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At least 19 records

A spatial beam property analyzer based on dispersive crystal diffraction for low-emittance X-ray light sources

Abstract The advent of low-emittance synchrotron X-ray sources and free-electron lasers urges the development of novel diagnostic techniques for measuring and monitoring the spatial source properties, especially the source sizes. This work introduces an X-ray beam property analyzer based on a multi-crystal diffraction geometry, including a crystal-based monochromator and a Laue crystal in a dispersive setting to the monochromator. By measuring the flat beam and the transmitted beam profiles, the system can provide a simultaneous high-sensitivity characterization of the source size, divergence, position, and angle in the diffraction plane of the multi-crystal system. Detailed theoretical modeling predicts the system’s feasibility as a versatile characterization tool for monitoring the X-ray source and beam properties. The experimental validation was conducted at a bending magnet beamline at the Swiss Light Source by varying the machine parameters. A measurement sensitivity of less than 10% of a source size of around 12 µm is demonstrated. The proposed system offers a compact setup with simple X-ray optics and can also be utilized for monitoring the electron source.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A spherical crystal diffraction imager for Sandia’s Z Pulsed Power Facility

Sandia’s Z Pulsed Power Facility is able to dynamically compress matter to extreme states with exceptional uniformity, duration, and size, which are ideal for investigating fundamental material properties of high energy density conditions. X-ray diffraction (XRD) is a key atomic scale probe since it provides direct observation of the compression and strain of the crystal lattice and is used to detect, identify, and quantify phase transitions. Because of the destructive nature of Z-Dynamic Material Property (DMP) experiments and low signal vs background emission levels of XRD, it is very challenging to detect a diffraction signal close to the Z-DMP load and to recover the data. We have developed a new Spherical Crystal Diffraction Imager (SCDI) diagnostic to relay and image the diffracted x-ray pattern away from the load debris field. The SCDI diagnostic utilizes the Z-Beamlet laser to generate 6.2-keV Mn–He α x rays to probe a shock-compressed material on the Z-DMP load. Finally, a spherically bent crystal composed of highly oriented pyrolytic graphite is used to collect and focus the diffracted x rays into a 1-in. thick tungsten housing, where an image plate is used to record the data.

47 OTHER INSTRUMENTATION↗

Locating anionic hydrogen in Ba 3 (Yb,Lu) 2 O 5 H 2 : A combined approach of X-ray diffraction, crystal chemistry, and DFT calculations

By a combination of x-ray diffraction, structural chemistry, and DFT calculations, the presence and location of anionic hydrogen in the two new, layered lanthanide oxyhydrides, Ba 3 Ln 2 O 5 H 2 (Ln ​= ​Yb, Lu) is inferred. Single crystals of the compounds have been synthesized from a molten barium flux with the addition of small amounts of BaH 2 . These phases crystallize in space group I4/mmm (#139, Z ​= ​2) with lattice parameters a ​= ​4.3336(2) Å and c ​= ​22.7197(6) Å, and a ​= ​4.3291(1) Å and c ​= ​22.597(1) Å, respectively. The Ba 3 Ln 2 O 5 H 2 phases comprise two different structural moieties: a perovskite double layer of stoichiometry Ba 2 Ln 2 O 5 H – formed by corner-connected LnO 5 tetragonal bi-pyramids with a terminating hydrogen anion, and a puckered rocksalt-type (BaH) + layer that is stretched along the c-axis. DFT calculations were used to arrive at hydrogen positions that minimize energy and are consistent with structural chemistry principles. Furthermore, the calculations show that the valence band edge is dominated by oxygen 2p orbitals with hydrogen 1s states admixed. The conduction band is formed by barium 5d-orbitals and Lu (Yb) 5d-orbitals. These are characteristics of materials with anionic H – . These new phases are isostructural with the Ba 3 Ln 2 O 5 Cl 2 (Ln ​= ​Gd–Lu) family of compounds with the chlorine atom in the same apical position as the hydrogen atom. Finally, steric effects limit the size of the lanthanide ion for Ba 3 Ln 2 O 5 H 2 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Crystal Diffraction Prediction and Partiality estimation using Gaussian basis functions

A small dataset with good data quality, useful as a benchmark. There exists a two-fold indexing ambiguity, so when processing with CrystFEL you will need to do: ambigator -o disambiguated.stream -y m-3 -w m-3m -j 72 ambiguous.stream Please check the README file for more information about the dataset. ----- Begin unit cell ----- CrystFEL unit cell file version 1.0 lattice_type = cubic centering = I a = 103.40 A b = 103.40 A c = 103.40 A al = 90.00 deg be = 90.00 deg ga = 90.00 deg ; Please note: this is the target unit cell. ; The actual unit cells produced by indexing depend on many other factors. ----- End unit cell -----

