Publisher: IUCr   (Total: 10 journals)   [Sort alphabetically]

Showing 1 - 10 of 10 Journals sorted by number of followers
Acta Crystallographica Section A: Foundations and Advances     Hybrid Journal   (Followers: 8, SJR: 5.99, CiteScore: 13)
Acta Crystallographica Section C: Structural Chemistry     Hybrid Journal   (Followers: 8, SJR: 0.834, CiteScore: 3)
Acta Crystallographica Section F: Structural Biology Communications     Hybrid Journal   (Followers: 8, SJR: 0.592, CiteScore: 1)
J. of Applied Crystallography     Hybrid Journal   (Followers: 7, SJR: 1.635, CiteScore: 3)
Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials     Hybrid Journal   (Followers: 6, SJR: 1.654, CiteScore: 5)
Acta Crystallographica Section D : Biological Crystallography     Hybrid Journal   (Followers: 5)
Acta Crystallographica Section E : Crystallographic Communications     Open Access   (Followers: 3, SJR: 0.153, CiteScore: 0)
J. of Synchrotron Radiation     Open Access   (Followers: 3, SJR: 1.65, CiteScore: 3)
IUCrData     Open Access   (Followers: 1)
IUCrJ     Open Access   (SJR: 3.212, CiteScore: 5)
Similar Journals
Journal Cover
Journal of Applied Crystallography
Journal Prestige (SJR): 1.635
Citation Impact (citeScore): 3
Number of Followers: 7  
 
  Hybrid Journal Hybrid journal (It can contain Open Access articles)
ISSN (Print) 0021-8898 - ISSN (Online) 1600-5767
Published by IUCr Homepage  [10 journals]
  • Resonant neutron scattering lengths

    • Free pre-print version: Loading...

      Authors: Von Dreele; R.B.
      Abstract: Unlike most of the periodic table, many rare-earth elements display considerable resonant scattering for thermal neutrons. Although this property is accompanied by strong neutron absorption, modern high-intensity neutron sources make diffraction experiments possible with these elements. Computation of scattering intensities is accomplished by fitting the variation in resonant scattering lengths (b0, b′ and b′′) to a semi-empirical Breit–Wigner formalism, which can be evaluated over the range of neutron energies useful for diffraction, typically E = 10–600 meV; λ = 0.4–2.8 Å (with good extrapolation to longer wavelengths).
      Keywords: resonant neutron scattering lengths; Breit–Wigner formula; rare earths
      Citation: urn:issn:1600-5767
      PubDate: 2024-07-17
      DOI: 10.1107/S1600576724005375
      Issue No: Vol. 57, No. 4 (2024)
       
  • Rapid detection of rare events from in situ X-ray diffraction data using
           machine learning

    • Free pre-print version: Loading...

      Authors: Zheng; W., Park, J.-S., Kenesei, P., Ali, A., Liu, Z., Foster, I., Schwarz, N., Kettimuthu, R., Miceli, A., Sharma, H.
      Abstract: High-energy X-ray diffraction methods can non-destructively map the 3D microstructure and associated attributes of metallic polycrystalline engineering materials in their bulk form. These methods are often combined with external stimuli such as thermo-mechanical loading to take snapshots of the evolving microstructure and attributes over time. However, the extreme data volumes and the high costs of traditional data acquisition and reduction approaches pose a barrier to quickly extracting actionable insights and improving the temporal resolution of these snapshots. This article presents a fully automated technique capable of rapidly detecting the onset of plasticity in high-energy X-ray microscopy data. The technique is computationally faster by at least 50 times than the traditional approaches and works for data sets that are up to nine times sparser than a full data set. This new technique leverages self-supervised image representation learning and clustering to transform massive data sets into compact, semantic-rich representations of visually salient characteristics (e.g. peak shapes). These characteristics can rapidly indicate anomalous events, such as changes in diffraction peak shapes. It is anticipated that this technique will provide just-in-time actionable information to drive smarter experiments that effectively deploy multi-modal X-ray diffraction methods spanning many decades of length scales.
      Keywords: high-energy diffraction microscopy; machine learning
      Citation: urn:issn:1600-5767
      PubDate: 2024-07-17
      DOI: 10.1107/S160057672400517X
      Issue No: Vol. 57, No. 4 (2024)
       
  • DFT2FEFFIT: a density-functional-theory-based structural toolkit to
           analyze EXAFS spectra

    • Free pre-print version: Loading...

      Authors: Manceau; A., Brossier, R., Mathon, O., Lomachenko, K.A., Retegan, M., Glatzel, P., Steinmann, S.N.
      Abstract: This article presents a Python-based program, DFT2FEFFIT, to regress theoretical extended X-ray absorption fine structure (EXAFS) spectra calculated from density functional theory structure models against experimental EXAFS spectra. To showcase its application, Ce-doped fluorapatite [Ca10(PO4)6F2] is revisited as a representative of a material difficult to analyze by conventional multi-shell least-squares fitting of EXAFS spectra. The software is open source and publicly available.
      Keywords: FEFF software; density functional theory; DFT; apatite; rare earth elements; cerium; EXAFS
      Citation: urn:issn:1600-5767
      PubDate: 2024-07-17
      DOI: 10.1107/S1600576724005454
      Issue No: Vol. 57, No. 4 (2024)
       
  • Demonstration of neutron time-of-flight diffraction with an event-mode
           imaging detector

    • Free pre-print version: Loading...

