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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.

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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Small-wedge synchrotron and serial XFEL datasets for Cysteinyl leukotriene GPCRs

Structural studies of challenging targets such as G protein-coupled receptors (GPCRs) have accelerated during the last several years due to the development of new approaches, including small-wedge and serial crystallography. Here, we describe the deposition of seven datasets consisting of X-ray diffraction images acquired from lipidic cubic phase (LCP) grown microcrystals of two human GPCRs, Cysteinyl leukotriene receptors 1 and 2 (CysLT 1 R and CysLT 2 R), in complex with various antagonists. Five datasets were collected using small-wedge synchrotron crystallography (SWSX) at the European Synchrotron Radiation Facility with multiple crystals under cryo-conditions. Two datasets were collected using X-ray free electron laser (XFEL) serial femtosecond crystallography (SFX) at the Linac Coherent Light Source, with microcrystals delivered at room temperature into the beam within LCP matrix by a viscous media microextrusion injector. All seven datasets have been deposited in the open-access databases Zenodo and CXIDB. Here, we describe sample preparation and annotate crystallization conditions for each partial and full datasets. We also document full processing pipelines and provide wrapper scripts for SWSX and SFX data processing. A Correction to this paper has been published: https://doi.org/10.1038/s41597-020-00759-w

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Eulerian finite element simulations of the drop weight impact test with a dislocation Density-based continuum model

During a drop weight impact test, the kinetic energy of the falling weight is transferred into the sample resting on the anvil. The plastic deformation in the sample is an important mechanism for the dissipation of the input kinetic energy. We use Eulerian finite element analysis to simulate the deformation and temperature evolution in a 1,3,5-trinitro-1,3,5-triazine (RDX) sample consisting of multiple crystals. In Eulerian finite element simulations, the mesh moves relative to the material. After every change of position between the mesh and the material, the state variables are interpolated to the new mesh position, i.e., advection. In an effort to reduce the advection errors, we use a rate form of a dislocation density-based continuum model by Luscher et al. Here, the simulations predict localization of plastic deformation, and plastic dissipation as a significant source of heat generation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

A polarization-switch effect of silicon crystals under multiple-beam diffraction geometry

On the basis of rigorous dynamical-theory calculations, a complete X-ray polarization-switch effect of silicon crystals at the exact multiple-beam diffraction condition is demonstrated in this paper. The underlying physical mechanism of this unique phenomenon can be revealed using a simple multiple-wave propagation and interference model. The constructive and destructive interference of the multiple detoured-diffraction beams along the direction of the primary diffracted beam directly leads to the complete polarization switch. This phenomenon can be realized using both synchrotron and laboratory X-ray sources at many discrete wavelengths, and used to design a novel crystal-based polarizer to achieve a 90° polarization rotation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Energy amplification in plasma crystals due to multiple torsions

Interacting torsions are examined within a two-dimensional monolayer crystal suspended in an argon complex plasma for 1–10 W discharge powers and pressures of 135–155 mTorr. Two torsions embedded in a lattice are shown to amplify the kinetic energy and range of motion of particles located between the torsions to nearly three times that observed in single torsion systems. It is also shown that multiple torsions can interact via amplified particle energy when separated by up to 14 interparticle distances (Δ). The torsion separation distance also showed a positive linear trend with power and a slightly positive correlation with the pressure. This amplification of energy is possible due to the fact that multiple torsions in a lattice increase the interparticle distance of the lattice by 16% more than single torsion systems, leading to additional freedom of motion in the lattice plane. These combined findings show that multiple torsions heat the lattice differently depending on their separation from the other torsion. The midpoint particles between torsions absorb the majority of energy from the two torsions, and energy addition at the midpoint is nonlinear. The addition of more torsions to the lattice may lead to melting of the plasma crystal.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

DXRD : a user-friendly suite of two- and multiple-beam dynamical X-ray diffraction programs

