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 Crystallography2022-11-21International 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 6, 2022textweekly62002-02-01T00:00+00:006552022-11-21Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallography1392urn:issn:1600-5767med@iucr.orgNovember 20222022-11-21Journal of Applied Crystallographyhttp://journals.iucr.org/logos/rss10j.gif
//journals.iucr.org/j/issues/2022/06/00/index.html
Still imageUnveiling the anisotropic fractal magnetic domain structure in bulk crystals of antiskyrmion host (Fe,Ni,Pd)3P by small-angle neutron scattering
http://scripts.iucr.org/cgi-bin/paper?un5006
Intermetallic Pd-doped (Fe,Ni)3P, which crystallizes in a non-centrosymmetric tetragonal structure with S4 symmetry, has recently been discovered to host magnetic antiskyrmions, antivortex-like topological spin textures. In this material, uniaxial magnetic anisotropy and dipolar interactions play a significant role, giving rise to finely branched magnetic domain patterns near the surface of bulk crystals, as revealed by a previous magnetic force microscopy (MFM) measurement. However, small-angle neutron scattering (SANS) is a more suitable method for characterizing bulk properties and fractal structures on the mesoscopic length scale. In this study, using SANS and MFM, the magnetic domain structure in bulk single crystals of (Fe0.63Ni0.30Pd0.07)3P is quantitatively investigated. The SANS results demonstrate that the magnetic domain structure exhibits anisotropic fractal character on length scales down to the width of the magnetic domain walls. The fractal features are gradually lost in magnetic fields, and different field dependencies are observed at 300 and 2 K due to a temperature-dependent anisotropy. This study quantifies the fractality of the highly anisotropic magnetic domain structures in an antiskyrmion material, and highlights the versatility of SANS for the study of fractal structures in magnetic systems.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Karube, K.Ukleev, V.Kagawa, F.Tokura, Y.Taguchi, Y.White, J.S.2022-10-14doi:10.1107/S1600576722008561International Union of CrystallographyThe anisotropic fractal magnetic domain structure in bulk single-crystal (Fe0.63Ni0.30Pd0.07)3P has been quantitatively characterized using small-angle neutron scattering.ENsmall-angle neutron scatteringfractalsmagnetic domainsantiskyrmionsIntermetallic Pd-doped (Fe,Ni)3P, which crystallizes in a non-centrosymmetric tetragonal structure with S4 symmetry, has recently been discovered to host magnetic antiskyrmions, antivortex-like topological spin textures. In this material, uniaxial magnetic anisotropy and dipolar interactions play a significant role, giving rise to finely branched magnetic domain patterns near the surface of bulk crystals, as revealed by a previous magnetic force microscopy (MFM) measurement. However, small-angle neutron scattering (SANS) is a more suitable method for characterizing bulk properties and fractal structures on the mesoscopic length scale. In this study, using SANS and MFM, the magnetic domain structure in bulk single crystals of (Fe0.63Ni0.30Pd0.07)3P is quantitatively investigated. The SANS results demonstrate that the magnetic domain structure exhibits anisotropic fractal character on length scales down to the width of the magnetic domain walls. The fractal features are gradually lost in magnetic fields, and different field dependencies are observed at 300 and 2 K due to a temperature-dependent anisotropy. This study quantifies the fractality of the highly anisotropic magnetic domain structures in an antiskyrmion material, and highlights the versatility of SANS for the study of fractal structures in magnetic systems.text/htmlUnveiling the anisotropic fractal magnetic domain structure in bulk crystals of antiskyrmion host (Fe,Ni,Pd)3P by small-angle neutron scatteringtext6552022-10-14Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Modeling the partitioning of amphiphilic molecules and co-solvents in biomembranes
http://scripts.iucr.org/cgi-bin/paper?in5068
Amphiphilic co-solvents can have a significant impact on the structure, organization and physical properties of lipid bilayers. Describing the mutual impact of partitioning and induced structure changes is therefore a crucial consideration for a range of topics such as anesthesia and other pharmacokinetic effects, as well as microbial solvent tolerance in the production of biofuels and other fermentation products, where molecules such as ethanol, butanol or acetic acid might be generated. Small-angle neutron scattering (SANS) is a key method for studying lipid and polymer bilayer structures, with many models for extracting bilayer structure (thickness, area per lipid etc.) from scattering data in use today. However, the molecular details of co-solvent partitioning are conflated with induced changes to bilayer structure, making interpretation and modeling of the scattering curves a challenge with the existing set of models. To address this, a model of a bilayer structure is presented which invokes a two-term partition constant accounting for the localization of the co-solvent within the bilayer. This model was validated using a series of SANS measurements of lipid vesicles in the presence of the co-solvent tetrahydrofuran (THF), showing several strategies of how to deploy the two-parameter partition constant model to describe scattering data and extract both structure and partitioning information from the data. Molecular dynamics simulations are then used to evaluate assumptions of the model, provide additional molecular scale details and illustrate its complementary nature to the data fitting procedure. This approach results in estimates of the partition coefficient for THF in 1,2-dimyristoyl-sn-glycero-3-phosphocholine at 35°C, along with an estimate of the fraction of THF residing in the hydrophobic core of the membrane. The authors envision that this model will be applicable to a wide range of other bilayer/amphiphile interactions and provide the associated code needed to implement this model as a fitting algorithm for scattering data in the SasView suite.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Tan, L.Smith, M.D.Scott, H.L.Yahya, A.Elkins, J.G.Katsaras, J.O'Neill, H.M.Pingali, S.V.Smith, J.C.Davison, B.H.Nickels, J.D.2022-10-14doi:10.1107/S1600576722008998International Union of CrystallographyPartitioning of small amphiphilic molecules into biomembranes and other lamellar structures induces structural changes and impacts the properties of the membrane. This work presents a model to describe the amount of co-solvent within the bilayer, its localization and the induced changes to the bilayer structure. The implementation of this model is shared as a fitting algorithm within SasView.ENsmall-angle neutron scatteringlipidsbiofuelsanesthesiatetrahydrofuranTHFAmphiphilic co-solvents can have a significant impact on the structure, organization and physical properties of lipid bilayers. Describing the mutual impact of partitioning and induced structure changes is therefore a crucial consideration for a range of topics such as anesthesia and other pharmacokinetic effects, as well as microbial solvent tolerance in the production of biofuels and other fermentation products, where molecules such as ethanol, butanol or acetic acid might be generated. Small-angle neutron scattering (SANS) is a key method for studying lipid and polymer bilayer structures, with many models for extracting bilayer structure (thickness, area per lipid etc.) from scattering data in use today. However, the molecular details of co-solvent partitioning are conflated with induced changes to bilayer structure, making interpretation and modeling of the scattering curves a challenge with the existing set of models. To address this, a model of a bilayer structure is presented which invokes a two-term partition constant accounting for the localization of the co-solvent within the bilayer. This model was validated using a series of SANS measurements of lipid vesicles in the presence of the co-solvent tetrahydrofuran (THF), showing several strategies of how to deploy the two-parameter partition constant model to describe scattering data and extract both structure and partitioning information from the data. Molecular dynamics simulations are then used to evaluate assumptions of the model, provide additional molecular scale details and illustrate its complementary nature to the data fitting procedure. This approach results in estimates of the partition coefficient for THF in 1,2-dimyristoyl-sn-glycero-3-phosphocholine at 35°C, along with an estimate of the fraction of THF residing in the hydrophobic core of the membrane. The authors envision that this model will be applicable to a wide range of other bilayer/amphiphile interactions and provide the associated code needed to implement this model as a fitting algorithm for scattering data in the SasView suite.text/htmlModeling the partitioning of amphiphilic molecules and co-solvents in biomembranestext6552022-10-14Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Electron diffraction characterization of nanocrystalline materials using a Rietveld-based approach. Part II. Application to microstructural analysis
