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) 2020 International Union of Crystallography2020-04-01International 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 53, Part 2, 2020textweekly62002-02-01T00:00+00:002532020-04-01Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallography312urn:issn:1600-5767med@iucr.orgApril 20202020-04-01Journal of Applied Crystallographyhttp://journals.iucr.org/logos/rss10j.gif
//journals.iucr.org/j/issues/2020/02/00/isscontsbdy.html
Still imageStrain tensor evaluation in polycrystalline materials by scanning high-energy X-ray diffraction
http://scripts.iucr.org/cgi-bin/paper?me6067
Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Borbély, A.2020-02-21doi:10.1107/S1600576720001661International Union of CrystallographyThe paper of Henningsson, Hall, Wright & Hektor [J. Appl. Cryst. (2020), 53, https://doi.org/10.1107/S1600576720001016] published in this journal issue presents a promising diffraction-tomography method for determining strain tensors at sub-micrometre scale in bulk polycrystalline materials.ENintragranular strainX-ray diffraction3DXRDtomographytext/htmlStrain tensor evaluation in polycrystalline materials by scanning high-energy X-ray diffractiontext2532020-02-21Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographyscientific commentaries312313Reconstructing intragranular strain fields in polycrystalline materials from scanning 3DXRD data
http://scripts.iucr.org/cgi-bin/paper?nb5257
Two methods for reconstructing intragranular strain fields are developed for scanning three-dimensional X-ray diffraction (3DXRD). The methods are compared with a third approach where voxels are reconstructed independently of their neighbours [Hayashi, Setoyama & Seno (2017). Mater. Sci. Forum, 905, 157–164]. The 3D strain field of a tin grain, located within a sample of approximately 70 grains, is analysed and compared across reconstruction methods. Implicit assumptions of sub-problem independence, made in the independent voxel reconstruction method, are demonstrated to introduce bias and reduce reconstruction accuracy. It is verified that the two proposed methods remedy these problems by taking the spatial properties of the inverse problem into account. Improvements in reconstruction quality achieved by the two proposed methods are further supported by reconstructions using synthetic diffraction data.Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Henningsson, N.A.Hall, S.A.Wright, J.P.Hektor, J.2020-02-21doi:10.1107/S1600576720001016International Union of CrystallographyMethods for reconstruction of intragranular strain tensor fields for scanning three-dimensional X-ray diffraction (3DXRD) are developed and evaluated.ENintragranular strainX-ray diffraction3DXRDtomographyTwo methods for reconstructing intragranular strain fields are developed for scanning three-dimensional X-ray diffraction (3DXRD). The methods are compared with a third approach where voxels are reconstructed independently of their neighbours [Hayashi, Setoyama & Seno (2017). Mater. Sci. Forum, 905, 157–164]. The 3D strain field of a tin grain, located within a sample of approximately 70 grains, is analysed and compared across reconstruction methods. Implicit assumptions of sub-problem independence, made in the independent voxel reconstruction method, are demonstrated to introduce bias and reduce reconstruction accuracy. It is verified that the two proposed methods remedy these problems by taking the spatial properties of the inverse problem into account. Improvements in reconstruction quality achieved by the two proposed methods are further supported by reconstructions using synthetic diffraction data.text/htmlReconstructing intragranular strain fields in polycrystalline materials from scanning 3DXRD datatext2532020-02-21Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographyresearch papers314325Classifying and analyzing small-angle scattering data using weighted k nearest neighbors machine learning techniques
http://scripts.iucr.org/cgi-bin/paper?vg5118
A consistent challenge for both new and expert practitioners of small-angle scattering (SAS) lies in determining how to analyze the data, given the limited information content of said data and the large number of models that can be employed. Machine learning (ML) methods are powerful tools for classifying data that have found diverse applications in many fields of science. Here, ML methods are applied to the problem of classifying SAS data for the most appropriate model to use for data analysis. The approach employed is built around the method of weighted k nearest neighbors (wKNN), and utilizes a subset of the models implemented in the SasView package (https://www.sasview.org/) for generating a well defined set of training and testing data. The prediction rate of the wKNN method implemented here using a subset of SasView models is reasonably good for many of the models, but has difficulty with others, notably those based on spherical structures. A novel expansion of the wKNN method was also developed, which uses Gaussian processes to produce local surrogate models for the classification, and this significantly improves the classification accuracy. Further, by integrating a stochastic gradient descent method during post-processing, it is possible to leverage the local surrogate model both to classify the SAS data with high accuracy and to predict the structural parameters that best describe the data. The linking of data classification and model fitting has the potential to facilitate the translation of measured data into results for both novice and expert practitioners of SAS.Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Archibald, R.K.Doucet, M.Johnston, T.Young, S.R.Yang, E.Heller, W.T.2020-02-18doi:10.1107/S1600576720000552International Union of CrystallographyIt is demonstrated how k nearest neighbor machine learning methods can be used to classify small-angle scattering data for the most appropriate model to use for data analysis. The results show the promise of machine learning for helping small-angle scattering practitioners translate measured data into scientific results.ENsmall-angle scattering datamachine learningmodelingSasViewA consistent challenge for both new and expert practitioners of small-angle scattering (SAS) lies in determining how to analyze the data, given the limited information content of said data and the large number of models that can be employed. Machine learning (ML) methods are powerful tools for classifying data that have found diverse applications in many fields of science. Here, ML methods are applied to the problem of classifying SAS data for the most appropriate model to use for data analysis. The approach employed is built around the method of weighted k nearest neighbors (wKNN), and utilizes a subset of the models implemented in the SasView package (https://www.sasview.org/) for generating a well defined set of training and testing data. The prediction rate of the wKNN method implemented here using a subset of SasView models is reasonably good for many of the models, but has difficulty with others, notably those based on spherical structures. A novel expansion of the wKNN method was also developed, which uses Gaussian processes to produce local surrogate models for the classification, and this significantly improves the classification accuracy. Further, by integrating a stochastic gradient descent method during post-processing, it is possible to leverage the local surrogate model both to classify the SAS data with high accuracy and to predict the structural parameters that best describe the data. The linking of data classification and model fitting has the potential to facilitate the translation of measured data into results for both novice and expert practitioners of SAS.text/htmlClassifying and analyzing small-angle scattering data using weighted k nearest neighbors machine learning techniquestext2532020-02-18Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographyresearch papers326334An in situ synchrotron study of the localized B2↔B19′ phase transformation in an Ni–Ti alloy subjected to uniaxial cyclic loading–unloading with incremental strains
http://scripts.iucr.org/cgi-bin/paper?kc5100
High-resolution in situ synchrotron X-ray diffraction was applied to study a cold-drawn and solution-treated 56Ni–44Ti wt% alloy subjected to uniaxial cyclic loading–unloading with incremental strains. The micro-mechanical behaviour associated with the partial and repeated B2↔B19′ phase transformation at the centre of the sample gauge length was studied with respect to the macroscopic stress–strain response. The lattice strains of the (110)B2 and different B19′ grain families are affected by (i) the transformation strain, the load-bearing capacity of both phases and the strain continuity maintained at/near the B2–B19′ interfaces at the centre of the gauge length, and (ii) the extent of transformation along the gauge length. With cycling and incremental strains (i) the elastic lattice strain and plastic strain in the remnant (110)B2 grain family gradually saturate at early cycles, whereas the plastic strain in the B19′ phase continues to increase. This contributes to accumulation of residual strains (degradation in superelasticity), greater non-linearity and change in the shape of the macroscopic stress–strain curve from plateau type to curvilinear elastic. (ii) The initial 〈111〉B2 fibre texture transforms to [120]B19′, [130]B19′, [150]B19′ and [010]B19′ orientations. Further increase in the applied strain with cycling results in the development of [130]B19′, [102]B19′, [102]B19′, [100]B19′ and [100]B19′ orientations.Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Bian, X.Saleh, A.A.Lynch, P.A.Davies, C.H.J.Gazder, A.A.Pereloma, E.V.2020-02-18doi:10.1107/S1600576720000370International Union of CrystallographyThis paper aims to expand the existing knowledge on the partial and repeated B2↔B19′ phase transformation under cyclic loading–unloading, by combining single peak fitting and Rietveld-based analysis.ENNiTishape memory alloycyclic loading–unloadingtextureRietveld refinementsynchrotron X-ray diffractionHigh-resolution in situ synchrotron X-ray diffraction was applied to study a cold-drawn and solution-treated 56Ni–44Ti wt% alloy subjected to uniaxial cyclic loading–unloading with incremental strains. The micro-mechanical behaviour associated with the partial and repeated B2↔B19′ phase transformation at the centre of the sample gauge length was studied with respect to the macroscopic stress–strain response. The lattice strains of the (110)B2 and different B19′ grain families are affected by (i) the transformation strain, the load-bearing capacity of both phases and the strain continuity maintained at/near the B2–B19′ interfaces at the centre of the gauge length, and (ii) the extent of transformation along the gauge length. With cycling and incremental strains (i) the elastic lattice strain and plastic strain in the remnant (110)B2 grain family gradually saturate at early cycles, whereas the plastic strain in the B19′ phase continues to increase. This contributes to accumulation of residual strains (degradation in superelasticity), greater non-linearity and change in the shape of the macroscopic stress–strain curve from plateau type to curvilinear elastic. (ii) The initial 〈111〉B2 fibre texture transforms to [120]B19′, [130]B19′, [150]B19′ and [010]B19′ orientations. Further increase in the applied strain with cycling results in the development of [130]B19′, [102]B19′, [102]B19′, [100]B19′ and [100]B19′ orientations.text/htmlAn in situ synchrotron study of the localized B2↔B19′ phase transformation in an Ni–Ti alloy subjected to uniaxial cyclic loading–unloading with incremental strainstext2532020-02-18Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographyresearch papers335348Nondestructive evaluation of 3D microstructure evolution in strontium titanate
http://scripts.iucr.org/cgi-bin/paper?nb5255