The DXRD program suite consisting of a series of dynamical theory programs is introduced for computing dynamical X-ray diffraction from single crystals. Its interactive graphical user interfaces (GUIs) allow general users to make complicated calculations with minimal effort. It can calculate plane-wave Darwin curves of single crystals (or multiple crystals) for both the Bragg and Laue cases, including grazing-incidence diffraction and backward diffraction (with Bragg angles approaching 90°). It is also capable of simulating rocking curves for divergent incident X-ray beams with finite bandwidths. A unique feature of DXRD is that it provides a convenient GUI-based multiple-beam diffraction program that can accurately compute arbitrary N-beam diffraction of any geometry using a universal 4N × 4N matrix method. DXRD also provides a mapping program for plotting all the multiple-beam diffraction lines (monochromator glitches) in the azimuth–energy coordinate system. All these functions make DXRD a convenient and powerful software tool for designing crystal-based synchrotron/X-ray optics (monochromators, analyzers, polarizers, phase plates etc.) and for crystal characterization, X-ray spectroscopy and X-ray diffraction teaching.

Bragg reflection↗
DOE OSTI2024

Advanced X-ray emission spectrometers

Spectroscopy systems require a crystal having specific properties for analyzing a spectrum of a sample, which is typically performed for measuring the presence of one element at a time. A two-dimensional (2D) crystal mount for performing simultaneous spectroscopy measurements includes a crystal holder having multiple rows of crystal mounts. Each crystal mount is positioned and orientated to physically support a crystal at a fixed position and fixed orientation relative to an optical axis. A sample provides radiation to analyzer crystals disposed in the crystal mounts, and a detector may detect radiation reflected from the analyzer crystals, for performing multiple simultaneous spectroscopy measurements.

Sun, Chengjun↗
DOE OSTI2024

Rapid Prototyping for Nanoparticle-Based Photonic Crystal Fiber Sensors

The advent of nanotechnology has motivated a revolution in the development of miniaturized sensors. Such sensors can be used for radiation detection, temperature sensing, radio-frequency sensing, strain sensing, and more. At the nanoscale, integrating the materials of interest into sensing platforms can be a common issue. One promising platform is photonic crystal fibers, which can draw in optically sensitive nanoparticles or have its optical properties changed by specialized nanomaterials. However, testing these sensors at scale is limited by the the need for specialized equipment to integrate these photonic crystal fibers into optical fiber systems. Having a method to enable rapid prototyping of new nanoparticle-based sensors in photonic crystal fibers would open up the field to a wider range of laboratories that could not have initially studied these materials in such a way before. This manuscript discusses the improved processes for cleaving, drawing, and rapidly integrating nanoparticle-based photonic crystal fibers into optical system setups. The method proposed in this manuscript achieved the following innovations: cleaving at a quality needed for nanoparticle integration could be done more reliably (≈100% acceptable cleaving yield versus ≈50% conventionally), nanoparticles could be drawn at scale through photonic crystal fibers in a safe manner (a method to draw multiple photonic crystal fibers at scale versus one fiber at a time), and the new photonic crystal fiber mount was able to be finely adjusted when increasing the optical coupling before inserting it into an optical system (before, expensive fusion splicing was the only other method).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Electron Nanocrystallography of Complex Materials and Processes

The proposed work is to develop Scanning CBED (SCBED) for the study of multi element crystals, including multiple principal elements alloys or high entropy alloys and relaxor-ferroelectric crystals. SCBED works like scanning transmission electron microscopy (STEM) but records the whole CBED at each probe position. Since CBED is a highly sensitive electron diffraction technique, SCBED combines the full benefits of CBED and STEM. Specifically, the SCBED based approach enables a quantitative determination of local atomic and electronic structures. The proposed work is thus to take advantage of SCBED for the study of complex multi-element crystals. The results from SCBED are expected to complement the methods of electron energy loss spectroscopy (EELS) near edge fine structure for probing local bonds, and X-ray and neutron scattering using the total scattering approach for probing local structure. Under the DOE BES support, we have developed SCBED to determine the structure of high entropy alloys, and we have coupled the work with in-situ compression study of dislocation dynamics to uncover the fundamental mechanisms of crystal slip.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Plant metacaspase: A case study of microcrystal structure determination and analysis