      Authors: Jäger; T.T., Losko, A.S., Wolfertz, A., Schmidt, S., Bertelsen, M., Khaplanov, A., Agnew, S.R., Funama, F., Morgano, M., Roth, M., Gochanour, J.R., Long, A.M., Lutterotti, L., Vogel, S.C.
      Abstract: Neutron diffraction beamlines have traditionally relied on deploying large detector arrays of 3He tubes or neutron-sensitive scintillators coupled with photomultipliers to efficiently probe crystallographic and microstructure information of a given material. Given the large upfront cost of custom-made data acquisition systems and the recent scarcity of 3He, new diffraction beamlines or upgrades to existing ones demand innovative approaches. This paper introduces a novel Timepix3-based event-mode imaging neutron diffraction detector system as well as first results of a silicon powder diffraction measurement made at the HIPPO neutron powder diffractometer at the Los Alamos Neutron Science Center. Notably, these initial measurements were conducted simultaneously with the 3He array on HIPPO, enabling direct comparison. Data reduction for this type of data was implemented in the MAUD code, enabling Rietveld analysis. Results from the Timepix3-based setup and HIPPO were benchmarked against McStas simulations, showing good agreement for peak resolution. With further development, systems such as the one presented here may substantially reduce the cost of detector systems for new neutron instrumentation as well as for upgrades of existing beamlines.
      Keywords: neutron diffraction; detector design; imaging detector
      Citation: urn:issn:1600-5767
      PubDate: 2024-07-11
      DOI: 10.1107/S1600576724004448
      Issue No: Vol. 57, No. 4 (2024)
       
  • Determination of the degree of crystallinity of polyphenylene sulfide
           composited with crystalline and non-crystalline fillers by applying the
           direct derivation method

    • Free pre-print version: Loading...

      Authors: Toraya; H.
      Abstract: A new procedure for determining the degree of crystallinity (DOC) has been recently proposed, and it has been verified using experimental and computer-generated powder diffractometry data [Toraya (2023). J. Appl. Cryst. 56, 1751–1763]. As an application to real materials like engineering plastics, this procedure is here applied to the DOC determination of plate-like polyphenylene sulfide (PPS) samples, composited with crystalline and non-crystalline fillers. The coexistence of partially crystallized polymer with non-crystalline fillers in target materials makes it difficult to separate the non-crystalline part of the partially crystallized polymer. This problem is here solved by the inverse application of the direct derivation (DD) method for quantitative phase analysis (QPA). The intensity–composition (IC) formula used in the DD method can derive the weight fractions of the individual components from just the total sums of observed intensities and the chemical composition data for these components [Toraya (2016). J. Appl. Cryst. 49, 1508–1516]. For the present purpose, the IC formula has been inversely applied to calculate the relative intensity ratios of individual components under the assumption that the chemical compositions and weight fractions of the respective components are known. The total halo intensity could then be separated into the non-crystalline part of the polymer and the non-crystalline filler. Analyzed results of PPS composites in four different DOCs are reported.
      Keywords: degree of crystallinity; direct derivation method; polyphenylene sulfide; PPS; non-crystalline fillers; engineering plastics; quantitative phase analysis
      Citation: urn:issn:1600-5767
      PubDate: 2024-07-11
      DOI: 10.1107/S1600576724005065
      Issue No: Vol. 57, No. 4 (2024)
       
  • Evolution of elliptical SAXS patterns in aligned systems

    • Free pre-print version: Loading...

      Authors: Murthy; N.S., Grubb, D.T.
      Abstract: Small-angle X-ray and neutron scattering (SAXS and SANS) patterns from certain semicrystalline polymers and liquid crystals contain discrete reflections from ordered assemblies and central diffuse scattering (CDS) from uncorrelated structures. Systems with imperfectly ordered lamellar structures aligned by stretching or by a magnetic field produce four distinct SAXS patterns: two-point `banana', four-point pattern, four-point `eyebrow' and four-point `butterfly'. The peak intensities of the reflections lie not on a layer line, or the arc of a circle, but on an elliptical trajectory. Modeling shows that randomly placed lamellar stacks modified by chain slip and stack rotation or interlamellar shear can create these forms. On deformation, the isotropic CDS becomes an equatorial streak with an oval, diamond or two-bladed propeller shape, which can be analyzed by separation into isotropic and oriented components. The streak has elliptical intensity contours, a natural consequence of the imperfect alignment of the elongated scattering objects. Both equatorial streaks and two- and four-point reflections can be fitted in elliptical coordinates with relatively few parameters. Equatorial streaks can be analyzed to obtain the size and orientation of voids, fibrils or surfaces. Analyses of the lamellar reflection yield lamellar spacing, stack orientation (interlamellar shear) angle α and chain slip angle ϕ, as well as the size distribution of the lamellar stacks. Currently available computational tools allow these microstructural parameters to be rapidly refined.
      Keywords: aligned objects; lamellar arrays; semicrystalline polymers; small-angle X-ray scattering; elliptical traces
      Citation: urn:issn:1600-5767
      PubDate: 2024-07-11
      DOI: 10.1107/S1600576724004503
      Issue No: Vol. 57, No. 4 (2024)
       
  • Exploring a nanostructured X-ray optical device for improved spatial
           resolution in laboratory X-ray diffraction imaging

    • Free pre-print version: Loading...

      Authors: Yamanashi; M.
      Abstract: Analytical methods with wide field range and high spatial resolution are required to observe the distribution of the crystal structure in micro-regions undergoing macroscopic chemical reactions. A recent X-ray diffraction (XRD) imaging method combines XRD with an X-ray optical device such as a glass polycapillary consisting of a bundle of numerous monocapillaries. The former provides the crystal structure, while the latter controls the shape of the incident or diffracted X-rays and retains the positional information of the sample. Although reducing the monocapillary pore size should improve the spatial resolution, manufacturing technology challenges must be overcome. Here, an anodic aluminium oxide (AAO) film, which forms self-ordered porous nanostructures by anodic oxidation in an electrolyte, is applied as an X-ray optical device. The AAO film (pore diameter: 110 nm; size of the disc: 11 mm; and thickness: 620 µm) was fabricated by anodization in a mixture of oxalic acid and ethylene glycol. The film was incorporated into a laboratory XRD instrument. Compared with using a glass polycapillary alone, using a combination of a glass polycapillary and the AAO film improved the spatial resolution of the XRD imaging method by 40%. This XRD imaging method should not only provide practical analysis in a laboratory environment but also support various observations of the crystal structure distribution.
      Keywords: X-ray diffraction imaging; X-ray optical devices; self-ordered nanostructure; anodization; porous anodic aluminium oxide
      Citation: urn:issn:1600-5767
      PubDate: 2024-07-11
      DOI: 10.1107/S1600576724005727
      Issue No: Vol. 57, No. 4 (2024)
       
  • Magnetic contrast layers with functional SiO2 coatings for soft-matter
           studies with polarized neutron reflectometry

    • Free pre-print version: Loading...

