Open-access and free articles in Acta Crystallographica Section A: Foundations and Advances
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Acta Crystallographica Section A: Foundations and Advances covers theoretical and fundamental aspects of the structure of matter. The journal is the prime forum for research in diffraction physics and the theory of crystallographic structure determination by diffraction methods using X-rays, neutrons and electrons. The structures include periodic and aperiodic crystals, and non-periodic disordered materials, and the corresponding Bragg, satellite and diffuse scattering, thermal motion and symmetry aspects. Spatial resolutions range from the subatomic domain in charge-density studies to nanodimensional imperfections such as dislocations and twin walls. The chemistry encompasses metals, alloys, and inorganic, organic and biological materials. Structure prediction and properties such as the theory of phase transformations are also covered.en-gbCopyright (c) 2021 International Union of CrystallographyInternational Union of CrystallographyInternational Union of Crystallographyhttps://journals.iucr.orgurn:issn:0108-7673Acta Crystallographica Section A: Foundations and Advances covers theoretical and fundamental aspects of the structure of matter. The journal is the prime forum for research in diffraction physics and the theory of crystallographic structure determination by diffraction methods using X-rays, neutrons and electrons. The structures include periodic and aperiodic crystals, and non-periodic disordered materials, and the corresponding Bragg, satellite and diffuse scattering, thermal motion and symmetry aspects. Spatial resolutions range from the subatomic domain in charge-density studies to nanodimensional imperfections such as dislocations and twin walls. The chemistry encompasses metals, alloys, and inorganic, organic and biological materials. Structure prediction and properties such as the theory of phase transformations are also covered.text/htmlOpen-access and free articles in Acta Crystallographica Section A Foundations and Advancestextyearly62002-01-01T00:00+00:00med@iucr.orgActa Crystallographica Section A Foundations and AdvancesCopyright (c) 2021 International Union of Crystallographyurn:issn:0108-7673Open-access and free articles in Acta Crystallographica Section A: Foundations and Advanceshttp://journals.iucr.org/logos/rss10a.gif
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Still imageOn incoherent diffractive imaging
http://scripts.iucr.org/cgi-bin/paper?iv5016
Incoherent diffractive imaging (IDI) promises structural analysis with atomic resolution based on intensity interferometry of pulsed X-ray fluorescence emission. However, its experimental realization is still pending and a comprehensive theory of contrast formation has not been established to date. Explicit expressions are derived for the equal-pulse two-point intensity correlations, as the principal measured quantity of IDI, with full control of the prefactors, based on a simple model of stochastic fluorescence emission. The model considers the photon detection statistics, the finite temporal coherence of the individual emissions, as well as the geometry of the scattering volume. The implications are interpreted in view of the most relevant quantities, including the fluorescence lifetime, the excitation pulse, as well as the extent of the scattering volume and pixel size. Importantly, the spatiotemporal overlap between any two emissions in the sample can be identified as a crucial factor limiting the contrast and its dependency on the sample size can be derived. The paper gives rigorous estimates for the optimum sample size, the maximum photon yield and the expected signal-to-noise ratio under optimal conditions. Based on these estimates, the feasibility of IDI experiments for plausible experimental parameters is discussed. It is shown in particular that the mean number of photons per detector pixel which can be achieved with X-ray fluorescence is severely limited and as a consequence imposes restrictive constraints on possible applications.https://creativecommons.org/licenses/by/4.0/urn:issn:2053-2733Lohse, L.M.Vassholz, M.Salditt, T.2021-08-27doi:10.1107/S2053273321007300International Union of CrystallographyStarting from a simple model of stochastic fluorescence emission, a theory is derived of contrast formation and signal-to-noise ratio for incoherent diffractive imaging; its feasibility for plausible experimental parameters is discussed.enFEMTOSECOND STUDIES; FREE-ELECTRON LASER; CORRELATED FLUCTUATIONS; DIFFRACT-THEN-DESTROY; SINGLE PARTICLES; XFELIncoherent diffractive imaging (IDI) promises structural analysis with atomic resolution based on intensity interferometry of pulsed X-ray fluorescence emission. However, its experimental realization is still pending and a comprehensive theory of contrast formation has not been established to date. Explicit expressions are derived for the equal-pulse two-point intensity correlations, as the principal measured quantity of IDI, with full control of the prefactors, based on a simple model of stochastic fluorescence emission. The model considers the photon detection statistics, the finite temporal coherence of the individual emissions, as well as the geometry of the scattering volume. The implications are interpreted in view of the most relevant quantities, including the fluorescence lifetime, the excitation pulse, as well as the extent of the scattering volume and pixel size. Importantly, the spatiotemporal overlap between any two emissions in the sample can be identified as a crucial factor limiting the contrast and its dependency on the sample size can be derived. The paper gives rigorous estimates for the optimum sample size, the maximum photon yield and the expected signal-to-noise ratio under optimal conditions. Based on these estimates, the feasibility of IDI experiments for plausible experimental parameters is discussed. It is shown in particular that the mean number of photons per detector pixel which can be achieved with X-ray fluorescence is severely limited and as a consequence imposes restrictive constraints on possible applications.text/htmlOn incoherent diffractive imagingtext775https://creativecommons.org/licenses/by/4.0/Acta Crystallographica Section A: Foundations and Advances2021-08-27480research papers2053-2733September 2021med@iucr.org4962053-2733Moiré, Euler and self-similarity – the lattice parameters of twisted hexagonal crystals
http://scripts.iucr.org/cgi-bin/paper?ug5017
A real-space approach for the calculation of the moiré lattice parameters for superstructures formed by a set of rotated hexagonal 2D crystals such as graphene or transition-metal dichalcogenides is presented. Apparent moiré lattices continuously form for all rotation angles, and their lattice parameter to a good approximation follows a hyperbolical angle dependence. Moiré crystals, i.e. moiré lattices decorated with a basis, require more crucial assessment of the commensurabilities and lead to discrete solutions and a non-continuous angle dependence of the moiré-crystal lattice parameter. In particular, this lattice parameter critically depends on the rotation angle, and continuous variation of the angle can lead to apparently erratic changes of the lattice parameter. The solutions form a highly complex pattern, which reflects number-theoretical relations between formation parameters of the moiré crystal. The analysis also provides insight into the special case of a 30° rotation of the constituting lattices, for which a dodecagonal quasicrystalline structure forms.https://creativecommons.org/licenses/by/4.0/urn:issn:2053-2733Feuerbacher, M.2021-08-19doi:10.1107/S2053273321007245International Union of CrystallographyThe moiré lattice parameters are calculated for superstructures