Metacaspases are highly conserved in plants and play essential roles in mediating programmed cell death, biotic and abiotic stress responses, and damage-induced innate immunity. Ca 2+ signaling induced by plant damage leads to activation of metacaspase from Arabidopsis thaliana (AtMC4), which subsequently processes a plant elicitor peptide to trigger downstream immuno-response. To understand the structural basis of AtMC4 activation by Ca 2+ , we previously determined its crystal structure and performed in-crystal Ca 2+ treatment to probe activation-associated conformational changes. To enable structure determination and in-crystal Ca 2+ activation analysis, we used microcrystals and related methods which were essential for our successful approach. Here, in this paper, we describe in detail the methods that we used for determination of AtMC4 structure using single-wavelength isomorphous replacement with anomalous signals assembled from 22 microcrystals. We also describe the method for in-crystal Ca 2+ soaking, microcrystal data collection, data assembly and analysis to obtain the activated structure of AtMC4 from 91 micro-sized crystals. The described methods may be useful to study other plant metacaspases and more broadly other plant enzymes for their structure determination and in-crystal functional characterization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Accelerating the identification of novel secondary metabolites in bioenergy plant root exudates using MicroED

Small molecule metabolites drive inter- and intraspecies communication and dependencies in diverse biological systems, yet a large proportion of these important chemical compounds remain uncharacterized in plants and microbes. Approximately 90% of the metabolites in root exudate profiles are unknown compounds, despite the importance of root exudate composition in plant-microbe interactions. We need advanced analytical capabilities that will support rapid discovery and structural elucidation of metabolites from biological samples that may be limited in quantity and high in complexity. To fill this gap, this project aimed to develop an integrated workflow involving metabolite extraction, separation, and crystallization from plant root exudates followed by characterization using nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry, and microcrystal electron diffraction (MicroED). Using crude root exudates from sorghum, this project successfully developed higher throughput exudate fractionation strategies to obtain pure compounds for crystallization and identified crystals in multiple fractions that diffracted. Additional efforts to increase the throughput of high-quality crystal generation for MicroED, such as crystallization screening and crystallization chaperone exploration, will be needed to further advance root exudate metabolite identification. The overall optimized sample preparation process can then be integrated with the existing data collection and data analysis pipelines for MicroED at PNNL to facilitate more rapid natural product discovery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Complementarity of neutron, XFEL and synchrotron crystallography for defining the structures of metalloenzymes at room temperature

Room-temperature macromolecular crystallography allows protein structures to be determined under close-to-physiological conditions, permits dynamic freedom in protein motions and enables time-resolved studies. In the case of metalloenzymes that are highly sensitive to radiation damage, such room-temperature experiments can present challenges, including increased rates of X-ray reduction of metal centres and site-specific radiation-damage artefacts, as well as in devising appropriate sample-delivery and data-collection methods. It can also be problematic to compare structures measured using different crystal sizes and light sources. In this study, structures of a multifunctional globin, dehaloperoxidase B (DHP-B), obtained using several methods of room-temperature crystallographic structure determination are described and compared. Here, data were measured from large single crystals and multiple microcrystals using neutrons, X-ray free-electron laser pulses, monochromatic synchrotron radiation and polychromatic (Laue) radiation light sources. These approaches span a range of 18 orders of magnitude in measurement time per diffraction pattern and four orders of magnitude in crystal volume. The first room-temperature neutron structures of DHP-B are also presented, allowing the explicit identification of the hydrogen positions. The neutron data proved to be complementary to the serial femtosecond crystallography data, with both methods providing structures free of the effects of X-ray radiation damage when compared with standard cryo-crystallography. Comparison of these room-temperature methods demonstrated the large differences in sample requirements, data-collection time and the potential for radiation damage between them. With regard to the structure and function of DHP-B, despite the results being partly limited by differences in the underlying structures, new information was gained on the protonation states of active-site residues which may guide future studies of DHP-B.

36 MATERIALS SCIENCE↗
DOE OSTI2024

In situ tuning of optomechanical crystals with nano-oxidation

Optomechanical crystals are a promising device platform for quantum transduction and sensing. Precise targeting of the optical and acoustic resonance frequencies of these devices is crucial for future advances on these fronts. However, fabrication disorder in these wavelength-scale nanoscale devices typically leads to inhomogeneous resonance frequencies. Here we achieve in situ , selective frequency tuning of optical and acoustic resonances in silicon optomechanical crystals via electric field-induced nano-oxidation using an atomic-force microscope. Our method can achieve a tuning range >2nm (0.13%) for the optical resonance wavelength in the telecom C-band, and >60MHz (1.2%) for the acoustic resonance frequency at 5 GHz. The tuning resolution of 1.1 pm for the optical wavelength and 150 kHz for the acoustic frequency allows us to spectrally align multiple optomechanical crystal resonators using a pattern generation algorithm. Our results establish a method for precise post-fabrication tuning of optomechanical crystals. This technique can enable coupled optomechanical resonator arrays, scalable resonant optomechanical circuits, and frequency matching of microwave-optical quantum transducers.

