Search NASA⌕ Search

SEARCH · Search NASA

Results for “diffraction”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,351 records · Page 75
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Reconstructing three-dimensional protein crystal intensities from sparse unoriented two-axis X-ray diffraction patterns

Recently, there has been a growing interest in adapting serial microcrystallography (SMX) experiments to existing storage ring (SR) sources. For very small crystals, however, radiation damage occurs before sufficient numbers of photons are diffracted to determine the orientation of the crystal. The challenge is to merge data from a large number of such `sparse' frames in order to measure the full reciprocal space intensity. To simulate sparse frames, a dataset was collected from a large lysozyme crystal illuminated by a dim X-ray source. The crystal was continuously rotated about two orthogonal axes to sample a subset of the rotation space. With the EMC algorithm [expand–maximize–compress; Loh & Elser (2009). Phys. Rev. E , 80 , 026705], it is shown that the diffracted intensity of the crystal can still be reconstructed even without knowledge of the orientation of the crystal in any sparse frame. Moreover, parallel computation implementations were designed to considerably improve the time and memory scaling of the algorithm. The results show that EMC-based SMX experiments should be feasible at SR sources.

Chemistry↗
DOE OSTI2018

Grating-based holographic diffraction methods for X-rays and neutrons: phase object approximation and dynamical theory

A method dubbed grating-based holography was recently used to determine the structure of colloidal fluids in the rectangular grooves of a diffraction grating from X-ray scattering measurements. Similar grating-based measurements have also been recently made with neutrons using a technique called spin-echo small-angle neutron scattering. The analysis of the X-ray diffraction data was done using an approximation that treats the X-ray phase change caused by the colloidal structure as a small perturbation to the overall phase pattern generated by the grating. In this paper, the adequacy of this weak phase approximation is explored for both X-ray and neutron grating holography. Additionally, it is found that there are several approximations hidden within the weak phase approximation that can lead to incorrect conclusions from experiments. In particular, the phase contrast for the empty grating is a critical parameter. Finally, while the approximation is found to be perfectly adequate for X-ray grating holography experiments performed to date, it cannot be applied to similar neutron experiments because the latter technique requires much deeper grating channels.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Correct interpretation of diffraction properties of quartz crystals for X-ray optics applications

Quartz has hundreds of strong Bragg reflections that may offer a great number of choices for making fixed-angle X-ray analyzers and polarizers at virtually any hard X-ray energies with selectable resolution. However, quartz crystals, unlike silicon and germanium, are chiral and may thus appear in two different forms of handedness that are mirror images. Furthermore, because of the threefold rotational symmetry along the c axis, the { h 1 h 2 h 3 L } and { h 2 h 1 h 3 L } Bragg reflections may have quite different Darwin bandwidth, reflectivity and angular acceptance, although they have the same Bragg angle. The design of X-ray optics from quartz crystals therefore requires unambiguous determination of the orientation, handedness and polarity of the crystals. The Laue method and single-axis diffraction technique can provide such information, but the variety of conventions used in the literature to describe quartz structures has caused widespread confusion. The current studies give detailed guidelines for design and fabrication of quartz X-ray optics, with special emphasis on the correct interpretation of Laue patterns in terms of the crystallography and diffraction properties of quartz. Furthermore, the quartz crystals examined were confirmed by X-ray topography to have acceptably low densities of dislocations and other defects, which is the foundation for developing high-resolution quartz-based X-ray optics.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Synthesizing pseudo-Kossel lines from neutron transmission data. II. Validation with neutron diffraction data