http://scripts.iucr.org/cgi-bin/paper?nb5333
This is the second in a two-paper series concerning the quantitative characterization of nanocrystalline materials using an electron-diffraction-based approach, in which a full-pattern fitting Rietveld-based refinement is applied to electron powder diffraction data in transmission electron microscopy (TEM). Part I [Sinha et al. (2022). J. Appl. Cryst. 55, 953–965] established a standard calibration protocol to determine the instrumental effects, with special emphasis on the camera length and the diameter of the selected area apertures. Possible application cases are now considered to demonstrate the capabilities of the approach, including the evaluation of the phase composition of TEM specimens, an operation that reveals new application fields for this powerful materials characterization technique. In this regard, different types of material specimen are examined: nanocrystalline yttrium oxide, silicon, titanium dioxide and debris from disc brake wear, each one featuring specific aspects to be tackled with the proposed methodology. To demonstrate the limits of the proposed approach as concerns the material characteristics, an analysis of a hematite sample obtained from the heat treatment of natural goethite, displaying a relatively coarse crystallite size, is performed and a critical discussion of the results is given.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Sinha, A.Ischia, G.Lutterotti, L.Gialanella, S.2022-10-27doi:10.1107/S160057672200886XInternational Union of CrystallographyQuantitative microstructural characterization of different nanocrystalline materials based on Rietveld refinement of electron diffraction patterns is presented to demonstrate the application of the methodology described in Part I [Sinha et al. (2022). J. Appl. Cryst. 55, 953–965].ENelectron diffractionRietveld refinementnanocrystalline materialsThis is the second in a two-paper series concerning the quantitative characterization of nanocrystalline materials using an electron-diffraction-based approach, in which a full-pattern fitting Rietveld-based refinement is applied to electron powder diffraction data in transmission electron microscopy (TEM). Part I [Sinha et al. (2022). J. Appl. Cryst. 55, 953–965] established a standard calibration protocol to determine the instrumental effects, with special emphasis on the camera length and the diameter of the selected area apertures. Possible application cases are now considered to demonstrate the capabilities of the approach, including the evaluation of the phase composition of TEM specimens, an operation that reveals new application fields for this powerful materials characterization technique. In this regard, different types of material specimen are examined: nanocrystalline yttrium oxide, silicon, titanium dioxide and debris from disc brake wear, each one featuring specific aspects to be tackled with the proposed methodology. To demonstrate the limits of the proposed approach as concerns the material characteristics, an analysis of a hematite sample obtained from the heat treatment of natural goethite, displaying a relatively coarse crystallite size, is performed and a critical discussion of the results is given.text/htmlElectron diffraction characterization of nanocrystalline materials using a Rietveld-based approach. Part II. Application to microstructural analysistext6552022-10-27Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Extending MIEZE spectroscopy towards thermal wavelengths
http://scripts.iucr.org/cgi-bin/paper?ei5087
A modulation of intensity with zero effort (MIEZE) setup is proposed for high-resolution neutron spectroscopy at momentum transfers up to 3 Å−1, energy transfers up to 20 meV and an energy resolution in the microelectronvolt range using both thermal and cold neutrons. MIEZE has two prominent advantages compared with classical neutron spin echo. The first is the possibility to investigate spin-depolarizing samples or samples in strong magnetic fields without loss of signal amplitude and intensity. This allows for the study of spin fluctuations in ferromagnets, and facilitates the study of samples with strong spin-incoherent scattering. The second advantage is that multi-analyzer setups can be implemented with comparatively little effort. The use of thermal neutrons increases the range of validity of the spin-echo approximation towards shorter spin-echo times. In turn, the thermal MIEZE option for greater ranges (TIGER) closes the gap between classical neutron spin-echo spectroscopy and conventional high-resolution neutron spectroscopy techniques such as triple-axis, time-of-flight and back-scattering. To illustrate the feasibility of TIGER, this paper presents the details of its implementation at the RESEDA beamline at FRM II by means of an additional velocity selector, polarizer and analyzer.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Jochum, J.K.Franz, C.Keller, T.Pfleiderer, C.2022-10-27doi:10.1107/S1600576722009505International Union of CrystallographyA modulation of intensity with zero effort (MIEZE) setup is proposed for high-resolution neutron spectroscopy at momentum transfers up to 3 Å−1, energy transfers up to 20 meV and an energy resolution in the microelectronvolt range using both thermal and cold neutrons.ENneutron resonant spin echoMIEZEquasielastic scatteringthermal neutronsA modulation of intensity with zero effort (MIEZE) setup is proposed for high-resolution neutron spectroscopy at momentum transfers up to 3 Å−1, energy transfers up to 20 meV and an energy resolution in the microelectronvolt range using both thermal and cold neutrons. MIEZE has two prominent advantages compared with classical neutron spin echo. The first is the possibility to investigate spin-depolarizing samples or samples in strong magnetic fields without loss of signal amplitude and intensity. This allows for the study of spin fluctuations in ferromagnets, and facilitates the study of samples with strong spin-incoherent scattering. The second advantage is that multi-analyzer setups can be implemented with comparatively little effort. The use of thermal neutrons increases the range of validity of the spin-echo approximation towards shorter spin-echo times. In turn, the thermal MIEZE option for greater ranges (TIGER) closes the gap between classical neutron spin-echo spectroscopy and conventional high-resolution neutron spectroscopy techniques such as triple-axis, time-of-flight and back-scattering. To illustrate the feasibility of TIGER, this paper presents the details of its implementation at the RESEDA beamline at FRM II by means of an additional velocity selector, polarizer and analyzer.text/htmlExtending MIEZE spectroscopy towards thermal wavelengthstext6552022-10-27Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Quantitative texture analysis at the WAND2 and HIDRA diffractometers
http://scripts.iucr.org/cgi-bin/paper?xx5003