Nondestructive X-ray diffraction contrast tomography imaging was used to characterize the microstructure evolution in a polycrystalline bulk strontium titanate specimen. Simultaneous acquisition of diffraction and absorption information allows for the reconstruction of shape and orientation of more than 800 grains in the specimen as well as porosity. Three-dimensional microstructure reconstructions of two coarsening states of the same specimen are presented alongside a detailed exploration of the crystallographic, topological and morphological characteristics of the evolving microstructure. The overall analysis of the 3D structure shows a clear signature of the grain boundary anisotropy, which can be correlated to surface energy anisotropy: the grain boundary plane distribution function shows an excess of 〈100〉-oriented interfaces with respect to a random structure. The results are discussed in the context of interface property anisotropy effects.Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Trenkle, A.Syha, M.Rheinheimer, W.Callahan, P. G.Nguyen, L.Ludwig, W.Lenthe, W.Echlin, M. P.Pollock, T. M.Weygand, D.De Graef, M.Hoffmann, M. J.Gumbsch, P.2020-02-21doi:10.1107/S160057672000093XInternational Union of CrystallographyX-ray diffraction contrast tomography is used to investigate the crystallographic, topological and morphological characteristics of the evolving microstructure in thermally aged strontium titanate samples. The analysis of the 3D structure shows a clear signature of the grain boundary anisotropy, which can be correlated to surface energy anisotropy: the grain boundary orientation distribution function shows an excess of 〈100〉-oriented interfaces with respect to a random structure.ENstrontium titanatediffraction contrast tomographygrain growth3D materials sciencemicrostructure evolutionNondestructive X-ray diffraction contrast tomography imaging was used to characterize the microstructure evolution in a polycrystalline bulk strontium titanate specimen. Simultaneous acquisition of diffraction and absorption information allows for the reconstruction of shape and orientation of more than 800 grains in the specimen as well as porosity. Three-dimensional microstructure reconstructions of two coarsening states of the same specimen are presented alongside a detailed exploration of the crystallographic, topological and morphological characteristics of the evolving microstructure. The overall analysis of the 3D structure shows a clear signature of the grain boundary anisotropy, which can be correlated to surface energy anisotropy: the grain boundary plane distribution function shows an excess of 〈100〉-oriented interfaces with respect to a random structure. The results are discussed in the context of interface property anisotropy effects.text/htmlNondestructive evaluation of 3D microstructure evolution in strontium titanatetext2532020-02-21Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographyresearch papers349359Evaluation of X-ray Bragg peak profiles with the variance method obtained by in situ measurement on Mg–Al alloys
http://scripts.iucr.org/cgi-bin/paper?nb5252
The microstructural evolution in randomly oriented Mg–Al samples is investigated in situ during compression by X-ray diffraction as a function of Al concentration. The diffraction data are evaluated by the variance method, which provides information about the dislocation density and spatial distribution of the dislocations. The dislocation density increases with increasing alloying content. Since the increment of the dislocation density above the yield point is linear, the mutual dislocation interaction type is determined from the Taylor equation. The results indicate the dominance of basal–basal dislocation interactions, but at higher alloying content the share of the basal–non-basal interactions increases. It is shown that the dynamics of dislocation wall formation also depend on Al content. Transmission electron microscopy observations are in agreement with the results obtained by X-ray line profile analysis.Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Farkas, G.Groma, I.Veselý, J.Máthis, K.2020-02-21doi:10.1107/S1600576720000709International Union of CrystallographyStatistical properties of the dislocation microstructure developing in Mg alloys deformed by compression have been determined by the variance method of X-ray line profile analysis.ENX-ray diffractionvariance methodmagnesium alloysdislocation structureprofile analysisThe microstructural evolution in randomly oriented Mg–Al samples is investigated in situ during compression by X-ray diffraction as a function of Al concentration. The diffraction data are evaluated by the variance method, which provides information about the dislocation density and spatial distribution of the dislocations. The dislocation density increases with increasing alloying content. Since the increment of the dislocation density above the yield point is linear, the mutual dislocation interaction type is determined from the Taylor equation. The results indicate the dominance of basal–basal dislocation interactions, but at higher alloying content the share of the basal–non-basal interactions increases. It is shown that the dynamics of dislocation wall formation also depend on Al content. Transmission electron microscopy observations are in agreement with the results obtained by X-ray line profile analysis.text/htmlEvaluation of X-ray Bragg peak profiles with the variance method obtained by in situ measurement on Mg–Al alloystext2532020-02-21Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographyresearch papers360368High-temperature X-ray scattering studies of atomic layer deposited IrO2
http://scripts.iucr.org/cgi-bin/paper?pd5111
IrO2 is an important material in numerous applications ranging from catalysis to the microelectronics industry, but despite this its behaviour upon annealing under different conditions has not yet been thoroughly studied. This work provides a detailed investigation of the annealing of IrO2 thin films using in situ high-temperature X-ray diffraction and X-ray reflectivity (HTXRR) measurements from room temperature up to 1000°C in oxygen, nitrogen, forming gas and vacuum. Complementary ex situ scanning electron microscopy and atomic force microscopy measurements were conducted. The combined data show the dependencies of crystalline properties and surface morphology on the annealing temperature and atmosphere. The reduction of IrO2 to Ir takes place at a temperature as low as 150°C in forming gas, but in oxygen IrO2 is stable up to 800°C and evaporates as a volatile oxide at higher temperatures. The IrO2 crystallite size remains constant in oxygen up to 400°C and increases above that, while in the more reducing atmospheres the Ir crystallites grow continuously above the phase-change temperature. The role of HTXRR in the analysis is shown to be important since its high sensitivity allows one to observe changes taking place in the film at temperatures much below the phase change.Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Heikkilä, M.J.Hämäläinen, J.Puukilainen, E.Leskelä, M.Ritala, M.2020-03-06doi:10.1107/S1600576720001053International Union of CrystallographyThe behaviour of IrO2 thin films during annealing in oxygen, nitrogen, forming gas and vacuum was studied using in situ high-temperature X-ray diffraction and X-ray reflectivity, and ex situ scanning electron microscopy and atomic force microscopy.ENIrO2atomic layer depositionALDhigh-temperature X-ray diffractionHTXRDhigh-temperature X-ray reflectivityHTXRRIrO2 is an important material in numerous applications ranging from catalysis to the microelectronics industry, but despite this its behaviour upon annealing under different conditions has not yet been thoroughly studied. This work provides a detailed investigation of the annealing of IrO2 thin films using in situ high-temperature X-ray diffraction and X-ray reflectivity (HTXRR) measurements from room temperature up to 1000°C in oxygen, nitrogen, forming gas and vacuum. Complementary ex situ scanning electron microscopy and atomic force microscopy measurements were conducted. The combined data show the dependencies of crystalline properties and surface morphology on the annealing temperature and atmosphere. The reduction of IrO2 to Ir takes place at a temperature as low as 150°C in forming gas, but in oxygen IrO2 is stable up to 800°C and evaporates as a volatile oxide at higher temperatures. The IrO2 crystallite size remains constant in oxygen up to 400°C and increases above that, while in the more reducing atmospheres the Ir crystallites grow continuously above the phase-change temperature. The role of HTXRR in the analysis is shown to be important since its high sensitivity allows one to observe changes taking place in the film at temperatures much below the phase change.text/htmlHigh-temperature X-ray scattering studies of atomic layer deposited IrO2text2532020-03-06Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographyresearch papers369380Effect of sample-preparation history on domain and crystal structure in a relaxor-ferroelectric single crystal
http://scripts.iucr.org/cgi-bin/paper?ks5640
The effect of sample-preparation procedures on single crystals of the relaxor-based ferroelectric Pb(Mg1/3Nb2/3)O3–31%PbTiO3 (PMN–31%PT) has been investigated. PMN–31%PT single crystals were treated using the general sample-preparation methods of mechanical polishing and Ar-ion milling. Similar domain structures were artificially induced in both the mechanically polished and the Ar-ion milled PMN–31%PT; this domain structure was not observed in the original PMN–31%PT single crystal. Macroscopic structural investigation using X-ray diffraction showed that these general sample-preparation methods induce a structural change from a monoclinic-like to a tetragonal-like structure. A study of local symmetry also indicated that Ar-ion milling induces a structural change from the original monoclinic-like crystal symmetry to a tetragonal-like crystal symmetry. It is also demonstrated that the conventional sample-preparation methods induce a poling-like effect on PMN–31%PT.Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Jeon, J.Oh, S.J.Kim, K.-H.2020-03-06doi:10.1107/S1600576720001235International Union of CrystallographyPhase transitions in relaxor-ferroelectric crystals during conventional sample preparation are investigated by a symmetry study.ENrelaxor-based ferrroelectricssample preparationsymmetry investigationsymmetry quantificationconvergent-beam electron diffractionThe effect of sample-preparation procedures on single crystals of the relaxor-based ferroelectric Pb(Mg1/3Nb2/3)O3–31%PbTiO3 (PMN–31%PT) has been investigated. PMN–31%PT single crystals were treated using the general sample-preparation methods of mechanical polishing and Ar-ion milling. Similar domain structures were artificially induced in both the mechanically polished and the Ar-ion milled PMN–31%PT; this domain structure was not observed in the original PMN–31%PT single crystal. Macroscopic structural investigation using X-ray diffraction showed that these general sample-preparation methods induce a structural change from a monoclinic-like to a tetragonal-like structure. A study of local symmetry also indicated that Ar-ion milling induces a structural change from the original monoclinic-like crystal symmetry to a tetragonal-like crystal symmetry. It is also demonstrated that the conventional sample-preparation methods induce a poling-like effect on PMN–31%PT.text/htmlEffect of sample-preparation history on domain and crystal structure in a relaxor-ferroelectric single crystaltext2532020-03-06Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographyresearch papers381386Robust surface structure analysis with reliable uncertainty estimation using the exchange Monte Carlo method
http://scripts.iucr.org/cgi-bin/paper?to5205
