Journal of Applied Crystallography
http://journals.iucr.org/j/issues/2016/04/00/isscontsbdy.html
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) 2016 International Union of Crystallography2016-06-23International 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 49, Part 4, 2016textweekly62002-02-01T00:00+00:004492016-06-23Copyright (c) 2016 International Union of CrystallographyJournal of Applied Crystallography1117urn:issn:1600-5767med@iucr.orgJune 20162016-06-23Journal of Applied Crystallographyhttp://journals.iucr.org/logos/rss10j.gif
http://journals.iucr.org/j/issues/2016/04/00/isscontsbdy.html
Still imageMeasurement and modeling of polarized specular neutron reflectivity in large magnetic fields
http://scripts.iucr.org/cgi-bin/paper?ge5021
The presence of a large applied magnetic field removes the degeneracy of the vacuum energy states for spin-up and spin-down neutrons. For polarized neutron reflectometry, this must be included in the reference potential energy of the Schrödinger equation that is used to calculate the expected scattering from a magnetic layered structure. For samples with magnetization that is purely parallel or antiparallel to the applied field which defines the quantization axis, there is no mixing of the spin states (no spin-flip scattering) and so this additional potential is constant throughout the scattering region. When there is non-collinear magnetization in the sample, however, there will be significant scattering from one spin state into the other, and the reference potentials will differ between the incoming and outgoing wavefunctions, changing the angle and intensities of the scattering. The theory of the scattering and recommended experimental practices for this type of measurement are presented, as well as an example measurement.Copyright (c) 2016 Brian B. Maranville et al.urn:issn:1600-5767Maranville, B.B.Kirby, B.J.Grutter, A.J.Kienzle, P.A.Majkrzak, C.F.Liu, Y.Dennis, C.L.2016-06-09doi:10.1107/S1600576716007135International Union of CrystallographyA procedure is described for polarized neutron reflectometry when the Zeeman corrections are significant, which occurs when both the magnetic anisotropy and the applied magnetic field are significant. Calculations and a recommended procedure for an example system are provided.ENpolarized neutron reflectometryapplied magnetic fieldsZeeman correctionsnon-collinear magnetizationThe presence of a large applied magnetic field removes the degeneracy of the vacuum energy states for spin-up and spin-down neutrons. For polarized neutron reflectometry, this must be included in the reference potential energy of the Schrödinger equation that is used to calculate the expected scattering from a magnetic layered structure. For samples with magnetization that is purely parallel or antiparallel to the applied field which defines the quantization axis, there is no mixing of the spin states (no spin-flip scattering) and so this additional potential is constant throughout the scattering region. When there is non-collinear magnetization in the sample, however, there will be significant scattering from one spin state into the other, and the reference potentials will differ between the incoming and outgoing wavefunctions, changing the angle and intensities of the scattering. The theory of the scattering and recommended experimental practices for this type of measurement are presented, as well as an example measurement.text/htmlMeasurement and modeling of polarized specular neutron reflectivity in large magnetic fieldstext4492016-06-09Copyright (c) 2016 Brian B. Maranville et al.Journal of Applied Crystallographyresearch papers00Investigation of dissimilar metal welds by energy-resolved neutron imaging
http://scripts.iucr.org/cgi-bin/paper?ks5507
A nondestructive study of the internal structure and compositional gradient of dissimilar metal-alloy welds through energy-resolved neutron imaging is described in this paper. The ability of neutrons to penetrate thick metal objects (up to several cm) provides a unique possibility to examine samples which are opaque to other conventional techniques. The presence of Bragg edges in the measured neutron transmission spectra can be used to characterize the internal residual strain within the samples and some microstructural features, e.g. texture within the grains, while neutron resonance absorption provides the possibility to map the degree of uniformity in mixing of the participating alloys and intermetallic formation within the welds. In addition, voids and other defects can be revealed by the variation of neutron attenuation across the samples. This paper demonstrates the potential of neutron energy-resolved imaging to measure all these characteristics simultaneously in a single experiment with sub-mm spatial resolution. Two dissimilar alloy welds are used in this study: Al autogenously laser welded to steel, and Ti gas metal arc welded (GMAW) to stainless steel using Cu as a filler alloy. The cold metal transfer variant of the GMAW process was used in joining the Ti to the stainless steel in order to minimize the heat input. The distributions of the lattice parameter and texture variation in these welds as well as the presence of voids and defects in the melt region are mapped across the welds. The depth of the thermal front in the Al–steel weld is clearly resolved and could be used to optimize the welding process. A highly textured structure is revealed in the Ti to stainless steel joint where copper was used as a filler wire. The limited diffusion of Ti into the weld region is also verified by the resonance absorption.Copyright (c) 2016 Anton S. Tremsin et al.urn:issn:1600-5767Tremsin, A.S.Ganguly, S.Meco, S.M.Pardal, G.R.Shinohara, T.Feller, W.B.2016-06-09doi:10.1107/S1600576716006725International