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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

Towards the spatial resolution of metalloprotein charge states by detailed modeling of XFEL crystallographic diffraction

Oxidation states of individual metal atoms within a metalloprotein can be assigned by examining X-ray absorption edges, which shift to higher energy for progressively more positive valence numbers. Indeed, X-ray crystallography is well suited for such a measurement, owing to its ability to spatially resolve the scattering contributions of individual metal atoms that have distinct electronic environments contributing to protein function. However, as the magnitude of the shift is quite small, about +2 eV per valence state for iron, it has only been possible to measure the effect when performed with monochromated X-ray sources at synchrotron facilities with energy resolutions in the range 2–3 × 10 −4 (Δ E / E ). This paper tests whether X-ray free-electron laser (XFEL) pulses, which have a broader bandpass (Δ E / E = 3 × 10 −3 ) when used without a monochromator, might also be useful for such studies. The program nanoBragg is used to simulate serial femtosecond crystallography (SFX) diffraction images with sufficient granularity to model the XFEL spectrum, the crystal mosaicity and the wavelength-dependent anomalous scattering factors contributed by two differently charged iron centers in the 110-amino-acid protein, ferredoxin. Bayesian methods are then used to deduce, from the simulated data, the most likely X-ray absorption curves for each metal atom in the protein, which agree well with the curves chosen for the simulation. The data analysis relies critically on the ability to measure the incident spectrum for each pulse, and also on the nanoBragg simulator to predict the size, shape and intensity profile of Bragg spots based on an underlying physical model that includes the absorption curves, which are then modified to produce the best agreement with the simulated data. This inference methodology potentially enables the use of SFX diffraction for the study of metalloenzyme mechanisms and, in general, offers a more detailed approach to Bragg spot data reduction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A unifying Bayesian framework for merging X-ray diffraction data

Novel X-ray methods are transforming the study of the functional dynamics of biomolecules. Key to this revolution is detection of often subtle conformational changes from diffraction data. Diffraction data contain patterns of bright spots known as reflections. To compute the electron density of a molecule, the intensity of each reflection must be estimated, and redundant observations reduced to consensus intensities. Systematic effects, however, lead to the measurement of equivalent reflections on different scales, corrupting observation of changes in electron density. Here, we present a modern Bayesian solution to this problem, which uses deep learning and variational inference to simultaneously rescale and merge reflection observations. We successfully apply this method to monochromatic and polychromatic single-crystal diffraction data, as well as serial femtosecond crystallography data. We find that this approach is applicable to the analysis of many types of diffraction experiments, while accurately and sensitively detecting subtle dynamics and anomalous scattering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Rational design of a genetically encoded NMR zinc sensor

Elucidating the biochemical roles of the essential metal ion, Zn 2+ , motivates detection strategies that are sensitive, selective, quantitative, and minimally invasive in living systems. Fluorescent probes have identified Zn 2+ in cells but complementary approaches employing nuclear magnetic resonance (NMR) are lacking. Recent studies of maltose binding protein (MBP) using ultrasensitive 129 Xe NMR spectroscopy identified a switchable salt bridge which causes slow xenon exchange and elicits strong hyperpolarized 129 Xe chemical exchange saturation transfer (hyper-CEST) NMR contrast. To engineer the first genetically encoded, NMR-active sensor for Zn 2+ , we converted the MBP salt bridge into a Zn 2+ binding site, while preserving the specific xenon binding cavity. The zinc sensor (ZS) at only 1 μM achieved ‘turn-on’ detection of Zn 2+ with pronounced hyper-CEST contrast. This made it possible to determine different Zn 2+ levels in a biological fluid via hyper-CEST. ZS was responsive to low-micromolar Zn 2+ , only modestly responsive to Cu 2+ , and nonresponsive to other biologically important metal ions, according to hyper-CEST NMR spectroscopy and isothermal titration calorimetry (ITC). Protein X-ray crystallography confirmed the identity of the bound Zn 2+ ion using anomalous scattering: Zn 2+ was coordinated with two histidine side chains and three water molecules. Penta-coordinate Zn 2+ forms a hydrogen-bond-mediated gate that controls the Xe exchange rate. Metal ion binding affinity, 129 Xe NMR chemical shift, and exchange rate are tunable parameters via protein engineering, which highlights the potential to develop proteins as selective metal ion sensors for NMR spectroscopy and imaging.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

AlphaFold -assisted structure determination of a bacterial protein of unknown function using X-ray and electron crystallography

Macromolecular crystallography generally requires the recovery of missing phase information from diffraction data to reconstruct an electron-density map of the crystallized molecule. Most recent structures have been solved using molecular replacement as a phasing method, requiring an a priori structure that is closely related to the target protein to serve as a search model; when no such search model exists, molecular replacement is not possible. New advances in computational machine-learning methods, however, have resulted in major advances in protein structure predictions from sequence information. Methods that generate predicted structural models of sufficient accuracy provide a powerful approach to molecular replacement. Taking advantage of these advances, AlphaFold predictions were applied to enable structure determination of a bacterial protein of unknown function (UniProtKB Q63NT7, NCBI locus BPSS0212) based on diffraction data that had evaded phasing attempts using MIR and anomalous scattering methods. Using both X-ray and micro-electron (microED) diffraction data, it was possible to solve the structure of the main fragment of the protein using a predicted model of that domain as a starting point. The use of predicted structural models importantly expands the promise of electron diffraction, where structure determination relies critically on molecular replacement.