formed by a set of rotated hexagonal 2D crystals such as graphene or transition-metal dichalcogenides, and the highly complex pattern of solutions is discussed.en2D MATERIALS; MOIRE PATTERN; TWISTED BILAYERS; TWISTRONICS; GRAPHENEA real-space approach for the calculation of the moiré lattice parameters for superstructures formed by a set of rotated hexagonal 2D crystals such as graphene or transition-metal dichalcogenides is presented. Apparent moiré lattices continuously form for all rotation angles, and their lattice parameter to a good approximation follows a hyperbolical angle dependence. Moiré crystals, i.e. moiré lattices decorated with a basis, require more crucial assessment of the commensurabilities and lead to discrete solutions and a non-continuous angle dependence of the moiré-crystal lattice parameter. In particular, this lattice parameter critically depends on the rotation angle, and continuous variation of the angle can lead to apparently erratic changes of the lattice parameter. The solutions form a highly complex pattern, which reflects number-theoretical relations between formation parameters of the moiré crystal. The analysis also provides insight into the special case of a 30° rotation of the constituting lattices, for which a dodecagonal quasicrystalline structure forms.text/htmlMoiré, Euler and self-similarity – the lattice parameters of twisted hexagonal crystalstext775https://creativecommons.org/licenses/by/4.0/Acta Crystallographica Section A: Foundations and Advances2021-08-19460research papers2053-2733September 2021med@iucr.org4712053-2733A fast algorithm to find reduced hyperplane unit cells and solve N-dimensional Bézout's identities
http://scripts.iucr.org/cgi-bin/paper?lu5010
Deformation twinning on a plane is a simple shear that transforms a unit cell attached to the plane into another unit cell equivalent by mirror symmetry or 180° rotation. Thus, crystallographic models of twinning require the determination of the short unit cells attached to the planes, or hyperplanes for dimensions higher than 3. Here, a method is presented to find them. Equivalently, it gives the solutions of the N-dimensional Bézout's identity associated with the Miller indices of the hyperplane.https://creativecommons.org/licenses/by/4.0/urn:issn:2053-2733Cayron, C.2021-08-13doi:10.1107/S2053273321006835International Union of CrystallographyThe paper describes a method to determine a short unit cell attached to any hyperplane given by its integer vector p. Equivalently, it gives all the solutions of the N-dimensional Bézout's identity associated with the coordinates of p.enN-DIMENSIONAL BEZOUT'S IDENTITY; HYPERPLANE UNIT CELL; INTEGER RELATION; TWINNINGDeformation twinning on a plane is a simple shear that transforms a unit cell attached to the plane into another unit cell equivalent by mirror symmetry or 180° rotation. Thus, crystallographic models of twinning require the determination of the short unit cells attached to the planes, or hyperplanes for dimensions higher than 3. Here, a method is presented to find them. Equivalently, it gives the solutions of the N-dimensional Bézout's identity associated with the Miller indices of the hyperplane.text/htmlA fast algorithm to find reduced hyperplane unit cells and solve N-dimensional Bézout's identitiestext5772021-08-13Acta Crystallographica Section A: Foundations and Advanceshttps://creativecommons.org/licenses/by/4.0/2053-2733research papers453med@iucr.orgSeptember 20214592053-2733A new density-modification procedure extending the application of the recent |ρ|-based phasing algorithm to larger crystal structures
http://scripts.iucr.org/cgi-bin/paper?ik5001
The incorporation of the new peakness-enhancing fast Fourier transform compatible ipp procedure (ipp = inner-pixel preservation) into the recently published SM algorithm based on |ρ| [Rius (2020). Acta Cryst A76, 489–493] improves its phasing efficiency for larger crystal structures with atomic resolution data. Its effectiveness is clearly demonstrated via a collection of test crystal structures (taken from the Protein Data Bank) either starting from random phase values or by using the randomly shifted modulus function (a Patterson-type synthesis) as initial ρ estimate. It has been found that in the presence of medium scatterers (e.g. S or Cl atoms) crystal structures with 1500 × c atoms in the unit cell (c = number of centerings) can be routinely solved. In the presence of strong scatterers like Fe, Cu or Zn atoms this number increases to around 5000 × c atoms. The implementation of this strengthened SM algorithm is simple, since it only includes a few easy-to-adjust parameters.https://creativecommons.org/licenses/by/4.0/urn:issn:2053-2733Rius, J.Torrelles, X.2021-06-21doi:10.1107/S2053273321004915International Union of CrystallographyThe insertion of a peakness-enhancing fast Fourier transform compatible module in the novel SM,|ρ| phasing algorithm improves its efficiency for larger crystal structures as shown with a collection of representative X-ray diffraction data sets taken from the Protein Data Bank.enSM PHASING ALGORITHM; IPP PROCEDURE; |[RHO]|-BASED PHASING RESIDUAL; DIRECT METHODS; ORIGIN-FREE MODULUS SUM FUNCTION; STRUCTURE SOLUTIONThe incorporation of the new peakness-enhancing fast Fourier transform compatible ipp procedure (ipp = inner-pixel preservation) into the recently published SM algorithm based on |ρ| [Rius (2020). Acta Cryst A76, 489–493] improves its phasing efficiency for larger crystal structures with atomic resolution data. Its effectiveness is clearly demonstrated via a collection of test crystal structures (taken from the Protein Data Bank) either starting from random phase values or by using the randomly shifted modulus function (a Patterson-type synthesis) as initial ρ estimate. It has been found that in the presence of medium scatterers (e.g. S or Cl atoms) crystal structures with 1500 × c atoms in the unit cell (c = number of centerings) can be routinely solved. In the presence of strong scatterers like Fe, Cu or Zn atoms this number increases to around 5000 × c atoms. The implementation of this strengthened SM algorithm is simple, since it only includes a few easy-to-adjust parameters.text/htmlA new density-modification procedure extending the application of the recent |ρ|-based phasing algorithm to larger crystal structurestext774https://creativecommons.org/licenses/by/4.0/Acta Crystallographica Section A: Foundations and Advances2021-06-21339research papers2053-2733July 2021med@iucr.org3472053-2733From crystal color symmetry to quantum spacetime
http://scripts.iucr.org/cgi-bin/paper?me6135
urn:issn:2053-2733Bojowald, M.Saxena, A.2021-05-27doi:10.1107/S2053273321005234International Union of CrystallographyThis perspective article elucidates both the importance and the implications of relativistic spacetime crystals as well as the renormalized blended coordinates transformation. It alludes to possible applications in materials science, condensed matter physics and quantum gravity.enCOLOR SYMMETRY; QUANTUM SPACETIME; RENORMALIZED BLENDED SPACETIME; RELATIVISTIC SPACETIME CRYSTALStext/htmlFrom crystal color symmetry to quantum spacetimetext774Acta Crystallographica Section A: Foundations and Advances2021-05-27239scientific commentaries2053-2733July 2021med@iucr.org2412053-2733A topological proof of the modified Euler characteristic based on the orbifold concept
http://scripts.iucr.org/cgi-bin/paper?ug5026