Union of CrystallographyEnergy-resolved neutron imaging is used for a nondestructive study of bulk internal microstructure, elemental composition and distribution of voids in dissimilar metal-alloy welds of ∼10 mm thickness. All these characteristics are measured simultaneously in one experiment with a few hundred micrometre spatial resolution.ENnondestructive testinglaser weldingdissimilar joiningmicrostructureneutron imagingA nondestructive study of the internal structure and compositional gradient of dissimilar metal-alloy welds through energy-resolved neutron imaging is described in this paper. The ability of neutrons to penetrate thick metal objects (up to several cm) provides a unique possibility to examine samples which are opaque to other conventional techniques. The presence of Bragg edges in the measured neutron transmission spectra can be used to characterize the internal residual strain within the samples and some microstructural features, e.g. texture within the grains, while neutron resonance absorption provides the possibility to map the degree of uniformity in mixing of the participating alloys and intermetallic formation within the welds. In addition, voids and other defects can be revealed by the variation of neutron attenuation across the samples. This paper demonstrates the potential of neutron energy-resolved imaging to measure all these characteristics simultaneously in a single experiment with sub-mm spatial resolution. Two dissimilar alloy welds are used in this study: Al autogenously laser welded to steel, and Ti gas metal arc welded (GMAW) to stainless steel using Cu as a filler alloy. The cold metal transfer variant of the GMAW process was used in joining the Ti to the stainless steel in order to minimize the heat input. The distributions of the lattice parameter and texture variation in these welds as well as the presence of voids and defects in the melt region are mapped across the welds. The depth of the thermal front in the Al–steel weld is clearly resolved and could be used to optimize the welding process. A highly textured structure is revealed in the Ti to stainless steel joint where copper was used as a filler wire. The limited diffusion of Ti into the weld region is also verified by the resonance absorption.text/htmlInvestigation of dissimilar metal welds by energy-resolved neutron imagingtext4492016-06-09Copyright (c) 2016 Anton S. Tremsin et al.Journal of Applied Crystallographyresearch papers00An approach to solving an ill posed inverse problem of residual stress depth profiling in thin films and compact solid materials
http://scripts.iucr.org/cgi-bin/paper?vg5045
The inverse problem of evaluating residual stresses σ(z) in real space using residual stresses σ(τ) in image space is discussed. This problem is ill posed and special solution methods are required in order to obtain a stable solution. Moreover, the real-space solution must be localized in reflecting layers only in multilayer systems. This requirement imposes strong restrictions on the solution methods and does not allow one to use methods based on the inverse Laplace transform employed for compact solid materials. Besides, in the case of solid materials, the use of the inverse Laplace transform often leads to extremely unstable solutions. The stable numerical solution of the discussed inverse problem can be found using a method based on the Tikhonov regularization. Given the measured data and their pointwise error estimation, this method provides stable approximate solutions for both solid materials and thin films in the form of piecewise functions defined solely in diffracting layers. The approximations are shown to converge to the exact function when the noise in the experimental data approaches zero. If the initial data satisfy certain constraints, the method provides a stable exact solution for the inverse problem. A freely available MATLAB package has been developed, and its efficiency was demonstrated in the numerical residual stress calculations carried out for solid materials and thin films.Copyright (c) 2016 International Union of Crystallographyurn:issn:1600-5767Tolstikhin, K.Scholtes, B.2016-06-09doi:10.1107/S1600576716007676International Union of CrystallographyAn approach to solving an ill posed inverse problem of determining actual residual stresses in thin films and compact solid materials using X-ray diffraction is described.ENresidual stressessteep gradientsthin filmsill posed problemsTikhonov regularizationThe inverse problem of evaluating residual stresses σ(z) in real space using residual stresses σ(τ) in image space is discussed. This problem is ill posed and special solution methods are required in order to obtain a stable solution. Moreover, the real-space solution must be localized in reflecting layers only in multilayer systems. This requirement imposes strong restrictions on the solution methods and does not allow one to use methods based on the inverse Laplace transform employed for compact solid materials. Besides, in the case of solid materials, the use of the inverse Laplace transform often leads to extremely unstable solutions. The stable numerical solution of the discussed inverse problem can be found using a method based on the Tikhonov regularization. Given the measured data and their pointwise error estimation, this method provides stable approximate solutions for both solid materials and thin films in the form of piecewise functions defined solely in diffracting layers. The approximations are shown to converge to the exact function when the noise in the experimental data approaches zero. If the initial data satisfy certain constraints, the method provides a stable exact solution for the inverse problem. A freely available MATLAB package has been developed, and its efficiency was demonstrated in the numerical residual stress calculations carried out for solid materials and thin films.text/htmlAn approach to solving an ill posed inverse problem of residual stress depth profiling in thin films and compact solid materialstext4492016-06-09Copyright (c) 2016 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Accurate optimization of amino acid form factors for computing small-angle X-ray scattering intensity of atomistic protein structures