Data collection and analysis strategies have been developed for efficient and reliable crystallographic texture measurements at two recently upgraded neutron diffractometers: the Wide Angle Neutron Diffractometer Squared (WAND2) and the High Intensity Diffractometer for Residual Stress Analysis (HIDRA) at the High Flux Isotope Reactor located at Oak Ridge National Laboratory. These methods are demonstrated using measurements on a variety of textured samples, including multi-phase steel composites and polycrystalline calcite (CaCO3). Reference measurements were also made at VULCAN, the engineering diffractometer located at the Spallation Neutron Source. The texture data obtained on the different instruments are in agreement, and WAND2 is more time efficient than HIDRA. Two analysis methods were investigated, single-peak fitting to obtain individual pole figures for inversion and Rietveld texture analysis using MAUD. The impact of the differences between the various textures obtained was evaluated through the calculation of diffraction elastic constants, which is one application of the texture data collected. Both instruments were found to provide texture data that are suitable for complementing other analyses, such as residual stress mapping.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Peterson, N.E.Fancher, C.M.Frontzek, M.Bunn, J.Payzant, A.An, K.Agnew, S.2022-10-27doi:10.1107/S1600576722009013International Union of CrystallographyCrystallographic texture measurement strategies have been developed and tested at two recently upgraded beamlines at the High Flux Isotope Reactor, Oak Ridge National Laboratory: WAND2 and HIDRA.ENcrystallographic textureneutron diffractionRietveld texture analysisData collection and analysis strategies have been developed for efficient and reliable crystallographic texture measurements at two recently upgraded neutron diffractometers: the Wide Angle Neutron Diffractometer Squared (WAND2) and the High Intensity Diffractometer for Residual Stress Analysis (HIDRA) at the High Flux Isotope Reactor located at Oak Ridge National Laboratory. These methods are demonstrated using measurements on a variety of textured samples, including multi-phase steel composites and polycrystalline calcite (CaCO3). Reference measurements were also made at VULCAN, the engineering diffractometer located at the Spallation Neutron Source. The texture data obtained on the different instruments are in agreement, and WAND2 is more time efficient than HIDRA. Two analysis methods were investigated, single-peak fitting to obtain individual pole figures for inversion and Rietveld texture analysis using MAUD. The impact of the differences between the various textures obtained was evaluated through the calculation of diffraction elastic constants, which is one application of the texture data collected. Both instruments were found to provide texture data that are suitable for complementing other analyses, such as residual stress mapping.text/htmlQuantitative texture analysis at the WAND2 and HIDRA diffractometerstext6552022-10-27Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Stabilizing ferroelectricity in alkaline-earth-metal-based perovskites (ABO3) via A- (Ca2+/Sr2+/Ba2+) and B-site (Ti4+) cationic radius ratio (RA/RB)
http://scripts.iucr.org/cgi-bin/paper?jl5045
Various distortion parameters for alkaline-earth-metal-based perovskites (A2+B4+O3) have been analyzed as a function of A- and B-site cationic radii RA and RB. The observed octahedral rotations and their associated mode amplitudes have shown an increasing trend with larger B-site cations, while a decreasing trend has been observed with larger A-site cations. Moreover, the analysis demonstrates that for incipient ferroelectrics like CaTiO3 and SrTiO3, having respective space groups Pnma (a−0b+0a−0) and Pm3m (a00a00a00), ferroelectric displacements are achieved via cation manipulation, which is governed by the RA/RB parameter. The increase in RA/RB through substitutions on the A site may suppress octahedral rotations as well as A-site anti-polar displacements in CaTiO3 and can consequently lead to a ferroelectrically distorted BaTiO3-like P4mm (a00a00c0+) phase via a cubic phase of SrTiO3, which has an intermediate RA/RB parameter. These results have been further corroborated by the calculated amplitudes of various frozen phonon modes associated with the cubic Pm3m Brillouin zone, responsible for symmetry breaking to tilt-oriented non-ferroelectric Pnma and ferroelectric P4mm phases.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Tripathi, A.Dubey, D.N.Kumar, H.Tripathi, S.2022-10-27doi:10.1107/S1600576722009414International Union of CrystallographyThis study establishes the structure–property correlation that eases the initial optimization process for various alkaline-earth-metal-based perovskites.ENferroelectricsalkaline earth metalsperovskitesoctahedral rotationssymmetry mode analysissuperlattice reflectionsVarious distortion parameters for alkaline-earth-metal-based perovskites (A2+B4+O3) have been analyzed as a function of A- and B-site cationic radii RA and RB. The observed octahedral rotations and their associated mode amplitudes have shown an increasing trend with larger B-site cations, while a decreasing trend has been observed with larger A-site cations. Moreover, the analysis demonstrates that for incipient ferroelectrics like CaTiO3 and SrTiO3, having respective space groups Pnma (a−0b+0a−0) and Pm3m (a00a00a00), ferroelectric displacements are achieved via cation manipulation, which is governed by the RA/RB parameter. The increase in RA/RB through substitutions on the A site may suppress octahedral rotations as well as A-site anti-polar displacements in CaTiO3 and can consequently lead to a ferroelectrically distorted BaTiO3-like P4mm (a00a00c0+) phase via a cubic phase of SrTiO3, which has an intermediate RA/RB parameter. These results have been further corroborated by the calculated amplitudes of various frozen phonon modes associated with the cubic Pm3m Brillouin zone, responsible for symmetry breaking to tilt-oriented non-ferroelectric Pnma and ferroelectric P4mm phases.text/htmlStabilizing ferroelectricity in alkaline-earth-metal-based perovskites (ABO3) via A- (Ca2+/Sr2+/Ba2+) and B-site (Ti4+) cationic radius ratio (RA/RB)text6552022-10-27Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Investigation of physical properties of Si crystallites in W/Si multilayers
http://scripts.iucr.org/cgi-bin/paper?jl5046
The structural inhomogeneities of silicon films embedded within W/Si multilayer mirrors were studied by X-ray reflection, grazing-incidence small-angle X-ray scattering (GISAXS) and X-ray photoelectron spectroscopy (XPS). In the diffuse scattering spectra, evidence of laterally and vertically ordered in-layer inhomogeneities was consistently observed. In particular, specific substructures resonant in nature (named here `ridges') were detected. The properties of the ridges were similar to the roughness determined by quasi-Bragg peaks of scattering, which required a high interlayer correlation of particles. The XPS showed the nanocrystalline nature of the Si particles in the amorphous matrix. The geometric characteristics and in-layer and inter-layer correlations of the nanoparticles were determined. In GISAXS imaging, the unusual splitting of the waists between the Bragg sheets into filament structures was observed, whose physical nature cannot yet be explained.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Chkhalo, N.I.Garakhin, S.A.Kumar, N.Nikolaev, K.V.Polkovnikov, V.N.Rogachev, A.Svechnikov, M.V.Tatarsky, D.A.Yakunin, S.N.2022-10-27doi:10.1107/S1600576722009529International Union of CrystallographyThe nature of the observed bulk inhomogeneities in the silicon layers in W/Si multilayers is established. In the diffuse scattering spectra, specific substructures, which are clearly resonant in nature, are observed. The physical nature of some of them is not established.ENmultilayer mirrorsX-ray diffusion scatteringnanoocrystallitesroughnessinterfacesThe structural inhomogeneities of silicon films embedded within W/Si multilayer mirrors were studied by X-ray reflection, grazing-incidence small-angle X-ray scattering (GISAXS) and X-ray photoelectron spectroscopy (XPS). In the diffuse scattering spectra, evidence of laterally and vertically ordered in-layer inhomogeneities was consistently observed. In particular, specific substructures resonant in nature (named here `ridges') were detected. The properties of the ridges were similar to the roughness determined by quasi-Bragg peaks of scattering, which required a high interlayer correlation of particles. The XPS showed the nanocrystalline nature of the Si particles in the amorphous matrix. The geometric characteristics and in-layer and inter-layer correlations of the nanoparticles were determined. In GISAXS imaging, the unusual splitting of the waists between the Bragg sheets into filament structures was observed, whose physical nature cannot yet be explained.text/htmlInvestigation of physical properties of Si crystallites in W/Si multilayerstext6552022-10-27Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Insights into the structural symmetry of YCrO3 from synchrotron X-ray diffraction