The notion of the Euler characteristic of a polyhedron or tessellation has been the subject of in-depth investigations by many authors. Two previous papers worked to explain the phenomenon of the vanishing (or zeroing) of the modified Euler characteristic of a polyhedron that underlies a periodic tessellation of a space under a crystallographic space group. The present paper formally expresses this phenomenon as a theorem about the vanishing of the Euler characteristic of certain topological spaces called topological orbifolds. In this new approach, it is explained that the theorem in question follows from the fundamental properties of the orbifold Euler characteristic. As a side effect of these considerations, a theorem due to Coxeter about the vanishing Euler characteristic of a honeycomb tessellation is re-proved in a context which frees the calculations from the assumptions made by Coxeter in his proof. The abstract mathematical concepts are visualized with down-to-earth examples motivated by concrete situations illustrating wallpaper and 3D crystallographic space groups. In a way analogous to the application of the classic Euler equation to completely bounded solids, the formula proven in this paper is applicable to such important crystallographic objects as asymmetric units and Dirichlet domains.https://creativecommons.org/licenses/by/4.0/urn:issn:2053-2733Naskręcki, B.Dauter, Z.Jaskolski, M.2021-06-21doi:10.1107/S2053273321004320International Union of CrystallographyThe vanishing of the modified Euler characteristic for symmetrically arranged space-filling polytopes is given a general proof based on the topological concept of orbifolds. The modified Euler characteristic is applicable to such important crystallographic objects as asymmetric units and Dirichlet domains.enEULER CHARACTERISTIC; ORBIFOLDS; SPACE-FILLING POLYHEDRA; SPACE GROUPS; ASYMMETRIC UNITSThe notion of the Euler characteristic of a polyhedron or tessellation has been the subject of in-depth investigations by many authors. Two previous papers worked to explain the phenomenon of the vanishing (or zeroing) of the modified Euler characteristic of a polyhedron that underlies a periodic tessellation of a space under a crystallographic space group. The present paper formally expresses this phenomenon as a theorem about the vanishing of the Euler characteristic of certain topological spaces called topological orbifolds. In this new approach, it is explained that the theorem in question follows from the fundamental properties of the orbifold Euler characteristic. As a side effect of these considerations, a theorem due to Coxeter about the vanishing Euler characteristic of a honeycomb tessellation is re-proved in a context which frees the calculations from the assumptions made by Coxeter in his proof. The abstract mathematical concepts are visualized with down-to-earth examples motivated by concrete situations illustrating wallpaper and 3D crystallographic space groups. In a way analogous to the application of the classic Euler equation to completely bounded solids, the formula proven in this paper is applicable to such important crystallographic objects as asymmetric units and Dirichlet domains.text/htmlA topological proof of the modified Euler characteristic based on the orbifold concepttext774https://creativecommons.org/licenses/by/4.0/Acta Crystallographica Section A: Foundations and Advances2021-06-21317research papers2053-2733July 2021med@iucr.org3262053-2733Resolution of a bent-crystal spectrometer for X-ray free-electron laser pulses: diamond versus silicon
http://scripts.iucr.org/cgi-bin/paper?wo5037
The resolution function of a spectrometer based on a strongly bent single crystal (bending radius of 10 cm or less) is evaluated. It is shown that the resolution is controlled by two parameters: (i) the ratio of the lattice spacing of the chosen reflection to the crystal thickness and (ii) a single parameter comprising crystal thickness, its bending radius, distance to a detector, and anisotropic elastic constants of the chosen crystal. The results allow the optimization of the parameters of bent-crystal spectrometers for the hard X-ray free-electron laser sources.https://creativecommons.org/licenses/by/4.0/urn:issn:2053-2733Kaganer, V.M.Petrov, I.Samoylova, L.2021-05-27doi:10.1107/S2053273321003697International Union of CrystallographyThe resolution function of a bent-crystal spectrometer for pulses of an X-ray free-electron laser is evaluated. Under appropriate conditions, the energy resolution reaches the ratio of the lattice spacing to the crystal thickness.enX-RAY FREE-ELECTRON LASERS; X-RAY SPECTROSCOPY; BENT CRYSTALS; DIAMOND CRYSTAL OPTICS; FEMTOSECOND X-RAY DIFFRACTIONThe resolution function of a spectrometer based on a strongly bent single crystal (bending radius of 10 cm or less) is evaluated. It is shown that the resolution is controlled by two parameters: (i) the ratio of the lattice spacing of the chosen reflection to the crystal thickness and (ii) a single parameter comprising crystal thickness, its bending radius, distance to a detector, and anisotropic elastic constants of the chosen crystal. The results allow the optimization of the parameters of bent-crystal spectrometers for the hard X-ray free-electron laser sources.text/htmlResolution of a bent-crystal spectrometer for X-ray free-electron laser pulses: diamond versus silicontext774https://creativecommons.org/licenses/by/4.0/Acta Crystallographica Section A: Foundations and Advances2021-05-27268research papers2053-2733July 2021med@iucr.org2762053-2733Relativistic spacetime crystals
http://scripts.iucr.org/cgi-bin/paper?ib5098
Periodic space crystals are well established and widely used in physical sciences. Time crystals have been increasingly explored more recently, where time is disconnected from space. Periodic relativistic spacetime crystals on the other hand need to account for the mixing of space and time in special relativity through Lorentz transformation, and have been listed only in 2D. This work shows that there exists a transformation between the conventional Minkowski spacetime (MS) and what is referred to here as renormalized blended spacetime (RBS); they are shown to be equivalent descriptions of relativistic physics in flat spacetime. There are two elements to this reformulation of MS, namely, blending and renormalization. When observers in two inertial frames adopt each other's clocks as their own, while retaining their original space coordinates, the observers become blended. This process reformulates the Lorentz boosts into Euclidean rotations while retaining the original spacetime hyperbola describing worldlines of constant spacetime length from the origin. By renormalizing the blended coordinates with an appropriate factor that is a function of the relative velocities between the various frames, the hyperbola is transformed into a Euclidean circle. With these two steps, one obtains the RBS coordinates complete with new light lines, but now with a Euclidean construction. One can now enumerate the RBS point and space groups in various dimensions with their mapping to the well known space crystal groups. The RBS point group for flat isotropic RBS spacetime is identified to be that of cylinders in various dimensions: mm2 which is that of a rectangle in 2D, (∞/m)m which is that of a cylinder in 3D, and that of a hypercylinder in 4D. An antisymmetry operation is introduced that can swap between space-like and time-like directions, leading to color spacetime groups. The formalism reveals RBS symmetries that are not readily apparent in the conventional MS formulation. Mathematica script is provided for plotting the MS and RBS geometries discussed in the work.https://creativecommons.org/licenses/by/4.0/urn:issn:2053-2733Gopalan, V.2021-05-27doi:10.1107/S2053273321003259International Union of CrystallographyBy appropriate reformulation of relativistic spacetime geometry, a direct mapping to Euclidean space crystals is shown. Using this mapping, hidden symmetries in relativistic spacetime crystals are uncovered.enSPACETIME; SPECIAL RELATIVITY; RENORMALIZED BLENDED SPACETIME; RELATIVISTIC SPACETIME CRYSTALSPeriodic space crystals are well established and widely used in physical sciences. Time crystals