http://scripts.iucr.org/cgi-bin/paper?vg5046
Structure modelling via small-angle X-ray scattering (SAXS) data generally requires intensive computations of scattering intensity from any given biomolecular structure, where the accurate evaluation of SAXS profiles using coarse-grained (CG) methods is vital to improve computational efficiency. To date, most CG SAXS computing methods have been based on a single-bead-per-residue approximation but have neglected structural correlations between amino acids. To improve the accuracy of scattering calculations, accurate CG form factors of amino acids are now derived using a rigorous optimization strategy, termed electron-density matching (EDM), to best fit electron-density distributions of protein structures. This EDM method is compared with and tested against other CG SAXS computing methods, and the resulting CG SAXS profiles from EDM agree better with all-atom theoretical SAXS data. By including the protein hydration shell represented by explicit CG water molecules and the correction of protein excluded volume, the developed CG form factors also reproduce the selected experimental SAXS profiles with very small deviations. Taken together, these EDM-derived CG form factors present an accurate and efficient computational approach for SAXS computing, especially when higher molecular details (represented by the q range of the SAXS data) become necessary for effective structure modelling.Copyright (c) 2016 International Union of Crystallographyurn:issn:1600-5767Tong, D.Yang, S.Lu, L.2016-06-20doi:10.1107/S1600576716007962International Union of CrystallographyCoarse-grained form factors are developed from a novel computational method for amino acid residues to enhance the computational efficiency of solution small-angle X-ray scattering modelling. The method is based on fitting the Fourier transform of protein electron density, and the resulting protein scattering intensity profiles are consistent with theoretical atomistic profiles and experimental data.ENsmall-angle X-ray scatteringform factorsproteinssolution X-ray scatteringcoarse grainingStructure modelling via small-angle X-ray scattering (SAXS) data generally requires intensive computations of scattering intensity from any given biomolecular structure, where the accurate evaluation of SAXS profiles using coarse-grained (CG) methods is vital to improve computational efficiency. To date, most CG SAXS computing methods have been based on a single-bead-per-residue approximation but have neglected structural correlations between amino acids. To improve the accuracy of scattering calculations, accurate CG form factors of amino acids are now derived using a rigorous optimization strategy, termed electron-density matching (EDM), to best fit electron-density distributions of protein structures. This EDM method is compared with and tested against other CG SAXS computing methods, and the resulting CG SAXS profiles from EDM agree better with all-atom theoretical SAXS data. By including the protein hydration shell represented by explicit CG water molecules and the correction of protein excluded volume, the developed CG form factors also reproduce the selected experimental SAXS profiles with very small deviations. Taken together, these EDM-derived CG form factors present an accurate and efficient computational approach for SAXS computing, especially when higher molecular details (represented by the q range of the SAXS data) become necessary for effective structure modelling.text/htmlAccurate optimization of amino acid form factors for computing small-angle X-ray scattering intensity of atomistic protein structurestext4492016-06-20Copyright (c) 2016 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Small-angle scattering and scale-dependent heterogeneity
http://scripts.iucr.org/cgi-bin/paper?ge5024
Although small-angle scattering is often discussed qualitatively in terms of material heterogeneity, when it comes to quantitative data analysis this notion becomes somehow hidden behind the concept of correlation function. In the present contribution, a quantitative measure of heterogeneity is defined, it is shown how it can be calculated from scattering data, and its structural significance for the purpose of material characterization is discussed. Conceptually, the procedure consists of using a finite probe volume to define a local average density at any point of the material; the heterogeneity is then quantitatively defined as the fluctuations of the local average density when the probe volume is moved systematically through the sample. Experimentally, it is shown that the so-defined heterogeneity can be estimated by projecting the small-angle scattering intensity onto the form factor of the chosen probe volume. Choosing probe volumes of various sizes and shapes enables one to comprehensively characterize the heterogeneity of a material over all its relevant length scales. General results are derived for asymptotically small and large probes in relation to the material surface area and integral range. It is also shown that the correlation function is equivalent to a heterogeneity calculated with a probe volume consisting