Hatipoglu, Utku (ORCID:0000000205119196)↗
DOE OSTI2020

Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray–derived conformational ensembles

How enzymes achieve their enormous rate enhancements remains a central question in biology, and our understanding to date has impacted drug development, influenced enzyme design, and deepened our appreciation of evolutionary processes. While enzymes position catalytic and reactant groups in active sites, physics requires that atoms undergo constant motion. Numerous proposals have invoked positioning or motions as central for enzyme function, but a scarcity of experimental data has limited our understanding of positioning and motion, their relative importance, and their changes through the enzyme’s reaction cycle. To examine positioning and motions and test catalytic proposals, we collected “room temperature” X-ray crystallography data for Pseudomonas putida ketosteroid isomerase (KSI), and we obtained conformational ensembles for this and a homologous KSI from multiple PDB crystal structures. Here, ensemble analyses indicated limited change through KSI’s reaction cycle. Active site positioning was on the 1- to 1.5-Å scale, and was not exceptional compared to noncatalytic groups. The KSI ensembles provided evidence against catalytic proposals invoking oxyanion hole geometric discrimination between the ground state and transition state or highly precise general base positioning. Instead, increasing or decreasing positioning of KSI’s general base reduced catalysis, suggesting optimized Ångstrom-scale conformational heterogeneity that allows KSI to efficiently catalyze multiple reaction steps. Ensemble analyses of surrounding groups for WT and mutant KSIs provided insights into the forces and interactions that allow and limit active-site motions. Most generally, this ensemble perspective extends traditional structure–function relationships, providing the basis for a new era of “ensemble–function” interrogation of enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Multi-crystal native-SAD phasing at 5 keV with a helium environment

De novo structure determination from single-wavelength anomalous diffraction using native sulfur or phospho­rus in biomolecules (native-SAD) is an appealing method to mitigate the labor-intensive production of heavy-atom derivatives and seleno­methio­nyl substitutions. The native-SAD method is particularly attractive for membrane proteins, which are difficult to produce and often recalcitrant to grow into decent-sized crystals. Native-SAD uses lower-energy X-rays to enhance anomalous signals from sulfur or phospho­rus. However, at lower energies, the scattering and absorption of air contribute to the background noise, reduce the signals and are thus adverse to native-SAD phasing. We have previously demonstrated native-SAD phasing at an energy of 5 keV in air at the NSLS-II FMX beamline. Here, the use of a helium path developed to reduce both the noise from background scattering and the air absorption of the diffracted X-ray beam are described. The helium path was used for collection of anomalous diffraction data at 5 keV for two proteins: thaumatin and the membrane protein TehA. Although anomalous signals from each individual crystal are very weak, robust anomalous signals are obtained from data assembled from micrometre-sized crystals. The thaumatin structure was determined from 15 microcrystals and the TehA structure from 18 microcrystals. These results demonstrate the usefulness of a helium environment in support of native-SAD phasing at 5 keV.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Terahertz Circular Dichroism Spectroscopy of Molecular Assemblies and Nanostructures

