Open-access and free articles in Acta Crystallographica Section A: Foundations of Crystallography
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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) 2018 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) 2018 International Union of Crystallographyurn:issn:0108-7673Open-access and free articles in Acta Crystallographica Section A: Foundations of Crystallographyhttp://journals.iucr.org/logos/rss10a.gif
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Still imageA method to estimate statistical errors of properties derived from charge-density modelling
http://scripts.iucr.org/cgi-bin/paper?ae5043
Estimating uncertainties of property values derived from a charge-density model is not straightforward. A methodology, based on calculation of sample standard deviations (SSD) of properties using randomly deviating charge-density models, is proposed with the MoPro software. The parameter shifts applied in the deviating models are generated in order to respect the variance–covariance matrix issued from the least-squares refinement. This `SSD methodology' procedure can be applied to estimate uncertainties of any property related to a charge-density model obtained by least-squares fitting. This includes topological properties such as critical point coordinates, electron density, Laplacian and ellipticity at critical points and charges integrated over atomic basins. Errors on electrostatic potentials and interaction energies are also available now through this procedure. The method is exemplified with the charge density of compound (E)-5-phenylpent-1-enylboronic acid, refined at 0.45 Å resolution. The procedure is implemented in the freely available MoPro program dedicated to charge-density refinement and modelling.https://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Fournier, B.Guillot, B.Lecomte, C.Escudero-Adán, E.C.Jelsch, C.2018-05-03doi:10.1107/S2053273318004308International Union of CrystallographyErrors on molecular properties including the topology of electron density and electrostatics are estimated from a sample of deviating models generated using the variance–covariance matrix issued at the end of the charge-density refinement.enMONTE CARLO METHODS; ELECTRON DENSITY; UNCERTAINTY; TOPOLOGY; INTERMOLECULAR INTERACTIONSEstimating uncertainties of property values derived from a charge-density model is not straightforward. A methodology, based on calculation of sample standard deviations (SSD) of properties using randomly deviating charge-density models, is proposed with the MoPro software. The parameter shifts applied in the deviating models are generated in order to respect the variance–covariance matrix issued from the least-squares refinement. This `SSD methodology' procedure can be applied to estimate uncertainties of any property related to a charge-density model obtained by least-squares fitting. This includes topological properties such as critical point coordinates, electron density, Laplacian and ellipticity at critical points and charges integrated over atomic basins. Errors on electrostatic potentials and interaction energies are also available now through this procedure. The method is exemplified with the charge density of compound (E)-5-phenylpent-1-enylboronic acid, refined at 0.45 Å resolution. The procedure is implemented in the freely available MoPro program dedicated to charge-density refinement and modelling.text/htmlA method to estimate statistical errors of properties derived from charge-density modellingtext743https://creativecommons.org/licenses/by/2.0/ukActa Crystallographica Section A: Foundations and Advances2018-05-03170research papers2053-2733May 2018med@iucr.org1832053-2733Spatial displacement of forward-diffracted X-ray beams by perfect crystals
http://scripts.iucr.org/cgi-bin/paper?sc5112
Time-delayed, narrow-band echoes generated by forward Bragg diffraction of an X-ray pulse by a perfect thin crystal are exploited for self-seeding at hard X-ray free-electron lasers. Theoretical predictions indicate that the retardation is strictly correlated to a transverse displacement of the echo pulses. This article reports the first experimental observation of the displaced echoes. The displacements are in good agreement with simulations relying on the dynamical diffraction theory. The echo signals are characteristic for a given Bragg reflection, the structure factor and the probed interplane distance. The reported results pave the way to exploiting the signals as an online diagnostic tool for hard X-ray free-electron laser seeding and for dynamical diffraction investigations of strain at the femtosecond timescale.https://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Rodriguez-Fernandez, A.Esposito, V.Sanchez, D.F.Finkelstein, K.D.Juranic, P.Staub, U.Grolimund, D.Reiche, S.Pedrini, B.2018-02-23doi:10.1107/S2053273318001419International Union of CrystallographyThe first experimental observation of transverse spatial echoes generated by forward Bragg diffraction of an X-ray beam propagating through a perfect thin crystal is reported.enX-RAY DYNAMICAL DIFFRACTION; PERFECT CRYSTALS; TRANSVERSE ECHO DISPLACEMENT; HARD X-RAY SELF-SEEDINGTime-delayed, narrow-band echoes generated by forward Bragg