http://scripts.iucr.org/cgi-bin/paper?vb5043
A high-resolution synchrotron X-ray diffraction study of a single-crystal YCrO3 compound was employed to obtain its crystallographic information, such as lattice parameters, atomic positions, bond lengths and angles, and local crystalline distortion size and mode. The measurements were taken at 120 K (below the antiferromagnetic transition temperature TN ≃ 141.5 K), 300 K (between TN and the ferroelectric transition temperature TC ≃ 473 K) and 500 K (above TC). Using the high intensity of synchrotron X-rays, it was possible to refine collected patterns with the previously proposed noncentrosymmetric monoclinic structural model (P1211, No. 4) and determine detailed structural parameters. Meanwhile, for a controlled study, the data were refined with the centrosymmetric orthorhombic space group (Pmnb, No. 62). The lattice constants a, b and c and the unit-cell volume increased nearly linearly upon heating. With the P1211 space group, the distributions of bond lengths and angles, as well as local distortion strengths, were observed to be more dispersed. This implies that (i) the local distortion mode of Cr2O6 at 120 K correlates with the formation of canted antiferromagnetic order by Cr1–Cr2 spin interactions, primarily via intermediate O3 and O4 ions; and (ii) the previously reported dielectric anomaly may have a microscopic origin in the strain-balanced Cr1—O3(O4) and Cr2—O5(O6) bonds as well as the local distortion modes of Cr1O6 and Cr2O6 octahedra at 300 K. Local crystalline distortion is shown to be an important factor in the formation of ferroelectric order. The comprehensive set of crystallographic information reported here allows for a complete understanding of the unique magnetic and ferroelectric properties of YCrO3.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Zhao, Q.Sun, K.Zhu, Y.Zhao, Z.Li, H.-F.2022-11-04doi:10.1107/S1600576722009438International Union of CrystallographyA high-resolution synchrotron X-ray diffraction study of a YCrO3 single crystal has allowed the structural parameters of the noncentrosymmetric P1211 space group to be obtained. The pathway of spin interactions was found for the formation of antiferromagnetism in YCrO3. Ferroelectricity in YCrO3 may originate from the strain-balanced Cr1—O3(O4) and Cr2—O5(O6) bonds and the local distortion modes of CrO6 octahedra in the P1211 space group. The relationship between microscopic and macroscopic properties has been revealed.ENferroelectricsorthochromatessingle crystalssynchrotron X-ray diffractioncrystal symmetryA high-resolution synchrotron X-ray diffraction study of a single-crystal YCrO3 compound was employed to obtain its crystallographic information, such as lattice parameters, atomic positions, bond lengths and angles, and local crystalline distortion size and mode. The measurements were taken at 120 K (below the antiferromagnetic transition temperature TN ≃ 141.5 K), 300 K (between TN and the ferroelectric transition temperature TC ≃ 473 K) and 500 K (above TC). Using the high intensity of synchrotron X-rays, it was possible to refine collected patterns with the previously proposed noncentrosymmetric monoclinic structural model (P1211, No. 4) and determine detailed structural parameters. Meanwhile, for a controlled study, the data were refined with the centrosymmetric orthorhombic space group (Pmnb, No. 62). The lattice constants a, b and c and the unit-cell volume increased nearly linearly upon heating. With the P1211 space group, the distributions of bond lengths and angles, as well as local distortion strengths, were observed to be more dispersed. This implies that (i) the local distortion mode of Cr2O6 at 120 K correlates with the formation of canted antiferromagnetic order by Cr1–Cr2 spin interactions, primarily via intermediate O3 and O4 ions; and (ii) the previously reported dielectric anomaly may have a microscopic origin in the strain-balanced Cr1—O3(O4) and Cr2—O5(O6) bonds as well as the local distortion modes of Cr1O6 and Cr2O6 octahedra at 300 K. Local crystalline distortion is shown to be an important factor in the formation of ferroelectric order. The comprehensive set of crystallographic information reported here allows for a complete understanding of the unique magnetic and ferroelectric properties of YCrO3.text/htmlInsights into the structural symmetry of YCrO3 from synchrotron X-ray diffractiontext6552022-11-04Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Magnetic neutron scattering from spherical nanoparticles with Néel surface anisotropy: analytical treatment
http://scripts.iucr.org/cgi-bin/paper?in5070
The magnetization profile and the related magnetic small-angle neutron scattering cross section of a single spherical nanoparticle with Néel surface anisotropy are analytically investigated. A Hamiltonian is employed that comprises the isotropic exchange interaction, an external magnetic field, a uniaxial magnetocrystalline anisotropy in the core of the particle and the Néel anisotropy at the surface. Using a perturbation approach, the determination of the magnetization profile can be reduced to a Helmholtz equation with Neumann boundary condition, whose solution is represented by an infinite series in terms of spherical harmonics and spherical Bessel functions. From the resulting infinite series expansion, the Fourier transform, which is algebraically related to the magnetic small-angle neutron scattering cross section, is analytically calculated. The approximate analytical solution for the spin structure is compared with the numerical solution using the Landau–Lifshitz equation, which accounts for the full nonlinearity of the problem. The signature of the Néel surface anisotropy can be identified in the magnetic neutron scattering observables, but its effect is relatively small, even for large values of the surface anisotropy constant.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Adams, M.P.Michels, A.Kachkachi, H.2022-11-04doi:10.1107/S1600576722008925International Union of CrystallographyThe magnetization profile and the ensuing magnetic neutron scattering signal from an inhomogeneously magnetized spherical nanoparticle with Néel surface anisotropy are derived analytically.ENmagnetic neutron scatteringsmall-angle neutron scatteringmagnetic nanoparticlessurface anisotropymicromagneticsThe magnetization profile and the related magnetic small-angle neutron scattering cross section of a single spherical nanoparticle with Néel surface anisotropy are analytically investigated. A Hamiltonian is employed that comprises the isotropic exchange interaction, an external magnetic field, a uniaxial magnetocrystalline anisotropy in the core of the particle and the Néel anisotropy at the surface. Using a perturbation approach, the determination of the magnetization profile can be reduced to a Helmholtz equation with Neumann boundary condition, whose solution is represented by an infinite series in terms of spherical harmonics and spherical Bessel functions. From the resulting infinite series expansion, the Fourier transform, which is algebraically related to the magnetic small-angle neutron scattering cross section, is analytically calculated. The approximate analytical solution for the spin structure is compared with the numerical solution using the Landau–Lifshitz equation, which accounts for the full nonlinearity of the problem. The signature of the Néel surface anisotropy can be identified in the magnetic neutron scattering observables, but its effect is relatively small, even for large values of the surface anisotropy constant.text/htmlMagnetic neutron scattering from spherical nanoparticles with Néel surface anisotropy: analytical treatmenttext6552022-11-04Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Magnetic neutron scattering from spherical nanoparticles with Néel surface anisotropy: atomistic simulations
http://scripts.iucr.org/cgi-bin/paper?in5071