      Authors: Dikaia; O., Luchini, A., Nylander, T., Grunin, A., Vorobiev, A., Goikhman, A.
      Abstract: This study introduces silicon substrates with a switchable magnetic contrast layer (MCL) for polarized neutron reflectometry (PNR) experiments at the solid–liquid interface to study soft-matter surface layers. During standard neutron reflectometry (NR) experiments on soft-matter samples, structural and compositional information is obtained by collecting experimental data with different isotopic contrasts on the same sample. This approach is normally referred to as contrast matching, and it can be achieved by using solvents with different isotopic contrast, e.g. different H2O/D2O ratios, and/or by selective deuteration of the molecules. However, some soft-matter systems might be perturbed by this approach, or it might be difficult to implement, particularly in the case of biological samples. In these scenarios, solid substrates with an MCL are an appealing alternative, as the magnetic contrast with the substrate can be used for partial recovery of information on the sample structure. More specifically, in this study, a magnetically soft Fe layer coated with SiO2 was produced by ion-beam sputter deposition on silicon substrates of different sizes. The structure was evaluated using X-ray reflectometry, atomic force microscopy, vibrating sample magnetometry and PNR. The collected data showed the high quality and repeatability of the MCL parameters, regardless of the substrate size or the thickness of the capping SiO2 layer. Previously proposed substrates with an iron MCL used an Au capping layer. The SiO2 capping layer proposed here allows reproduction of the typical surface of a standard silicon substrate used for NR experiments and is compatible with a large variety of soft-matter samples. This application is demonstrated with ready-to-use 50 × 50 × 10 mm substrates in PNR experiments for the characterization of a lipid bilayer in a single solvent contrast. Overall, the article highlights the potential of PNR with an MCL for the investigation of soft-matter samples.
      Keywords: polarized neutron reflectometry; magnetic contrast layers; thin films; ion-beam sputter deposition; iron; silicon oxide
      Citation: urn:issn:1600-5767
      PubDate: 2024-07-11
      DOI: 10.1107/S1600576724005387
      Issue No: Vol. 57, No. 4 (2024)
       
  • On the magnitude of error in the determination of rotation axes

    • Free pre-print version: Loading...

      Authors: Morawiec; A.
      Abstract: Rotation axes (together with rotation angles) are often used to describe crystal orientations and misorientations, and they are also needed to characterize some properties of crystalline materials. Since experimental orientation data are subject to errors, the directions of the axes obtained from such data are also inaccurate. A natural question arises: given the resolution of input rotations, what is the average error of the rotation axes' Assuming that rotation data characterized by a rotation angle ω deviate from the actual data by error rotations with fixed angle δ but which are otherwise random, the average error of the rotation axes of the data is expressed analytically as a function of ω and δ. A scheme for using this formula in practical cases when rotation errors δ follow the von Mises–Fisher distribution is also described. Finally, the impact of crystal symmetry on the determination of the average errors of the axis directions is discussed. The presented results are important for assessing the reliability of rotation axes in studies where the directions of crystal rotations play a role, e.g. in identifying deformation slip mechanisms.
      Keywords: crystal orientation; misorientation; rotation axes; crystallographic texture; slip systems
      Citation: urn:issn:1600-5767
      PubDate: 2024-07-04
      DOI: 10.1107/S1600576724004692
      Issue No: Vol. 57, No. 4 (2024)
       
  • Mix and measure II: joint high-energy laboratory powder diffraction and
           microtomography for cement hydration studies

    • Free pre-print version: Loading...

      Authors: Fernandez-Sanchez; J., Cuesta, A., Shirani, S., Redondo-Soto, C., De la Torre, A.G., Santacruz, I., Salcedo, I.R., Leon-Reina, L., Aranda, M.A.G.
      Abstract: Portland cements (PCs) and cement blends are multiphase materials of different fineness, and quantitatively analysing their hydration pathways is very challenging. The dissolution (hydration) of the initial crystalline and amorphous phases must be determined, as well as the formation of labile (such as ettringite), reactive (such as portlandite) and amorphous (such as calcium silicate hydrate gel) components. The microstructural changes with hydration time must also be mapped out. To address this robustly and accurately, an innovative approach is being developed based on in situ measurements of pastes without any sample conditioning. Data are sequentially acquired by Mo Kα1 laboratory X-ray powder diffraction (LXRPD) and microtomography (µCT), where the same volume is scanned with time to reduce variability. Wide capillaries (2 mm in diameter) are key to avoid artefacts, e.g. self-desiccation, and to have excellent particle averaging. This methodology is tested in three cement paste samples: (i) a commercial PC 52.5 R, (ii) a blend of 80 wt% of this PC and 20 wt% quartz, to simulate an addition of supplementary cementitious materials, and (iii) a blend of 80 wt% PC and 20 wt% limestone, to simulate a limestone Portland cement. LXRPD data are acquired at 3 h and 1, 3, 7 and 28 days, and µCT data are collected at 12 h and 1, 3, 7 and 28 days. Later age data can also be easily acquired. In this methodology, the amounts of the crystalline phases are directly obtained from Rietveld analysis and the amorphous phase contents are obtained from mass-balance calculations. From the µCT study, and within the attained spatial resolution, three components (porosity, hydrated products and unhydrated cement particles) are determined. The analyses quantitatively demonstrate the filler effect of quartz and limestone in the hydration of alite and the calcium aluminate phases. Further hydration details are discussed.
      Keywords: Portland cements; cement blends; in situ studies; Rietveld quantitative phase analysis; X-ray imaging; filler effect
      Citation: urn:issn:1600-5767
      PubDate: 2024-07-04
      DOI: 10.1107/S1600576724004527
      Issue No: Vol. 57, No. 4 (2024)
       
  • Subgradient-projection-based stable phase-retrieval algorithm for X-ray
           ptychography

    • Free pre-print version: Loading...