of two points only. The interest of scale-dependent heterogeneity for practical data analysis is illustrated with experimental small-angle X-ray scattering patterns measured on a micro- and mesoporous material, on a gel, and on a semi-crystalline polyethylene sample. Using different types of probes to analyse a given scattering pattern enables one to focus on different structural characteristics of the material, which is particularly useful in the case of hierarchical structures.Copyright (c) 2016 International Union of Crystallographyurn:issn:1600-5767Gommes, C.J.2016-06-23doi:10.1107/S1600576716007810International Union of CrystallographyA quantitative measure for the scale-dependent heterogeneity of a structure is designed, which can be calculated from small-angle scattering data. This measure generalizes the notion of correlation function, and it leads to novel data analysis procedures.ENsmall-angle scatteringscale-dependent heterogeneityAlthough small-angle scattering is often discussed qualitatively in terms of material heterogeneity, when it comes to quantitative data analysis this notion becomes somehow hidden behind the concept of correlation function. In the present contribution, a quantitative measure of heterogeneity is defined, it is shown how it can be calculated from scattering data, and its structural significance for the purpose of material characterization is discussed. Conceptually, the procedure consists of using a finite probe volume to define a local average density at any point of the material; the heterogeneity is then quantitatively defined as the fluctuations of the local average density when the probe volume is moved systematically through the sample. Experimentally, it is shown that the so-defined heterogeneity can be estimated by projecting the small-angle scattering intensity onto the form factor of the chosen probe volume. Choosing probe volumes of various sizes and shapes enables one to comprehensively characterize the heterogeneity of a material over all its relevant length scales. General results are derived for asymptotically small and large probes in relation to the material surface area and integral range. It is also shown that the correlation function is equivalent to a heterogeneity calculated with a probe volume consisting of two points only. The interest of scale-dependent heterogeneity for practical data analysis is illustrated with experimental small-angle X-ray scattering patterns measured on a micro- and mesoporous material, on a gel, and on a semi-crystalline polyethylene sample. Using different types of probes to analyse a given scattering pattern enables one to focus on different structural characteristics of the material, which is particularly useful in the case of hierarchical structures.text/htmlSmall-angle scattering and scale-dependent heterogeneitytext4492016-06-23Copyright (c) 2016 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Characterization of crystal structure and precipitation crystallography of a new MgxAl2−xGd phase in an Mg97Al1Gd2 alloy
http://scripts.iucr.org/cgi-bin/paper?ks5516
The composition, crystal structure and precipitation crystallography of a newly found precipitate are characterized by Cs-corrected scanning transmission electron microscopy. The composition of the plate-like precipitate could be expressed as MgxAl2−xGd (x = 0.38), and its crystal structure is the same as the face-centered cubic type Laves phases Mg2Gd and Al2Gd, with a lattice parameter of 7.92 Å (space group No. 227, Fd\overline 3m). The orientation relationship between the matrix and precipitate is found to be (0001)m//(111)p and [10\overline 10]m//[1\overline 10]p, and the habit plane is parallel to the (0001)m//(111)p plane. In addition, this preferred crystallography of phase transformation is well explained on the basis of the atomic matching at the interface.Copyright (c) 2016 International Union of Crystallographyurn:issn:1600-5767Gu, X.-F.Furuhara, T.2016-06-23doi:10.1107/S1600576716008980International Union of CrystallographyThe composition, crystal structure and precipitation crystallography of a newfound MgxAl2−xGd precipitate are characterized by Cs-corrected scanning transmission electron microscopy.ENMg–Al–GdLaves phaseorientation relationshipsinterfacesatomic matchingThe composition, crystal structure and precipitation crystallography of a newly found precipitate are characterized by Cs-corrected scanning transmission electron microscopy. The composition of the plate-like precipitate could be expressed as MgxAl2−xGd (x = 0.38), and its crystal structure is the same as the face-centered cubic type Laves phases Mg2Gd and Al2Gd, with a lattice parameter of 7.92 Å (space group No. 227, Fd\overline 3m). The orientation relationship between the matrix and precipitate is found to be (0001)m//(111)p and [10\overline 10]m//[1\overline 10]p, and the habit plane is parallel to the (0001)m//(111)p plane. In addition, this preferred crystallography of phase transformation is well explained on the basis of the atomic matching at the interface.text/htmlCharacterization of crystal structure and precipitation crystallography of a new MgxAl2−xGd phase in an Mg97Al1Gd2 alloytext4492016-06-23Copyright (c) 2016 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Facile usage of a MYTHEN 1K with a Huber 5021 diffractometer and angular calibration in operando experiments
http://scripts.iucr.org/cgi-bin/paper?kc5032