diffraction of an X-ray pulse by a perfect thin crystal are exploited for self-seeding at hard X-ray free-electron lasers. Theoretical predictions indicate that the retardation is strictly correlated to a transverse displacement of the echo pulses. This article reports the first experimental observation of the displaced echoes. The displacements are in good agreement with simulations relying on the dynamical diffraction theory. The echo signals are characteristic for a given Bragg reflection, the structure factor and the probed interplane distance. The reported results pave the way to exploiting the signals as an online diagnostic tool for hard X-ray free-electron laser seeding and for dynamical diffraction investigations of strain at the femtosecond timescale.text/htmlSpatial displacement of forward-diffracted X-ray beams by perfect crystalstext2742018-02-23Acta Crystallographica Section A: Foundations and Advanceshttps://creativecommons.org/licenses/by/2.0/uk2053-2733research papers75med@iucr.orgMarch 2018872053-2733The development of powder profile refinement at the Reactor Centre Netherlands at Petten
http://scripts.iucr.org/cgi-bin/paper?ib5058
With thousands of references to `Rietveld refinement' it is forgotten that the method did not suddenly appear in a flash of inspiration of a single person, but was the result of the work of three individuals working in the 1960s at the Reactor Centre Netherlands at Petten, Loopstra, van Laar and Rietveld. This paper outlines the origins of `profile refinement', as it was called at Petten, and also looks at why it took so long for the scientific community to recognize its importance. With the recent passing of Hugo Rietveld, the death of Bert Loopstra in 1998 and before other pioneers also disappear, it is important to set down a first-hand account.https://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733van Laar, B.Schenk, H.2018-03-01doi:10.1107/S2053273317018435International Union of CrystallographyAround 1965 at the Reactor Centre Netherlands at Petten, Loopstra, van Laar and Rietveld developed `profile refinement'. Although Loopstra had the idea, van Laar worked it out mathematically and Rietveld wrote the computer program, the essential contributions of the first two are forgotten when using `Rietveld refinement'.enPOWDER PROFILE REFINEMENT; PROFILE REFINEMENT; RIETVELD REFINEMENTWith thousands of references to `Rietveld refinement' it is forgotten that the method did not suddenly appear in a flash of inspiration of a single person, but was the result of the work of three individuals working in the 1960s at the Reactor Centre Netherlands at Petten, Loopstra, van Laar and Rietveld. This paper outlines the origins of `profile refinement', as it was called at Petten, and also looks at why it took so long for the scientific community to recognize its importance. With the recent passing of Hugo Rietveld, the death of Bert Loopstra in 1998 and before other pioneers also disappear, it is important to set down a first-hand account.text/htmlThe development of powder profile refinement at the Reactor Centre Netherlands at Pettentext2742018-03-01Acta Crystallographica Section A: Foundations and Advanceshttps://creativecommons.org/licenses/by/2.0/uk2053-2733scientific comment88med@iucr.orgMarch 2018922053-2733Quasicrystals: What do we know? What do we want to know? What can we know?
http://scripts.iucr.org/cgi-bin/paper?ib5056
More than 35 years and 11 000 publications after the discovery of quasicrystals by Dan Shechtman, quite a bit is known about their occurrence, formation, stability, structures and physical properties. It has also been discovered that quasiperiodic self-assembly is not restricted to intermetallics, but can take place in systems on the meso- and macroscales. However, there are some blank areas, even in the centre of the big picture. For instance, it has still not been fully clarified whether quasicrystals are just entropy-stabilized high-temperature phases or whether they can be thermodynamically stable at 0 K as well. More studies are needed for developing a generally accepted model of quasicrystal growth. The state of the art of quasicrystal research is briefly reviewed and the main as-yet unanswered questions are addressed, as well as the experimental limitations to finding answers to them. The focus of this discussion is on quasicrystal structure analysis as well as on quasicrystal stability and growth mechanisms.https://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Steurer, W.2018-01-01doi:10.1107/S2053273317016540International Union of CrystallographyThe state of the art of quasicrystal research is critically reviewed. Fundamental questions that are still unanswered are discussed and experimental limitations are considered.enQUASICRYSTALS; STRUCTURE ANALYSIS; HIGHER-DIMENSIONAL CRYSTALLOGRAPHY; STABILITY OF QUASICRYSTALS; QUASICRYSTAL GROWTHMore than 35 years and 11 000 publications after the discovery of quasicrystals by Dan Shechtman, quite a bit is known about their occurrence, formation, stability, structures and physical properties. It has also been discovered that quasiperiodic self-assembly is not restricted to intermetallics, but can take place in systems on the meso- and macroscales. However, there are