A new method to recover the orientation matrix of a single crystal with a known unit cell by analyzing synthesized pseudo-Kossel lines from time-of-flight neutron transmission data has been outlined in a companion article [Dessieux et al. (2023). J. Appl. Cryst. 56, https://dx.doi.org/10.1107/S1600576723001346; referred to here as Article I]. In this work, validation of this new technique is presented by employing experimental neutron transmission and diffraction measurements performed on two copper single-crystal specimens. Time-of-flight spectra were recorded during rotation (ω) of the single crystals about a vertical axis perpendicular to the incident neutron beam. The λ–ω maps recorded in transmission are utilized to determine the crystal orientation with respect to the neutron beam, following the procedure presented in Article I. Further, to validate the indexing procedure, the crystal orientations are compared with those obtained via conventional methods using the diffraction data. The resulting pseudo-Kossel lines across the 2D detectors are also observed for the first time.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Oblique diffraction geometry for the observation of several non-coplanar Bragg reflections under identical illumination

A method to determine the strain tensor and local lattice rotation with dark-field X-ray microscopy is presented. Using a set of at least three non-coplanar symmetry-equivalent Bragg reflections, the illuminated volume of the sample can be kept constant for all reflections, facilitating easy registration of the measured lattice variations. This requires an oblique diffraction geometry,i.e.the diffraction plane is neither horizontal nor vertical. We derive a closed analytical expression that allows determination of the strain and lattice rotation from the deviation of experimental observables (e.g.goniometer angles) from their nominal values for an unstrained lattice.

Chemistry↗
DOE OSTI2026

Machine learning approaches for crystallographic classification from synthetic 2D X-ray diffraction data

Crystallographic structure identification is crucial for understanding material properties; however, current methodologies often depend on labor-intensive and time-consuming analyses of 2D X-ray diffraction (XRD) patterns. To address these limitations, this study employs synthetic 2D XRD patterns combined with deep learning (DL) techniques to enable automated and high-throughput classification of the seven crystal systems and 230 space groups. We introduce the novel Auto Diffraction Pipeline, designed to generate synthetic 2D XRD spot patterns from crystallographic information files under diverse conditions, including varying zone axes, atomic substitution, atomic depletion and mechanical loading. These conditions enhance the realism of synthetic data, mitigating the scarcity of experimental datasets and enabling the creation of large representative training sets. Convolutional neural networks were trained and validated on these synthetic datasets to classify crystallographic structures across multiple scenarios. Our results demonstrate that integrating synthetic 2D XRD patterns with DL facilitates rapid, accurate and automated crystallographic classification, promoting the wider adoption of data-driven approaches in materials science.

Shahnazari, Ayoub [Univ. of Rochester, NY (United ↗
DOE OSTI2023

A MHz X-ray diffraction set-up for dynamic compression experiments in the diamond anvil cell

An experimental platform for dynamic diamond anvil cell (dDAC) research has been developed at the High Energy Density (HED) Instrument at the European X-ray Free Electron Laser (European XFEL). Advantage was taken of the high repetition rate of the European XFEL (up to 4.5 MHz) to collect pulse-resolved MHz X-ray diffraction data from samples as they are dynamically compressed at intermediate strain rates (≤10 3 s −1 ), where up to 352 diffraction images can be collected from a single pulse train. The set-up employs piezo-driven dDACs capable of compressing samples in ≥340 µs, compatible with the maximum length of the pulse train (550 µs). Results from rapid compression experiments on a wide range of sample systems with different X-ray scattering powers are presented. A maximum compression rate of 87 TPa s −1 was observed during the fast compression of Au, while a strain rate of ∼1100 s −1 was achieved during the rapid compression of N 2 at 23 TPa s −1 .

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2017

Raw diffraction data preservation and reuse: Overview, update on practicalities and metadata requirements

A topical review is presented of the rapidly developing interest in and storage options for the preservation and reuse of raw data within the scientific domain of the IUCr and its Commissions, each of which operates within a great diversity of instrumentation. A résumé is included of the case for raw diffraction data deposition. An overall context is set by highlighting the initiatives of science policy makers towards an `Open Science' model within which crystallographers will increasingly work in the future; this will bring new funding opportunities but also new codes of procedure within open science frameworks. Skills education and training for crystallographers will need to be expanded. Overall, there are now the means and the organization for the preservation of raw crystallographic diffraction data via different types of archive, such as at universities, discipline-specific repositories (Integrated Resource for Reproducibility in Macromolecular Crystallography, Structural Biology Data Grid), general public data repositories (Zenodo, ResearchGate) and centralized neutron and X-ray facilities. Formulation of improved metadata descriptors for the raw data types of each of the IUCr Commissions is in progress; some detailed examples are provided. Lastly, a number of specific case studies are presented, including an example research thread that provides complete open access to raw data.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2017