The exchange Monte Carlo (MC) method is implemented in a surface structure refinement software using Bayesian inference. The MC calculation successfully reproduces crystal truncation rod intensity profiles from perovskite oxide ultrathin films, which involves about 60 structure parameters, starting from a simple model structure in which the ultrathin film and substrate surface have an atomic arrangement identical to the substrate bulk crystal. This shows great tolerance of the initial model in the surface structure search. The MC software is provided on the web. One of the advantages of using the MC method is the precise estimation of uncertainty of the obtained parameters. However, the parameter uncertainty is largely underestimated when one assumes that the diffraction measurements at each scattering vector are independent. The underestimation is caused by the correlation of experimental error. A means of estimation of uncertainty based on the effective number of observations is demonstrated.Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Nagai, K.Anada, M.Nakanishi-Ohno, Y.Okada, M.Wakabayashi, Y.2020-03-06doi:10.1107/S1600576720001314International Union of CrystallographyThe exchange Monte Carlo method is implemented for analyses of surface X-ray scattering.ENsurface diffractionBayesian inferenceMonte Carlooxide filmsepitaxial filmsThe exchange Monte Carlo (MC) method is implemented in a surface structure refinement software using Bayesian inference. The MC calculation successfully reproduces crystal truncation rod intensity profiles from perovskite oxide ultrathin films, which involves about 60 structure parameters, starting from a simple model structure in which the ultrathin film and substrate surface have an atomic arrangement identical to the substrate bulk crystal. This shows great tolerance of the initial model in the surface structure search. The MC software is provided on the web. One of the advantages of using the MC method is the precise estimation of uncertainty of the obtained parameters. However, the parameter uncertainty is largely underestimated when one assumes that the diffraction measurements at each scattering vector are independent. The underestimation is caused by the correlation of experimental error. A means of estimation of uncertainty based on the effective number of observations is demonstrated.text/htmlRobust surface structure analysis with reliable uncertainty estimation using the exchange Monte Carlo methodtext2532020-03-06Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographyresearch papers387392General approaches for shear-correcting coordinate transformations in Bragg coherent diffraction imaging. Part I
http://scripts.iucr.org/cgi-bin/paper?to5203
This two-part article series provides a generalized description of the scattering geometry of Bragg coherent diffraction imaging (BCDI) experiments, the shear distortion effects inherent in the 3D image obtained from presently used methods and strategies to mitigate this distortion. Part I starts from fundamental considerations to present the general real-space coordinate transformation required to correct this shear, in a compact operator formulation that easily lends itself to implementation with available software packages. Such a transformation, applied as a final post-processing step following phase retrieval, is crucial for arriving at an undistorted, correctly oriented and physically meaningful image of the 3D crystalline scatterer. As the relevance of BCDI grows in the field of materials characterization, the available sparse literature that addresses the geometric theory of BCDI and the subsequent analysis methods are generalized here. This geometrical aspect, specific to coherent Bragg diffraction and absent in 2D transmission CDI experiments, gains particular importance when it comes to spatially resolved characterization of 3D crystalline materials in a reliable nondestructive manner. This series of articles describes this theory, from the diffraction in Bragg geometry to the corrections needed to obtain a properly rendered digital image of the 3D scatterer. Part I of this series provides the experimental BCDI community with the general form of the 3D real-space distortions in the phase-retrieved object, along with the necessary post-retrieval correction method. Part II builds upon the geometric theory developed in Part I with the formalism to correct the shear distortions directly on an orthogonal grid within the phase-retrieval algorithm itself, allowing more physically realistic constraints to be applied. Taken together, Parts I and II provide the X-ray science community with a set of generalized BCDI shear-correction techniques crucial to the final rendering of a 3D crystalline scatterer and for the development of new BCDI methods and experiments.Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Maddali, S.Li, P.Pateras, A.Timbie, D.Delegan, N.Crook, A.L.Lee, H.Calvo-Almazan, I.Sheyfer, D.Cha, W.Heremans, F.J.Awschalom, D.D.Chamard, V.Allain, M.Hruszkewycz, S.O.2020-03-06doi:10.1107/S1600576720001363International Union of CrystallographyThis article provides a unifying description of the diffraction and signal acquisition geometries of a 3D Bragg coherent diffraction imaging (BCDI) measurement, obtained from fundamental considerations of Fourier-conjugate spaces. Rigorously derived and presented in a compact operator notation, this approach can be easily generalized to any set of BCDI degrees of freedom.ENBragg coherent diffraction imagingphase retrievalshear correctioncoordinate transformationscattering geometryBragg ptychographyconjugate spacesThis two-part article series provides a generalized description of the scattering geometry of Bragg coherent diffraction imaging (BCDI) experiments, the shear distortion effects inherent in the 3D image obtained from presently used methods and strategies to mitigate this distortion. Part I starts from fundamental considerations to present the general real-space coordinate transformation required to correct this shear, in a compact operator formulation that easily lends itself to implementation with available software packages. Such a transformation, applied as a final post-processing step following phase retrieval, is crucial for arriving at an undistorted, correctly oriented and physically meaningful image of the 3D crystalline scatterer. As the relevance of BCDI grows in the field of materials characterization, the available sparse literature that addresses the geometric theory of BCDI and the subsequent analysis methods are generalized here. This geometrical aspect, specific to coherent Bragg diffraction and absent in 2D transmission CDI experiments, gains particular importance when it comes to spatially resolved characterization of 3D crystalline materials in a reliable nondestructive manner. This series of articles describes this theory, from the diffraction in Bragg geometry to the corrections needed to obtain a properly rendered digital image of the 3D scatterer. Part I of this series provides the experimental BCDI community with the general form of the 3D real-space distortions in the phase-retrieved object, along with the necessary post-retrieval correction method. Part II builds upon the geometric theory developed in Part I with the formalism to correct the shear distortions directly on an orthogonal grid within the phase-retrieval algorithm itself, allowing more physically realistic constraints to be applied. Taken together, Parts I and II provide the X-ray science community with a set of generalized BCDI shear-correction techniques crucial to the final rendering of a 3D crystalline scatterer and for the development of new BCDI methods and experiments.text/htmlGeneral approaches for shear-correcting coordinate transformations in Bragg coherent diffraction imaging. Part Itext2532020-03-06Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographyresearch papers393403General approaches for shear-correcting coordinate transformations in Bragg coherent diffraction imaging. Part II
http://scripts.iucr.org/cgi-bin/paper?to5204
X-ray Bragg coherent diffraction imaging (BCDI) has been demonstrated as a powerful 3D microscopy approach for the investigation of sub-micrometre-scale crystalline particles. The approach is based on the measurement of a series of coherent Bragg diffraction intensity patterns that are numerically inverted to retrieve an image of the spatial distribution of the relative phase and amplitude of the Bragg structure factor of the diffracting sample. This 3D information, which is collected through an angular rotation of the sample, is necessarily obtained in a non-orthogonal frame in Fourier space that must be eventually reconciled. To deal with this, the approach currently favored by practitioners (detailed in Part I) is to perform the entire inversion in conjugate non-orthogonal real- and Fourier-space frames, and to transform the 3D sample image into an orthogonal frame as a post-processing step for result analysis. In this article, which is a direct follow-up of Part I, two different transformation strategies are demonstrated, which enable the entire inversion procedure of the measured data set to be performed in an orthogonal frame. The new approaches described here build mathematical and numerical frameworks that apply to the cases of evenly and non-evenly sampled data along the direction of sample rotation (i.e. the rocking curve). The value of these methods is that they rely on the experimental geometry, and they incorporate significantly more information about that geometry into the design of the phase-retrieval Fourier transformation than the strategy presented in Part I. Two important outcomes are (1) that the resulting sample image is correctly interpreted in a shear-free frame and (2) physically realistic constraints of BCDI phase retrieval that are difficult to implement with current methods are easily incorporated. Computing scripts are also given to aid readers in the implementation of the proposed formalisms.Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Li, P.Maddali, S.Pateras, A.Calvo-Almazan, I.Hruszkewycz, S.O.Cha, W.Chamard, V.Allain, M.2020-03-06doi:10.1107/S1600576720001375International Union of CrystallographyNew phase-retrieval methods to directly invert Bragg coherent diffraction imaging data on an orthogonal grid under even and uneven signal sampling conditions are described.ENBragg coherent diffraction imagingFourier synthesisnon-orthogonal Fourier samplingcoordinate transformationshear correctionBragg ptychographyX-ray Bragg coherent diffraction imaging (BCDI) has been demonstrated as a powerful 3D microscopy approach for the investigation of sub-micrometre-scale crystalline particles. The approach is based on the measurement of a series of coherent Bragg diffraction intensity patterns that are numerically inverted to retrieve an image of the spatial distribution of the relative phase and amplitude of the Bragg structure factor of the diffracting sample. This 3D information, which is collected through an angular rotation of the sample, is necessarily obtained in a non-orthogonal frame in Fourier space that must be eventually reconciled. To deal with this, the approach currently favored by practitioners (detailed in Part I) is to perform the entire inversion in conjugate non-orthogonal real- and Fourier-space frames, and to transform the 3D sample image into an orthogonal frame as a post-processing step for result analysis. In this article, which is a direct follow-up of Part I, two different transformation strategies are demonstrated, which enable the entire inversion procedure of the measured data set to be performed in an orthogonal frame. The new approaches described here build mathematical and numerical frameworks that apply to the cases of evenly and non-evenly sampled data along the direction of sample rotation (i.e. the rocking curve). The value of these methods is that they rely on the experimental geometry, and they incorporate significantly more information about that geometry into the design of the phase-retrieval Fourier transformation than the strategy presented in Part I. Two important outcomes are (1) that the resulting sample image is correctly interpreted in a shear-free frame and (2) physically realistic constraints of BCDI phase retrieval that are difficult to implement with current methods are easily incorporated. Computing scripts are also given to aid readers in the implementation of the proposed formalisms.text/htmlGeneral approaches for shear-correcting coordinate transformations in Bragg coherent diffraction imaging. Part IItext2532020-03-06Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographyresearch papers404418Effects of the crystallographic texture on the contractile strain ratio of Ti–3Al–2.5V tubing
http://scripts.iucr.org/cgi-bin/paper?ks5642