A dilute ensemble of randomly oriented non-interacting spherical nanomagnets is considered, and its magnetization structure and ensuing neutron scattering response are investigated by numerically solving the Landau–Lifshitz equation. Taking into account the isotropic exchange interaction, an external magnetic field, a uniaxial magnetic anisotropy for the particle core, and in particular the Néel surface anisotropy, the magnetic small-angle neutron scattering cross section and pair-distance distribution function are calculated from the obtained equilibrium spin structures. The numerical results are compared with the well known analytical expressions for uniformly magnetized particles and provide guidance to the experimentalist. In addition, the effect of a particle-size distribution function is modelled.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Adams, M.P.Michels, A.Kachkachi, H.2022-11-04doi:10.1107/S1600576722008949International Union of CrystallographyBased on the Landau–Lifshitz equation, atomistic simulations of the magnetic neutron scattering from inhomogeneously magnetized spherical nanoparticles with a strong surface anisotropy are carried out.ENmagnetic neutron scatteringsmall-angle neutron scatteringmagnetic nanoparticlessurface anisotropymicromagneticsA dilute ensemble of randomly oriented non-interacting spherical nanomagnets is considered, and its magnetization structure and ensuing neutron scattering response are investigated by numerically solving the Landau–Lifshitz equation. Taking into account the isotropic exchange interaction, an external magnetic field, a uniaxial magnetic anisotropy for the particle core, and in particular the Néel surface anisotropy, the magnetic small-angle neutron scattering cross section and pair-distance distribution function are calculated from the obtained equilibrium spin structures. The numerical results are compared with the well known analytical expressions for uniformly magnetized particles and provide guidance to the experimentalist. In addition, the effect of a particle-size distribution function is modelled.text/htmlMagnetic neutron scattering from spherical nanoparticles with Néel surface anisotropy: atomistic simulationstext6552022-11-04Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Three-dimensional model of a split-crystal X-ray and neutron interferometer
http://scripts.iucr.org/cgi-bin/paper?ei5084
The observation of neutron interference using a crystal interferometer having a separate analyser opens the way to the construction and operation of interferometers with vast arm separation and length. Setting the design specifications requires a three-dimensional dynamical theory model of their operation. This paper develops the required three-dimensional mathematical framework, which also comprises coherent and incoherent illuminations; it is applied to study the visibility of the interference fringes.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Sasso, C.P.Mana, G.Massa, E.2022-11-04doi:10.1107/S1600576722008962International Union of CrystallographyThe observation of neutron interference using a split-crystal interferometer opens the way to realizing interferometers with vast arm separation and length. Setting the design specifications requires a three-dimensional model of their operation. Also, the spatial coherence of the source affects the interference visibility. This paper presents a novel formalism to model crystal interferometers, operating with both coherent and partially coherent X-rays and neutrons, in three dimensions.ENdynamical theory of X-ray diffractionsplit-crystal interferometrycrystal neutron interferometrycrystal X-ray interferometryX-ray coherenceneutron coherenceThe observation of neutron interference using a crystal interferometer having a separate analyser opens the way to the construction and operation of interferometers with vast arm separation and length. Setting the design specifications requires a three-dimensional dynamical theory model of their operation. This paper develops the required three-dimensional mathematical framework, which also comprises coherent and incoherent illuminations; it is applied to study the visibility of the interference fringes.text/htmlThree-dimensional model of a split-crystal X-ray and neutron interferometertext6552022-11-04Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Efficient data reduction for time-of-flight neutron scattering experiments on single crystals
http://scripts.iucr.org/cgi-bin/paper?fs5205
Event-mode data collection presents remarkable new opportunities for time-of-flight neutron scattering studies of collective excitations, diffuse scattering from short-range atomic and magnetic structures, and neutron crystallography. In these experiments, large volumes of the reciprocal space are surveyed, often using different wavelengths and counting times. These data then have to be added together, with accurate propagation of the counting errors. This paper presents a statistically correct way of adding and histogramming the data for single-crystal time-of-flight neutron scattering measurements. In order to gain a broader community acceptance, particular attention is given to improving the efficiency of calculations.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Savici, A.T.Gigg, M.A.Arnold, O.Tolchenov, R.Whitfield, R.E.Hahn, S.E.Zhou, W.Zaliznyak, I.A.2022-11-04doi:10.1107/S1600576722009645International Union of CrystallographyIn neutron scattering experiments, data sets with different statistical significance are collected. A new method is presented to efficiently calculate the weights of single-crystal time-of-flight measurements, and to add together the various contributions.ENtime-of-flight neutron scatteringalgorithmssingle crystalsEvent-mode data collection presents remarkable new opportunities for time-of-flight neutron scattering studies of collective excitations, diffuse scattering from short-range atomic and magnetic structures, and neutron crystallography. In these experiments, large volumes of the reciprocal space are surveyed, often using different wavelengths and counting times. These data then have to be added together, with accurate propagation of the counting errors. This paper presents a statistically correct way of adding and histogramming the data for single-crystal time-of-flight neutron scattering measurements. In order to gain a broader community acceptance, particular attention is given to improving the efficiency of calculations.text/htmlEfficient data reduction for time-of-flight neutron scattering experiments on single crystalstext6552022-11-04Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Progressive alignment of crystals: reproducible and efficient assessment of crystal structure similarity
http://scripts.iucr.org/cgi-bin/paper?tu5028
During in silico crystal structure prediction of organic molecules, millions of candidate structures are often generated. These candidates must be compared to remove duplicates prior to further analysis (e.g. optimization with electronic structure methods) and ultimately compared with structures determined experimentally. The agreement of predicted and experimental structures forms the basis of evaluating the results from the Cambridge Crystallographic Data Centre (CCDC) blind assessment of crystal structure prediction, which further motivates the pursuit of rigorous alignments. Evaluating crystal structure packings using coordinate root-mean-square deviation (RMSD) for N molecules (or N asymmetric units) in a reproducible manner requires metrics to describe the shape of the compared molecular clusters to account for alternative approaches used to prioritize selection of molecules. Described here is a flexible algorithm called Progressive Alignment of Crystals (PAC) to evaluate crystal packing similarity using coordinate RMSD and introducing the radius of gyration (Rg) as a metric to quantify the shape of the superimposed clusters. It is shown that the absence of metrics to describe cluster shape adds ambiguity to the results of the CCDC blind assessments because it is not possible to determine whether the superposition algorithm has prioritized tightly packed molecular clusters (i.e. to minimize Rg) or prioritized reduced RMSD (i.e. via possibly elongated clusters with relatively larger Rg). For example, it is shown that when the PAC algorithm described here uses single linkage to prioritize molecules for inclusion in the superimposed clusters, the results are nearly identical to those calculated by the widely used program COMPACK. However, the lower Rg values obtained by the use of average linkage are favored for molecule prioritization because the resulting RMSDs more equally reflect the importance of packing along each dimension. It is shown that the PAC algorithm is faster than COMPACK when using a single process and its utility for biomolecular crystals is demonstrated. Finally, parallel scaling up to 64 processes in the open-source code Force Field X is presented.