some blank areas, even in the centre of the big picture. For instance, it has still not been fully clarified whether quasicrystals are just entropy-stabilized high-temperature phases or whether they can be thermodynamically stable at 0 K as well. More studies are needed for developing a generally accepted model of quasicrystal growth. The state of the art of quasicrystal research is briefly reviewed and the main as-yet unanswered questions are addressed, as well as the experimental limitations to finding answers to them. The focus of this discussion is on quasicrystal structure analysis as well as on quasicrystal stability and growth mechanisms.text/htmlQuasicrystals: What do we know? What do we want to know? What can we know?text1742018-01-01Acta Crystallographica Section A: Foundations and Advanceshttps://creativecommons.org/licenses/by/2.0/uk2053-2733topical reviews1med@iucr.orgJanuary 2018112053-2733Small-angle X-ray scattering tensor tomography: model of the three-dimensional reciprocal-space map, reconstruction algorithm and angular sampling requirements
http://scripts.iucr.org/cgi-bin/paper?vk5021
Small-angle X-ray scattering tensor tomography, which allows reconstruction of the local three-dimensional reciprocal-space map within a three-dimensional sample as introduced by Liebi et al. [Nature (2015), 527, 349–352], is described in more detail with regard to the mathematical framework and the optimization algorithm. For the case of trabecular bone samples from vertebrae it is shown that the model of the three-dimensional reciprocal-space map using spherical harmonics can adequately describe the measured data. The method enables the determination of nanostructure orientation and degree of orientation as demonstrated previously in a single momentum transfer q range. This article presents a reconstruction of the complete reciprocal-space map for the case of bone over extended ranges of q. In addition, it is shown that uniform angular sampling and advanced regularization strategies help to reduce the amount of data required.https://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Liebi, M.Georgiadis, M.Kohlbrecher, J.Holler, M.Raabe, J.Usov, I.Menzel, A.Schneider, P.Bunk, O.Guizar-Sicairos, M.2018-01-01doi:10.1107/S205327331701614XInternational Union of CrystallographyThe mathematical framework and reconstruction algorithm for small-angle scattering tensor tomography are introduced in detail, as well as strategies which help to reduce the amount of data and therewith the measurement time required. Experimental validation is provided for the application to trabecular bone.enSMALL-ANGLE X-RAY SCATTERING; TENSOR TOMOGRAPHY; SPHERICAL HARMONICS; BONESmall-angle X-ray scattering tensor tomography, which allows reconstruction of the local three-dimensional reciprocal-space map within a three-dimensional sample as introduced by Liebi et al. [Nature (2015), 527, 349–352], is described in more detail with regard to the mathematical framework and the optimization algorithm. For the case of trabecular bone samples from vertebrae it is shown that the model of the three-dimensional reciprocal-space map using spherical harmonics can adequately describe the measured data. The method enables the determination of nanostructure orientation and degree of orientation as demonstrated previously in a single momentum transfer q range. This article presents a reconstruction of the complete reciprocal-space map for the case of bone over extended ranges of q. In addition, it is shown that uniform angular sampling and advanced regularization strategies help to reduce the amount of data required.text/htmlSmall-angle X-ray scattering tensor tomography: model of the three-dimensional reciprocal-space map, reconstruction algorithm and angular sampling requirementstext1742018-01-01Acta Crystallographica Section A: Foundations and Advanceshttps://creativecommons.org/licenses/by/2.0/uk2053-2733research papers12med@iucr.orgJanuary 2018242053-2733{\bb Z}-module defects in crystals
http://scripts.iucr.org/cgi-bin/paper?td5044
An analysis is presented of the new types of defects that can appear in crystalline structures where the positions of the atoms and the unit cell belong to the same {\bb Z}-module, i.e. are irrational projections of an N > 3-dimensional (N-D) lattice Λ as in the case of quasicrystals. Beyond coherent irrationally oriented twins already discussed in a previous paper [Quiquandon et al. (2016). Acta Cryst. A72, 55–61], new two-dimensional translational defects are expected, the translation vectors of which, being projections of nodes of Λ, have irrational coordinates with respect to the unit-cell reference frame. Partial dislocations, called here module dislocations, are the linear defects bounding these translation faults. A specific case arises when the Burgers vector B is the projection of a non-zero vector of Λ that is perpendicular to the physical space. This new kind of dislocation is called a scalar dislocation since, because its Burgers vector in physical space is zero, it generates no displacement field and has no interaction with external stress fields and other dislocations.https://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Sirindil, A.Quiquandon, M.Gratias, D.2017-10-26doi:10.1107/S2053273317013882International