Cydia pomonella granulovirus hull protein↗

Microgravity crystallization of perdeuterated tryptophan synthase for neutron diffraction

Abstract Biologically active vitamin B 6 -derivative pyridoxal 5′-phosphate (PLP) is an essential cofactor in amino acid metabolic pathways. PLP-dependent enzymes catalyze a multitude of chemical reactions but, how reaction diversity of PLP-dependent enzymes is achieved is still not well understood. Such comprehension requires atomic-level structural studies of PLP-dependent enzymes. Neutron diffraction affords the ability to directly observe hydrogen positions and therefore assign protonation states to the PLP cofactor and key active site residues. The low fluxes of neutron beamlines require large crystals (≥0.5 mm 3 ). Tryptophan synthase (TS), a Fold Type II PLP-dependent enzyme, crystallizes in unit gravity with inclusions and high mosaicity, resulting in poor diffraction. Microgravity offers the opportunity to grow large, well-ordered crystals by reducing gravity-driven convection currents that impede crystal growth. We developed the Toledo Crystallization Box (TCB), a membrane-barrier capillary-dialysis device, to grow neutron diffraction-quality crystals of perdeuterated TS in microgravity. Here, we present the design of the TCB and its implementation on Center for Advancement of Science in Space (CASIS) supported International Space Station (ISS) Missions Protein Crystal Growth (PCG)-8 and PCG-15. The TCB demonstrated the ability to improve X-ray diffraction and mosaicity on PCG-8. In comparison to ground control crystals of the same size, microgravity-grown crystals from PCG-15 produced higher quality neutron diffraction data. Neutron diffraction data to a resolution of 2.1 Å has been collected using microgravity-grown perdeuterated TS crystals from PCG-15.

59 BASIC BIOLOGICAL SCIENCES↗

At-wavelength characterization of X-ray wavefronts in Bragg diffraction from crystals

The advent of next-generation synchrotron radiation sources and X-ray free-electron lasers calls for high-quality Bragg-diffraction crystal optics to preserve the X-ray beam coherence and wavefront. This requirement brings new challenges in characterizing crystals in Bragg diffraction in terms of Bragg-plane height errors and wavefront phase distortions. Here, a quantitative methodology to characterize crystal optics using a state-of-the-art at-wavelength wavefront sensing technique and statistical analysis is proposed. The method was tested at the 1-BM-B optics testing beamline at the Advanced Photon Source for measuring silicon and diamond crystals in a self-referencing single-crystal mode and an absolute double-crystal mode. The phase error sensitivity of the technique is demonstrated to be at the λ/100 level required by most applications, such as the characterization of diamond crystals for cavity-based X-ray free-electron lasers.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Noncollinear magnetic structure and magnetoelectric coupling in buckled honeycomb Co 4 Nb 2 O 9 : A single-crystal neutron diffraction study

Through an analysis of single-crystal neutron diffraction data, we present the magnetic structure and magnetoelectric properties of Co 4 Nb 2 O 9 under various magnetic fields. In zero field, neutron diffraction experiments below T N =27K reveal that the Co 2+ moments order in the (ab) plane without any spin canting along the c axis, manifested by the magnetic symmetry C2/c'. Along each Co chain parallel to the c axis, the moments of nearest-neighbor Co atoms order ferromagnetically with a small cant away from the next-nearest-neighbor Co moments. Under the applied magnetic field H ∥ a, three magnetic domains were aligned with their major magnetic moments perpendicular to the magnetic field with no other observable magnetic transitions. The influences of magnetic fields on the magnetic structures associated with the observed magnetoelectric coupling are discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Artifact identification in X-ray diffraction data using machine learning methods