A facile usage of a MYTHEN 1K detector with a Huber 5021 six-circle diffractometer is described in detail. A mechanical support has been custom designed for the first time to combine the MYTHEN 1K detector with a point detector, which can be used as a reference point for each individual pixel of the MYTHEN 1K during measurements. The MYTHEN 1K is mounted on the arm of the 2θ circle of the Huber diffractometer with an intrinsic angular resolution of ∼0.0038°, and its pitch angle can be automatically adjusted with an accuracy of 0.0072°. Standard procedures are discussed for its calibration. Programs have been written in the SPEC environment for simultaneous data conversion, integration and acquisition. The X-ray powder diffraction patterns of standard samples were measured in the Debye–Scherrer geometry and matched well with those of references. The angular shift due to sample-to-center displacement in the `flat-plate transmission' geometry, which is frequently employed in operando experiments, has been successfully investigated and can be efficiently corrected. One operando experiment using the MYTHEN 1K is presented. This work provides a straightforward procedure to use the MYTHEN 1K detector properly in Debye–Scherrer geometry, and could facilitate its application at other synchrotron facilities.Copyright (c) 2016 International Union of Crystallographyurn:issn:1600-5767Gao, M.Gu, Y.Li, L.Gong, Z.Gao, X.Wen, W.2016-06-23doi:10.1107/S1600576716008566International Union of CrystallographyA mechanical assembly has been successfully designed to combine a MYTHEN 1K with a point detector, and is proved facile for the angular calibration of individual pixels. In `flat-plate transmission' geometry, which is frequently used in various operando experiments, straightforward corrections can be efficiently made to compensate for sample displacement away from the diffractometer center.ENMYTHEN 1KX-ray powder diffractionsynchrotron radiationDebye–Scherrer geometryA facile usage of a MYTHEN 1K detector with a Huber 5021 six-circle diffractometer is described in detail. A mechanical support has been custom designed for the first time to combine the MYTHEN 1K detector with a point detector, which can be used as a reference point for each individual pixel of the MYTHEN 1K during measurements. The MYTHEN 1K is mounted on the arm of the 2θ circle of the Huber diffractometer with an intrinsic angular resolution of ∼0.0038°, and its pitch angle can be automatically adjusted with an accuracy of 0.0072°. Standard procedures are discussed for its calibration. Programs have been written in the SPEC environment for simultaneous data conversion, integration and acquisition. The X-ray powder diffraction patterns of standard samples were measured in the Debye–Scherrer geometry and matched well with those of references. The angular shift due to sample-to-center displacement in the `flat-plate transmission' geometry, which is frequently employed in operando experiments, has been successfully investigated and can be efficiently corrected. One operando experiment using the MYTHEN 1K is presented. This work provides a straightforward procedure to use the MYTHEN 1K detector properly in Debye–Scherrer geometry, and could facilitate its application at other synchrotron facilities.text/htmlFacile usage of a MYTHEN 1K with a Huber 5021 diffractometer and angular calibration in operando experimentstext4492016-06-23Copyright (c) 2016 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Symmetrized Bingham distribution for representing texture: parameter estimation with respect to crystal and sample symmetries
http://scripts.iucr.org/cgi-bin/paper?nb5173
The quaternion Bingham distribution has been used to model preferred crystallographic orientation, or crystallographic texture, in polycrystalline materials in the materials science and geological communities. A primary difficulty in applying the Bingham distribution has been the lack of an efficient method for fitting the distribution parameters with respect to the material's underlying crystallographic symmetry or any statistical sample symmetry due to processing. This paper presents a symmetrized distribution, based on the quaternion Bingham, which can account for any general combination of crystallographic or sample symmetries. A numerical scheme is also introduced for estimating the parameters of the symmetrized distribution based on the well known expectation maximization algorithm.Copyright (c) 2016 International Union of Crystallographyurn:issn:1600-5767Niezgoda, S.R.Magnuson, E.A.Glover, J.2016-06-09doi:10.1107/S160057671600649XInternational Union of CrystallographyThis short communication presents a symmetrized Bingham distribution for the modeling of crystallographic texture which can account for arbitrary crystallographic and statistical sample (resulting from material processing) symmetries. Additionally, an efficient computational scheme is presented for parameter estimation.ENtextureBingham distributionparameter estimationsymmetrymicrotextureThe quaternion Bingham distribution has been used to model preferred crystallographic orientation, or crystallographic texture, in polycrystalline materials in the materials science and geological communities. A primary difficulty in applying the Bingham distribution has been the lack of an efficient method for fitting the distribution parameters with respect to the material's underlying crystallographic symmetry or any statistical sample symmetry due to processing. This paper presents a symmetrized distribution, based on the quaternion Bingham, which can account for any general combination of crystallographic or sample symmetries. A numerical scheme is also introduced for estimating the parameters of the symmetrized distribution based on the well known expectation maximization algorithm.text/htmlSymmetrized Bingham distribution for representing texture: parameter estimation with respect to crystal and sample symmetriestext4492016-06-09Copyright (c) 2016 International Union of CrystallographyJournal of Applied Crystallographyshort communications00Dragonfly: an implementation of the expand–maximize–compress algorithm for single-particle imaging