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Nessler, A.J.Okada, O.Hermon, M.J.Nagata, H.Schnieders, M.J.2022-11-21doi:10.1107/S1600576722009670International Union of CrystallographyEvaluating crystal structure packings using coordinate root-mean-square deviation (RMSD) for N molecules (or N asymmetric units) in a reproducible manner requires metrics to describe the shape of the compared molecular clusters to account for alternative approaches used to prioritize selection of molecules. Described here is a fast algorithm called Progressive Alignment of Crystals (PAC) to evaluate crystal packing similarity using coordinate RMSD and introducing the radius of gyration as a metric to quantify the shape of the superimposed clusters.ENstructure comparisoncrystal packingcrystal structure predictionradius of gyrationMPI parallelizationDuring in silico crystal structure prediction of organic molecules, millions of candidate structures are often generated. These candidates must be compared to remove duplicates prior to further analysis (e.g. optimization with electronic structure methods) and ultimately compared with structures determined experimentally. The agreement of predicted and experimental structures forms the basis of evaluating the results from the Cambridge Crystallographic Data Centre (CCDC) blind assessment of crystal structure prediction, which further motivates the pursuit of rigorous alignments. Evaluating crystal structure packings using coordinate root-mean-square deviation (RMSD) for N molecules (or N asymmetric units) in a reproducible manner requires metrics to describe the shape of the compared molecular clusters to account for alternative approaches used to prioritize selection of molecules. Described here is a flexible algorithm called Progressive Alignment of Crystals (PAC) to evaluate crystal packing similarity using coordinate RMSD and introducing the radius of gyration (Rg) as a metric to quantify the shape of the superimposed clusters. It is shown that the absence of metrics to describe cluster shape adds ambiguity to the results of the CCDC blind assessments because it is not possible to determine whether the superposition algorithm has prioritized tightly packed molecular clusters (i.e. to minimize Rg) or prioritized reduced RMSD (i.e. via possibly elongated clusters with relatively larger Rg). For example, it is shown that when the PAC algorithm described here uses single linkage to prioritize molecules for inclusion in the superimposed clusters, the results are nearly identical to those calculated by the widely used program COMPACK. However, the lower Rg values obtained by the use of average linkage are favored for molecule prioritization because the resulting RMSDs more equally reflect the importance of packing along each dimension. It is shown that the PAC algorithm is faster than COMPACK when using a single process and its utility for biomolecular crystals is demonstrated. Finally, parallel scaling up to 64 processes in the open-source code Force Field X is presented.text/htmlProgressive alignment of crystals: reproducible and efficient assessment of crystal structure similaritytext6552022-11-21Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Band-gap assessment from X-ray powder diffraction using artificial intelligence
http://scripts.iucr.org/cgi-bin/paper?jl5044
X-ray diffraction is a phenomenon that stems from the interaction of the electron density of a crystalline material and the electric field of the X-ray waves. The product of this interaction, the diffraction pattern, provides a picture of the reciprocal space of the atomic distribution in terms of intensities of certain scattering wavevectors. In this manner, a correlation between those intensities seen in a diffraction pattern and the electronic properties of a material is suggested. This correlation, if it exists, may not be directly proposed using analytical expressions. This article shows for the first time the feasibility of assessing the band gap of metal–organic frameworks (MOFs) and organic and inorganic materials from their X-ray powder diffraction pattern. The band gaps were assessed with convolutional neural networks (CNNs). These CNNs were developed using simulated X-ray powder diffraction patterns and the band gaps calculated with density functional theory. The diffraction patterns were simulated with different crystal sizes, from 10 nm to the macrocrystalline size. In addition, the reported band gaps of MOFs and organic compounds in the Quantum MOF Database and the Organic Materials Database data sets were used, which were calculated with the PBE functional. Furthermore, the band gaps calculated by Kim et al. [Sci. Data (2020), 7, 387] for inorganic compounds with the HSE functional were used. The developed CNNs were tested with simulated diffraction patterns of compounds different from those used to train the CNNs, as well as with experimentally recorded diffraction patterns. The developed CNNs allowed the assessment of the band gap of the compounds with a root-mean-square error as low as 0.492 eV after training with over 64 000 diffraction patterns.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Gómez-Peralta, J.I.Bokhimi, X.García-Peña, N.G.Quintana-Owen, P.Rodríguez-Gattorno, G.2022-11-21doi:10.1107/S1600576722009797International Union of CrystallographyThe band gaps of metal–organic framework, organic and inorganic materials were assessed from X-ray powder diffraction patterns. The assessments were done with convolutional neural networks.ENX-ray powder diffractionartificial intelligenceband-gap estimationmetal–organic frameworksorganic materialsX-ray diffraction is a phenomenon that stems from the interaction of the electron density of a crystalline material and the electric field of the X-ray waves. The product of this interaction, the diffraction pattern, provides a picture of the reciprocal space of the atomic distribution in terms of intensities of certain scattering wavevectors. In this manner, a correlation between those intensities seen in a diffraction pattern and the electronic properties of a material is suggested. This correlation, if it exists, may not be directly proposed using analytical expressions. This article shows for the first time the feasibility of assessing the band gap of metal–organic frameworks (MOFs) and organic and inorganic materials from their X-ray powder diffraction pattern. The band gaps were assessed with convolutional neural networks (CNNs). These CNNs were developed using simulated X-ray powder diffraction patterns and the band gaps calculated with density functional theory. The diffraction patterns were simulated with different crystal sizes, from 10 nm to the macrocrystalline size. In addition, the reported band gaps of MOFs and organic compounds in the Quantum MOF Database and the Organic Materials Database data sets were used, which were calculated with the PBE functional. Furthermore, the band gaps calculated by Kim et al. [Sci. Data (2020), 7, 387] for inorganic compounds with the HSE functional were used. The developed CNNs were tested with simulated diffraction patterns of compounds different from those used to train the CNNs, as well as with experimentally recorded diffraction patterns. The developed CNNs allowed the assessment of the band gap of the compounds with a root-mean-square error as low as 0.492 eV after training with over 64 000 diffraction patterns.text/htmlBand-gap assessment from X-ray powder diffraction using artificial intelligencetext6552022-11-21Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographyresearch papers10Automatic bad-pixel mask maker for X-ray pixel detectors with application to serial crystallography
http://scripts.iucr.org/cgi-bin/paper?te5097