      Authors: Akaishi; N., Yamada, K., Yatabe, K., Takayama, Y.
      Abstract: X-ray ptychography is a lensless imaging technique that visualizes the nanostructure of a thick specimen which cannot be observed with an electron microscope. It reconstructs a complex-valued refractive index of the specimen from observed diffraction patterns. This reconstruction problem is called phase retrieval (PR). For further improvement in the imaging capability, including expansion of the depth of field, various PR algorithms have been proposed. Since a high-quality PR method is built upon a base PR algorithm such as ePIE, developing a well performing base PR algorithm is important. This paper proposes an improved iterative algorithm named CRISP. It exploits subgradient projection which allows adaptive step size and can be expected to avoid yielding a poor image. The proposed algorithm was compared with ePIE, which is a simple and fast-convergence algorithm, and its modified algorithm, rPIE. The experiments confirmed that the proposed method improved the reconstruction performance for both simulation and real data.
      Keywords: hard X-ray ptychography; phase retrieval; subgradient projection
      Citation: urn:issn:1600-5767
      PubDate: 2024-07-04
      DOI: 10.1107/S1600576724004709
      Issue No: Vol. 57, No. 4 (2024)
       
  • On the analysis of two-time correlation functions: equilibrium versus
           non-equilibrium systems

    • Free pre-print version: Loading...

      Authors: Ragulskaya; A., Starostin, V., Zhang, F., Gutt, C., Schreiber, F.
      Abstract: X-ray photon correlation spectroscopy (XPCS) is a powerful tool for the investigation of dynamics covering a broad range of timescales and length scales. The two-time correlation function (TTC) is commonly used to track non-equilibrium dynamical evolution in XPCS measurements, with subsequent extraction of one-time correlations. While the theoretical foundation for the quantitative analysis of TTCs is primarily established for equilibrium systems, where key parameters such as the diffusion coefficient remain constant, non-equilibrium systems pose a unique challenge. In such systems, different projections (`cuts') of the TTC may lead to divergent results if the underlying fundamental parameters themselves are subject to temporal variations. This article explores widely used approaches for TTC calculations and common methods for extracting relevant information from correlation functions, particularly in the light of comparing dynamics in equilibrium and non-equilibrium systems.
      Keywords: two-time correlation functions; X-ray photon correlation spectroscopy; data analysis
      Citation: urn:issn:1600-5767
      PubDate: 2024-07-04
      DOI: 10.1107/S1600576724004618
      Issue No: Vol. 57, No. 4 (2024)
       
  • Automated pipeline processing X-ray diffraction data from dynamic
           compression experiments on the Extreme Conditions Beamline of PETRA III

    • Free pre-print version: Loading...

      Authors: Karnevskiy; M., Glazyrin, K., Yu, Y., Mondal, A., Sanchez-Valle, C., Marquardt, H., Husband, R.J., O'Bannon, E., Prescher, C., Barty, A., Liermann, H.-P.
      Abstract: Presented and discussed here is the implementation of a software solution that provides prompt X-ray diffraction data analysis during fast dynamic compression experiments conducted within the dynamic diamond anvil cell technique. It includes efficient data collection, streaming of data and metadata to a high-performance cluster (HPC), fast azimuthal data integration on the cluster, and tools for controlling the data processing steps and visualizing the data using the DIOPTAS software package. This data processing pipeline is invaluable for a great number of studies. The potential of the pipeline is illustrated with two examples of data collected on ammonia–water mixtures and multiphase mineral assemblies under high pressure. The pipeline is designed to be generic in nature and could be readily adapted to provide rapid feedback for many other X-ray diffraction techniques, e.g. large-volume press studies, in situ stress/strain studies, phase transformation studies, chemical reactions studied with high-resolution diffraction etc.
      Keywords: high-performance computing; pipeline data processing; batch pipeline processing; high-pressure studies; diamond anvil cells; dynamic compression; X-ray diffraction; visualization; analysis
      Citation: urn:issn:1600-5767
      PubDate: 2024-07-04
      DOI: 10.1107/S1600576724004114
      Issue No: Vol. 57, No. 4 (2024)
       
  • X-ray tensor tomography for small-grained polycrystals with strong texture

    • Free pre-print version: Loading...

      Authors: Carlsen; M., Appel, C., Hearn, W., Olsson, M., Menzel, A., Liebi, M.
      Abstract: Small-angle X-ray tensor tomography and the related wide-angle X-ray tensor tomography are X-ray imaging techniques that tomographically reconstruct the anisotropic scattering density of extended samples. In previous studies, these methods have been used to image samples where the scattering density depends slowly on the direction of scattering, typically modeling the directionality, i.e. the texture, with a spherical harmonics expansion up until order ℓ = 8 or lower. This study investigates the performance of several established algorithms from small-angle X-ray tensor tomography on samples with a faster variation as a function of scattering direction and compares their expected and achieved performance. The various algorithms are tested using wide-angle scattering data from an as-drawn steel wire with known texture to establish the viability of the tensor tomography approach for such samples and to compare the performance of existing algorithms.
      Keywords: tensor tomography; texture analysis; wide- and small-angle X-ray scattering; SAXS; WAXS
      Citation: urn:issn:1600-5767
      PubDate: 2024-06-27
      DOI: 10.1107/S1600576724004588
      Issue No: Vol. 57, No. 4 (2024)
       
  • Determination of α lamellae orientation in a β-Ti alloy using electron
           backscatter diffraction

    • Free pre-print version: Loading...