In situ synchrotron high-energy X-ray powder diffraction (XRD) is highly utilized by researchers to analyze the crystallographic structures of materials in functional devices ( e.g. battery materials) or in complex sample environments ( e.g. diamond anvil cells or syntheses reactors). An atomic structure of a material can be identified by its diffraction pattern along with a detailed analysis of the Rietveld refinement which yields rich information on the structure and the material, such as crystallite size, microstrain and defects. For in situ experiments, a series of XRD images is usually collected on the same sample under different conditions ( e.g. adiabatic conditions) yielding different states of matter, or is simply collected continuously as a function of time to track the change of a sample during a chemical or physical process. In situ experiments are usually performed with area detectors and collect images composed of diffraction patterns. For an ideal powder, the diffraction pattern should be a series of concentric Debye–Scherrer rings with evenly distributed intensities in each ring. For a realistic sample, one may observe different characteristics other than the typical ring pattern, such as textures or preferred orientations and single-crystal diffraction spots. Textures or preferred orientations usually have several parts of a ring that are more intense than the rest, whereas single-crystal diffraction spots are localized intense spots owing to diffraction of large crystals, typically >10 µm. In this work, an investigation of machine learning methods is presented for fast and reliable identification and separation of the single-crystal diffraction spots in XRD images. The exclusion of artifacts during an XRD image integration process allows a precise analysis of the powder diffraction rings of interest. When it is trained with small subsets of highly diverse datasets, the gradient boosting method can consistently produce high-accuracy results. The method dramatically decreases the amount of time spent identifying and separating single-crystal diffraction spots in comparison with the conventional method.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Takagi–Taupin dynamical X-ray diffraction simulations of asymmetric X-ray diffraction from crystals: the effects of surface undulations

Dynamical X-ray diffraction simulations from crystals with surface undulations are reported. The Takagi–Taupin equations are applied and used to derive results in good agreement with experimental data reported in a separate paper [Macrander, Pereira, Huang, Kasman, Qian, Wojcik & Assoufid (2020). J. Appl. Cryst. 53, 789–792]. The development of Uragami [J. Phys. Soc. Jpn, (1969), 27, 147–154] is followed. Although previous work by Olekhnovich & Olekhnovich [Acta. Cryst. (1980), A36, 22–27] treated a crystal in the shape of a round cylinder, there do not seem to be any reports of previous dynamical X-ray diffraction treatments specifically for surface undulations. The significance of the present work is that it bridges the diffraction treatment of more classical dynamical diffraction theory, which assumes a flat surface, and the simple kinematic diffraction theory. Finally, the kinematic theory has, to date, been the primary means of simulating X-ray diffraction from surfaces.

36 MATERIALS SCIENCE↗

Operando single crystal neutron diffraction reveals insight into the field response mechanisms in the hydrogen-bonded KH 2 PO 4 ferroelectric

The mechanism that facilitates polarization reorientation in KH 2 PO 4 (KDP) was investigated using operando single-crystal neutron diffraction. Diffraction data were measured from a KDP single crystal during the application of alternating electric fields and were then binned into 40 increments to enable field-dependent single-crystal structure refinements. The field-dependent structures are compared with an as-grown crystal to determine how the lattice and atomic sites evolve in response to the applied electric fields. These analyses provide evidence that the reorientation of the macroscopic polarization is facilitated through a cooperative change in hydrogen bonding, which results in the reversal of the spontaneous dipole. In addition, a decrease in secondary extinction near the coercive field indicates that the inversion of the macroscopic polarization is achieved through the nucleation and subsequent growth of new domains.

36 MATERIALS SCIENCE↗

Toward an Autonomous Workflow for Single Crystal Neutron Diffraction

The operation of the neutron facility relies heavily on beamline scientists. Some experiments can take one or two days with experts making decisions along the way. Leveraging the computing power of HPC platforms and AI advances in image analyses, here we demonstrate an autonomous workflow for the single-crystal neutron diffraction experiments. The workflow consists of three components: an inference service that provides real-time AI segmentation on the image stream from the experiments conducted at the neutron facility, a continuous integration service that launches distributed training jobs on Summit to update the AI model on newly collected images, and a frontend web service to display the AI tagged images to the expert. Ultimately, the feedback can be directly fed to the equipment at the edge in deciding the next-step experiment without requiring an expert in the loop. With the analyses of the requirements and benchmarks of the performance for each component, this effort serves as the first step toward an autonomous workflow for real-time experiment steering at ORNL neutron facilities.

Yin, Junqi↗

Machine-learning-assisted automation of single-crystal neutron diffraction

Neutron scattering is a powerful but expensive technique to study materials and discover new matter. Advanced detector technology has significantly improved the efficiency of neutron experiments, increasing the complexity of neutron data reduction and analysis. Machine learning (ML) brings new directions for neutron diffraction data reduction and experiment operation. Here, this work presents an ML-assisted data reduction and analysis method for precise recognition of Bragg peaks and the corresponding regions of interest; it can then automatically screen and align a measured crystal using the recognized peaks, and subsequently plan and optimize the data collection with user-provided information and uncertainty quantification values of detected peaks. This method shows robust performance in different complex sample environments and enables automated single-crystal neutron diffraction.