X-ray crystallography has witnessed a massive development over the past decade, driven by large increases in the intensity and brightness of X-ray sources and enabled by employing high-frame-rate X-ray detectors. The analysis of large data sets is done via automatic algorithms that are vulnerable to imperfections in the detector and noise inherent with the detection process. By improving the model of the behaviour of the detector, data can be analysed more reliably and data storage costs can be significantly reduced. One major requirement is a software mask that identifies defective pixels in diffraction frames. This paper introduces a methodology and program based upon concepts of machine learning, called robust mask maker (RMM), for the generation of bad-pixel masks for large-area X-ray pixel detectors based on modern robust statistics. It is proposed to discriminate normally behaving pixels from abnormal pixels by analysing routine measurements made with and without X-ray illumination. Analysis software typically uses a Bragg peak finder to detect Bragg peaks and an indexing method to detect crystal lattices among those peaks. Without proper masking of the bad pixels, peak finding methods often confuse the abnormal values of bad pixels in a pattern with true Bragg peaks and flag such patterns as useful regardless, leading to storage of enormous uninformative data sets. Also, it is computationally very expensive for indexing methods to search for crystal lattices among false peaks and the solution may be biased. This paper shows how RMM vastly improves peak finders and prevents them from labelling bad pixels as Bragg peaks, by demonstrating its effectiveness on several serial crystallography data sets.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Sadri, A.Hadian-Jazi, M.Yefanov, O.Galchenkova, M.Kirkwood, H.Mills, G.Sikorski, M.Letrun, R.de Wijn, R.Vakili, M.Oberthuer, D.Komadina, D.Brehm, W.Mancuso, A.P.Carnis, J.Gelisio, L.Chapman, H.N.2022-11-21doi:10.1107/S1600576722009815International Union of CrystallographyAttention is focused on perhaps the biggest bottleneck in data analysis for serial crystallography at X-ray free-electron lasers, which has not received serious enough examination to date. An effective and reliable way is presented to identify anomalies in detectors, using machine learning and recently developed mathematical methods in the field referred to as `robust statistics'.ENbad-pixel masksrobust mask makermachine learningrobust statisticsserial crystallographyX-ray crystallography has witnessed a massive development over the past decade, driven by large increases in the intensity and brightness of X-ray sources and enabled by employing high-frame-rate X-ray detectors. The analysis of large data sets is done via automatic algorithms that are vulnerable to imperfections in the detector and noise inherent with the detection process. By improving the model of the behaviour of the detector, data can be analysed more reliably and data storage costs can be significantly reduced. One major requirement is a software mask that identifies defective pixels in diffraction frames. This paper introduces a methodology and program based upon concepts of machine learning, called robust mask maker (RMM), for the generation of bad-pixel masks for large-area X-ray pixel detectors based on modern robust statistics. It is proposed to discriminate normally behaving pixels from abnormal pixels by analysing routine measurements made with and without X-ray illumination. Analysis software typically uses a Bragg peak finder to detect Bragg peaks and an indexing method to detect crystal lattices among those peaks. Without proper masking of the bad pixels, peak finding methods often confuse the abnormal values of bad pixels in a pattern with true Bragg peaks and flag such patterns as useful regardless, leading to storage of enormous uninformative data sets. Also, it is computationally very expensive for indexing methods to search for crystal lattices among false peaks and the solution may be biased. This paper shows how RMM vastly improves peak finders and prevents them from labelling bad pixels as Bragg peaks, by demonstrating its effectiveness on several serial crystallography data sets.text/htmlAutomatic bad-pixel mask maker for X-ray pixel detectors with application to serial crystallographytext6552022-11-21Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Small-angle X-ray microdiffraction from fibrils embedded in tissue thin sections
http://scripts.iucr.org/cgi-bin/paper?fs5212
Small-angle X-ray scattering (SAXS) from fibrils embedded in a fixed, thin section of tissue includes contributions from the fibrils, the polymeric matrix surrounding the fibrils, other constituents of the tissue, and cross-terms due to the spatial correlation between fibrils and neighboring molecules. This complex mixture severely limits the amount of information that can be extracted from scattering studies. However, availability of micro- and nano-beams has made the measurement of scattering from very small volumes possible, which, in some cases, may be dominated by a single fibrillar constituent. In such cases, information about the predominant species may be accessible. Nevertheless, even in these cases, the correlations between the positions of fibrils and other constituents have a significant impact on the observed scattering. Here, strategies are proposed to extract partial information about fibril structure and tissue organization on the basis of SAXS from samples of this type. It is shown that the spatial correlation function of the fibril in the direction perpendicular to the fibril axis can be computed and contains information about the predominant fibril structure and the organization of the surrounding tissue matrix. This has significant advantages over approaches based on techniques developed for X-ray solution scattering. Examples of correlation calculations in different types of samples are given to demonstrate the information that can be obtained from these measurements.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Nepal, P.Al Bashit, A.Yang, L.Makowski, L.2022-11-21doi:10.1107/S1600576722009955International Union of CrystallographyThe availability of micro- and nano-X-ray beams makes measurement of scattering from very small volumes possible, opening possibilities for deriving in situ structural information on fibrillar constituents in complex materials and tissues. This work outlines a set of strategies for confronting major technical obstacles to extract useful structural information from scattering derived from these samples.ENsmall-angle X-ray scatteringSAXSscanning microdiffractionamyloidsAlzheimer's diseaseSmall-angle X-ray scattering (SAXS) from fibrils embedded in a fixed, thin section of tissue includes contributions from the fibrils, the polymeric matrix surrounding the fibrils, other constituents of the tissue, and cross-terms due to the spatial correlation between fibrils and neighboring molecules. This complex mixture severely limits the amount of information that can be extracted from scattering studies. However, availability of micro- and nano-beams has made the measurement of scattering from very small volumes possible, which, in some cases, may be dominated by a single fibrillar constituent. In such cases, information about the predominant species may be accessible. Nevertheless, even in these cases, the correlations between the positions of fibrils and other constituents have a significant impact on the observed scattering. Here, strategies are proposed to extract partial information about fibril structure and tissue organization on the basis of SAXS from samples of this type. It is shown that the spatial correlation function of the fibril in the direction perpendicular to the fibril axis can be computed and contains information about the predominant fibril structure and the organization of the surrounding tissue matrix. This has significant advantages over approaches based on techniques developed for X-ray solution scattering. Examples of correlation calculations in different types of samples are given to demonstrate the information that can be obtained from these measurements.text/htmlSmall-angle X-ray microdiffraction from fibrils embedded in tissue thin sectionstext6552022-11-21Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Stochastic atomic modeling and optimization with fullrmc
http://scripts.iucr.org/cgi-bin/paper?yr5090