Chemical, physical, biological and materials engineering disciplines use a variety of chiroptical spectroscopies to probe geometrical and optical asymmetry in molecules and particles. Electronic (ECD) and vibrational (VCD) circular dichroism are the most common of these techniques and collectively enable the studies of electronic and vibronic transitions with energies between 0.1 and 5.0 eV. The vibrational states with characteristic energies in the range of 0.001–0.01 eV carry valuable information about concerted intermolecular motions in molecules and crystals involving multiple atoms. These vibronic transitions located in the terahertz (THz) part of the spectrum become increasingly more important for the chemistry, physics, and biology of complex molecules and materials However, the methodology and hardware of THz circular dichroism (TCD) are much less developed than the chiroptical spectroscopies for ultraviolet, visible, near- and mid infrared photons. In this report we provide theoretical foundations, practical implementations, comparative assessments, and exemplary applications of TCD spectroscopy. We show that the sign, intensity, and position of TCD peaks are highly sensitive to the three-dimensional structure and long-range organization of molecular crystals, which offer unique capabilities to study (bio) molecules, their crystals, and nanoscale assemblies and apply the novel data processing methodologies. TCD also offers a convenient toolbox to identify new physical phenomena, such as chiral phonons and their propagation in nanostructured matter. We also discuss the major challenges, emerging opportunities and promising research directions, including broad investigation of chiral phonons observed in chiral (nano) crystals and emerging machine learning methodologies for TCD in biological and nanoscale structures. Ubiquity of low-frequency vibrations with rotational components in biomolecular structures, combined with sharpness of peaks in TCD spectra, enables a variety of technological translations.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Tunable coherent mixed-dimensional perovskite heterojunctions and quantum wells grown from solution

Coherent heterojunctions, quantum wells and multiple quantum wells are needed for high-performance devices; these are generally grown via a dedicated vapour phase epitaxy process. Here we demonstrate the growth of coherent perovskite heterojunctions and quantum wells made of mixed-dimensional perovskites using a solution process. By exploiting the solubility difference of methylammonium (MA + ) and 4-(aminomethyl)piperidinium (4AMP 2+ ), we assemble layered perovskites with different layer numbers. The resulting 4AMP-MA n–1 Pb n I 3n+1 materials each with different layer numbers or bandgaps form quantum wells. Heterojunctions and quantum wells made of 4AMP-MA 2 Pb 3 I 10 (n = 3) and 4AMP-MAPb 2 I 7 (n = 2) with various barrier thickness are tailored by the solution temperature profile during crystal growth. Multiple quantum wells have been formed by cycling temperature profiles. The planar heterojunction and quantum wells have lattice matching without interfacial defects, and exhibit strong thermal stability. Type I band alignment at the n = 2/n = 3 heterojunction is confirmed by both computation and optical studies. In conclusion, this study opens a new direction for the development of sophisticated perovskite heterojunction and quantum well devices.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2023

Crystallographic Characterization of Sodium Ions in a Bacterial Leucine/Sodium Symporter

Na + is the most abundant ion in living organisms and plays essential roles in regulating nutrient uptake, muscle contraction, and neurotransmission. The identification of Na + in protein structures is crucial for gaining a deeper understanding of protein function in a physiological context. LeuT, a bacterial homolog of the neurotransmitter:sodium symporter family, uses the Na + gradient to power the uptake of amino acids into cells and has been used as a paradigm for the study of Na + -dependent transport systems. We have devised a low-energy multi-crystal approach for characterizing low-Z (Z ≤ 20) anomalous scattering ions such as Na + , Mg 2+ , K + , and Ca 2+ by combining Bijvoet-difference Fourier syntheses for ion detection and f” refinements for ion speciation. Using the approach, we experimentally identify two Na + bound near the central leucine binding site in LeuT. Using LeuT microcrystals, we also demonstrate that Na + may be depleted to study conformational changes in the LeuT transport cycle.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Desolvation Processes in Channel Solvates of Niclosamide

The antiparasitic drug niclosamide (NCL) is notable for its ability to crystallize in multiple 1:1 channel solvate forms, none of which are isostructural. Here, using a combination of time-resolved synchrotron powder X-ray diffraction and thermogravimetry, the process-induced desolvation mechanisms of methanol and acetonitrile solvates are investigated. Structural changes in both solvates follow a complicated molecular-level trajectory characterized by a sudden shift in lattice parameters several degrees below the temperature where the desolvated phase first appears. Model fitting of kinetic data obtained under isothermal heating conditions suggests that the desolvation is rate-limited by the nucleation of the solvent-free product. The desolvation pathways identified in these systems stand in contrast to previous investigations of the NCL channel hydrate, where water loss by diffusion initially yields an anhydrous isomorph that converts to the thermodynamic polymorph at significantly higher temperatures. Taking the view that each solvate lattice is a unique “pre-organized” precursor, a comparison of the pathways from different starting topologies to the same final product provides the opportunity to reevaluate assumptions of how various factors (e.g., solvent binding strength, density) influence solid-state desolvation processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