47 OTHER INSTRUMENTATION↗

Symmetrization of Strong Hydrogen Bond under High Pressure in Bihydroxide-Ion-Containing NaCu 2 (SO 4 ) 2 ·H 3 O 2 Revealed by Experimental Charge Density, Single-Crystal Electron Diffraction, and Neutron Diffraction Studies

In minerals and inorganic compounds, strong hydrogen bonding can lead to the formation of complex ionic species such as the H 3 O 2 – bihydroxide anion and Zundel cation H 5 O 2 + . We studied [NaCu 2 (SO 4 ) 2 ·H 3 O 2 ] natrochalcite, which contains bihydroxide anions and undergoes hydrogen bond symmetrization at the lowest pressure reported so far among inorganic compounds. Hydrogen bond symmetrization leads to changes in the bulk modulus, seismic wave velocities, and proton mobility and plays a primary role in high-temperature superconductivity, but its characteristics are not well understood due to a lack of systematic studies and limitations of experimental methods sensitive to this subtle change. In this work, we applied experimental charge density analysis based on in situ single-crystal X-ray diffraction data, along with the single-crystal neutron and electron diffraction experiments, to probe the behavior of hydrogen atoms during the hydrogen bond symmetrization process under high-pressure conditions. On the way to the symmetrical H-bonding, natrochalcite undergoes a series of complex redistributions of electron density, which we trace with multipole refinement and detailed analysis of changes in the Laplacian of electron density values. Additionally, we deconvoluted the equation of state (volume of the unit cell vs pressure relation) into the atomic equation of states describing dependencies of atomic charges or volumes vs pressure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Noncollinear antiferromagnetic order in the buckled honeycomb lattice of magnetoelectric Co 4 Ta 2 O 9 determined by single-crystal neutron diffraction

Co 4 Ta 2 O 9 exhibits a three-dimensional magnetic lattice based on the buckled honeycomb motif. It shows unusual magnetoelectric effects, including the sign change and nonlinearity. These effects cannot be understood without the detailed knowledge of the magnetic structure. Herein, we report neutron diffraction and direction-dependent magnetic susceptibility measurements on Co 4 Ta 2 O 9 single crystals. In this work, below 20.3 K, we find a long-range antiferromagnetic order in the alternating buckled and flat honeycomb layers of Co 2+ ions stacked along the c axis. Within experimental accuracy, the magnetic moments lie in the ab plane. They form a canted antiferromagnetic structure with a tilt angle of ~14° at 15 K in the buckled layers, while the magnetic moments in each flat layer are collinear. This is directly evidenced by a finite (0, 0, 3) magnetic Bragg peak intensity, which would be absent in the collinear magnetic order. The magnetic space group is C2/c'. It is different from the previously reported C2/c' group, also found in the isostructural Co 4 Nb 2 O 9 . The revised magnetic structure successfully explains the major features of the magnetoelectric tensor of Co 4 Ta 2 O 9 within the framework of the spin-flop model.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Europium c -axis ferromagnetism in Eu ( Co 1 - x Ni x ) 2 - y As 2 : A single-crystal neutron diffraction study

Here we report neutron diffraction results for the body-centered-tetragonal series Eu⁢(Co 1-x ⁢Ni x ) 2-y As 2 , x=0.10, 0.20, 0.42, and 0.82, y≤0.10, that detail changes to the magnetic ordering with nominal hole doping. We report the antiferromagnetic (AFM) propagation vectors, magnetic transition temperatures, and the ordered magnetic moments. We find a nonmonotonic change of the AFM propagation vector with x, with a minimum occurring at the tetragonal to collapsed-tetragonal phase crossover. For x=0.10 and 0.82 we find c-axis helix ordering of the Eu magnetic moments (spins) similar to x=0 and 1, with the spins oriented within the ab-plane. For x=0.20 and 0.42 we find higher-temperature c-axis ferromagnetic (FM) order and lower-temperature c-axis cone order. Using the extinction conditions for the space group, we discovered that the Eu spins are ordered in the higher-temperature c-axis FM phase for intermediate values of x, contrary to a previous report suggesting only Co/Ni spin ordering. Although we cannot directly confirm that the Co/Ni spins are also ordered, we suggest that c-axis itinerant-FM ordering of the Co/Ni spins could provide a molecular field that drives FM ordering of the Eu spins, which in turn provides the anisotropy for the lower-temperature c-axis cone order.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