On automatic determination of quasicrystal orientations by indexing of detected reflections
Automatic crystal orientation determination and orientation mapping are important tools for research on polycrystalline materials. The most common methods of automatic orientation determination rely on detecting and indexing individual diffraction reflections, but these methods have not been used for orientation mapping of quasicrystalline materials. The paper describes the necessary changes to existing software designed for orientation determination of periodic crystals so that it can be applied to quasicrystals. The changes are implemented in one such program. The functioning of the modified program is illustrated by an ...
Source: Acta Crystallographica Section A - June 2, 2023 Category: Chemistry Authors: Morawiec, A. Tags: quasicrystals orientation mapping diffraction indexing EBSD microstructure research papers Source Type: research
Crystal search – feasibility study of a real-time deep learning process for crystallization well images
To avoid the time-consuming and often monotonous task of manual inspection of crystallization plates, a Python-based program to automatically detect crystals in crystallization wells employing deep learning techniques was developed. The program uses manually scored crystallization trials deposited in a database of an in-house crystallization robot as a training set. Since the success rate of such a system is able to catch up with manual inspection by trained persons, it will become an important tool for crystallographers working on biological samples. Four network architectures were compared and the SqueezeNet architecture...
Source: Acta Crystallographica Section A - June 2, 2023 Category: Chemistry Authors: Thielmann, Y. Luft, T. Zint, N. Koepke, J. Tags: biocrystallization high-throughput screening deep learning neural network U-Net AlexNet VggNet ResNet SqueezeNet BOINC research papers Source Type: research
New benchmarks in the modelling of X-ray atomic form factors
Analytical representations of X-ray atomic form factor data have been determined. The original data, f0(s;Z), are reproduced to a high degree of accuracy. The mean absolute errors calculated for all s = sin θ / λ and Z values in question are primarily determined by the precision of the published data. The inverse Mott – Bethe formula is the underlying basis with the electron scattering factor expressed by an expansion in Gaussian basis functions. The number of Gaussians depends upon the element and the data and is in the range 6 – 20. The refinement procedure, conducted to obtain the parameters of the models, is ...
Source: Acta Crystallographica Section A - June 2, 2023 Category: Chemistry Authors: Thorkildsen, G. Tags: atomic form factors analytical representations inverse Mott – Bethe formula research papers Source Type: research
On the combinatorics of crystal structures. II. Number of Wyckoff sequences of a given subdivision complexity
Wyckoff sequences are a way of encoding combinatorial information about crystal structures of a given symmetry. In particular, they offer an easy access to the calculation of a crystal structure's combinatorial, coordinational and configurational complexity, taking into account the individual multiplicities (combinatorial degrees of freedom) and arities (coordinational degrees of freedom) associated with each Wyckoff position. However, distinct Wyckoff sequences can yield the same total numbers of combinatorial and coordinational degrees of freedom. In this case, they share the same value for their Shannon entropy based su...
Source: Acta Crystallographica Section A - May 11, 2023 Category: Chemistry Authors: Hornfeck, W. Č erven ý , K. Tags: Wyckoff sequences combinatorics Shannon entropy structural complexity research papers Source Type: research
Boris Gruber's contributions to mathematical crystallography
Boris Gruber made fundamental contributions to the study of crystal lattices, leading to a finer classification of lattice types than those of Paul Niggli and Boris Delaunay before him. (Source: Acta Crystallographica Section A)
Source: Acta Crystallographica Section A - May 5, 2023 Category: Chemistry Authors: Grimmer, H. Tags: Boris Gruber crystal lattices lattice characters Buerger cells Niggli cell Bravais types genera scientific commentaries Source Type: research
Fourier-synthesis approach for static charge-density reconstruction from theoretical structure factors of CaB6
In a pilot study, electron-density (ED) and ED Laplacian distributions were reconstructed for the challenging case of CaB6 (Pearson symbol cP7) with conceptually fractional B — B bonds from quantum-chemically calculated structure-factor sets with resolutions 0.5 Å – 1 ≤ [sin( θ )/ λ ]max ≤ 5.0 Å – 1 by means of Fourier-synthesis techniques. Convergence of norm deviations of the distributions obtained with respect to the reference ones was obtained in the valence region of the unit cell. The QTAIM (quantum theory of atoms in molecules) atomic charges, and the ED and ED Laplacian values at the character...
Source: Acta Crystallographica Section A - May 5, 2023 Category: Chemistry Authors: Bergner, C. Grin, Y. Wagner, F.R. Tags: electron density Fourier transformation Fourier synthesis hexaborides Laplacian research papers Source Type: research
Revisited relativistic Dirac – Hartree – Fock X-ray scattering factors. II. Chemically relevant cations and selected monovalent anions for atoms with Z = 3 – 112
The previously described approach for determination of the relativistic atomic X-ray scattering factors (XRSFs) at the Dirac – Hartree – Fock level [Olukayode et al. (2023). Acta Cryst. A79, 59 – 79] has been used to evaluate the XRSFs for a total of 318 species including all chemically relevant cations [Greenwood& Earnshaw (1997). Chemistry of the Elements], six monovalent anions (O − , F − , Cl − , Br − , I − , At − ), the ns1np3 excited (valence) states of carbon and silicon, and several exotic cations (Db5+, Sg6+, Bh7+, Hs8+ and Cn2+) for which the chemical compounds have been recently identified, thu...