have been increasingly explored more recently, where time is disconnected from space. Periodic relativistic spacetime crystals on the other hand need to account for the mixing of space and time in special relativity through Lorentz transformation, and have been listed only in 2D. This work shows that there exists a transformation between the conventional Minkowski spacetime (MS) and what is referred to here as renormalized blended spacetime (RBS); they are shown to be equivalent descriptions of relativistic physics in flat spacetime. There are two elements to this reformulation of MS, namely, blending and renormalization. When observers in two inertial frames adopt each other's clocks as their own, while retaining their original space coordinates, the observers become blended. This process reformulates the Lorentz boosts into Euclidean rotations while retaining the original spacetime hyperbola describing worldlines of constant spacetime length from the origin. By renormalizing the blended coordinates with an appropriate factor that is a function of the relative velocities between the various frames, the hyperbola is transformed into a Euclidean circle. With these two steps, one obtains the RBS coordinates complete with new light lines, but now with a Euclidean construction. One can now enumerate the RBS point and space groups in various dimensions with their mapping to the well known space crystal groups. The RBS point group for flat isotropic RBS spacetime is identified to be that of cylinders in various dimensions: mm2 which is that of a rectangle in 2D, (∞/m)m which is that of a cylinder in 3D, and that of a hypercylinder in 4D. An antisymmetry operation is introduced that can swap between space-like and time-like directions, leading to color spacetime groups. The formalism reveals RBS symmetries that are not readily apparent in the conventional MS formulation. Mathematica script is provided for plotting the MS and RBS geometries discussed in the work.text/htmlRelativistic spacetime crystalstext774https://creativecommons.org/licenses/by/4.0/Acta Crystallographica Section A: Foundations and Advances2021-05-27242research papers2053-2733July 2021med@iucr.org2562053-2733Combining X-rays, neutrons and electrons, and NMR, for precision and accuracy in structure–function studies
http://scripts.iucr.org/cgi-bin/paper?ae5100
The distinctive features of the physics-based probes used in understanding the structure of matter focusing on biological sciences, but not exclusively, are described in the modern context. This is set in a wider scope of holistic biology and the scepticism about `reductionism', what is called the `molecular level', and how to respond constructively. These topics will be set alongside the principles of accuracy and precision, and their boundaries. The combination of probes and their application together is the usual way of realizing accuracy. The distinction between precision and accuracy can be blurred by the predictive force of a precise structure, thereby lending confidence in its potential accuracy. These descriptions will be applied to the comparison of cryo and room-temperature protein crystal structures as well as the solid state of a crystal and the same molecules studied by small-angle X-ray scattering in solution and by electron microscopy on a sample grid. Examples will include: time-resolved X-ray Laue crystallography of an enzyme Michaelis complex formed directly in a crystal equivalent to in vivo; a new iodoplatin for radiation therapy predicted from studies of platin crystal structures; and the field of colouration of carotenoids, as an effective assay of function, i.e. their colouration, when unbound and bound to a protein. The complementarity of probes, as well as their combinatory use, is then at the foundation of real (biologically relevant), probe-artefacts-free, structure–function studies. The foundations of our methodologies are being transformed by colossal improvements in technologies of X-ray and neutron sources and their beamline instruments, as well as improved electron microscopes and NMR spectrometers. The success of protein structure prediction from gene sequence recently reported by CASP14 also opens new doors to change and extend the foundations of the structural sciences.https://creativecommons.org/licenses/by/4.0/urn:issn:2053-2733Helliwell, J.R.2021-05-04doi:10.1107/S205327332100317XInternational Union of CrystallographyThe distinctive features of the probes used in understanding the structure of matter focusing on biological sciences, but not exclusively, are described in the modern context to minimize the consequences of artefactual information in data interpretation. The precision and accuracy of both data and technique are revisited. A variety of structural results are described that reach beyond reductionism to the whole biological organism. All these aspects open new doors to change and extend the foundations of the structural sciences.enX-RAYS; NEUTRONS; ELECTRONS; NMR; STRUCTURE AND FUNCTIONThe distinctive features of the physics-based probes used in understanding the structure of matter focusing on biological sciences, but not exclusively, are described in the modern context. This is set in a wider scope of holistic biology and the scepticism about `reductionism', what is called the `molecular level', and how to respond constructively. These topics will be set alongside the principles of accuracy and precision, and their boundaries. The combination of probes and their application together is the usual way of realizing accuracy. The distinction between precision and accuracy can be blurred by the predictive force of a precise structure, thereby lending confidence in its potential accuracy. These descriptions will be applied to the comparison of cryo and room-temperature protein crystal structures as well as the solid state of a crystal and the same molecules studied by small-angle X-ray scattering in solution and by electron microscopy on a sample grid. Examples will include: time-resolved X-ray Laue crystallography of an enzyme Michaelis complex formed directly in a crystal equivalent to in vivo; a new iodoplatin for radiation therapy predicted from studies of platin crystal structures; and the field of colouration of carotenoids, as an effective assay of function, i.e. their colouration, when unbound and bound to a protein. The complementarity of probes, as well as their combinatory use, is then at the foundation of real (biologically relevant), probe-artefacts-free, structure–function studies. The foundations of our methodologies are being transformed by colossal improvements in technologies of X-ray and neutron sources and their beamline instruments, as well as improved electron microscopes and NMR spectrometers. The success of protein structure prediction from gene sequence recently reported by CASP14 also opens new doors to change and extend the foundations of the structural sciences.text/htmlCombining X-rays, neutrons and electrons, and NMR, for precision and accuracy in structure–function studiestext773https://creativecommons.org/licenses/by/4.0/Acta Crystallographica Section A: Foundations and Advances2021-05-04173lead articles2053-2733May 2021med@iucr.org1852053-2733Diffraction line profiles from polydisperse crystalline systems. Corrigenda
http://scripts.iucr.org/cgi-bin/paper?me6128
Equation (16) and some entries in Table 1 in the article by Scardi & Leoni [(2001), Acta Cryst. A57, 604–613] are corrected.Copyright (c) 2021 International Union of Crystallographyurn:issn:2053-2733Scardi, P.2021-03-17doi:10.1107/S2053273321002813International Union of CrystallographyErrors in the article by Scardi & Leoni [(2001), Acta Cryst. A57, 604–613] are corrected.enLINE PROFILE ANALYSIS; LPA; WHOLE POWDER PATTERN MODELLING; WPPM; CRYSTALLINE DOMAIN SIZE; CORRIGENDAEquation (16) and some entries in Table 1 in the article by Scardi & Leoni [(2001), Acta Cryst. A57, 604–613] are corrected.text/htmlDiffraction line profiles from polydisperse crystalline systems. Corrigendatext773Copyright (c) 2021 International Union of CrystallographyActa Crystallographica Section A: Foundations and Advances2021-03-17232addenda and errata2053-2733May 2021med@iucr.org2322053-2733A new electron diffraction approach for structure refinement applied to Ca3Mn2O7
