal X-ray diffractometer is presented.ENcrystallographic educationteaching materialsfour-circle X-ray diffractometersThis article presents the design and manufacture of an automated scale model of a four-circle single-crystal X-ray diffractometer that can be used for scientific dissemination. The purpose of this device is to reach out to the wider public and students to introduce them in an entertaining way to one of the laboratory apparatuses to which they do not usually have access, to talk to them about crystallography in the broadest sense, to develop concepts in various fields of science and technology, and to initiate interest and discussions. The main technical aspects of the project are described, with the expectation that such an approach could be useful to anyone involved in scientific dissemination and could be developed for other laboratory equipment and other disciplines. This kind of device can also be the subject of scientific and technological projects in close collaboration with educational institutions.text/htmlCRISTAL-ITE: a single-crystal X-ray diffractometer scale model for scientific disseminationtext1552022-02-01Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographyteaching and education00The Euler characteristic as a basis for teaching topology concepts to crystallographers
http://scripts.iucr.org/cgi-bin/paper?gj5277
The simple Euler polyhedral formula, expressed as an alternating count of the bounding faces, edges and vertices of any polyhedron, V − E + F = 2, is a fundamental concept in several branches of mathematics. Obviously, it is important in geometry, but it is also well known in topology, where a similar telescoping sum is known as the Euler characteristic χ of any finite space. The value of χ can also be computed for the unit polyhedra (such as the unit cell, the asymmetric unit or Dirichlet domain) which build, in a symmetric fashion, the infinite crystal lattices in all space groups. In this application χ has a modified form (χm) and value because the addends have to be weighted according to their symmetry. Although derived in geometry (in fact in crystallography), χm has an elegant topological interpretation through the concept of orbifolds. Alternatively, χm can be illustrated using the theorems of Harriot and Descartes, which predate the discovery made by Euler. Those historical theorems, which focus on angular defects of polyhedra, are beautifully expressed in the formula of de Gua de Malves. In a still more general interpretation, the theorem of Gauss–Bonnet links the Euler characteristic with the general curvature of any closed space. This article presents an overview of these interesting aspects of mathematics with Euler's formula as the leitmotif. Finally, a game is designed, allowing readers to absorb the concept of the Euler characteristic in an entertaining way.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Naskręcki, B.Jaskolski, M.Dauter, Z.2022-02-01doi:10.1107/S160057672101205XInternational Union of CrystallographyThe concept of the Euler characteristic as a property of space-filling polyhedra in crystallography is discussed in a didactic way; a number of other aspects, all of fundamental importance in mathematics, are covered. A game is designed to allow the readers to absorb the concept of the Euler characteristic in an entertaining way.ENHarriot theoremDescartes' theoremEuler's polyhedral formulamodified Euler characteristicspace-filling polyhedraasymmetric unitDirichlet domainsThe simple Euler polyhedral formula, expressed as an alternating count of the bounding faces, edges and vertices of any polyhedron, V − E + F = 2, is a fundamental concept in several branches of mathematics. Obviously, it is important in geometry, but it is also well known in topology, where a similar telescoping sum is known as the Euler characteristic χ of any finite space. The value of χ can also be computed for the unit polyhedra (such as the unit cell, the asymmetric unit or Dirichlet domain) which build, in a symmetric fashion, the infinite crystal lattices in all space groups. In this application χ has a modified form (χm) and value because the addends have to be weighted according to their symmetry. Although derived in geometry (in fact in crystallography), χm has an elegant topological interpretation through the concept of orbifolds. Alternatively, χm can be illustrated using the theorems of Harriot and Descartes, which predate the discovery made by Euler. Those historical theorems, which focus on angular defects of polyhedra, are beautifully expressed in the formula of de Gua de Malves. In a still more general interpretation, the theorem of Gauss–Bonnet links the Euler characteristic with the general curvature of any closed space. This article presents an overview of these interesting aspects of mathematics with Euler's formula as the leitmotif. Finally, a game is designed, allowing readers to absorb the concept of the Euler characteristic in an entertaining way.text/htmlThe Euler characteristic as a basis for teaching topology concepts to crystallographerstext1552022-02-01Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographyteaching and education00Parent grain reconstruction from partially or fully transformed microstructures in MTEX
http://scripts.iucr.org/cgi-bin/paper?nb5309