Source: Acta Crystallographica Section A - May 1, 2023 Category: Chemistry Authors: Olukayode, S. Froese Fischer, C. Volkov, A. Tags: relativistic X-ray scattering factors for ions relativistic Dirac – Hartree Fock interpolation of X-ray scattering factors research papers Source Type: research
Parallelohedra, old and new
It is shown that from a skewed, skeletal (edges and vertices), truncated octahedron, skewed skeletons can be derived of the other four convex parallelohedra found by Fedorov in 1885. In addition, three new nonconvex parallelohedra are produced, a counterexample to a statement by Gr ü nbaum. This opens several new ways to view atomic positions in crystals, and new avenues in geometry. (Source: Acta Crystallographica Section A)
Source: Acta Crystallographica Section A - March 31, 2023 Category: Chemistry Authors: Senechal, M. Taylor, J.E. Tags: nonconvex parallelohedra zonohedra research papers Source Type: research
A fast two-stage algorithm for non-negative matrix factorization in smoothly varying data
This article reports the study of algorithms for non-negative matrix factorization (NMF) in various applications involving smoothly varying data such as time or temperature series diffraction data on a dense grid of points. Utilizing the continual nature of the data, a fast two-stage algorithm is developed for highly efficient and accurate NMF. In the first stage, an alternating non-negative least-squares framework is used in combination with the active set method with a warm-start strategy for the solution of subproblems. In the second stage, an interior point method is adopted to accelerate the local convergence. The con...
Source: Acta Crystallographica Section A - February 24, 2023 Category: Chemistry Authors: Gu, R. Billinge, S.J.L. Du, Q. Tags: non-negative matrix factorization smoothly varying data pair distribution function interior point method research papers Source Type: research
Borromean rings redux. A missing link found – a Borromean triplet of Borromean triplets
This paper describes a nine-component Borromean structure – a Borromean triplet of Borromean triplets – that was missing from an earlier enumeration. (Source: Acta Crystallographica Section A)
Source: Acta Crystallographica Section A - February 17, 2023 Category: Chemistry Authors: O'Keeffe, M. Treacy, M.M.J. Tags: Borromean structure Borromean triplet of Borromean triplets catenanes short communications Source Type: research
Crystal diffraction prediction and partiality estimation using Gaussian basis functions
This article gives a computationally efficient way of calculating approximate crystal diffraction patterns given varying distributions of the incoming beam, crystal shapes and other potentially hidden parameters. This approach models each pixel of a diffraction pattern and improves data processing of integrated peak intensities by enabling the correction of partially recorded reflections. The fundamental idea is to express the distributions as weighted sums of Gaussian functions. The approach is demonstrated on serial femtosecond crystallography data sets, showing a significant decrease in the required number of patterns t...
Source: Acta Crystallographica Section A - February 17, 2023 Category: Chemistry Authors: Brehm, W. White, T. Chapman, H.N. Tags: partiality estimation diffraction prediction merging serial snapshot crystallography research papers Source Type: research
Twenty-Fifth General Assembly and International Congress of Crystallography, Prague, Czech Republic, 14 – 21 August 2021
(Source: Acta Crystallographica Section A)
Source: Acta Crystallographica Section A - February 16, 2023 Category: Chemistry Authors: Ashcroft, A.T. Tags: International Union of Crystallography IUCr General Assembly International Congress of Crystallography Source Type: research
Three-periodic nets, tilings and surfaces. A short review and new results
A brief introductory review is provided of the theory of tilings of 3-periodic nets and related periodic surfaces. Tilings have a transitivity [p q r s] indicating the vertex, edge, face and tile transitivity. Proper, natural and minimal-transitivity tilings of nets are described. Essential rings are used for finding the minimal-transitivity tiling for a given net. Tiling theory is used to find all edge- and face-transitive tilings (q = r = 1) and to find seven, one, one and 12 examples of tilings with transitivity [1 1 1 1], [1 1 1 2], [2 1 1 1] and [2 1 1 2], respectively. These are all minimal-transitivity t...
Source: Acta Crystallographica Section A - February 13, 2023 Category: Chemistry Authors: Delgado-Friedrichs, O. O'Keeffe, M. Proserpio, D.M. Treacy, M.M.J. Tags: tilings nets 3-periodic nets 3-periodic tilings essential rings research papers Source Type: research
Dynamical diffraction of high-energy electrons by light-atom structures: a multiple forward scattering interpretation
Because of the strong electron – atom interaction, the kinematic theory of diffraction cannot be used to describe the scattering of electrons by an assembly of atoms due to the strong dynamical diffraction that needs to be taken into account. In this paper, the scattering of high-energy electrons by a regular array of light atoms is solved exactly by applying the T-matrix formalism to the corresponding Schr ö dinger's equation in spherical coordinates. The independent atom model is used, where each atom is represented by a sphere with an effective constant potential. The validity of the forward scattering approximation ...
Source: Acta Crystallographica Section A - February 9, 2023 Category: Chemistry Authors: Drevon, T.R. Waterman, D.G. Krissinel, E. Tags: high-energy electron diffraction T-matrix multiple scattering independent atom approximation research papers Source Type: research
A general force field by machine learning on experimental crystal structures. Calculations of intermolecular Gibbs energy with FlexCryst
Machine learning was employed on the experimental crystal structures of the Cambridge Structural Database (CSD) to derive an intermolecular force field for all available types of atoms (general force field). The obtained pairwise interatomic potentials of the general force field allow for the fast and accurate calculation of intermolecular Gibbs energy. The approach is based on three postulates regarding Gibbs energy: the lattice energy must be below zero, the crystal structure must be a local minimum, and, if available, the experimental and the calculated lattice energy must coincide. The parametrized general force field ...
Source: Acta Crystallographica Section A - February 9, 2023 Category: Chemistry Authors: Hofmann, D.W.M. Kuleshova, L.N. Tags: machine learning Gibbs energy crystal structure analysis force field intermolecular interactions research papers Source Type: research