http://scripts.iucr.org/cgi-bin/paper?lu5005
The digital large-angle convergent-beam electron diffraction (D-LACBED) technique is applied to Ca3Mn2O7 for a range of temperatures. Bloch-wave simulations are used to examine the effects that changes in different parameters have on the intensity in D-LACBED patterns, and atomic coordinates, thermal atomic displacement parameters and apparent occupancy are refined to achieve a good fit between simulation and experiment. The sensitivity of the technique to subtle changes in structure is demonstrated. Refined structures are in good agreement with previous determinations of Ca3Mn2O7 and show the decay of anti-phase oxygen octahedral tilts perpendicular to the c axis of the A21am unit cell with increasing temperature, as well as the robustness of oxygen octahedral tilts about the c axis up to ∼400°C. The technique samples only the zero-order Laue zone and is therefore insensitive to atom displacements along the electron-beam direction. For this reason it is not possible to distinguish between in-phase and anti-phase oxygen octahedral tilting about the c axis using the [110] data collected in this study.https://creativecommons.org/licenses/by/4.0/urn:issn:2053-2733Beanland, R.Smith, K.Vaněk, P.Zhang, H.Hubert, A.Evans, K.Römer, R.A.Kamba, S.2021-03-17doi:10.1107/S2053273321001546International Union of CrystallographyThe `digital' large-angle convergent-beam electron diffraction (D-LACBED) method uses computer control of a transmission electron microscope to collect hundreds of diffraction patterns from a region a few nanometres in size, which are combined into a single data set. The sensitivity of the resulting patterns to crystal structure is explored using the Ruddlesden–Popper oxide Ca3Mn2O7 and it is found that refinement of atomic coordinates can be performed to sub-picometre precision.enDIGITAL DIFFRACTION; ELECTRON DIFFRACTION; CA3MN2O7; CBED; LACBEDThe digital large-angle convergent-beam electron diffraction (D-LACBED) technique is applied to Ca3Mn2O7 for a range of temperatures. Bloch-wave simulations are used to examine the effects that changes in different parameters have on the intensity in D-LACBED patterns, and atomic coordinates, thermal atomic displacement parameters and apparent occupancy are refined to achieve a good fit between simulation and experiment. The sensitivity of the technique to subtle changes in structure is demonstrated. Refined structures are in good agreement with previous determinations of Ca3Mn2O7 and show the decay of anti-phase oxygen octahedral tilts perpendicular to the c axis of the A21am unit cell with increasing temperature, as well as the robustness of oxygen octahedral tilts about the c axis up to ∼400°C. The technique samples only the zero-order Laue zone and is therefore insensitive to atom displacements along the electron-beam direction. For this reason it is not possible to distinguish between in-phase and anti-phase oxygen octahedral tilting about the c axis using the [110] data collected in this study.text/htmlA new electron diffraction approach for structure refinement applied to Ca3Mn2O7text773https://creativecommons.org/licenses/by/4.0/Acta Crystallographica Section A: Foundations and Advances2021-03-17196research papers2053-2733May 2021med@iucr.org2072053-2733A discussion on `Domain formation and phase transitions in the wurtzite-based heterovalent ternaries: a Landau theory analysis'
http://scripts.iucr.org/cgi-bin/paper?ug5021
Heterovalent ternary nitrides are considered one of the promising classes of materials for photovoltaics, combining attractive physical properties with low toxicity and element abundance. One of the front-runner systems under consideration is ZnSnN2. Although it is nominally a ternary compound, no clear crystallographic evidence for cation ordering has been observed so far. An attempt to elucidate this discrepancy [Quayle (2020). Acta Cryst. A76, 410–420] was the trigger for an intensive discussion between the authors, and an agreement was reached to elaborate on some points in order to set things in perspective. Rather than using a conventional comment–answer scheme, this is published in the form of a joint discussion to celebrate constructive criticism and collegiality.https://creativecommons.org/licenses/by/4.0/urn:issn:2053-2733Quayle, P.C.Breternitz, J.2021-03-23doi:10.1107/S2053273321001376International Union of CrystallographyA scientific exchange on an earlier paper [Quayle (2020). Acta Cryst. A76, 410–420] has led to the clarification of some of the points.enGROUP-SUBGROUP RELATIONSHIPS; NITRIDE MATERIALS; WURTZITE TYPEHeterovalent ternary nitrides are considered one of the promising classes of materials for photovoltaics, combining attractive physical properties with low toxicity and element abundance. One of the front-runner systems under consideration is ZnSnN2. Although it is nominally a ternary compound, no clear crystallographic evidence for cation ordering has been observed so far. An attempt to elucidate this discrepancy [Quayle (2020). Acta Cryst. A76, 410–420] was the trigger for an intensive discussion between the authors, and an agreement was reached to elaborate on some points in order to set things in perspective. Rather than using a conventional comment–answer scheme, this is published in the form of a joint discussion to celebrate constructive criticism and collegiality.text/htmlA discussion on `Domain formation and phase transitions in the wurtzite-based heterovalent ternaries: a Landau theory analysis'text773https://creativecommons.org/licenses/by/4.0/Acta Crystallographica Section A: Foundations and Advances2021-03-23217research papers2053-2733May 2021med@iucr.org2212053-2733Nothing trumps good data
http://scripts.iucr.org/cgi-bin/paper?me6117
urn:issn:2053-2733Pinkerton, A.A.2021-01-29doi:10.1107/S2053273321000759International Union of CrystallographyThe advantages of a powerful new tool for determining the electron density of small inorganic systems using high-quality powder diffraction data from the MYTHEN microstrip detector [Svane et al. (2021). Acta Cryst. A77, 85–95] are considered.enELECTRON DENSITY; DATA QUALITY; CHARGE DENSITY; POWDER DIFFRACTION; MYTHEN DETECTORtext/htmlNothing trumps good datatext772Acta Crystallographica Section A: Foundations and Advances2021-01-2983scientific commentaries2053-2733March 2021med@iucr.org842053-2733Coordination sequences of crystals are of quasi-polynomial type
http://scripts.iucr.org/cgi-bin/paper?pl5008
The coordination sequence of a graph measures how many vertices the graph has at each distance from a fixed vertex and is a generalization of the coordination number. Here it is proved that the coordination sequence of the graph obtained from a crystal is of quasi-polynomial type, as had been postulated by Grosse-Kunstleve et al. [Acta Cryst. (1996), A52, 879–889].https://creativecommons.org/licenses/by/4.0/urn:issn:2053-2733Nakamura, Y.Sakamoto, R.Mase, T.Nakagawa, J.2021-02-18doi:10.1107/S2053273320016769International Union of CrystallographyIt is proved that the coordination sequence of the graph obtained from a crystal is of quasi-polynomial type, as had been postulated by Grosse-Kunstleve et al. [Acta Cryst. (1996), A52, 879–889] in their study of coordination sequences of zeolites.enCOORDINATION SEQUENCES; GRAPH THEORY; HILBERT POLYNOMIAL; MONOID THEORYThe coordination sequence of a graph measures how many vertices the graph has at each distance from a fixed vertex and is a generalization of the coordination number. Here it is proved that the coordination sequence of the graph obtained from a crystal is of quasi-polynomial type, as had been postulated by Grosse-Kunstleve et al. [Acta Cryst. (1996), A52, 879–889].text/htmlCoordination sequences of crystals are of quasi-polynomial typetext772https://creativecommons.org/licenses/by/4.0/Acta Crystallographica Section A: Foundations and Advances2021-02-18138research papers2053-2733March 2021med@iucr.org1482053-2733Multipole electron densities and structural parameters from synchrotron powder X-ray diffraction data obtained with a MYTHEN detector system (OHGI)