Merging single-shot XFEL diffraction data from inorganic nanoparticles: a new approach to size and orientation determination

X-ray free-electron lasers (XFELs) provide new opportunities for structure determination of biomolecules, viruses and nanomaterials. With unprecedented peak brilliance and ultra-short pulse duration, XFELs can tolerate higher X-ray doses by exploiting the femtosecond-scale exposure time, and can thus go beyond the resolution limits achieved with conventional X-ray diffraction imaging techniques. Using XFELs, it is possible to collect scattering information from single particles at high resolution, however particle heterogeneity and unknown orientations complicate data merging in three-dimensional space. Using the Linac Coherent Light Source (LCLS), synthetic inorganic nanocrystals with a core–shell architecture were used as a model system for proof-of-principle coherent diffractive single-particle imaging experiments. To deal with the heterogeneity of the core–shell particles, new computational methods have been developed to extract the particle size and orientation from the scattering data to assist data merging. The size distribution agrees with that obtained by electron microscopy and the merged data support a model with a core–shell architecture.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Solving protein structure from sparse serial microcrystal diffraction data at a storage-ring synchrotron source

In recent years, the success of serial femtosecond crystallography and the paucity of beamtime at X-ray free-electron lasers have motivated the development of serial microcrystallography experiments at storage-ring synchrotron sources. However, especially at storage-ring sources, if a crystal is too small it will have suffered significant radiation damage before diffracting a sufficient number of X-rays into Bragg peaks for peak-indexing software to determine the crystal orientation. As a consequence, the data frames of small crystals often cannot be indexed and are discarded. Introduced here is a method based on the expand–maximize–compress (EMC) algorithm to solve protein structures, specifically from data frames for which indexing methods fail because too few X-rays are diffracted into Bragg peaks. The method is demonstrated on a real serial microcrystallography data set whose signals are too weak to be indexed by conventional methods. In spite of the daunting background scatter from the sample-delivery medium, it was still possible to solve the protein structure at 2.1 Å resolution. The ability of the EMC algorithm to analyze weak data frames will help to reduce sample consumption. Furthermore, it will also allow serial microcrystallography to be performed with crystals that are otherwise too small to be feasibly analyzed at storage-ring sources.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2017

Solvent exchange in a metal–organic framework single crystal monitored by dynamic in situ X-ray diffraction

Understanding the processes by which porous solid-state materials adsorb and release guest molecules would represent a significant step towards developing rational design principles for functional porous materials. To elucidate the process of liquid exchange in these materials, dynamic in situ X-ray diffraction techniques have been developed which utilize liquid-phase chemical stimuli. Using these time-resolved diffraction techniques, the ethanol solvation process in a flexible metal–organic framework [Co(AIP)(bpy) 0.5 (H 2 O)]·2H 2 O was examined. The measurements provide important insight into the nature of the chemical transformation in this system including the presence of a previously unreported neat ethanol solvate structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Inflexible stoichiometry in bulk pyrite FeS 2 as viewed by in situ and high-resolution X-ray diffraction

Non-stoichiometry is considered to be one of the main problems limiting iron pyrite, FeS 2 , as a photovoltaic absorber material. Although some historical diffraction experiments have implied a large solubility range of FeS 2-δ with δ up to 0.25, the current consensus based on calculated formation energies of intrinsic defects has lent support to line-compound behavior. Here it is shown that pyrite stoichiometry is relatively inflexible in both reductive conditions and in autogenous sulfur partial pressure, which produces samples with precise stoichiometry of FeS 2 even at different Fe/S ratios. By properly standardizing in situ gas-flow X-ray diffraction measurements, no significant changes in the lattice parameter of FeS 2 can be resolved, which portrays iron pyrite as prone to forming sulfur-deficient compounds, but not intrinsic defects in the manner of NiS 2-δ .