http://scripts.iucr.org/cgi-bin/paper?zf5002
Single-particle imaging (SPI) with X-ray free-electron lasers has the potential to change fundamentally how biomacromolecules are imaged. The structure would be derived from millions of diffraction patterns, each from a different copy of the macromolecule before it is torn apart by radiation damage. The challenges posed by the resultant data stream are staggering: millions of incomplete, noisy and un-oriented patterns have to be computationally assembled into a three-dimensional intensity map and then phase reconstructed. In this paper, the Dragonfly software package is described, based on a parallel implementation of the expand–maximize–compress reconstruction algorithm that is well suited for this task. Auxiliary modules to simulate SPI data streams are also included to assess the feasibility of proposed SPI experiments at the Linac Coherent Light Source, Stanford, California, USA.Copyright (c) 2016 Kartik Ayyer et al.urn:issn:1600-5767Ayyer, K.Lan, T.-Y.Elser, V.Loh, N.D.2016-06-20doi:10.1107/S1600576716008165International Union of CrystallographyA description is given of a single-particle X-ray imaging reconstruction and simulation package using the expand–maximize–compress algorithm, named Dragonfly.ENsingle-particle imagingX-ray free-electron lasersXFELsexpand–maximize–compress reconstruction algorithmSingle-particle imaging (SPI) with X-ray free-electron lasers has the potential to change fundamentally how biomacromolecules are imaged. The structure would be derived from millions of diffraction patterns, each from a different copy of the macromolecule before it is torn apart by radiation damage. The challenges posed by the resultant data stream are staggering: millions of incomplete, noisy and un-oriented patterns have to be computationally assembled into a three-dimensional intensity map and then phase reconstructed. In this paper, the Dragonfly software package is described, based on a parallel implementation of the expand–maximize–compress reconstruction algorithm that is well suited for this task. Auxiliary modules to simulate SPI data streams are also included to assess the feasibility of proposed SPI experiments at the Linac Coherent Light Source, Stanford, California, USA.text/htmlDragonfly: an implementation of the expand–maximize–compress algorithm for single-particle imagingtext4492016-06-20Copyright (c) 2016 Kartik Ayyer et al.Journal of Applied Crystallographycomputer programs00CFEL–ASG Software Suite (CASS): usage for free-electron laser experiments with biological focus
http://scripts.iucr.org/cgi-bin/paper?zw5003
CASS [Foucar et al. (2012). Comput. Phys. Commun. 183, 2207–2213] is a well established software suite for experiments performed at any sort of light source. It is based on a modular design and can easily be adapted for use at free-electron laser (FEL) experiments that have a biological focus. This article will list all the additional functionality and enhancements of CASS for use with FEL experiments that have been introduced since the first publication. The article will also highlight some advanced experiments with biological aspects that have been performed.Copyright (c) 2016 Lutz Foucarurn:issn:1600-5767Foucar, L.2016-06-23doi:10.1107/S1600576716009201International Union of CrystallographyAn overview of how the well established CFEL–ASG Software Suite (CASS) can be used for serial femtosecond crystallography data is given.ENfree-electron lasersFELsdata analysisfemtosecond crystallographySFXsingle-particle experimentspump–probe techniquesfluorescencecomputer programsCASS [Foucar et al. (2012). Comput. Phys. Commun. 183, 2207–2213] is a well established software suite for experiments performed at any sort of light source. It is based on a modular design and can easily be adapted for use at free-electron laser (FEL) experiments that have a biological focus. This article will list all the additional functionality and enhancements of CASS for use with FEL experiments that have been introduced since the first publication. The article will also highlight some advanced experiments with biological aspects that have been performed.text/htmlCFEL–ASG Software Suite (CASS): usage for free-electron laser experiments with biological focustext4492016-06-23Copyright (c) 2016 Lutz FoucarJournal of Applied Crystallographycomputer programs00SPGGEN: a computer program for retrieval of space-group information in several settings and generator-containing space-group symbols
http://scripts.iucr.org/cgi-bin/paper?po5066
A brief outline of the algorithm for the derivation of a space group is followed by a detailed description of the explicit space-group symbols here employed. These space-group symbols are unique insofar as they contain explicitly the generators of the space group dealt with. Next, the implementation of the above in a computer program, SPGGEN, is briefly discussed and the options presented by the program are outlined. Briefly, these options are (i) conventional derivation of the space group from an explicit symbol, including a user-defined one; (ii) such derivation from the conventional space-group number only; (iii) introduction of a general setting into the derivation; (iv) introduction of a Cartesian setting into the derivation; and (v) treatment of some non-conventional settings of orthorhombic space groups. This is followed by a detailed comparison with International Tables for Crystallography, Vol. A, and by examples of the output of SPGGEN. A complete tabulation of the explicit three-dimensional space-group symbols is readily accessed.Copyright (c) 2016 International Union of Crystallographyurn:issn:1600-5767Shmueli, U.2016-06-09doi:10.1107/S1600576716007330International Union of CrystallographyA computer program for the retrieval of space-group information in several settings is presented, and the generator-containing space-group symbols on which the program is based are described and fully detailed for three-dimensional space groups.ENspace groupsexplicit symbolsgeneratorsgeneral settingCartesian settingcomputer programsA brief outline of the algorithm for the derivation of a space group is followed by a detailed description of the explicit space-group symbols here employed. These space-group symbols are unique insofar as they contain explicitly the generators of the space group dealt with. Next, the implementation of the above in a computer program, SPGGEN, is briefly discussed and the options presented by the program are outlined. Briefly, these options are (i) conventional derivation of the space group from an explicit symbol, including a user-defined one; (ii) such derivation from the conventional space-group number only; (iii) introduction of a general setting into the derivation; (iv) introduction of a Cartesian setting into the derivation; and (v) treatment of some non-conventional settings of orthorhombic space groups. This is followed by a detailed comparison with International Tables for Crystallography, Vol. A, and by examples of the output of SPGGEN. A complete tabulation of the explicit three-dimensional space-group symbols is readily accessed.text/htmlSPGGEN: a computer program for retrieval of space-group information in several settings and generator-containing space-group symbolstext4492016-06-09Copyright (c) 2016 International Union of CrystallographyJournal of Applied Crystallographycomputer programs00EosFit7-GUI: a new graphical user interface for equation of state calculations, analyses and teaching
http://scripts.iucr.org/cgi-bin/paper?kc5039
EosFit7-GUI is a full graphical user interface designed to simplify the analysis of thermal expansion and equations of state (EoSs). The software allows users to easily perform least-squares fitting of EoS parameters to diffraction data collected as a function of varying pressure, temperature or both. It has been especially designed to allow rapid graphical evaluation of both parametric data and the EoS fitted to the data, making it useful both for data analysis and for teaching.Copyright (c) 2016 International Union of Crystallographyurn:issn:1600-5767Gonzalez-Platas, J.Alvaro, M.Nestola, F.Angel, R.2016-06-20doi:10.1107/S1600576716008050International Union of CrystallographyEosFit7-GUI is a new full graphical user interface for analysing and fitting equations of state.ENequations of statethermal expansionhigh pressurehigh temperaturelow temperatureelasticityEosFit7-GUI is a full graphical user interface designed to simplify the analysis of thermal expansion and equations of state (EoSs). The software allows users to easily perform least-squares fitting of EoS parameters to diffraction data collected as a function of varying pressure, temperature or both. It has been especially designed to allow rapid graphical evaluation of both parametric data and the EoS fitted to the data, making it useful both for data analysis and for teaching.text/htmlEosFit7-GUI: a new graphical user interface for equation of state calculations, analyses and teachingtext4492016-06-20Copyright (c) 2016 International Union of CrystallographyJournal of Applied Crystallographycomputer programs00A portable light-delivery device for in situ photocrystallographic experiments in the home laboratory
http://scripts.iucr.org/cgi-bin/paper?kc5038
Photocrystallographic experiments provide valuable information on how crystalline samples interact with light, yielding light-induced structural changes. Studied processes include, among others, solid state chemical reactions, as well as isolation and characterization of various metastable states. Thus, some instrumentation development efforts in the field have been dedicated to facilitating such experiments using a home X-ray source. In this contribution, a portable, easy-to-use and adjustable light-delivery device for home single-crystal diffractometers is described. The whole system consists of adjustable laser-focusing optics and a holder, which can be conveniently attached to a goniometer, as an additional sample conditioning device. The light-delivery device was designed to reduce any goniometer movement limitations. It allows one to conveniently perform photocrystallographic experiments without violation of the X-ray safety protocols, even when changing the light source is necessary. Test in situ photocrystallographic experiments performed on the literature-reported Ni(NO2)2(dppe) complex [dppe is bis(diphenylphosphino)ethane] confirm the effectiveness and applicability of the device for conducting linkage isomer single-crystal-to-single-crystal transformations.Copyright (c) 2016 International Union of Crystallographyurn:issn:1600-5767Kamiński, R.Jarzembska, K.N.Kutyła, S.E.Kamiński, M.2016-06-20doi:10.1107/S1600576716008128International Union of CrystallographyA portable light-delivery device for home in situ photocrystallographic experiments is described and tested.ENlight-delivery devicesin situ photocrystallographysingle-crystal-to-single-crystal transformationslinkage isomersPhotocrystallographic experiments provide valuable information on how crystalline samples interact with light, yielding light-induced structural changes. Studied processes include, among others, solid state chemical reactions, as well as isolation and characterization of various metastable states. Thus, some instrumentation development efforts in the