      Authors: Harcuba; P., Šmilauerová, J., Janeček, M., Ilavský, J., Holý, V.
      Abstract: The spatial orientation of α lamellae in a metastable β-Ti matrix of Timetal LCB (Ti–6.8 Mo–4.5 Fe–1.5 Al in wt%) was examined and the orientation of the hexagonal close-packed α lattice in the α lamella was determined. For this purpose, a combination of methods of small-angle X-ray scattering, scanning electron microscopy and electron backscatter diffraction was used. The habit planes of α laths are close to {111}β, which corresponds to (1320)α in the hexagonal coordinate system of the α phase. The longest α lamella direction lies approximately along one of the 〈110〉β directions which are parallel to the specific habit plane. Taking into account the average lattice parameters of the β and α phases in aged conditions in Timetal LCB, it was possible to index all main axes and faces of an α lath not only in the cubic coordinate system of the parent β phase but also in the hexagonal system of the α phase.
      Keywords: metastable titanium alloys; α phase; habit planes; orientation relationships
      Citation: urn:issn:1600-5767
      PubDate: 2024-06-27
      DOI: 10.1107/S160057672400400X
      Issue No: Vol. 57, No. 4 (2024)
       
  • Updating direct methods II. Reduction of the structural complexity when
           triplet invariants are estimated via the Patterson map

    • Free pre-print version: Loading...

      Authors: Burla; M.C., Giacovazzo, C., Polidori, G.
      Abstract: Direct methods have practically solved the phase problem for small–medium-size molecules but have substantially failed in macromolecular crystallography. They have two main limitations: a strong dependence on structural complexity and the need to work with atomic-resolution data. Many attempts have been made to broaden their field of applicability, for example the use of some a priori information to make the estimate of the triplet invariant phases more effective. Unfortunately none of these new approaches allowed the successful application of direct methods to proteins and nucleic acids. Direct methods are still a niche tool in macromolecular crystallography. In a recent publication [Giacovazzo (2019). Acta Cryst. A75, 142–157] the method of joint probability distributions has been modified to take into account new sources of prior information, one of which is relevant to this article: the Patterson map. In practice, it has been shown that with prior knowledge of the interatomic vectors one is able to modify the classic Cochran reliability parameter for estimating the triplet invariant phases. The article was essentially theoretical in nature, and no attempt was described to test the practical usefulness of the new probabilistic formulas. This work is therefore the first application of the new method. It is shown that the use of the Patterson map as prior information substantially improves the Cochran estimate of triplet phases; the phase error distribution for the new estimates, even if it is related to macromolecular structures, becomes similar to that obtained for medium-size structures. In some ways, it is as if the use of the Patterson information reduces the structural complexity, thus allowing a more general use of direct methods in macromolecular crystallography. Atomic resolution no longer seems to be a necessary ingredient for the applicability of direct methods; tests show that the apparent reduction in structural complexity also occurs in macromolecular structures with experimental data having a resolution of 2.3 Å. A number of test structures have been used to show the potential of the new technique.
      Keywords: direct methods; Patterson maps; ab initio solution of macromolecules
      Citation: urn:issn:1600-5767
      PubDate: 2024-06-27
      DOI: 10.1107/S1600576724004345
      Issue No: Vol. 57, No. 4 (2024)
       
  • Approaches and challenges in whole-nanoparticle refinements from neutron
           total-scattering data

    • Free pre-print version: Loading...

      Authors: Cladek; B., Zhang, Y., Maier, R., Ravel, B., Tucker, M.G., Levin, I.
      Abstract: This study considers critical data reduction steps and data analysis approaches required to determine explicitly the atomic arrangements in nanoparticles from time-of-flight neutron total scattering. A practical procedure is described for removing parasitic backgrounds caused by the incoherent scattering of hydrogen inevitably present in most nanoparticle samples and normalizing the recovered coherent scattering intensities onto an absolute scale. A model-free analysis is presented of a pair-distribution function derived from total scattering that can be used to determine thermal expansion coefficients and particle sizes directly from experimental data without knowledge of the material's structure. Finally, atomistic whole-nanoparticle refinements of yttrium-doped ceria nanoparticles from neutron total-scattering data are demonstrated using the reverse Monte Carlo method implemented in the RMCProfile software. These results reveal a strong dependence of the cation–oxygen and oxygen–oxygen distances on the coordination numbers, which leads to gradients of these distances near the particle surface. The details are dependent on the surface coverage by ligands and adsorbates and on the structure of grain boundaries in nanocrystalline agglomerates. The refined models confirm the expectations of more substantial disorder at particle surfaces, with a distorted surface layer extending over several coordination shells. The results highlight the feasibility of whole-nanoparticle refinements from neutron data, calling for further development of data reduction and analysis procedures.
      Keywords: nanoparticles; structure; atomistic models; total scattering; neutrons
      Citation: urn:issn:1600-5767
      PubDate: 2024-06-27
      DOI: 10.1107/S1600576724004321
      Issue No: Vol. 57, No. 4 (2024)
       
  • Quality assessment of the wide-angle detection option planned at the
           high-intensity/extended Q-range SANS diffractometer KWS-2 combining
           experiments and McStas simulations

    • Free pre-print version: Loading...

      Authors: Radulescu; A.
      Abstract: For a reliable characterization of materials and systems featuring multiple structural levels, a broad length scale from a few ångström to hundreds of nanometres must be analyzed and an extended Q range must be covered in X-ray and neutron scattering experiments. For certain samples or effects, it is advantageous to perform such characterization with a single instrument. Neutrons offer the unique advantage of contrast variation and matching by D-labeling, which is of great value in the characterization of natural or synthetic polymers. Some time-of-flight small-angle neutron scattering (TOF-SANS) instruments at neutron spallation sources can cover an extended Q range by using a broad wavelength band and a multitude of detectors. The detectors are arranged to cover a wide range of scattering angles with a resolution that allows both large-scale morphology and crystalline structure to be resolved simultaneously. However, for such analyses, the SANS instruments at steady-state sources operating in conventional monochromatic pinhole mode rely on additional wide-angle neutron scattering (WANS) detectors. The resolution must be tuned via a system of choppers and a TOF data acquisition option to reliably measure the atomic to mesoscale structures. The KWS-2 SANS diffractometer at Jülich Centre for Neutron Science allows the exploration of a wide Q range using conventional pinhole and lens focusing modes and an adjustable resolution Δλ/λ between 2 and 20%. This is achieved through the use of a versatile mechanical velocity selector combined with a variable slit opening and rotation frequency chopper. The installation of WANS detectors planned on the instrument required a detailed analysis of the quality of the data measured over a wide angular range with variable resolution. This article presents an assessment of the WANS performance by comparison with a McStas [Willendrup, Farhi & Lefmann (2004). Physica B, 350, E735–E737] simulation of ideal experimental conditions at the instrument.
      Keywords: small-angle neutron scattering; SANS; wide-angle neutron scattering; WANS; McStas simulations; semi-crystalline materials
      Citation: urn:issn:1600-5767
      PubDate: 2024-06-27
      DOI: 10.1107/S160057672400493X
      Issue No: Vol. 57, No. 4 (2024)
       