http://scripts.iucr.org/cgi-bin/paper?pl5010
Powder X-ray diffraction has some inherent advantages over traditional single-crystal X-ray diffraction in accurately determining electron densities and structural parameters due to the lower requirements for sample crystallinity, simpler corrections and measurement simultaneity. For some simple inorganic materials, it has been shown that these advantages can compensate for disadvantages such as peak overlap and error-prone background subtraction. Although it is challenging to extend powder X-ray diffraction-based electron-density studies to organic materials with significant peak overlap, previous results using a dedicated vacuum diffractometer with a large image-plate camera (AVID) demonstrated that it can be done. However, the vacuum setup with the off-line detector system was found to prohibit a widespread use. Fast microstrip detectors, which have been employed at a number of powder diffraction beamlines, have the potential to facilitate electron-density studies. Nevertheless, no electron-density studies even for materials with slight peak overlap have been performed with microstrip detectors. One of the most critical problems has been a difference in sensitivity between microstrip channels, which substantially defines the dynamic range of a detector. Recently, a robust approach to this problem has been developed and applied to a total scattering measurement system (OHGI) with 15 MYTHEN microstrip modules. In the present study, synchrotron powder X-ray diffraction data obtained with OHGI are evaulated in terms of multipole electron densities and structural parameters (atomic positions and displacement parameters). These results show that, even without a dedicated setup and perfect samples, electron-density modelling can be carried out on high-quality powder X-ray diffraction data. However, it was also found that the required prior information about the sample prohibits widespread use of the method. With the presently obtainable data quality, electron densities of molecular crystals in general are not reliably obtained from powder data, but it is an excellent, possibly superior, alternative to single-crystal measurements for small-unit-cell inorganic solids. If aspherical atomic scattering factors can be obtained from other means (multipole databases, theoretical calculations), then atomic positions (including for hydrogen) and anisotropic atomic displacement parameters (non-hydrogen atoms) of excellent accuracy can be refined from synchrotron powder X-ray diffraction data on organic crystals.https://creativecommons.org/licenses/by/4.0/urn:issn:2053-2733Svane, B.Tolborg, K.Kato, K.Iversen, B.B.2021-01-28doi:10.1107/S2053273320016605International Union of CrystallographyMultipole electron densities and structural parameters of inorganic and organic materials were evaluated on the basis of synchrotron powder X-ray diffraction data obtained with a MYTHEN detector system (OHGI).enELECTRON DENSITY; STRUCTURAL PARAMETERS; POWDER DIFFRACTION; MOLECULAR CRYSTALS; SYNCHROTRON RADIATIONPowder X-ray diffraction has some inherent advantages over traditional single-crystal X-ray diffraction in accurately determining electron densities and structural parameters due to the lower requirements for sample crystallinity, simpler corrections and measurement simultaneity. For some simple inorganic materials, it has been shown that these advantages can compensate for disadvantages such as peak overlap and error-prone background subtraction. Although it is challenging to extend powder X-ray diffraction-based electron-density studies to organic materials with significant peak overlap, previous results using a dedicated vacuum diffractometer with a large image-plate camera (AVID) demonstrated that it can be done. However, the vacuum setup with the off-line detector system was found to prohibit a widespread use. Fast microstrip detectors, which have been employed at a number of powder diffraction beamlines, have the potential to facilitate electron-density studies. Nevertheless, no electron-density studies even for materials with slight peak overlap have been performed with microstrip detectors. One of the most critical problems has been a difference in sensitivity between microstrip channels, which substantially defines the dynamic range of a detector. Recently, a robust approach to this problem has been developed and applied to a total scattering measurement system (OHGI) with 15 MYTHEN microstrip modules. In the present study, synchrotron powder X-ray diffraction data obtained with OHGI are evaulated in terms of multipole electron densities and structural parameters (atomic positions and displacement parameters). These results show that, even without a dedicated setup and perfect samples, electron-density modelling can be carried out on high-quality powder X-ray diffraction data. However, it was also found that the required prior information about the sample prohibits widespread use of the method. With the presently obtainable data quality, electron densities of molecular crystals in general are not reliably obtained from powder data, but it is an excellent, possibly superior, alternative to single-crystal measurements for small-unit-cell inorganic solids. If aspherical atomic scattering factors can be obtained from other means (multipole databases, theoretical calculations), then atomic positions (including for hydrogen) and anisotropic atomic displacement parameters (non-hydrogen atoms) of excellent accuracy can be refined from synchrotron powder X-ray diffraction data on organic crystals.text/htmlMultipole electron densities and structural parameters from synchrotron powder X-ray diffraction data obtained with a MYTHEN detector system (OHGI)text772https://creativecommons.org/licenses/by/4.0/Acta Crystallographica Section A: Foundations and Advances2021-01-2885research papers2053-2733March 2021med@iucr.org952053-2733Arithmetic proof of the multiplicity-weighted Euler characteristic for symmetrically arranged space-filling polyhedra
http://scripts.iucr.org/cgi-bin/paper?pl5009