Union of CrystallographyNew kinds of defects can appear in crystals where the atoms and unit cell sit on the nodes of {\bb Z}-modules, i.e. on three-dimensional projections of N-dimensional lattices. These defects are the result of the symmetry breaking due to the projection of the structure from N to three dimensions. Examples are given that illustrate the processes. A new kind of dislocation, here called a `scalar dislocation', is expected; it generates no deformation and has no interaction with stress fields.en{\BB Z}-MODULES; INTERMETALLIC ALLOYS; DEFECTS; TWINS; DISLOCATIONSAn analysis is presented of the new types of defects that can appear in crystalline structures where the positions of the atoms and the unit cell belong to the same {\bb Z}-module, i.e. are irrational projections of an N > 3-dimensional (N-D) lattice Λ as in the case of quasicrystals. Beyond coherent irrationally oriented twins already discussed in a previous paper [Quiquandon et al. (2016). Acta Cryst. A72, 55–61], new two-dimensional translational defects are expected, the translation vectors of which, being projections of nodes of Λ, have irrational coordinates with respect to the unit-cell reference frame. Partial dislocations, called here module dislocations, are the linear defects bounding these translation faults. A specific case arises when the Burgers vector B is the projection of a non-zero vector of Λ that is perpendicular to the physical space. This new kind of dislocation is called a scalar dislocation since, because its Burgers vector in physical space is zero, it generates no displacement field and has no interaction with external stress fields and other dislocations.text/html{\bb Z}-module defects in crystalstext6732017-10-26Acta Crystallographica Section A: Foundations and Advanceshttps://creativecommons.org/licenses/by/2.0/uk2053-2733research papers427med@iucr.orgNovember 20174372053-2733Introducing the holo-TIE approach to cellular imaging
http://scripts.iucr.org/cgi-bin/paper?me0655
Copyright (c) 2017 International Union of Crystallographyurn:issn:2053-2733Robinson, I.2017-06-29doi:10.1107/S2053273317009500International Union of CrystallographyThe new holo-TIE approach to cellular imaging described by Krenkel et al. [Acta Cryst. (2017), A73, 282–292] is discussed.enX-RAY TOMOGRAPHY; COHERENT DIFFRACTION IMAGING; BIOLOGICAL IMAGING; CONTRAST-TRANSFER FUNCTIONtext/htmlIntroducing the holo-TIE approach to cellular imagingtext734Copyright (c) 2017 International Union of CrystallographyActa Crystallographica Section A: Foundations and Advances2017-06-29281scientific commentaries2053-2733July 2017med@iucr.org2812053-2733High-resolution X-ray diffraction with no sample preparation
http://scripts.iucr.org/cgi-bin/paper?sc5103
It is shown that energy-dispersive X-ray diffraction (EDXRD) implemented in a back-reflection geometry is extremely insensitive to sample morphology and positioning even in a high-resolution configuration. This technique allows high-quality X-ray diffraction analysis of samples that have not been prepared and is therefore completely non-destructive. The experimental technique was implemented on beamline B18 at the Diamond Light Source synchrotron in Oxfordshire, UK. The majority of the experiments in this study were performed with pre-characterized geological materials in order to elucidate the characteristics of this novel technique and to develop the analysis methods. Results are presented that demonstrate phase identification, the derivation of precise unit-cell parameters and extraction of microstructural information on unprepared rock samples and other sample types. A particular highlight was the identification of a specific polytype of a muscovite in an unprepared mica schist sample, avoiding the time-consuming and difficult preparation steps normally required to make this type of identification. The technique was also demonstrated in application to a small number of fossil and archaeological samples. Back-reflection EDXRD implemented in a high-resolution configuration shows great potential in the crystallographic analysis of cultural heritage artefacts for the purposes of scientific research such as provenancing, as well as contributing to the formulation of conservation strategies. Possibilities for moving the technique from the synchrotron into museums are discussed. The avoidance of the need to extract samples from high-value and rare objects is a highly significant advantage, applicable also in other potential research areas such as palaeontology, and the study of meteorites and planetary materials brought to Earth by sample-return missions.http://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Hansford, G.M.Turner, S.M.R.Degryse, P.Shortland, A.J.2017-06-29doi:10.1107/S2053273317008592International Union of CrystallographyA novel, high-resolution X-ray diffraction (XRD) technique that provides completely non-destructive, high-quality XRD analyses of unprepared samples is demonstrated. The method shows great potential in the characterization of cultural heritage artefacts.enENERGY-DISPERSIVE XRD; BACK-REFLECTION GEOMETRY; SAMPLE PREPARATION; NON-DESTRUCTIVE ANALYSIS; CULTURAL HERITAGE ARTEFACTS; SYNCHROTRON EXPERIMENTSIt is shown