  • Inferring effective electrostatic interaction of charge-stabilized
           colloids from scattering using deep learning

    • Free pre-print version: Loading...

      Authors: Tung; C.-H., Chen, M.-Z., Chen, H.-L., Huang, G.-R., Porcar, L., Chang, M.-C., Carrillo, J.-M., Wang, Y., Sumpter, B.G., Shinohara, Y., Do, C., Chen, W.-R.
      Abstract: An innovative strategy is presented that incorporates deep auto-encoder networks into a least-squares fitting framework to address the potential inversion problem in small-angle scattering. To evaluate the performance of the proposed approach, a detailed case study focusing on charged colloidal suspensions was carried out. The results clearly indicate that a deep learning solution offers a reliable and quantitative method for studying molecular interactions. The approach surpasses existing deterministic approaches with respect to both numerical accuracy and computational efficiency. Overall, this work demonstrates the potential of deep learning techniques in tackling complex problems in soft-matter structures and beyond.
      Keywords: charge-stabilized colloids; small-angle scattering; deep learning; structure factors; potential inversion
      Citation: urn:issn:1600-5767
      PubDate: 2024-06-27
      DOI: 10.1107/S1600576724004515
      Issue No: Vol. 57, No. 4 (2024)
       
  • TORO Indexer: a PyTorch-based indexing algorithm for kilohertz serial
           crystallography

    • Free pre-print version: Loading...

      Authors: Gasparotto; P., Barba, L., Stadler, H.-C., Assmann, G., Mendonça, H., Ashton, A.W., Janousch, M., Leonarski, F., Béjar, B.
      Abstract: Serial crystallography (SX) involves combining observations from a very large number of diffraction patterns coming from crystals in random orientations. To compile a complete data set, these patterns must be indexed (i.e. their orientation determined), integrated and merged. Introduced here is TORO (Torch-powered robust optimization) Indexer, a robust and adaptable indexing algorithm developed using the PyTorch framework. TORO is capable of operating on graphics processing units (GPUs), central processing units (CPUs) and other hardware accelerators supported by PyTorch, ensuring compatibility with a wide variety of computational setups. In tests, TORO outpaces existing solutions, indexing thousands of frames per second when running on GPUs, which positions it as an attractive candidate to produce real-time indexing and user feedback. The algorithm streamlines some of the ideas introduced by previous indexers like DIALS real-space grid search [Gildea, Waterman, Parkhurst, Axford, Sutton, Stuart, Sauter, Evans & Winter (2014). Acta Cryst. D70, 2652–2666] and XGandalf [Gevorkov, Yefanov, Barty, White, Mariani, Brehm, Tolstikova, Grigat & Chapman (2019). Acta Cryst. A75, 694–704] and refines them using faster and principled robust optimization techniques which result in a concise code base consisting of less than 500 lines. On the basis of evaluations across four proteins, TORO consistently matches, and in certain instances outperforms, established algorithms such as XGandalf and MOSFLM [Powell (1999). Acta Cryst. D55, 1690–1695], occasionally amplifying the quality of the consolidated data while achieving superior indexing speed. The inherent modularity of TORO and the versatility of PyTorch code bases facilitate its deployment into a wide array of architectures, software platforms and bespoke applications, highlighting its prospective significance in SX.
      Keywords: PyTorch indexer; robust optimization; real-time indexing algorithms; serial crystallography; macromolecular crystallography; X-ray image acquisition; Torch scripts
      Citation: urn:issn:1600-5767
      PubDate: 2024-06-18
      DOI: 10.1107/S1600576724003182
      Issue No: Vol. 57, No. 4 (2024)
       
  • Tracking copper nanofiller evolution in polysiloxane during processing
           into SiOC ceramic

    • Free pre-print version: Loading...

      Authors: Loughney; P.A., Cuillier, P., Pruyn, T.L., Doan-Nguyen, V.
      Abstract: Polymer-derived ceramics (PDCs) remain at the forefront of research for a variety of applications including ultra-high-temperature ceramics, energy storage and functional coatings. Despite their wide use, questions remain about the complex structural transition from polymer to ceramic and how local structure influences the final microstructure and resulting properties. This is further complicated when nanofillers are introduced to tailor structural and functional properties, as nanoparticle surfaces can interact with the matrix and influence the resulting structure. The inclusion of crystalline nanofiller produces a mixed crystalline–amorphous composite, which poses characterization challenges. With this study, we aim to address these challenges with a local-scale structural study that probes changes in a polysiloxane matrix with incorporated copper nanofiller. Composites were processed at three unique temperatures to capture mixing, pyrolysis and initial crystallization stages for the pre-ceramic polymer. We observed the evolution of the nanofiller with electron microscopy and applied synchrotron X-ray diffraction with differential pair distribution function (d-PDF) analysis to monitor changes in the matrix's local structure and interactions with the nanofiller. The application of the d-PDF to PDC materials is novel and informs future studies to understand interfacial interactions between nanofiller and matrix throughout PDC processing.
      Keywords: polymer-derived ceramics; polysiloxane; X-ray total scattering; pair distribution function; nanofillers
      Citation: urn:issn:1600-5767
      PubDate: 2024-06-18
      DOI: 10.1107/S1600576724003133
      Issue No: Vol. 57, No. 4 (2024)
       
  • Quantitative selection of sample structures in small-angle scattering
           using Bayesian methods

    • Free pre-print version: Loading...