The contractile strain ratio (CSR) is an important property and a quality control factor of cold-worked and stress-relieved Ti–3Al–2.5V tubing. In this work, the CSR values of three thin-walled Ti–3Al–2.5V tubing samples were obtained by uniaxial tensile tests, and the crystallographic textures of the tubing samples were characterized by orientation distribution functions (ODFs) which were determined on the basis of a series of pole figures obtained by X-ray diffraction. A quantitative method is proposed for exploring the correlation between the CSR values and the ODF data of the tubing samples, including the following steps: Firstly, taking advantage of the ODF data, the volume fraction (V%) of crystallites that lie within a certain range of Euler angles (φ1, Φ, φ2) can be calculated, and the calculation is performed on each set of Euler angles (φ1, Φ, φ2). Secondly, each V% is resolved into an effective fraction in the orientation of the ideal radial texture {0002}〈10\overline 10〉 corresponding to the Euler angles of (0, 0, 0), and the equivalent radial texture (ERT) is obtained as the sum of all such effective fractions. Thirdly, similarly to the previous step, the equivalent tangential texture (ETT) is calculated. The CSR will be related to the ratio of the ERT to the ETT, named the equivalent texture ratio (ETR). The CSR values of the tubing samples are 1.38, 1.96 and 2.19 and their ETR values are 1.33, 1.72 and 1.87, respectively. In particular, the CSR and the ETR of the tubing with a random distribution of the basal poles in the radial–tangential plane are both unity. It is found from the above data that the CSR increases approximately linearly with the ETR. Since the three-dimensional orientations of crystallites and the orientation distributions throughout the Euler space are taken into account in the calculations of the ETR, the proposed method can be used for predicting and explaining the mechanical anisotropy of Ti–3Al–2.5V tubing more accurately.Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Wang, W.Yuan, L.Li, Y.Zhang, H.Zhang, W.Wang, Y.2020-03-13doi:10.1107/S1600576720001879International Union of CrystallographyBased on measurements of the contractile strain ratio (CSR) and the textures of three thin-walled Ti–3Al–2.5V tubing samples, a quantitative method is proposed for exploring the correlation between the CSR values and the orientation distribution function data of the tubing samples.ENtextureorientation distribution functionODFcontractile strain ratioCSRtitanium alloy tubingX-ray diffractionThe contractile strain ratio (CSR) is an important property and a quality control factor of cold-worked and stress-relieved Ti–3Al–2.5V tubing. In this work, the CSR values of three thin-walled Ti–3Al–2.5V tubing samples were obtained by uniaxial tensile tests, and the crystallographic textures of the tubing samples were characterized by orientation distribution functions (ODFs) which were determined on the basis of a series of pole figures obtained by X-ray diffraction. A quantitative method is proposed for exploring the correlation between the CSR values and the ODF data of the tubing samples, including the following steps: Firstly, taking advantage of the ODF data, the volume fraction (V%) of crystallites that lie within a certain range of Euler angles (φ1, Φ, φ2) can be calculated, and the calculation is performed on each set of Euler angles (φ1, Φ, φ2). Secondly, each V% is resolved into an effective fraction in the orientation of the ideal radial texture {0002}〈10\overline 10〉 corresponding to the Euler angles of (0, 0, 0), and the equivalent radial texture (ERT) is obtained as the sum of all such effective fractions. Thirdly, similarly to the previous step, the equivalent tangential texture (ETT) is calculated. The CSR will be related to the ratio of the ERT to the ETT, named the equivalent texture ratio (ETR). The CSR values of the tubing samples are 1.38, 1.96 and 2.19 and their ETR values are 1.33, 1.72 and 1.87, respectively. In particular, the CSR and the ETR of the tubing with a random distribution of the basal poles in the radial–tangential plane are both unity. It is found from the above data that the CSR increases approximately linearly with the ETR. Since the three-dimensional orientations of crystallites and the orientation distributions throughout the Euler space are taken into account in the calculations of the ETR, the proposed method can be used for predicting and explaining the mechanical anisotropy of Ti–3Al–2.5V tubing more accurately.text/htmlEffects of the crystallographic texture on the contractile strain ratio of Ti–3Al–2.5V tubingtext2532020-03-13Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographyresearch papers419423Quantitative phase analysis of slag hydrating in an alkaline environment
http://scripts.iucr.org/cgi-bin/paper?pd5110
An X-ray diffraction (XRD)-based evaluation of the crystalline and amorphous phases in slag hydrating in an alkaline environment is presented. A method is developed for the quantification of the amorphous phases present in hydrating slag in a sodium hydroxide solution. In hydrating slag, the amorphous reaction product is identified as calcium aluminosilicate hydrate. A water-soluble sodium-based amorphous reaction product is also produced. The XRD-based quantification method relies on the direct decomposition of the XRD intensity pattern of the total amorphous phase present in partially hydrated slag into the intensity patterns of the amorphous unreacted slag, the hydrate and the sodium-based product. The unreacted slag content in partially hydrated slag is also determined from the decomposition of the intensity signature of the total amorphous phase. An independent verification of the amorphous unreacted slag content in hydrating slag is obtained from measurements of blends of unhydrated and partially hydrated slag. The XRD-based phase-quantification procedure developed here provides a basis for evaluating the extent of reaction in hydrating slag.Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Reddy, K.C.Subramaniam, K.V.L.2020-03-13doi:10.1107/S1600576720001399International Union of CrystallographyA total-intensity method for amorphous phase quantification is presented, which allows for determining the mass fractions of amorphous components in an alkali-activated slag. The method is applied to determine the unreacted slag in an alkali-activated slag.ENslagX-ray methodshydrationamorphous phasesquantitative phase analysisAn X-ray diffraction (XRD)-based evaluation of the crystalline and amorphous phases in slag hydrating in an alkaline environment is presented. A method is developed for the quantification of the amorphous phases present in hydrating slag in a sodium hydroxide solution. In hydrating slag, the amorphous reaction product is identified as calcium aluminosilicate hydrate. A water-soluble sodium-based amorphous reaction product is also produced. The XRD-based quantification method relies on the direct decomposition of the XRD intensity pattern of the total amorphous phase present in partially hydrated slag into the intensity patterns of the amorphous unreacted slag, the hydrate and the sodium-based product. The unreacted slag content in partially hydrated slag is also determined from the decomposition of the intensity signature of the total amorphous phase. An independent verification of the amorphous unreacted slag content in hydrating slag is obtained from measurements of blends of unhydrated and partially hydrated slag. The XRD-based phase-quantification procedure developed here provides a basis for evaluating the extent of reaction in hydrating slag.text/htmlQuantitative phase analysis of slag hydrating in an alkaline environmenttext2532020-03-13Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographyresearch papers424434Manual measurement of angles in backscattered and transmission Kikuchi diffraction patterns
http://scripts.iucr.org/cgi-bin/paper?nb5262
A historical tool for crystallographic analysis is provided by the Hilton net, which can be used for manually surveying the crystal lattice as it is manifested by the Kikuchi bands in a gnomonic projection. For a quantitative analysis using the Hilton net, the projection centre as the relative position of the signal source with respect to the detector plane needs to be known. Interplanar angles are accessible with a precision and accuracy which is estimated to be ≤0.3°. Angles between any directions, e.g. zone axes, are directly readable. Finally, for the rare case of an unknown projection-centre position, its determination is demonstrated by adapting an old approach developed for photogrammetric applications. It requires the indexing of four zone axes [uvw]i in a backscattered Kikuchi diffraction pattern of a known phase collected under comparable geometric conditions.Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Nolze, G.Tokarski, T.Cios, G.Winkelmann, A.2020-03-25doi:10.1107/S1600576720000692International Union of CrystallographyProcedures are demonstrated which enable a manual determination of the angles between lattice planes and directions from electron backscatter diffraction patterns of unknown phases. The determination of the projection centre is described for cases where it is unknown.ENelectron backscatter diffractionEBSDangle measurementgnomonic projectionsKikuchi patternsHilton netA historical tool for crystallographic analysis is provided by the Hilton net, which can be used for manually surveying the crystal lattice as it is manifested by the Kikuchi bands in a gnomonic projection. For a quantitative analysis using the Hilton net, the projection centre as the relative position of the signal source with respect to the detector plane needs to be known. Interplanar angles are accessible with a precision and accuracy which is estimated to be ≤0.3°. Angles between any directions, e.g. zone axes, are directly readable. Finally, for the rare case of an unknown projection-centre position, its determination is demonstrated by adapting an old approach developed for photogrammetric applications. It requires the indexing of four zone axes [uvw]i in a backscattered Kikuchi diffraction pattern of a known phase collected under comparable geometric conditions.text/htmlManual measurement of angles in backscattered and transmission Kikuchi diffraction patternstext2532020-03-25Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographyresearch papers435443In-house texture measurement using a compact neutron source
http://scripts.iucr.org/cgi-bin/paper?ks5635
In order to improve the instrumental accessibility of neutron diffraction techniques, many emerging compact neutron sources and in-house neutron diffractometers are being developed, even though the precision level of neutron diffraction experiments performed on such instruments was thought to be incomparable with that of large-scale neutron facilities. As a challenging project, the RIKEN accelerator-driven compact neutron source (RANS) was employed here to establish the technical environment for texture measurements, and the recalculated pole figures and orientation distribution functions of an interstitial-free steel sheet obtained from RANS were compared with the results from another two neutron diffractometers well established for texture measurement. These quantitative comparisons revealed that the precise neutron diffraction texture measurement at RANS has been realized successfully, and the fine region division of the neutron detector panel is invaluable for improving the stereographic resolution of texture measurements. Moreover, through selectively using the parts of the obtained neutron diffraction patterns that exhibit good statistics, the Rietveld texture analysis improves the reliability of the texture measurement to a certain extent. These technical research results may accelerate the development of other easily accessible techniques for evaluation of engineering materials using compact neutron sources, and also help to improve the data-collection efficiency for various time-resolved scattering experiments at large-scale neutron facilities.Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Xu, P.G.Ikeda, Y.Hakoyama, T.Takamura, M.Otake, Y.Suzuki, H.2020-03-25doi:10.1107/S1600576720002551International Union of CrystallographyThe RIKEN compact neutron source and related neutron diffractometer were successfully upgraded for precise in-house texture measurement, as judged by comparison with two other well established neutron diffractometers. This provides a good example for the technical development and the scientific application of neutron diffraction techniques based on compact neutron sources.ENcompact neutron sourcestexture measurementneutron diffractiontexture measurement reliabilityinstrumental accessibilityIn order to improve the instrumental accessibility of neutron diffraction techniques, many emerging compact neutron sources and in-house neutron diffractometers are being developed, even though the precision level of neutron diffraction experiments performed on such instruments was thought to be incomparable with that of large-scale neutron facilities. As a challenging project, the RIKEN accelerator-driven compact neutron source (RANS) was employed here to establish the technical environment for texture measurements, and the recalculated pole figures and orientation distribution functions of an interstitial-free steel sheet obtained from RANS were compared with the results from another two neutron diffractometers well established for texture measurement. These quantitative comparisons revealed that the precise neutron diffraction texture measurement at RANS has been realized successfully, and the fine region division of the neutron detector panel is invaluable for improving the stereographic resolution of texture measurements. Moreover, through selectively using the parts of the obtained neutron diffraction patterns that exhibit good statistics, the Rietveld texture analysis improves the reliability of the texture measurement to a certain extent. These technical research results may accelerate the development of other easily accessible techniques for evaluation of engineering materials using compact neutron sources, and also help to improve the data-collection efficiency for various time-resolved scattering experiments at large-scale neutron facilities.text/htmlIn-house texture measurement using a compact neutron sourcetext2532020-03-25Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographyresearch papers444454Determination of the melting temperature of spherical nanoparticles in dilute solution as a function of their radius by exclusively using the small-angle X-ray scattering technique
http://scripts.iucr.org/cgi-bin/paper?vh5111
In this investigation the dependence on radius of the melting temperature of dilute sets of spherical nanocrystals with wide radius distributions was determined by a novel procedure exclusively using the results of small-angle X-ray scattering (SAXS) measurements. This procedure is based on the sensitivity of the SAXS function to small and rather sharp variations in the size and electron density of nanocrystals at their melting temperature. The input for this procedure is a set of experimental SAXS intensity functions at selected q values for varying sample temperatures. In practice, the sample is heated from a minimum temperature, lower than the melting temperature of the smallest nanocrystals, up to a temperature higher than the melting temperature of the largest nanocrystals. The SAXS intensity is recorded in situ at different temperatures during the heating process. This novel procedure was applied to three samples composed of dilute sets of spherical Bi nanocrystals with wide radius distributions embedded in a sodium borate glass. The function relating the melting temperature of Bi nanocrystals with their radius – determined by using the procedure proposed here – agrees very well with the results reported in previous experimental studies using different methods. The results reported here also evidence the predicted size-dependent contraction of Bi nanocrystals induced by the large surface-to-volume ratio of small nanocrystals and an additional size-independent compressive stress caused by the solid glass matrix in which liquid Bi nanodroplets are initially formed. This last effect is a consequence of the increase in the volume of Bi nanoparticles upon crystallization and also of differences in the thermal expansion coefficients of the crystalline phase of Bi and the glass matrix. This additional stress leads to a depression of about 10 K in the melting temperature of the Bi nanocrystals confined in the glass. The procedure described here also allowed the determination of the specific masses and thermal expansion coefficients of Bi nanoparticles in both liquid and crystalline phases.Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Kellermann, G.Pereira, F.L.C.Craievich, A.F.2020-03-25doi:10.1107/S1600576720002101International Union of CrystallographyThe dependence on radius of the melting temperature of dilute sets of spherical nanocrystals with wide radius distributions was determined by a novel procedure exclusively using the results of small-angle X-ray scattering measurements. The same procedure also allowed determination of the thermal expansion coefficients of nanoparticles in both liquid and crystalline phases.ENsmall-angle X-ray scatteringSAXSmeltingnanoparticlesthermal expansionsize-dependent contractionIn this investigation the dependence on radius of the melting temperature of dilute sets of spherical nanocrystals with wide radius distributions was determined by a novel procedure exclusively using the results of small-angle X-ray scattering (SAXS) measurements. This procedure is based on the sensitivity of the SAXS function to small and rather sharp variations in the size and electron density of nanocrystals at their melting temperature. The input for this procedure is a set of experimental SAXS intensity functions at selected q values for varying sample temperatures. In practice, the sample is heated from a minimum temperature, lower than the melting temperature of the smallest nanocrystals, up to a temperature higher than the melting temperature of the largest nanocrystals. The SAXS intensity is recorded in situ at different temperatures during the heating process. This novel procedure was applied to three samples composed of dilute sets of spherical Bi nanocrystals with wide radius distributions embedded in a sodium borate glass. The function relating the melting temperature of Bi nanocrystals with their radius – determined by using the procedure proposed here – agrees very well with the results reported in previous experimental studies using different methods. The results reported here also evidence the predicted size-dependent contraction of Bi nanocrystals induced by the large surface-to-volume ratio of small nanocrystals and an additional size-independent compressive stress caused by the solid glass matrix in which liquid Bi nanodroplets are initially formed. This last effect is a consequence of the increase in the volume of Bi nanoparticles upon crystallization and also of differences in the thermal expansion coefficients of the crystalline phase of Bi and the glass matrix. This additional stress leads to a depression of about 10 K in the melting temperature of the Bi nanocrystals confined in the glass. The procedure described here also allowed the determination of the specific masses and thermal expansion coefficients of Bi nanoparticles in both liquid and crystalline phases.text/htmlDetermination of the melting temperature of spherical nanoparticles in dilute solution as a function of their radius by exclusively using the small-angle X-ray scattering techniquetext2532020-03-25Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographyresearch papers455463Exact resolution function for double-disk chopper neutron time-of-flight spectrometers: application to reflectivity
http://scripts.iucr.org/cgi-bin/paper?ge5071
The exact resolution function of the transfer vector for the HERMÈS reflectometer at the Laboratoire Léon Brillouin is calculated as an example of a neutron time-of-flight spectrometer with a double-disk chopper. The calculation accounts for the wavelength distribution of the incident beam, the tilt of the chopper axis, collimation and gravity, without an assumption of Gaussian distributions or the independence of these different contributions. A numerical implementation is provided. It is shown that data fitting using this exact resolution function allows much better results to be reached than with the usual approximation by a Gaussian profile.Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Lairez, D.Chennevière, A.Ott, F.2020-03-25doi:10.1107/S1600576720001764International Union of CrystallographyThe different random variables that contribute to the final resolution of a time-of-flight neutron reflectometer are presented, and their exact distribution functions are considered and appropriately convoluted. The whole resolution function that accounts for all terms is writen analytically, a Python implementation is provided and it is shown how data fitting is improved compared with the usual approximation of a Gaussian profile.ENtime-of-flight spectrometersHERMÈS reflectometerneutronsresolutionreflectivityexact resolution functiondata fittingThe exact resolution function of the transfer vector for the HERMÈS reflectometer at the Laboratoire Léon Brillouin is calculated as an example of a neutron time-of-flight spectrometer with a double-disk chopper. The calculation accounts for the wavelength distribution of the incident beam, the tilt of the chopper axis, collimation and gravity, without an assumption of Gaussian distributions or the independence of these different contributions. A numerical implementation is provided. It is shown that data fitting using this exact resolution function allows much better results to be reached than with the usual approximation by a Gaussian profile.text/htmlExact resolution function for double-disk chopper neutron time-of-flight spectrometers: application to reflectivitytext2532020-03-25Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographyresearch papers464476Application of a high-throughput microcrystal delivery system to serial femtosecond crystallography
http://scripts.iucr.org/cgi-bin/paper?yr5056
Microcrystal delivery methods are pivotal in the use of serial femtosecond crystallography (SFX) to resolve the macromolecular structures of proteins. Here, the development of a novel technique and instruments for efficiently delivering microcrystals for SFX are presented. The new method, which relies on a one-dimensional fixed-target system that includes a microcrystal container, consumes an extremely low amount of sample compared with conventional two-dimensional fixed-target techniques at ambient temperature. This novel system can deliver soluble microcrystals without highly viscous carrier media and, moreover, can be used as a microcrystal growth device for SFX. Diffraction data collection utilizing this advanced technique along with a real-time visual servo scan system has been successfully demonstrated for the structure determination of proteinase K microcrystals at 1.85 Å resolution.Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Lee, D.Park, S.Lee, K.Kim, J.Park, G.Nam, K.H.Baek, S.Chung, W.K.Lee, J.-L.Cho, Y.Park, J.2020-03-25doi:10.1107/S1600576720002423International Union of CrystallographyA new one-dimensional fixed-target sample delivery method combined with a real-time visual servo scan system has been developed for serial femtosecond crystallography. The developed high-throughput microcrystal delivery system shows significant improvements for microcrystal delivery efficiency at an optimal crystal stability and significantly reduced sample consumption to reveal protein structures utilizing X-ray free-electron laser pulses.ENhigh-throughput microcrystal deliveryHT-MCDmicrocrystal delivery systemsserial femtosecond crystallographyX-ray free-electron lasersXFELsMicrocrystal delivery methods are pivotal in the use of serial femtosecond crystallography (SFX) to resolve the macromolecular structures of proteins. Here, the development of a novel technique and instruments for efficiently delivering microcrystals for SFX are presented. The new method, which relies on a one-dimensional fixed-target system that includes a microcrystal container, consumes an extremely low amount of sample compared with conventional two-dimensional fixed-target techniques at ambient temperature. This novel system can deliver soluble microcrystals without highly viscous carrier media and, moreover, can be used as a microcrystal growth device for SFX. Diffraction data collection utilizing this advanced technique along with a real-time visual servo scan system has been successfully demonstrated for the structure determination of proteinase K microcrystals at 1.85 Å resolution.text/htmlApplication of a high-throughput microcrystal delivery system to serial femtosecond crystallographytext2532020-03-25Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographyresearch papers477485X-ray characterization of self-standing bent Si crystal plates for Large Hadron Collider beam extraction