McAuliffe, Rebecca D.↗
DOE OSTI2018

Undistorted linear Bi chains with hypervalent bonding in La 3 TiBi 5 from single-crystal X-ray diffraction

The crystal structure of the lanthanum titanium bis­muthide La 3 TiBi 5 (Pearson code hP18, Wyckoff sequence b d g2) has been established from single-crystal X-ray diffraction data and analyzed in detail using first-principles calculations. There are no anomalies pertaining to the atomic displacement parameter of the Ti site, previously reported based on a powder X-ray diffraction analysis of this compound. The anionic substructure contains columns of face-sharing TiBi 6 octa­hedra and linear Bi chains. Due to a significant La(5d) and Bi(6p) orbital mixing, a perfectly one-dimensional character of the Bi chains is not realised, while a three-dimensional electronic structure is established instead. The latter fact explains the stability of the polyanionic pnictide units against Peierls distortions. The hypervalent bonding in the Bi chains is reflected in a rather long Bi—Bi distance of 3.2264 (4) Å and a typical pattern of bonding and anti­bonding inter­actions, as revealed by electronic structure calculations.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Dicarbonyl[10,10-dimethyl-5,15-bis(pentafluorophenyl)biladiene]ruthenium(II): discovery of the first ruthenium tetrapyrrole cis -dicarbonyl complex by X-ray and electron diffraction

Dicarbon­yl[10,10-dimethyl-5,15-bis­(penta­fluoro­phen­yl)biladiene]ruthenium(II), [Ru(C 33 H 16 F 10 N 4 )(CO) 2 ] or Ru(CO) 2 [DMBil1], is the first reported ruthenium(II) cis-dicarbonyl tetra­pyrrole complex. The neutral complex sports two carbonyls and an oligo­tetra­pyrrolic biladiene ligand. Notably, the biladiene adopts a coordination geometry that is well distorted from square planar and much more closely approximates a seesaw arrangement. Accordingly, Ru(CO) 2 [DMBil1] is not only the first ruthenium cis-dicarbonyl with a tetra­pyrrole ligand, but also the first metal biladiene complex in which the tetra­pyrrole does not adopt a (pseudo-)square-planar coordination geometry. Ru(CO) 2 [DMBil1] is weakly luminescent, displaying λ em = 552 nm upon excitation at λ ex = 500 nm, supports two reversible 1 e – reductions at –1.45 and –1.73 V (versus Fc + /Fc), and has significant absorption features at 481 and 531 nm, suggesting suitability for photo­catalytic and photosensitization applications. While the structure of Ru(CO) 2 [DMBil1] was initially determined by X-ray diffraction, a traditionally acceptable quality structure could not be obtained (despite multiple attempts) because of consistently poor crystal quality. Furthermore, an independent structure obtained from electron diffraction experiments corroborates the structure of this unusual biladiene complex.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Crystallization and X-ray diffraction analysis of the HMG domain of the chondrogenesis master regulator Sox9 in complex with a ChIP-Seq-identified DNA element

Sox9 is a fundamental sex-determining gene and the master regulator of chondrogenesis, and is involved in the development of various vital organs such as testes, kidney, heart and brain, and in skeletal development. Similar to other known Sox transcription factors, Sox9 recognizes and binds DNA with the consensus sequence C(T/A)TTG(T/A)(T/A) through the highly conserved HMG domain. Nonetheless, the molecular basis of the functional specificity of Sox9 in key developmental processes is still unclear. As an initial step towards a mechanistic understanding of Sox9 transcriptional regulation, the current work describes the details of the purification of the mouse Sox9 HMG domain (mSox9HMG), its crystallization in complex with a ChIP-Seq-identified FOXP2 promoter DNA element and the X-ray diffraction data analysis of this complex. The mSox9HMG–FOXP2 promoter DNA complex was crystallized by the hanging-drop vapour-diffusion method using 20% PEG 3350 in 200 m M sodium/potassium phosphate with 100 m M bis-tris propane at pH 8.5. The crystals diffracted to 2.7 Å resolution and the complex crystallized in the tetragonal space group P 4 1 2 1 2, with unit-cell parameters a = b = 99.49, c = 45.89 Å. Crystal-packing parameters revealed that asymmetric unit contained one mSox9HMG–FOXP2 promoter DNA complex with an estimated solvent content of 64%.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2016