A versatile generic framework for parent grain reconstruction from fully or partially transformed child microstructures has been integrated into the open-source crystallographic toolbox MTEX. The framework extends traditional parent grain reconstruction, phase transformation and variant analysis to all parent–child crystal symmetry combinations. The inherent versatility of the universally applicable parent grain reconstruction methods and the ability to conduct in-depth variant analysis are showcased via example workflows that can be programmatically modified by users to suit their specific applications. This is highlighted by three applications, namely α′-to-γ reconstruction in a lath martensitic steel, α-to-β reconstruction in a Ti alloy, and a two-step reconstruction from α′ to ɛ to γ in a twinning and transformation-induced plasticity steel. Advanced orientation relationship discovery and analysis options, including variant analysis, are demonstrated via the add-on function library ORTools.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Niessen, F.Nyyssönen, T.Gazder, A.A.Hielscher, R.2022-02-01doi:10.1107/S1600576721011560International Union of CrystallographyA versatile generic framework for parent grain reconstruction from fully or partially transformed child microstructures has been integrated into the open-source crystallographic toolbox MTEX. The framework extends traditional parent grain reconstruction, phase transformation and variant analysis to all parent–child crystal symmetry combinations and allows the programmatic creation of individual workflows to reconstruct parent grains.ENelectron backscattering diffractionphase transformationsorientation relationships (ORs)parent phase reconstructionA versatile generic framework for parent grain reconstruction from fully or partially transformed child microstructures has been integrated into the open-source crystallographic toolbox MTEX. The framework extends traditional parent grain reconstruction, phase transformation and variant analysis to all parent–child crystal symmetry combinations. The inherent versatility of the universally applicable parent grain reconstruction methods and the ability to conduct in-depth variant analysis are showcased via example workflows that can be programmatically modified by users to suit their specific applications. This is highlighted by three applications, namely α′-to-γ reconstruction in a lath martensitic steel, α-to-β reconstruction in a Ti alloy, and a two-step reconstruction from α′ to ɛ to γ in a twinning and transformation-induced plasticity steel. Advanced orientation relationship discovery and analysis options, including variant analysis, are demonstrated via the add-on function library ORTools.text/htmlParent grain reconstruction from partially or fully transformed microstructures in MTEXtext1552022-02-01Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographycomputer programs00SGTools: a suite of tools for processing and analyzing large data sets from in situ X-ray scattering experiments
http://scripts.iucr.org/cgi-bin/paper?iu5012
In situ synchrotron small-angle X-ray scattering (SAXS) is a powerful tool for studying dynamic processes during material preparation and application. The processing and analysis of large data sets generated from in situ X-ray scattering experiments are often tedious and time consuming. However, data processing software for in situ experiments is relatively rare, especially for grazing-incidence small-angle X-ray scattering (GISAXS). This article presents an open-source software suite (SGTools) to perform data processing and analysis for SAXS and GISAXS experiments. The processing modules in this software include (i) raw data calibration and background correction; (ii) data reduction by multiple methods; (iii) animation generation and intensity mapping for in situ X-ray scattering experiments; and (iv) further data analysis for the sample with an order degree and interface correlation. This article provides the main features and framework of SGTools. The workflow of the software is also elucidated to allow users to develop new features. Three examples are demonstrated to illustrate the use of SGTools for dealing with SAXS and GISAXS data. Finally, the limitations and future features of the software are also discussed.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Zhao, N.Yang, C.Bian, F.Guo, D.Ouyang, X.2022-02-01doi:10.1107/S1600576721012267International Union of CrystallographyData processing and analysis tools are presented that are suitable for the large data sets generated from in situ small-angle X-ray scattering experiments.ENsmall-angle X-ray scatteringSAXSgrazing-incidence small-angle X-ray scatteringGISAXSdata processingin situ experimentsIn situ synchrotron small-angle X-ray scattering (SAXS) is a powerful tool for studying dynamic processes during material preparation and application. The processing and analysis of large data sets generated from in situ X-ray scattering experiments are often tedious and time consuming. However, data processing software for in situ experiments is relatively rare, especially for grazing-incidence small-angle X-ray scattering (GISAXS). This article presents an open-source software suite (SGTools) to perform data processing and analysis for SAXS and GISAXS experiments. The processing modules in this software include (i) raw data calibration and background correction; (ii) data reduction by multiple methods; (iii) animation generation and intensity mapping for in situ X-ray scattering experiments; and (iv) further data analysis for the sample with an order degree and interface correlation. This article provides the main features and framework of SGTools. The workflow of the software is also elucidated to allow users to develop new features. Three examples are demonstrated to illustrate the use of SGTools for dealing with SAXS and GISAXS data. Finally, the limitations and future features of the software are also discussed.text/htmlSGTools: a suite of tools for processing and analyzing large data sets from in situ X-ray scattering experimentstext1552022-02-01Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographycomputer programs00Collecting Experiments. Making Big Data Biology. By Bruno J. Strasser. Chicago University Press, 2019. Pp. 392. Price USD 45.00. ISBN 9780226635040.
http://scripts.iucr.org/cgi-bin/paper?xo0187
Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Helliwell, J.R.2022-02-01doi:10.1107/S1600576721012140International Union of CrystallographyBook review.ENbook reviewsbiologybig datatext/htmlCollecting Experiments. Making Big Data Biology. By Bruno J. Strasser. Chicago University Press, 2019. Pp. 392. Price USD 45.00. ISBN 9780226635040.text1552022-02-01Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographybook reviews00