Understanding materials' atomic structure with a high level of confidence and certainty is often regarded as a very arduous and sometimes impossible task, especially for newer, emerging technology materials exhibiting limited long-range order. Nevertheless, information about atomic structural properties is very valuable for materials science and synthesis. For non-crystalline amorphous and nanoscale materials, using conventional structural determination methods is impossible. Reverse Monte Carlo (RMC) modeling is commonly used to derive models of materials from experimental diffraction data. Here, the latest developments in the fullrmc software package are discussed. Despite its name, fullrmc provides a very flexible modeling framework for solving atomic structures with many methods beyond RMC. The stochastic nature of fullrmc allows it to explore all possible dimensions and degrees of freedom for atomic modeling and create statistical solutions to match measurements. Differing versions of fullrmc are provided as open source or for cloud computing access. The latter includes a modern web-based graphical user interface that incorporates advanced computing and structure-building modules and machine-learning-based components. The main features of fullrmc are presented, including constraint types, boundary conditions, density shape functions and the two running modes: stochastic using a Monte Carlo algorithm and optimization using a genetic algorithm. Capabilities include tools for statistical, mesoscopic and nanoscopic approaches, atomic or coarse-grained models, and smart artificial-intelligence-ready loss functions.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Aoun, B.2022-10-14doi:10.1107/S1600576722008536International Union of Crystallographyfullrmc is an open-source framework to model and optimize atomic and molecular materials. It is enabled with reinforcement machine learning and designed to solve complex crystalline, amorphous atomic or molecular structures up to the nanoscopic scale.ENreverse Monte Carlostochastic atomic and molecular modelingtheoretical optimizationloss functionsartificial intelligenceUnderstanding materials' atomic structure with a high level of confidence and certainty is often regarded as a very arduous and sometimes impossible task, especially for newer, emerging technology materials exhibiting limited long-range order. Nevertheless, information about atomic structural properties is very valuable for materials science and synthesis. For non-crystalline amorphous and nanoscale materials, using conventional structural determination methods is impossible. Reverse Monte Carlo (RMC) modeling is commonly used to derive models of materials from experimental diffraction data. Here, the latest developments in the fullrmc software package are discussed. Despite its name, fullrmc provides a very flexible modeling framework for solving atomic structures with many methods beyond RMC. The stochastic nature of fullrmc allows it to explore all possible dimensions and degrees of freedom for atomic modeling and create statistical solutions to match measurements. Differing versions of fullrmc are provided as open source or for cloud computing access. The latter includes a modern web-based graphical user interface that incorporates advanced computing and structure-building modules and machine-learning-based components. The main features of fullrmc are presented, including constraint types, boundary conditions, density shape functions and the two running modes: stochastic using a Monte Carlo algorithm and optimization using a genetic algorithm. Capabilities include tools for statistical, mesoscopic and nanoscopic approaches, atomic or coarse-grained models, and smart artificial-intelligence-ready loss functions.text/htmlStochastic atomic modeling and optimization with fullrmctext6552022-10-14Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographycomputer programs00Updates in SASfit for fitting analytical expressions and numerical models to small-angle scattering patterns
http://scripts.iucr.org/cgi-bin/paper?yr5094
Small-angle scattering is an increasingly common method for characterizing particle ensembles in a wide variety of sample types and for diverse areas of application. SASfit has been one of the most comprehensive and flexible curve-fitting programs for decades, with many specialized tools for various fields. Here, a selection of enhancements and additions to the SASfit program are presented that may be of great benefit to interested and advanced users alike: (a) further development of the technical basis of the program, such as new numerical algorithms currently in use, a continuous integration practice for automated building and packaging of the software, and upgrades on the plug-in system for easier adoption by third-party developers; (b) a selection of new form factors for anisotropic scattering patterns and updates to existing form factors to account for multiple scattering effects; (c) a new type of a very flexible distribution called metalog [Keelin (2016). Decis. Anal. 13, 243–277], and regularization techniques such as the expectation-maximization method [Dempster et al. (1977). J. R. Stat. Soc. Ser. B (Methodological), 39, 1–22; Richardson (1972) J. Opt. Soc. Am. 62, 55; Lucy (1974). Astron. J. 79, 745; Lucy (1994). Astron. Astrophys. 289, 983–994], which is compared with fits of analytical size distributions via the non-linear least-squares method; and (d) new structure factors, especially for ordered nano- and meso-scaled material systems, as well as the Ornstein–Zernike solver for numerical determination of particle interactions and the resulting structure factor when no analytical solution is available, with the aim of incorporating its effects into the small-angle scattering intensity model used for fitting with SASfit.Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Kohlbrecher, J.Breßler, I.2022-11-21doi:10.1107/S1600576722009037International Union of CrystallographyRecent enhancements and additions to the SASfit program are discussed, including anisotropic scattering models, flexible distributions, regularization techniques such as the expectation-maximization method, and new structure factors, especially for ordered nano- and meso-scaled material. The Ornstein–Zernike solver for numerical structure factors is also introduced.ENsmall-angle scatteringSASfitnumerical modelsstructure factorsform factorsregularization techniquesSmall-angle scattering is an increasingly common method for characterizing particle ensembles in a wide variety of sample types and for diverse areas of application. SASfit has been one of the most comprehensive and flexible curve-fitting programs for decades, with many specialized tools for various fields. Here, a selection of enhancements and additions to the SASfit program are presented that may be of great benefit to interested and advanced users alike: (a) further development of the technical basis of the program, such as new numerical algorithms currently in use, a continuous integration practice for automated building and packaging of the software, and upgrades on the plug-in system for easier adoption by third-party developers; (b) a selection of new form factors for anisotropic scattering patterns and updates to existing form factors to account for multiple scattering effects; (c) a new type of a very flexible distribution called metalog [Keelin (2016). Decis. Anal. 13, 243–277], and regularization techniques such as the expectation-maximization method [Dempster et al. (1977). J. R. Stat. Soc. Ser. B (Methodological), 39, 1–22; Richardson (1972) J. Opt. Soc. Am. 62, 55; Lucy (1974). Astron. J. 79, 745; Lucy (1994). Astron. Astrophys. 289, 983–994], which is compared with fits of analytical size distributions via the non-linear least-squares method; and (d) new structure factors, especially for ordered nano- and meso-scaled material systems, as well as the Ornstein–Zernike solver for numerical determination of particle interactions and the resulting structure factor when no analytical solution is available, with the aim of incorporating its effects into the small-angle scattering intensity model used for fitting with SASfit.text/htmlUpdates in SASfit for fitting analytical expressions and numerical models to small-angle scattering patternstext6552022-11-21Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographycomputer programs00The Knowledge Machine: How an Unreasonable Idea Created Modern Science. By Michael Strevens. Penguin, 2022. Pp. 368. Price GBP 7.99 (Kindle), GBP 9.95 (paperback). ISBN 9780141981260.
http://scripts.iucr.org/cgi-bin/paper?xo0193
Copyright (c) 2022 International Union of Crystallographyurn:issn:1600-5767Helliwell, J.R.2022-11-04doi:10.1107/S1600576722010275International Union of CrystallographyBook review.ENbook reviewshistory of sciencephilosophy of sciencetext/htmlThe Knowledge Machine: How an Unreasonable Idea Created Modern Science. By Michael Strevens. Penguin, 2022. Pp. 368. Price GBP 7.99 (Kindle), GBP 9.95 (paperback). ISBN 9780141981260.text6552022-11-04Copyright (c) 2022 International Union of CrystallographyJournal of Applied Crystallographybook reviews00