that energy-dispersive X-ray diffraction (EDXRD) implemented in a back-reflection geometry is extremely insensitive to sample morphology and positioning even in a high-resolution configuration. This technique allows high-quality X-ray diffraction analysis of samples that have not been prepared and is therefore completely non-destructive. The experimental technique was implemented on beamline B18 at the Diamond Light Source synchrotron in Oxfordshire, UK. The majority of the experiments in this study were performed with pre-characterized geological materials in order to elucidate the characteristics of this novel technique and to develop the analysis methods. Results are presented that demonstrate phase identification, the derivation of precise unit-cell parameters and extraction of microstructural information on unprepared rock samples and other sample types. A particular highlight was the identification of a specific polytype of a muscovite in an unprepared mica schist sample, avoiding the time-consuming and difficult preparation steps normally required to make this type of identification. The technique was also demonstrated in application to a small number of fossil and archaeological samples. Back-reflection EDXRD implemented in a high-resolution configuration shows great potential in the crystallographic analysis of cultural heritage artefacts for the purposes of scientific research such as provenancing, as well as contributing to the formulation of conservation strategies. Possibilities for moving the technique from the synchrotron into museums are discussed. The avoidance of the need to extract samples from high-value and rare objects is a highly significant advantage, applicable also in other potential research areas such as palaeontology, and the study of meteorites and planetary materials brought to Earth by sample-return missions.text/htmlHigh-resolution X-ray diffraction with no sample preparationtext734http://creativecommons.org/licenses/by/2.0/ukActa Crystallographica Section A: Foundations and Advances2017-06-29293research papers2053-2733July 2017med@iucr.org3112053-2733Three-dimensional single-cell imaging with X-ray waveguides in the holographic regime
http://scripts.iucr.org/cgi-bin/paper?ib5053
X-ray tomography at the level of single biological cells is possible in a low-dose regime, based on full-field holographic recordings, with phase contrast originating from free-space wave propagation. Building upon recent progress in cellular imaging based on the illumination by quasi-point sources provided by X-ray waveguides, here this approach is extended in several ways. First, the phase-retrieval algorithms are extended by an optimized deterministic inversion, based on a multi-distance recording. Second, different advanced forms of iterative phase retrieval are used, operational for single-distance and multi-distance recordings. Results are compared for several different preparations of macrophage cells, for different staining and labelling. As a result, it is shown that phase retrieval is no longer a bottleneck for holographic imaging of cells, and how advanced schemes can be implemented to cope also with high noise and inconsistencies in the data.http://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Krenkel, M.Toepperwien, M.Alves, F.Salditt, T.2017-06-29doi:10.1107/S2053273317007902International Union of CrystallographyPhase-contrast X-ray imaging of biological cells in two and three dimensions can be carried out with a low dose, based on free propagation and a setting of optimized wavefronts in cone-beam geometry. In order to reach the required contrast level, images have to be recorded in the holographic regime. The main result of this work is holographic recordings of a quality that is fully amenable to quantitative phase retrieval, beyond previous approximations. Different approaches to sample preparations, data recording and phase retrieval are compared.enX-RAY HOLOGRAPHY; PHASE RETRIEVAL; X-RAY TOMOGRAPHY; X-RAY WAVEGUIDES; COHERENT IMAGINGX-ray tomography at the level of single biological cells is possible in a low-dose regime, based on full-field holographic recordings, with phase contrast originating from free-space wave propagation. Building upon recent progress in cellular imaging based on the illumination by quasi-point sources provided by X-ray waveguides, here this approach is extended in several ways. First, the phase-retrieval algorithms are extended by an optimized deterministic inversion, based on a multi-distance recording. Second, different advanced forms of iterative phase retrieval are used, operational for single-distance and multi-distance recordings. Results are compared for several different preparations of macrophage cells, for different staining and labelling. As a result, it is shown that phase retrieval is no longer a bottleneck for holographic imaging of cells, and how advanced schemes can be implemented to cope also with high noise and inconsistencies in the data.text/htmlThree-dimensional single-cell imaging with X-ray waveguides in the holographic regimetext734http://creativecommons.org/licenses/by/2.0/ukActa Crystallographica Section A: Foundations and Advances2017-06-29282research papers2053-2733July 2017med@iucr.org2922053-2733