      Authors: Hayashi; Y., Katakami, S., Kuwamoto, S., Nagata, K., Mizumaki, M., Okada, M.
      Abstract: Small-angle scattering (SAS) is a key experimental technique for analyzing nanoscale structures in various materials. In SAS data analysis, selecting an appropriate mathematical model for the scattering intensity is critical, as it generates a hypothesis of the structure of the experimental sample. Traditional model selection methods either rely on qualitative approaches or are prone to overfitting. This paper introduces an analytical method that applies Bayesian model selection to SAS measurement data, enabling a quantitative evaluation of the validity of mathematical models. The performance of the method is assessed through numerical experiments using artificial data for multicomponent spherical materials, demonstrating that this proposed analysis approach yields highly accurate and interpretable results. The ability of the method to analyze a range of mixing ratios and particle size ratios for mixed components is also discussed, along with its precision in model evaluation by the degree of fitting. The proposed method effectively facilitates quantitative analysis of nanoscale sample structures in SAS, which has traditionally been challenging, and is expected to contribute significantly to advancements in a wide range of fields.
      Keywords: small-angle X-ray scattering; small-angle neutron scattering; nanostructure analysis; model selection; Bayesian inference
      Citation: urn:issn:1600-5767
      PubDate: 2024-06-18
      DOI: 10.1107/S1600576724004138
      Issue No: Vol. 57, No. 4 (2024)
       
  • Patching-based deep-learning model for the inpainting of Bragg coherent
           diffraction patterns affected by detector gaps

    • Free pre-print version: Loading...

      Authors: Masto; M., Favre-Nicolin, V., Leake, S., Schülli, T., Richard, M.-I., Bellec, E.
      Abstract: A deep-learning algorithm is proposed for the inpainting of Bragg coherent diffraction imaging (BCDI) patterns affected by detector gaps. These regions of missing intensity can compromise the accuracy of reconstruction algorithms, inducing artefacts in the final result. It is thus desirable to restore the intensity in these regions in order to ensure more reliable reconstructions. The key aspect of the method lies in the choice of training the neural network with cropped sections of diffraction data and subsequently patching the predictions generated by the model along the gap, thus completing the full diffraction peak. This approach enables access to a greater amount of experimental data for training and offers the ability to average overlapping sections during patching. As a result, it produces robust and dependable predictions for experimental data arrays of any size. It is shown that the method is able to remove gap-induced artefacts on the reconstructed objects for both simulated and experimental data, which becomes essential in the case of high-resolution BCDI experiments.
      Keywords: Bragg coherent diffraction imaging; image inpainting; deep learning
      Citation: urn:issn:1600-5767
      PubDate: 2024-06-18
      DOI: 10.1107/S1600576724004163
      Issue No: Vol. 57, No. 4 (2024)
       
  • Accurate space-group prediction from composition

    • Free pre-print version: Loading...

      Authors: Venkatraman; V., Carvalho, P.A.
      Abstract: Predicting crystal symmetry simply from chemical composition has remained challenging. Several machine-learning approaches can be employed, but the predictive value of popular crystallographic databases is relatively modest due to the paucity of data and uneven distribution across the 230 space groups. In this work, virtually all crystallographic information available to science has been compiled and used to train and test multiple machine-learning models. Composition-driven random-forest classification relying on a large set of descriptors showed the best performance. The predictive models for crystal system, Bravais lattice, point group and space group of inorganic compounds are made publicly available as easy-to-use software downloadable from https://gitlab.com/vishsoft/cosy.
      Keywords: space groups; random forests; machine learning; data sets; prediction
      Citation: urn:issn:1600-5767
      PubDate: 2024-06-18
      DOI: 10.1107/S1600576724004497
      Issue No: Vol. 57, No. 4 (2024)
       
  • A simple protocol for determining the zone axis direction from
           selected-area electron diffraction spot patterns of cubic materials

    • Free pre-print version: Loading...

      Authors: Weirich; T.E.
      Abstract: Using the well known Rn ratio method, a protocol has been elaborated for determining the lattice direction for the 15 most common cubic zone axis spot patterns. The method makes use of the lengths of the three shortest reciprocal-lattice vectors in each pattern and the angles between them. No prior pattern calibration is required for the method to work, as the Rn ratio method is based entirely on geometric relationships. In the first step the pattern is assigned to one of three possible pattern types according to the angles that are measured between the three reciprocal-lattice vectors. The lattice direction [uvw] and possible Bravais type(s) and Laue indices of the corresponding reflections can then be determined by using lookup tables. In addition to determining the lattice direction, this simple geometric analysis allows one to distinguish between the P, I and F Bravais lattices for spot patterns aligned along [013], [112], [114] and [233]. Moreover, the F lattice can always be uniquely identified from the [011] and [123] patterns.
      Keywords: electron diffraction; zone axis spot pattern; orientation determination; cubic symmetry; ratio method
      Citation: urn:issn:1600-5767
      PubDate: 2024-06-18
      DOI: 10.1107/S1600576724004333
      Issue No: Vol. 57, No. 4 (2024)
       
  • A study of stress, composition and grain interaction gradients in
           energy-dispersive X-ray stress analysis on materials with cubic symmetry

    • Free pre-print version: Loading...