http://scripts.iucr.org/cgi-bin/paper?ks5641
Bent crystals can be used to deflect high-energy charged particles for beam extraction and/or beam collimation at accelerator facilities, thanks to the channelling phenomenon. In the present paper, two perfect silicon mono-crystals were bent using two different methods: sandblasting and the application of a carbon fibre composite. In particular, these samples were obtained for the realization of bent crystal prototypes to be used to steer the 7 TeV proton beam of the Large Hadron Collider in the context of the CRYSBEAM project. The two bending methods were selected since they allow a very homogeneous curvature of the crystals to be obtained, which is essential for high channelling efficiency. Moreover, the deformation obtained is self-standing, i.e. there is no need for any external device to keep the samples bent. Self-standing curvature can be useful because the presence of an external bender could be a severe limitation in the collider beam-pipe. The curvature of the samples was measured through high-energy X-ray diffraction at the ID11 beamline of the European Synchrotron Radiation Facility in Grenoble, France. Since the diffraction efficiencies obtained were in good agreement with theoretical expectations, it follows that the manufacturing techniques did not damage the samples, i.e. the crystallographic quality was preserved. Finally, the crystal quality of the sandblasted sample was investigated in detail at the synchrotron source at Karlsruhe Institute of Technology by X-ray white-beam topography. The measurements showed no diffusion of defects from the machined surfaces to the crystal bulk.Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Camattari, R.Romagnoni, M.Bandiera, L.Bagli, E.Mazzolari, A.Sytov, A.Haaga, S.Kabukcuoglu, M.Bode, S.Hänschke, D.Danilewsky, A.Baumbach, T.Bellucci, V.Guidi, V.Cavoto, G.2020-03-30doi:10.1107/S1600576720002800International Union of CrystallographyTwo perfect silicon mono-crystals were bent to be used to deflect high-energy charged particle beams in the context of beam extraction and/or beam collimation at accelerator facilities, such as for steering the 7 TeV proton beam of the Large Hadron Collider. The sample curvature and quality were tested at the ID11 beamline of the European Synchrotron Radiation Facility via hard X-ray diffraction and at the Karlsruhe Institute of Technology synchrotron via X-ray white-beam topography.ENself-standing bent crystalshard X-ray diffractionX-ray white-beam topographychannellingLarge Hadron ColliderLHC beam extractionBent crystals can be used to deflect high-energy charged particles for beam extraction and/or beam collimation at accelerator facilities, thanks to the channelling phenomenon. In the present paper, two perfect silicon mono-crystals were bent using two different methods: sandblasting and the application of a carbon fibre composite. In particular, these samples were obtained for the realization of bent crystal prototypes to be used to steer the 7 TeV proton beam of the Large Hadron Collider in the context of the CRYSBEAM project. The two bending methods were selected since they allow a very homogeneous curvature of the crystals to be obtained, which is essential for high channelling efficiency. Moreover, the deformation obtained is self-standing, i.e. there is no need for any external device to keep the samples bent. Self-standing curvature can be useful because the presence of an external bender could be a severe limitation in the collider beam-pipe. The curvature of the samples was measured through high-energy X-ray diffraction at the ID11 beamline of the European Synchrotron Radiation Facility in Grenoble, France. Since the diffraction efficiencies obtained were in good agreement with theoretical expectations, it follows that the manufacturing techniques did not damage the samples, i.e. the crystallographic quality was preserved. Finally, the crystal quality of the sandblasted sample was investigated in detail at the synchrotron source at Karlsruhe Institute of Technology by X-ray white-beam topography. The measurements showed no diffusion of defects from the machined surfaces to the crystal bulk.text/htmlX-ray characterization of self-standing bent Si crystal plates for Large Hadron Collider beam extractiontext2532020-03-30Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographyresearch papers486493Experimental determination of precision, resolution, accuracy and trueness of time-of-flight neutron diffraction strain measurements
http://scripts.iucr.org/cgi-bin/paper?ks5645
A simple statistical analysis which yields the precision, resolution, accuracy and trueness of diffraction-based lattice strain measurements is discussed. The procedure consists of measuring the thermal expansion induced in each component of an ideal non-reacting two-component crystalline powder sample in situ. One component, with a high coefficient of thermal expansion (CTE), serves as an internal thermometer. The quantities of interest are obtained by determining the smallest statistically significant thermal lattice strain which can be detected through diffraction analysis in the second, low-CTE, component in response to controlled temperature changes. This procedure also provides a robust check of the alignment of the diffraction system and is able to reveal the presence of systematic errors. The application of this technique to a time-of-flight engineering diffractometer/strain scanner is presented.Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Noyan, I.C.Bunn, J.R.Tippett, M.K.Payzant, E.A.Clausen, B.Brown, D.W.2020-03-30doi:10.1107/S1600576720002150International Union of CrystallographyStatistical analysis of thermal lattice strains can be used to characterize the precision, resolution, accuracy and trueness of diffraction-based lattice strain measurements. These strains can also be used to check the alignment of the diffractometer.ENprecisionresolutionaccuracytruenesstime of flightA simple statistical analysis which yields the precision, resolution, accuracy and trueness of diffraction-based lattice strain measurements is discussed. The procedure consists of measuring the thermal expansion induced in each component of an ideal non-reacting two-component crystalline powder sample in situ. One component, with a high coefficient of thermal expansion (CTE), serves as an internal thermometer. The quantities of interest are obtained by determining the smallest statistically significant thermal lattice strain which can be detected through diffraction analysis in the second, low-CTE, component in response to controlled temperature changes. This procedure also provides a robust check of the alignment of the diffraction system and is able to reveal the presence of systematic errors. The application of this technique to a time-of-flight engineering diffractometer/strain scanner is presented.text/htmlExperimental determination of precision, resolution, accuracy and trueness of time-of-flight neutron diffraction strain measurementstext2532020-03-30Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographyresearch papers494511Monte Carlo simulation of neutron scattering by a textured polycrystal
http://scripts.iucr.org/cgi-bin/paper?in5032
A method of simulating the neutron scattering by a textured polycrystal is presented. It is based on an expansion of the scattering cross sections in terms of the spherical harmonics of the incident and scattering directions, which is derived from the generalized Fourier expansion of the polycrystal orientation distribution function. The method has been implemented in a Monte Carlo code as a component of the McStas software package, and it has been validated by computing some pole figures of a Zircaloy-4 plate and a Zr–2.5Nb pressure tube, and by simulating an ideal transmission experiment. The code can be used to estimate the background generated by components of neutron instruments such as pressure cells, whose walls are made of alloys with significant crystallographic texture. As a first application, the effect of texture on the signal-to-noise ratio was studied in a simple model of a diffraction experiment, in which a sample is placed inside a pressure cell made of a zirconium alloy. With this setting, the results of two simulations were compared: one in which the pressure-cell wall has a uniform distribution of grain orientations, and another in which the pressure cell has the texture of a Zr–2.5Nb pressure tube. The results showed that the effect of the texture of the pressure cell on the noise of a diffractogram is very important. Thus, the signal-to-noise ratio can be controlled by appropriate choice of the texture of the pressure-cell walls.Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Laliena, V.Vicente-Álvarez, M.Á.Campo, J.2020-03-30doi:10.1107/S1600576720002290International Union of CrystallographyA method of simulating the diffraction of thermal neutrons by polycrystalline materials, using the generalized Fourier transform of the orientation distribution function, is developed and implemented in a Monte Carlo code in the McStas software package. Simulations to validate the code and a first application are also presented.ENneutron diffractioncrystallographic textureMonte Carlo simulationsA method of simulating the neutron scattering by a textured polycrystal is presented. It is based on an expansion of the scattering cross sections in terms of the spherical harmonics of the incident and scattering directions, which is derived from the generalized Fourier expansion of the polycrystal orientation distribution function. The method has been implemented in a Monte Carlo code as a component of the McStas software package, and it has been validated by computing some pole figures of a Zircaloy-4 plate and a Zr–2.5Nb pressure tube, and by simulating an ideal transmission experiment. The code can be used to estimate the background generated by components of neutron instruments such as pressure cells, whose walls are made of alloys with significant crystallographic texture. As a first application, the effect of texture on the signal-to-noise ratio was studied in a simple model of a diffraction experiment, in which a sample is placed inside a pressure cell made of a zirconium alloy. With this setting, the results of two simulations were compared: one in which the pressure-cell wall has a uniform distribution of grain orientations, and another in which the pressure cell has the texture of a Zr–2.5Nb pressure tube. The results showed that the effect of the texture of the pressure cell on the noise of a diffractogram is very important. Thus, the signal-to-noise ratio can be controlled by appropriate choice of the texture of the pressure-cell walls.text/htmlMonte Carlo simulation of neutron scattering by a textured polycrystaltext2532020-03-30Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographyresearch papers512529In meso crystallogenesis. Compatibility of the lipid cubic phase with the synthetic digitonin analogue, glyco-diosgenin
http://scripts.iucr.org/cgi-bin/paper?gj5240