The puzzling observation that the famous Euler's formula for three-dimensional polyhedra V − E + F = 2 or Euler characteristic χ = V − E + F − I = 1 (where V, E, F are the numbers of the bounding vertices, edges and faces, respectively, and I = 1 counts the single solid itself) when applied to space-filling solids, such as crystallographic asymmetric units or Dirichlet domains, are modified in such a way that they sum up to a value one unit smaller (i.e. to 1 or 0, respectively) is herewith given general validity. The proof provided in this paper for the modified Euler characteristic, χm = Vm − Em + Fm − Im = 0, is divided into two parts. First, it is demonstrated for translational lattices by using a simple argument based on parity groups of integer-indexed elements of the lattice. Next, Whitehead's theorem, about the invariance of the Euler characteristic, is used to extend the argument from the unit cell to its asymmetric unit components.https://creativecommons.org/licenses/by/4.0/urn:issn:2053-2733Naskręcki, B.Dauter, Z.Jaskolski, M.2021-02-04doi:10.1107/S2053273320016186International Union of CrystallographyA mathematical proof based on arithmetic argument is presented for the modified Euler characteristic \chi_{\rm m}=\sum_{i=0}^N (-1)^i \sum _{j=1}^{n(i)} 1/m(ij)=0 (where the first summation runs from 0-dimensional vertices to the N-dimensional cell or `interior'), applicable to symmetrically arranged space-filling polytopes in N-dimensional space, where the contribution of each jth i-dimensional element of the polytope is weighted by a factor inversely proportional to its multiplicity m(ij).enEULER'S FORMULA; MULTIPLICITY-WEIGHTED EULER CHARACTERISTIC; SPACE-FILLING POLYHEDRA; POLYTOPES; ASYMMETRIC UNIT; DIRICHLET DOMAINSThe puzzling observation that the famous Euler's formula for three-dimensional polyhedra V − E + F = 2 or Euler characteristic χ = V − E + F − I = 1 (where V, E, F are the numbers of the bounding vertices, edges and faces, respectively, and I = 1 counts the single solid itself) when applied to space-filling solids, such as crystallographic asymmetric units or Dirichlet domains, are modified in such a way that they sum up to a value one unit smaller (i.e. to 1 or 0, respectively) is herewith given general validity. The proof provided in this paper for the modified Euler characteristic, χm = Vm − Em + Fm − Im = 0, is divided into two parts. First, it is demonstrated for translational lattices by using a simple argument based on parity groups of integer-indexed elements of the lattice. Next, Whitehead's theorem, about the invariance of the Euler characteristic, is used to extend the argument from the unit cell to its asymmetric unit components.text/htmlArithmetic proof of the multiplicity-weighted Euler characteristic for symmetrically arranged space-filling polyhedratext772https://creativecommons.org/licenses/by/4.0/Acta Crystallographica Section A: Foundations and Advances2021-02-04126research papers2053-2733March 2021med@iucr.org1292053-2733Symmetry relations in wurtzite nitrides and oxide nitrides and the curious case of Pmc21
http://scripts.iucr.org/cgi-bin/paper?ug5020
Binary III–V nitrides such as AlN, GaN and InN in the wurtzite-type structure have long been considered as potent semiconducting materials because of their optoelectronic properties, amongst others. With rising concerns over the utilization of scarce elements, a replacement of the trivalent cations by others in ternary and multinary nitrides has led to the development of different variants of nitrides and oxide nitrides crystallizing in lower-symmetry variants of wurtzite. This work presents the symmetry relationships between these structural types specific to nitrides and oxide nitrides and updates some prior work on this matter. The non-existence of compounds crystallizing in Pmc21, formally the highest subgroup of the wurtzite type fulfilling Pauling's rules for 1:1:2 stoichiometries, has been puzzling scientists for a while; a rationalization is given, from a crystallographic basis, of why this space group is unlikely to be adopted.https://creativecommons.org/licenses/by/4.0/urn:issn:2053-2733Breternitz, J.Schorr, S.2021-03-23doi:10.1107/S2053273320015971International Union of CrystallographyBinary and multinary nitrides in a wurtzitic arrangement are very interesting semiconductor materials. The group–subgroup relationship between the different structural types is established.enGROUP-SUBGROUP RELATIONSHIPS; NITRIDE MATERIALS; WURTZITE TYPEBinary III–V nitrides such as AlN, GaN and InN in the wurtzite-type structure have long been considered as potent semiconducting materials because of their optoelectronic properties, amongst others. With rising concerns over the utilization of scarce elements, a replacement of the trivalent cations by others in ternary and multinary nitrides has led to the development of different variants of nitrides and oxide nitrides crystallizing in lower-symmetry variants of wurtzite. This work presents the symmetry relationships between these structural types specific to nitrides and oxide nitrides and updates some prior work on this matter. The non-existence of compounds crystallizing in Pmc21, formally the highest subgroup of the wurtzite type fulfilling Pauling's rules for 1:1:2 stoichiometries, has been puzzling scientists for a while; a rationalization is given, from a crystallographic basis, of why this space group is unlikely to be adopted.text/htmlSymmetry relations in wurtzite nitrides and oxide nitrides and the curious case of Pmc21text773https://creativecommons.org/licenses/by/4.0/Acta Crystallographica Section A: Foundations and Advances2021-03-23208research papers2053-2733May 2021med@iucr.org2162053-2733Small-angle X-ray scattering from GaN nanowires on Si(111): facet truncation rods, facet roughness and Porod's law
http://scripts.iucr.org/cgi-bin/paper?iv5011
Small-angle X-ray scattering from GaN nanowires grown on Si(111) is measured in the grazing-incidence geometry and modelled by means of a Monte Carlo simulation that takes into account the orientational distribution of the faceted nanowires and the roughness of their side facets. It is found that the scattering intensity at large wavevectors does not follow Porod's law I(q) ∝ q−4. The intensity depends on the orientation of the side facets with respect to the incident X-ray beam. It is maximum when the scattering vector is directed along a facet normal, reminiscent of surface truncation rod scattering. At large wavevectors q, the scattering intensity is reduced by surface roughness. A root-mean-square roughness of 0.9 nm, which is the height of just 3–4 atomic steps per micrometre-long facet, already gives rise to a strong intensity reduction.https://creativecommons.org/licenses/by/4.0/urn:issn:2053-2733Kaganer, V.M.Konovalov, O.V.Fernández-Garrido, S.2021-01-05doi:10.1107/S205327332001548XInternational Union of CrystallographyThe intensity of small-angle X-ray scattering from GaN nanowires on Si(111) depends on the orientation of the side facets with respect to the incident beam. This reminiscence of truncation rod scattering gives rise to a deviation from Porod's law. A roughness of just 3–4 atomic steps per micrometre-long side facet notably changes the intensity curves.enNANOWIRES; POROD'S LAW; FACET TRUNCATION RODS; SMALL-ANGLE X-RAY SCATTERING; SAXS; GRAZING-INCIDENCE SMALL-ANGLE X-RAY SCATTERING; GISAXSSmall-angle X-ray scattering from GaN nanowires grown on Si(111) is measured in the grazing-incidence geometry and modelled by means of a Monte Carlo simulation that takes into account the orientational distribution of the faceted nanowires and the roughness of their side facets. It is found that the scattering intensity at large wavevectors does not follow Porod's law I(q) ∝ q−4. The intensity depends on the orientation of the side facets with respect to the incident X-ray beam. It is maximum when the scattering vector is directed along a facet normal, reminiscent of surface truncation rod scattering. At large wavevectors q, the scattering intensity is reduced by surface roughness. A root-mean-square roughness of 0.9 nm, which is the height of just 3–4 atomic steps per micrometre-long facet, already gives rise to a strong intensity reduction.text/htmlSmall-angle X-ray scattering from GaN nanowires on Si(111): facet truncation rods, facet roughness and Porod's lawtext1772021-01-05Acta Crystallographica Section A: Foundations and Advanceshttps://creativecommons.org/licenses/by/4.0/2053-2733research papers42med@iucr.orgJanuary 2021532053-2733Macromolecular phasing using diffraction from multiple crystal forms
http://scripts.iucr.org/cgi-bin/paper?sc5137