field have been dedicated to facilitating such experiments using a home X-ray source. In this contribution, a portable, easy-to-use and adjustable light-delivery device for home single-crystal diffractometers is described. The whole system consists of adjustable laser-focusing optics and a holder, which can be conveniently attached to a goniometer, as an additional sample conditioning device. The light-delivery device was designed to reduce any goniometer movement limitations. It allows one to conveniently perform photocrystallographic experiments without violation of the X-ray safety protocols, even when changing the light source is necessary. Test in situ photocrystallographic experiments performed on the literature-reported Ni(NO2)2(dppe) complex [dppe is bis(diphenylphosphino)ethane] confirm the effectiveness and applicability of the device for conducting linkage isomer single-crystal-to-single-crystal transformations.text/htmlA portable light-delivery device for in situ photocrystallographic experiments in the home laboratorytext4492016-06-20Copyright (c) 2016 International Union of CrystallographyJournal of Applied Crystallographylaboratory notes00Small-angle neutron scattering spectrometer Suanni equipped with ultra-thin biconcave focusing lenses
http://scripts.iucr.org/cgi-bin/paper?vg5041
The small-angle neutron scattering (SANS) spectrometer Suanni at the liquid hydrogen cold neutron source of the 20 MW China Mianyang Research Reactor has recently been upgraded. Ultra-thin biconcave MgF2 lenses with a central thickness down to 0.2 mm have been installed between the collimator chamber and the sample stage. The lenses are able to improve the flux without too excessive an increase in the neutron beam size on the detector. A smaller minimum Q (Qmin) can be obtained by decreasing the beam size without changing the total length of the spectrometer. By testing the central beam profiles under different neutron wavelengths (∼0.56–1 nm) with both traditional pinhole SANS (PSANS) and focusing SANS (FSANS) geometries, the gain factor thanks to the neutron lenses is about one order of magnitude. Given the loss of intensity due to the absorption of neutrons by the lenses, the benefits of the focusing can only be realized if it is possible to increase the aperture size. With an identical source aperture, FSANS can minimize the nominal Qmin from 7.20 × 10−3 nm−1 (for PSANS) to 5.55 × 10−3 nm−1 at a neutron wavelength of 1 nm. The practical benefit provided by the lenses is verified with a solution of poly(methyl methacrylate) nanospheres, which yields a scattering intensity one order of magnitude higher and a better resolution with the FSANS geometry than with that of PSANS.Copyright (c) 2016 International Union of Crystallographyurn:issn:1600-5767Chen, L.Sun, L.Wang, Y.Wang, Y.Zou, L.Yan, G.Chen, J.Tian, Q.Peng, M.Gong, J.Chen, B.Sun, G.Liu, D.2016-06-20doi:10.1107/S1600576716007950International Union of CrystallographyThe small-angle neutron scattering (SANS) spectrometer Suanni at the China Mianyang Research Reactor has successfully been upgraded from a pinhole SANS instrument to a focusing SANS instrument with ultra-thin biconcave MgF2 focusing lenses. It is found that introducing lenses in the current experimental methodology can either enhance the flux or achieve a smaller Qmin.ENsmall-angle neutron scatteringfocusing SANSpinhole SANSbiconcave lensesminimum Qhigh intensityThe small-angle neutron scattering (SANS) spectrometer Suanni at the liquid hydrogen cold neutron source of the 20 MW China Mianyang Research Reactor has recently been upgraded. Ultra-thin biconcave MgF2 lenses with a central thickness down to 0.2 mm have been installed between the collimator chamber and the sample stage. The lenses are able to improve the flux without too excessive an increase in the neutron beam size on the detector. A smaller minimum Q (Qmin) can be obtained by decreasing the beam size without changing the total length of the spectrometer. By testing the central beam profiles under different neutron wavelengths (∼0.56–1 nm) with both traditional pinhole SANS (PSANS) and focusing SANS (FSANS) geometries, the gain factor thanks to the neutron lenses is about one order of magnitude. Given the loss of intensity due to the absorption of neutrons by the lenses, the benefits of the focusing can only be realized if it is possible to increase the aperture size. With an identical source aperture, FSANS can minimize the nominal Qmin from 7.20 × 10−3 nm−1 (for PSANS) to 5.55 × 10−3 nm−1 at a neutron wavelength of 1 nm. The practical benefit provided by the lenses is verified with a solution of poly(methyl methacrylate) nanospheres, which yields a scattering intensity one order of magnitude higher and a better resolution with the FSANS geometry than with that of PSANS.text/htmlSmall-angle neutron scattering spectrometer Suanni equipped with ultra-thin biconcave focusing lensestext4492016-06-20Copyright (c) 2016 International Union of CrystallographyJournal of Applied Crystallographylaboratory notes00Quantum Confined Laser Devices. Optical Gain and Recombination in Semiconductors. By Peter Blood. Oxford University Press, 2015. Pp. 432. Price GBP 28.99. ISBN 9780199644520
http://scripts.iucr.org/cgi-bin/paper?xo0044
Copyright (c) 2016 International Union of Crystallographyurn:issn:1600-5767Tomm, J.W.2016-06-23doi:10.1107/S1600576716009547International Union of CrystallographyENbook reviewstext/htmlQuantum Confined Laser Devices. Optical Gain and Recombination in Semiconductors. By Peter Blood. Oxford University Press, 2015. Pp. 432. Price GBP 28.99. ISBN 9780199644520text4492016-06-23Copyright (c) 2016 International Union of CrystallographyJournal of Applied Crystallographybook reviews00