Digitonin has long been used as a mild detergent for extracting proteins from membranes for structure and function studies. As supplied commercially, digitonin is inhomogeneous and requires lengthy pre-treatment for reliable downstream use. Glyco-diosgenin (GDN) is a recently introduced synthetic surfactant with features that mimic digitonin. It is available in homogeneously pure form. GDN is proving to be a useful detergent, particularly in the area of single-particle cryo-electron microscopic studies of membrane integral proteins. With a view to using it as a detergent for crystallization trials by the in meso or lipid cubic phase method, it was important to establish the carrying capacity of the cubic mesophase for GDN. This was quantified in the current study using small-angle X-ray scattering for mesophase identification and phase microstructure characterization as a function of temperature and GDN concentration. The data show that the lipid cubic phase formed by hydrated monoolein tolerates GDN to concentrations orders of magnitude in excess of those used for membrane protein studies. Thus, having GDN in a typical membrane protein preparation should not deter use of the in meso method for crystallogenesis.Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767van Dalsen, L.Weichert, D.Caffrey, M.2020-03-25doi:10.1107/S1600576720002289International Union of CrystallographyThe lipid cubic phase is compatible with the synthetic digitonin analogue, GDN, over a considerable range of concentrations, indeed well beyond those likely to be encountered in typical membrane crystallization studies. Thus, based on its compatibility with the cubic phase, there is every reason to use GDN as a detergent for preparing membrane proteins that are subsequently subjected to in meso crystallogenesis.ENin meso methodmembrane proteinmild non-ionic detergentsmall-angle X-ray scatteringX-ray crystal structureDigitonin has long been used as a mild detergent for extracting proteins from membranes for structure and function studies. As supplied commercially, digitonin is inhomogeneous and requires lengthy pre-treatment for reliable downstream use. Glyco-diosgenin (GDN) is a recently introduced synthetic surfactant with features that mimic digitonin. It is available in homogeneously pure form. GDN is proving to be a useful detergent, particularly in the area of single-particle cryo-electron microscopic studies of membrane integral proteins. With a view to using it as a detergent for crystallization trials by the in meso or lipid cubic phase method, it was important to establish the carrying capacity of the cubic mesophase for GDN. This was quantified in the current study using small-angle X-ray scattering for mesophase identification and phase microstructure characterization as a function of temperature and GDN concentration. The data show that the lipid cubic phase formed by hydrated monoolein tolerates GDN to concentrations orders of magnitude in excess of those used for membrane protein studies. Thus, having GDN in a typical membrane protein preparation should not deter use of the in meso method for crystallogenesis.text/htmlIn meso crystallogenesis. Compatibility of the lipid cubic phase with the synthetic digitonin analogue, glyco-diosgenintext2532020-03-25Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographyshort communications530535Simulation of small-angle X-ray scattering data of biological macromolecules in solution
http://scripts.iucr.org/cgi-bin/paper?vh5110
This article presents IMSIM, an application to simulate two-dimensional small-angle X-ray scattering patterns and, further, one-dimensional profiles from biological macromolecules in solution. IMSIM implements a statistical approach yielding two-dimensional images in TIFF, CBF or EDF format, which may be readily processed by existing data-analysis pipelines. Intensities and error estimates of one-dimensional patterns obtained from the radial average of the two-dimensional images exhibit the same statistical properties as observed with actual experimental data. With initial input on an absolute scale, [cm−1]/c[mg ml−1], the simulated data frames may also be scaled to absolute scale such that the forward scattering after subtraction of the background is proportional to the molecular weight of the solute. The effects of changes of concentration, exposure time, flux, wavelength, sample–detector distance, detector dimensions, pixel size, and the mask as well as incident beam position can be considered for the simulation. The simulated data may be used in method development, for educational purposes, and also to determine the most suitable beamline setup for a project prior to the application and use of the actual beamtime. IMSIM is available as part of the ATSAS software package (3.0.0) and is freely available for academic use (http://www.embl-hamburg.de/biosaxs/download.html).Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Franke, D.Hajizadeh, N.R.Svergun, D.I.2020-02-18doi:10.1107/S1600576720000527International Union of CrystallographyAn application is presented to simulate images on an area detector for isotropic small-angle X-ray scattering, explicitly accounting for the experimental geometry and yielding radially averaged 1D scattering patterns with statistically appropriate variations.ENsmall-angle X-ray scatteringSAXSdata simulationcomputer programssolution scatteringThis article presents IMSIM, an application to simulate two-dimensional small-angle X-ray scattering patterns and, further, one-dimensional profiles from biological macromolecules in solution. IMSIM implements a statistical approach yielding two-dimensional images in TIFF, CBF or EDF format, which may be readily processed by existing data-analysis pipelines. Intensities and error estimates of one-dimensional patterns obtained from the radial average of the two-dimensional images exhibit the same statistical properties as observed with actual experimental data. With initial input on an absolute scale, [cm−1]/c[mg ml−1], the simulated data frames may also be scaled to absolute scale such that the forward scattering after subtraction of the background is proportional to the molecular weight of the solute. The effects of changes of concentration, exposure time, flux, wavelength, sample–detector distance, detector dimensions, pixel size, and the mask as well as incident beam position can be considered for the simulation. The simulated data may be used in method development, for educational purposes, and also to determine the most suitable beamline setup for a project prior to the application and use of the actual beamtime. IMSIM is available as part of the ATSAS software package (3.0.0) and is freely available for academic use (http://www.embl-hamburg.de/biosaxs/download.html).text/htmlSimulation of small-angle X-ray scattering data of biological macromolecules in solutiontext2532020-02-18Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographycomputer programs536539Visualization of texture components using MTEX
http://scripts.iucr.org/cgi-bin/paper?nb5247
Knowledge of the appearance of texture components and fibres in pole figures, in inverse pole figures and in Euler space is fundamental for texture analysis. For cubic crystal systems, such as steels, an extensive literature exists and, for example, the book by Matthies, Vinel & Helming [Standard Distributions in Texture Analysis: Maps for the Case of Cubic Orthorhomic Symmetry, (1987), Akademie-Verlag Berlin] provides an atlas to identify texture components. For lower crystal symmetries, however, equivalent comprehensive overviews that can serve as guidance for the interpretation of experimental textures do not exist. This paper closes this gap by providing a set of scripts for the MTEX package [Bachmann, Hielscher & Schaeben (2010). Solid State Phenom. 160, 63–68] that allow the texture practitioner to compile such an atlas for a given material system, thus aiding orientation distribution function analysis also for non-cubic systems.Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Rafailov, G.Caspi, E.N.Hielscher, R.Tiferet, E.Schneck, R.Vogel, S.C.2020-02-18doi:10.1107/S1600576719014742International Union of CrystallographyKnowledge of the appearance of texture components and fibres in pole figures, in inverse pole figures and in Euler space is fundamental for texture analysis; an MTEX-based tool is presented to predict their appearance to enable subsequent quantitative texture analysis.ENtexturepole figuresinverse pole figuresorientation distribution functionODFMTEXKnowledge of the appearance of texture components and fibres in pole figures, in inverse pole figures and in Euler space is fundamental for texture analysis. For cubic crystal systems, such as steels, an extensive literature exists and, for example, the book by Matthies, Vinel & Helming [Standard Distributions in Texture Analysis: Maps for the Case of Cubic Orthorhomic Symmetry, (1987), Akademie-Verlag Berlin] provides an atlas to identify texture components. For lower crystal symmetries, however, equivalent comprehensive overviews that can serve as guidance for the interpretation of experimental textures do not exist. This paper closes this gap by providing a set of scripts for the MTEX package [Bachmann, Hielscher & Schaeben (2010). Solid State Phenom. 160, 63–68] that allow the texture practitioner to compile such an atlas for a given material system, thus aiding orientation distribution function analysis also for non-cubic systems.text/htmlVisualization of texture components using MTEXtext2532020-02-18Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographycomputer programs540548RADDOSE-XFEL: femtosecond time-resolved dose estimates for macromolecular X-ray free-electron laser experiments
http://scripts.iucr.org/cgi-bin/paper?jo5054
For macromolecular structure determination at synchrotron sources, radiation damage remains a major limiting factor. Estimation of the absorbed dose (J kg−1) during data collection at these sources by programs such as RADDOSE-3D has allowed direct comparison of radiation damage between experiments carried out with different samples and beam parameters. This has enabled prediction of roughly when radiation damage will manifest so it can potentially be avoided. X-ray free-electron lasers (XFELs), which produce intense X-ray pulses only a few femtoseconds in duration, can be used to generate diffraction patterns before most of the radiation damage processes have occurred and hence hypothetically they enable the determination of damage-free atomic resolution structures. In spite of this, several experimental and theoretical studies have suggested that structures from XFELs are not always free of radiation damage. There are currently no freely available programs designed to calculate the dose absorbed during XFEL data collection. This article presents an extension to RADDOSE-3D called RADDOSE-XFEL, which calculates the time-resolved dose during XFEL experiments. It is anticipated that RADDOSE-XFEL could be used to facilitate the study of radiation damage at XFELs and ultimately be used prior to data collection so that experimenters can plan their experiments to avoid radiation damage manifesting in their structures.Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Dickerson, J.L.McCubbin, P.T.N.Garman, E.F.2020-02-18doi:10.1107/S1600576720000643International Union of CrystallographyA new extension to RADDOSE-3D, RADDOSE-XFEL, is presented. RADDOSE-XFEL estimates the dose absorbed during macromolecular X-ray free-electron laser experiments by tracking physical phenomena on the femtosecond timescale.ENradiation damagedoseX-ray free-electron lasersXFELsprotein crystallographyserial femtosecond crystallographycomputer programsFor macromolecular structure determination at synchrotron sources, radiation damage remains a major limiting factor. Estimation of the absorbed dose (J kg−1) during data collection at these sources by programs such as RADDOSE-3D has allowed direct comparison of radiation damage between experiments carried out with different samples and beam parameters. This has enabled prediction of roughly when radiation damage will manifest so it can potentially be avoided. X-ray free-electron lasers (XFELs), which produce intense X-ray pulses only a few femtoseconds in duration, can be used to generate diffraction patterns before most of the radiation damage processes have occurred and hence hypothetically they enable the determination of damage-free atomic resolution structures. In spite of this, several experimental and theoretical studies have suggested that structures from XFELs are not always free of radiation damage. There are currently no freely available programs designed to calculate the dose absorbed during XFEL data collection. This article presents an extension to RADDOSE-3D called RADDOSE-XFEL, which calculates the time-resolved dose during XFEL experiments. It is anticipated that RADDOSE-XFEL could be used to facilitate the study of radiation damage at XFELs and ultimately be used prior to data collection so that experimenters can plan their experiments to avoid radiation damage manifesting in their structures.text/htmlRADDOSE-XFEL: femtosecond time-resolved dose estimates for macromolecular X-ray free-electron laser experimentstext2532020-02-18Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographycomputer programs549560τompas: a free and integrated tool for online crystallographic analysis in transmission electron microscopy