A phasing algorithm for macromolecular crystallography is proposed that utilizes diffraction data from multiple crystal forms – crystals of the same molecule with different unit-cell packings (different unit-cell parameters or space-group symmetries). The approach is based on the method of iterated projections, starting with no initial phase information. The practicality of the method is demonstrated by simulation using known structures that exist in multiple crystal forms, assuming some information on the molecular envelope and positional relationships between the molecules in the different unit cells. With incorporation of new or existing methods for determination of these parameters, the approach has potential as a method for ab initio phasing.https://creativecommons.org/licenses/by/4.0/urn:issn:2053-2733Metz, M.Arnal, R.D.Brehm, W.Chapman, H.N.Morgan, A.J.Millane, R.P.2021-01-05doi:10.1107/S2053273320013650International Union of CrystallographyA phasing algorithm for protein crystallography using diffraction data from multiple crystal forms is proposed. The algorithm is evaluated by simulation, and practical aspects and potential for ab initio phasing are discussed.enMULTIPLE CRYSTAL FORMS; AB INITIO PHASING; ITERATIVE PROJECTION ALGORITHMS; X-RAY FREE-ELECTRON LASERS; XFELSA phasing algorithm for macromolecular crystallography is proposed that utilizes diffraction data from multiple crystal forms – crystals of the same molecule with different unit-cell packings (different unit-cell parameters or space-group symmetries). The approach is based on the method of iterated projections, starting with no initial phase information. The practicality of the method is demonstrated by simulation using known structures that exist in multiple crystal forms, assuming some information on the molecular envelope and positional relationships between the molecules in the different unit cells. With incorporation of new or existing methods for determination of these parameters, the approach has potential as a method for ab initio phasing.text/htmlMacromolecular phasing using diffraction from multiple crystal formstext1772021-01-05Acta Crystallographica Section A: Foundations and Advanceshttps://creativecommons.org/licenses/by/4.0/2053-2733research papers19med@iucr.orgJanuary 2021352053-2733A cloud platform for atomic pair distribution function analysis: PDFitc
http://scripts.iucr.org/cgi-bin/paper?ae5091
A cloud web platform for analysis and interpretation of atomic pair distribution function (PDF) data (PDFitc) is described. The platform is able to host applications for PDF analysis to help researchers study the local and nanoscale structure of nanostructured materials. The applications are designed to be powerful and easy to use and can, and will, be extended over time through community adoption and development. The currently available PDF analysis applications, structureMining, spacegroupMining and similarityMapping, are described. In the first and second the user uploads a single PDF and the application returns a list of best-fit candidate structures, and the most likely space group of the underlying structure, respectively. In the third, the user can upload a set of measured or calculated PDFs and the application returns a matrix of Pearson correlations, allowing assessment of the similarity between different data sets. structureMining is presented here as an example to show the easy-to-use workflow on PDFitc. In the future, as well as using the PDFitc applications for data analysis, it is hoped that the community will contribute their own codes and software to the platform.https://creativecommons.org/licenses/by/4.0/urn:issn:2053-2733Yang, L.Culbertson, E.A.Thomas, N.K.Vuong, H.T.Kjær, E.T.S.Jensen, K.M.Ø.Tucker, M.G.Billinge, S.J.L.2021-01-05doi:10.1107/S2053273320013066International Union of CrystallographyA new web platform is presented for the pair distribution function (PDF) community to use and share advanced PDF analysis software in the cloud.enPAIR DISTRIBUTION FUNCTION; PDF; DATA ANALYSIS; WEB APPLICATIONS; CLOUD COMPUTINGA cloud web platform for analysis and interpretation of atomic pair distribution function (PDF) data (PDFitc) is described. The platform is able to host applications for PDF analysis to help researchers study the local and nanoscale structure of nanostructured materials. The applications are designed to be powerful and easy to use and can, and will, be extended over time through community adoption and development. The currently available PDF analysis applications, structureMining, spacegroupMining and similarityMapping, are described. In the first and second the user uploads a single PDF and the application returns a list of best-fit candidate structures, and the most likely space group of the underlying structure, respectively. In the third, the user can upload a set of measured or calculated PDFs and the application returns a matrix of Pearson correlations, allowing assessment of the similarity between different data sets. structureMining is presented here as an example to show the easy-to-use workflow on PDFitc. In the future, as well as using the PDFitc applications for data analysis, it is hoped that the community will contribute their own codes and software to the platform.text/htmlA cloud platform for atomic pair distribution function analysis: PDFitctext1772021-01-05Acta Crystallographica Section A: Foundations and Advanceshttps://creativecommons.org/licenses/by/4.0/2053-2733research papers2med@iucr.orgJanuary 202162053-2733Algorithms for target transformations of lattice basis vectors
http://scripts.iucr.org/cgi-bin/paper?ae5090
Simple algorithms are proposed for the transformation of lattice basis vectors to a specific target. In the first case, one of the new basis vectors is aligned to a predefined lattice direction, while in the second case, two of the new basis vectors are brought to a lattice plane with predefined Miller indices. The multi-dimensional generalization of the algorithm is available in the supporting materials. The algorithms are useful for such crystallographic operations as simulation of zone planes (i.e. geometry of electron diffraction patterns) or transformation of a unit cell for surface or cleavage energy calculations. The most general multi-dimensional version of the algorithm may be useful for the analysis of quasiperiodic crystals or as an alternative method of calculating Bézout coefficients. The algorithms are demonstrated both graphically and numerically.https://creativecommons.org/licenses/by/4.0/urn:issn:2053-2733Gorfman, S.2020-10-29doi:10.1107/S2053273320012668International Union of CrystallographyPresented here are algorithms for the transformation of lattice basis vectors to a specific target. The algorithms are useful for crystallographic operations in direct and reciprocal spaces alike. The algorithms are demonstrated graphically and numerically.enCRYSTAL LATTICE; TRANSFORMATIONS; LATTICE PLANES; ZONESSimple algorithms are proposed for the transformation of lattice basis vectors to a specific target. In the first case, one of the new basis vectors is aligned to a predefined lattice direction, while in the second case, two of the new basis vectors are brought to a lattice plane with predefined Miller indices. The multi-dimensional generalization of the algorithm is available in the supporting materials. The algorithms are useful for such crystallographic operations as simulation of zone planes (i.e. geometry of electron diffraction patterns) or transformation of a unit cell for surface or cleavage energy calculations. The most general multi-dimensional version of the algorithm may be useful for the analysis of quasiperiodic crystals or as an alternative method of calculating Bézout coefficients. The algorithms are demonstrated both graphically and numerically.text/htmlAlgorithms for target transformations of lattice basis vectorstext6762020-10-29Acta Crystallographica Section A: Foundations and Advanceshttps://creativecommons.org/licenses/by/4.0/2053-2733research papers713med@iucr.orgNovember 20207182053-2733