      Authors: Genzel; C., Klaus, M.
      Abstract: The influence of various combinations of residual stress, composition and grain interaction gradients in polycrystalline materials with cubic symmetry on energy-dispersive X-ray stress analysis is theoretically investigated. For the evaluation of the simulated sin2ψ distributions, two different strategies are compared with regard to their suitability for separating the individual gradients. It is shown that the separation of depth gradients of the strain-free lattice parameter a0(z) from residual stress gradients σ(z) is only possible if the data analysis is carried out in section planes parallel to the surface. The impact of a surface layer z* that is characterized by a direction-dependent grain interaction model in contrast to the volume of the material is quantified by comparing a ferritic and an austenitic steel, which feature different elastic anisotropy. It is shown to be of minor influence on the resulting residual stress depth profiles if the data evaluation is restricted to reflections hkl with orientation factors Γhkl close to the model-independent orientation Γ*. Finally, a method is proposed that allows the thickness of the anisotropic surface layer z* to be estimated on the basis of an optimization procedure.
      Keywords: X-ray stress analysis; energy-dispersive diffraction; grain interaction; composition gradients; stress gradients
      Citation: urn:issn:1600-5767
      PubDate: 2024-06-07
      DOI: 10.1107/S1600576724003996
      Issue No: Vol. 57, No. 4 (2024)
       
  • Accessing self-diffusion on nanosecond time and nanometre length scales
           with minute kinetic resolution

    • Free pre-print version: Loading...

      Authors: Beck; C., Roosen-Runge, F., Grimaldo, M., Zeller, D., Peters, J., Schreiber, F., Seydel, T.
      Abstract: Neutron spectroscopy uniquely and non-destructively accesses diffusive dynamics in soft and biological matter, including for instance proteins in hydrated powders or in solution, and more generally dynamic properties of condensed matter on the molecular level. Given the limited neutron flux resulting in long counting times, it is important to optimize data acquisition for the specific question, in particular for time-resolved (kinetic) studies. The required acquisition time was recently significantly reduced by measurements of discrete energy transfers rather than quasi-continuous neutron scattering spectra on neutron backscattering spectrometers. Besides this reduction in acquisition times, smaller amounts of samples can be measured with better statistics, and most importantly, kinetically changing samples, such as aggregating or crystallizing samples, can be followed. However, given the small number of discrete energy transfers probed in this mode, established analysis frameworks for full spectra can break down. Presented here are new approaches to analyze measurements of diffusive dynamics recorded within fixed windows in energy transfer, and these are compared with the analysis of full spectra. The new approaches are tested by both modeled scattering functions and a comparative analysis of fixed energy window data and full spectra on well understood reference samples. This new approach can be employed successfully for kinetic studies of the dynamics focusing on the short-time apparent center-of-mass diffusion.
      Keywords: quasielastic neutron spectroscopy; data analysis; self-diffusion; single-crystal monochromators
      Citation: urn:issn:1600-5767
      PubDate: 2024-06-07
      DOI: 10.1107/S1600576724003820
      Issue No: Vol. 57, No. 4 (2024)
       
  • Observation of quasi-Bragg scattering by Goebel mirrors

    • Free pre-print version: Loading...

      Authors: Reunov; D.G., Akhsakhalyan, A.A., Akhsakhalyan, A.D., Chkhalo, N.I., Shaposhnikov, R.A., Drozdov, Y.N.
      Abstract: This paper reports the first observation of quasi-Bragg scattering from collimating Goebel mirrors in a real instrument. On the basis of the experimental data obtained and the numerical analysis performed, it is concluded that it is necessary to take into account the effect of quasi-Bragg scattering when constructing real devices with multilayer mirrors for use in X-ray diffractometry and in spectroscopy, especially for small-angle scattering with position-sensitive detectors.
      Keywords: X-ray optics; Goebel mirrors; multilayer mirrors; quasi-Bragg scattering
      Citation: urn:issn:1600-5767
      PubDate: 2024-06-07
      DOI: 10.1107/S1600576724004126
      Issue No: Vol. 57, No. 4 (2024)
       
 
JournalTOCs
School of Mathematical and Computer Sciences
Heriot-Watt University
Edinburgh, EH14 4AS, UK
Email: journaltocs@hw.ac.uk
Tel: +00 44 (0)131 4513762
 


Your IP address: 3.235.182.206
 
Home (Search)
API
About JournalTOCs
News (blog, publications)
JournalTOCs on Twitter   JournalTOCs on Facebook

JournalTOCs © 2009-
JournalTOCs
 
 

Publisher: IUCr   (Total: 10 journals)   [Sort alphabetically]

Showing 1 - 10 of 10 Journals sorted by number of followers
Acta Crystallographica Section A: Foundations and Advances     Hybrid Journal   (Followers: 8, SJR: 5.99, CiteScore: 13)
Acta Crystallographica Section C: Structural Chemistry     Hybrid Journal   (Followers: 8, SJR: 0.834, CiteScore: 3)
Acta Crystallographica Section F: Structural Biology Communications     Hybrid Journal   (Followers: 8, SJR: 0.592, CiteScore: 1)
J. of Applied Crystallography     Hybrid Journal   (Followers: 7, SJR: 1.635, CiteScore: 3)
Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials     Hybrid Journal   (Followers: 6, SJR: 1.654, CiteScore: 5)
Acta Crystallographica Section D : Biological Crystallography     Hybrid Journal   (Followers: 5)
Acta Crystallographica Section E : Crystallographic Communications     Open Access   (Followers: 3, SJR: 0.153, CiteScore: 0)
J. of Synchrotron Radiation     Open Access   (Followers: 3, SJR: 1.65, CiteScore: 3)
IUCrData     Open Access   (Followers: 1)
IUCrJ     Open Access   (SJR: 3.212, CiteScore: 5)
Similar Journals
Similar Journals
A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z  All
HOME > Browse the 3359 Publishers covered by JournalTOCs 4 5 6 7 8 9 10 11  
PublisherTotal Journals
4 5 6 7 8 9 10 11  
 
JournalTOCs
School of Mathematical and Computer Sciences
Heriot-Watt University
Edinburgh, EH14 4AS, UK
Email: journaltocs@hw.ac.uk
Tel: +00 44 (0)131 4513762
 


Your IP address: 3.235.182.206
 
Home (Search)
API
About JournalTOCs
News (blog, publications)
JournalTOCs on Twitter   JournalTOCs on Facebook

JournalTOCs © 2009-