http://scripts.iucr.org/cgi-bin/paper?ks5644
τompas (TEM online multi-purpose analyzing system) is a free and integrated software tool designed to perform online crystallographic analysis in transmission electron microscopy (TEM) experiments. By using sample holder tilt angles as input, τompas can simultaneously simulate pole figures, Kikuchi patterns and feature projections, providing graphical views of the sample crystallography. These simulations are further employed to navigate sample tilting and to quickly interpret experimental Kikuchi patterns and images by image matching, giving self-consistent indices of features and crystal orientations. These functions are integrated with mouse operations to improve work efficiency. τompas is distributed as a small cross-platform program that can be installed on a microscope computer to cooperate with other tools.Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Xie, R.-X.Zhang, W.-Z.2020-02-21doi:10.1107/S1600576720000801International Union of Crystallographyτompas is a software tool designed to facilitate transmission electron microscopy (TEM) experiments with real-time simulation of pole figures, Kikuchi patterns and feature projections according to sample holder tilt angles. τompas can replace a significant number of crystallographic calculations, making it convenient for performing online crystallographic analysis in conventional TEM.ENtransmission electron microscopy (TEM)Kikuchi patternselectron diffractiontrace analysisτompas (TEM online multi-purpose analyzing system) is a free and integrated software tool designed to perform online crystallographic analysis in transmission electron microscopy (TEM) experiments. By using sample holder tilt angles as input, τompas can simultaneously simulate pole figures, Kikuchi patterns and feature projections, providing graphical views of the sample crystallography. These simulations are further employed to navigate sample tilting and to quickly interpret experimental Kikuchi patterns and images by image matching, giving self-consistent indices of features and crystal orientations. These functions are integrated with mouse operations to improve work efficiency. τompas is distributed as a small cross-platform program that can be installed on a microscope computer to cooperate with other tools.text/htmlτompas: a free and integrated tool for online crystallographic analysis in transmission electron microscopytext2532020-02-21Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographycomputer programs561568IMRPS: Inserted and Modified Residues in Protein Structures. A database
http://scripts.iucr.org/cgi-bin/paper?ei5050
Modified residues present in proteins are the result of post-translational modifications (PTMs). These PTMs increase the functional diversity of the proteome and influence various biological processes and diseased conditions. Therefore, identification and understanding of PTMs in various protein structures is of great significance. In view of this, an online database, Inserted and Modified Residues in Protein Structures (IMRPS), has been developed. IMRPS is a derived database that furnishes information on the residues modified and inserted in the protein structures available in the Protein Data Bank (PDB). The database is equipped with a graphical user interface and has an option to view the data for non-redundant protein structures (25 and 90%) as well. A quality criteria cutoff has been incorporated to assist in displaying the specific set of PDB codes. The entire protein structure along with the inserted or modified residues can be visualized in JSmol. This database will be updated regularly (presently, every three months) and can be accessed through the URL http://cluster.physics.iisc.ac.in/imrps/.Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Santhosh, R.Bankoti, N.Gurudarshan, M.Jeyakanthan, J.Sekar, K.2020-03-13doi:10.1107/S1600576720001880International Union of CrystallographyIMRPS is an interactive database for identifying and displaying the inserted and modified residues present in the protein structures available in the Protein Data Bank.ENpost-translational modificationsinserted residuesmodified residuesprotein structuresknowledgebaseModified residues present in proteins are the result of post-translational modifications (PTMs). These PTMs increase the functional diversity of the proteome and influence various biological processes and diseased conditions. Therefore, identification and understanding of PTMs in various protein structures is of great significance. In view of this, an online database, Inserted and Modified Residues in Protein Structures (IMRPS), has been developed. IMRPS is a derived database that furnishes information on the residues modified and inserted in the protein structures available in the Protein Data Bank (PDB). The database is equipped with a graphical user interface and has an option to view the data for non-redundant protein structures (25 and 90%) as well. A quality criteria cutoff has been incorporated to assist in displaying the specific set of PDB codes. The entire protein structure along with the inserted or modified residues can be visualized in JSmol. This database will be updated regularly (presently, every three months) and can be accessed through the URL http://cluster.physics.iisc.ac.in/imrps/.text/htmlIMRPS: Inserted and Modified Residues in Protein Structures. A databasetext2532020-03-13Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographycomputer programs569573PtychoShelves, a versatile high-level framework for high-performance analysis of ptychographic data
http://scripts.iucr.org/cgi-bin/paper?zy5001
Over the past decade, ptychography has been proven to be a robust tool for non-destructive high-resolution quantitative electron, X-ray and optical microscopy. It allows for quantitative reconstruction of the specimen's transmissivity, as well as recovery of the illuminating wavefront. Additionally, various algorithms have been developed to account for systematic errors and improved convergence. With fast ptychographic microscopes and more advanced algorithms, both the complexity of the reconstruction task and the data volume increase significantly. PtychoShelves is a software package which combines high-level modularity for easy and fast changes to the data-processing pipeline, and high-performance computing on CPUs and GPUs.Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Wakonig, K.Stadler, H.-C.Odstrčil, M.Tsai, E.H.R.Diaz, A.Holler, M.Usov, I.Raabe, J.Menzel, A.Guizar-Sicairos, M.2020-03-13doi:10.1107/S1600576720001776International Union of CrystallographyA new computer program for analysing ptychographic data combines both high-level simplicity and high-performance computing on large-scale computing clusters. It is available with a royalty-free non-exclusive licence for academic and non-commercial purposes.ENptychographyPtychoShelvesMATLABhigh-performance computingphase retrievalsynchrotronsOver the past decade, ptychography has been proven to be a robust tool for non-destructive high-resolution quantitative electron, X-ray and optical microscopy. It allows for quantitative reconstruction of the specimen's transmissivity, as well as recovery of the illuminating wavefront. Additionally, various algorithms have been developed to account for systematic errors and improved convergence. With fast ptychographic microscopes and more advanced algorithms, both the complexity of the reconstruction task and the data volume increase significantly. PtychoShelves is a software package which combines high-level modularity for easy and fast changes to the data-processing pipeline, and high-performance computing on CPUs and GPUs.text/htmlPtychoShelves, a versatile high-level framework for high-performance analysis of ptychographic datatext2532020-03-13Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographycomputer programs574586RaDMaX online: a web-based program for the determination of strain and damage profiles in irradiated crystals using X-ray diffraction
http://scripts.iucr.org/cgi-bin/paper?nb5270
RaDMaX online is a major update to the previously published RaDMaX (radiation damage in materials analysed with X-ray diffraction) software [Souilah, Boulle & Debelle (2016). J. Appl. Cryst. 49, 311–316]. This program features a user-friendly interface that allows retrieval of strain and disorder depth profiles in irradiated crystals from the simulation of X-ray diffraction data recorded in symmetrical θ/2θ mode. As compared with its predecessor, RaDMaX online has been entirely rewritten in order to be able to run within a simple web browser, therefore avoiding the necessity to install any programming environment on the users' computers. The RaDMaX online web application is written in Python and developed within a Jupyter notebook implementing graphical widgets and interactive plots. RaDMaX online is free and open source and can be accessed on the internet at https://aboulle.github.io/RaDMaX-online/.Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Boulle, A.Mergnac, V.2020-03-25doi:10.1107/S1600576720002514International Union of CrystallographyRaDMaX online is a web-based program for the determination of strain and disorder depth profiles in ion-irradiated materials from the simulation of X-ray diffraction data. It can be accessed at https://aboulle.github.io/RaDMaX-online/.ENX-ray diffractionPythoncomputingweb developmentradiation damageRaDMaX online is a major update to the previously published RaDMaX (radiation damage in materials analysed with X-ray diffraction) software [Souilah, Boulle & Debelle (2016). J. Appl. Cryst. 49, 311–316]. This program features a user-friendly interface that allows retrieval of strain and disorder depth profiles in irradiated crystals from the simulation of X-ray diffraction data recorded in symmetrical θ/2θ mode. As compared with its predecessor, RaDMaX online has been entirely rewritten in order to be able to run within a simple web browser, therefore avoiding the necessity to install any programming environment on the users' computers. The RaDMaX online web application is written in Python and developed within a Jupyter notebook implementing graphical widgets and interactive plots. RaDMaX online is free and open source and can be accessed on the internet at https://aboulle.github.io/RaDMaX-online/.text/htmlRaDMaX online: a web-based program for the determination of strain and damage profiles in irradiated crystals using X-ray diffractiontext2532020-03-25Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographylaboratory notes587593The Whats of a Scientific Life. By John R. Helliwell. CRC Press, 2019. Pp. 120. Price GBP 50.00 (hardback). ISBN 9780367233020.
http://scripts.iucr.org/cgi-bin/paper?xo0162
Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Lecomte, C.2020-03-13doi:10.1107/S1600576720000138International Union of CrystallographyBook review.ENbook reviewstext/htmlThe Whats of a Scientific Life. By John R. Helliwell. CRC Press, 2019. Pp. 120. Price GBP 50.00 (hardback). ISBN 9780367233020.text2532020-03-13Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographybook reviews594595Being an Interdisciplinary Academic: How Institutions Shape University Careers. By Catherine Lyall. Palgrave Pivot, 2019. Pp. 154. Price EUR 51.99 (hardcover). ISBN 978-3-030-18658-6.
http://scripts.iucr.org/cgi-bin/paper?xo0168
Copyright (c) 2020 International Union of Crystallographyurn:issn:1600-5767Helliwell, J.R.2020-03-13doi:10.1107/S1600576720002630International Union of CrystallographyBook review.ENbook reviewsinterdisciplinaritytext/htmlBeing an Interdisciplinary Academic: How Institutions Shape University Careers. By Catherine Lyall. Palgrave Pivot, 2019. Pp. 154. Price EUR 51.99 (hardcover). ISBN 978-3-030-18658-6.text2532020-03-13Copyright (c) 2020 International Union of CrystallographyJournal of Applied Crystallographybook reviews596597