Cloning, expression, purification, crystallization and X-ray diffraction analysis of dihydrodipicolinate synthase from the human pathogenic bacterium Bartonella henselae strain Houston-1 at 2.1 Å resolution

The enzyme dihydrodipicolinate synthase catalyzes the committed step in the synthesis of diaminopimelate and lysine to facilitate peptidoglycan and protein synthesis. Dihydrodipicolinate synthase catalyzes the condensation of L-aspartate 4-semialdehyde and pyruvate to synthesize L-2,3-dihydrodipicolinate. Here, the cloning, expression, purification, crystallization and X-ray diffraction analysis of dihydrodipicolinate synthase from the pathogenic bacterium Bartonella henselae , the causative bacterium of cat-scratch disease, are presented. Protein crystals were grown in conditions consisting of 20%( w / v ) PEG 4000, 100 m M sodium citrate tribasic pH 5.5 and were shown to diffract to ~2.10 Å resolution. They belonged to space group P 2 1 2 1 2 1 , with unit-cell parameters a = 79.96, b = 106.33, c = 136.25 Å. The final R values were R r.i.m. = 0.098, R work = 0.183, R free = 0.233.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

X-ray diffraction analysis and in vitro characterization of the UAM2 protein from Oryza sativa

The role of seemingly non-enzymatic proteins in complexes interconverting UDP-arabinopyranose and UDP-arabinofuranose (UDP-arabinosemutases; UAMs) in the plant cytosol remains unknown. To shed light on their function, crystallographic and functional studies of the seemingly non-enzymatic UAM2 protein from Oryza sativa (OsUAM2) were undertaken. Here, X-ray diffraction data are reported, as well as analysis of the oligomeric state in the crystal and in solution. OsUAM2 crystallizes readily but forms highly radiation-sensitive crystals with limited diffraction power, requiring careful low-dose vector data acquisition. Using size-exclusion chromatography, it is shown that the protein is monomeric in solution. Finally, limited proteolysis was employed to demonstrate DTT-enhanced proteolytic digestion, indicating the existence of at least one intramolecular disulfide bridge or, alternatively, a requirement for a structural metal ion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Preliminary results of neutron and X-ray diffraction data collection on a lytic polysaccharide monooxygenase under reduced and acidic conditions

Lytic polysaccharide monooxygenases (LPMOs) are copper-center enzymes that are involved in the oxidative cleavage of the glycosidic bond in crystalline cellulose and other polysaccharides. The LPMO reaction is initiated by the addition of a reductant and oxygen to ultimately form an unknown activated copper–oxygen species that is responsible for polysaccharide-substrate H-atom abstraction. Given the sensitivity of metalloproteins to radiation damage, neutron protein crystallo­graphy provides a nondestructive technique for structural characterization while also informing on the positions of H atoms. Neutron cryo-crystallography permits the trapping of catalytic intermediates, thereby providing insight into the protonation states and chemical nature of otherwise short-lived species in the reaction mechanism. Here, to characterize the reaction-mechanism intermediates of LPMO9D from Neurospora crassa, a cryo-neutron diffraction data set was collected from an ascorbate-reduced crystal. A second neutron diffraction data set was collected at room temperature from an LPMO9D crystal exposed to low-pH conditions to probe the protonation states of ionizable groups involved in catalysis under acidic conditions.

Neurospora crassa↗