molecular replacement↗
DOE OSTI2020

K 2P channel C-type gating involves asymmetric selectivity filter order-disorder transitions

K 2P potassium channels regulate cellular excitability using their selectivity filter (C-type) gate. C-type gating mechanisms, best characterized in homotetrameric potassium channels, remain controversial and are attributed to selectivity filter pinching, dilation, or subtle structural changes. The extent to which such mechanisms control C-type gating of innately heterodimeric K 2P s is unknown. Here, combining K 2P 2.1 (TREK-1) x-ray crystallography in different potassium concentrations, potassium anomalous scattering, molecular dynamics, and electrophysiology, we uncover unprecedented, asymmetric, potassium-dependent conformational changes that underlie K 2P C-type gating. These asymmetric order-disorder transitions, enabled by the K 2P heterodimeric architecture, encompass pinching and dilation, disrupt the S1 and S2 ion binding sites, require the uniquely long K 2P SF2-M4 loop and conserved “M3 glutamate network,” and are suppressed by the K 2P C-type gate activator ML335. These findings demonstrate that two distinct C-type gating mechanisms can operate in one channel and underscore the SF2-M4 loop as a target for K 2P channel modulator development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Nickel Binding to the c-Src SH3 Domain Facilitates Crystallization

Introduction: Numerous X-ray crystal structures of the c-Src SH3 domain have provideda large sampling of atomic-level information for this important signaling domain. Multiple crystalforms have been reported, with variable crystal lattice contacts and chemical crystallizationconditions. Materials and Methods: We crystallized the c-Src SH3 domain in a crystallization buffercontaining NiCl2. Results: A unique crystal structure of the Src SH3 domain in the trigonal space group H32 isdetermined to 1.45 Å resolution. Crystal packing and anomalous scattering reveal that this crystalform is mediated by two ordered nickel ions provided by the crystallization buffer. Nickelcoordination occurs in a 2:2 stoichiometry, which dimerizes two SH3 domain monomers across apseudo-twofold rotation axis and involves the native N-terminal c-Src SH3 amino acid sequence, asurface-exposed histidine residue, and ordered water molecules. Discussion: This study provides an example of metal-mediated crystallization and metal binding byN-terminal protein residues, contrasting with the Amino-Terminal Copper and Nickel Binding(ATCUN) motif. Conclusion: Alternative avenues help widen the potential for future crystallography-based studiesof the c-Src SH3 domain.

Biochemistry & Molecular Biology↗
DOE OSTI2020

Chemical and structural investigation of the paroxetine-human serotonin transporter complex

Antidepressants target the serotonin transporter (SERT) by inhibiting serotonin reuptake. Structural and biochemical studies aiming to understand binding of small-molecules to conformationally dynamic transporters like SERT often require thermostabilizing mutations and antibodies to stabilize a specific conformation, leading to questions about relationships of these structures to the bonafide conformation and inhibitor binding poses of wild-type transporter. To address these concerns, we determined the structures of ΔN72/ΔC13 and ts2-inactive SERT bound to paroxetine analogues using single-particle cryo-EM and x-ray crystallography, respectively. We synthesized enantiopure analogues of paroxetine containing either bromine or iodine instead of fluorine. We exploited the anomalous scattering of bromine and iodine to define the pose of these inhibitors and investigated inhibitor binding to Asn177 mutants of ts2-active SERT. These studies provide mutually consistent insights into how paroxetine and its analogues bind to the central substrate-binding site of SERT, stabilize the outward-open conformation, and inhibit serotonin transport.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1977

Crater morphometry from bistatic radar

In the present paper, bistatic radar techniques are discussed which can be used to identify and measure the dimensions of anomalously scattering regions on planetary surfaces. The morphometric potential of the bistatic radar is demonstrated by an example in which spectral features in Apollo 14 echoes are correlated with parts of the lunar crater Lansberg. Crater dimensions, including width of interior walls and extent of the ejecta blanket, are determined from a quantitative analysis. It is shown that the technique can be generalized for scattering areas at arbitrary positions with respect to the ground track, and could easily be inverted for characterization of a 'blind' target, such as Venus.

Simpson, R. A.↗
NASA NTRS1986

Three dimensional simulation of the operation of a hollow cathode electron emitter on the Shuttle orbiter

Several researchers have suggested using hollow cathodes as plasma contactors for electrodynamic tethers, particularly to prevent the shuttle orbiter from charging to large negative potentials. Previous studies have shown that fluid models with anomalous scattering can describe the electron transport in hollow cathode generated plasmas. An improved theory of the hollow cathode plasmas is developed and computational results using the theory are compared with laboratory experiment. Numerical predictions for a hollow cathode plasma source of the type considered for use on the shuttle are presented as are three-dimensional NASCAP/LEO calculations of the emitted ion trajectories and the resulting potentials in the vicinity of the orbiter. The computer calculations show that the hollow cathode plasma source makes vastly superior contact with the ionospheric plasma compared with either an electron gun or passive ion collection by the orbiter.

Davis, V. A.↗
NASA NTRS1987

Hollow cathodes as electron emitting plasma contactors Theory and computer modeling

Several researchers have suggested using hollow cathodes as plasma contactors for electrodynamic tethers, particularly to prevent the Shuttle Orbiter from charging to large negative potentials. Previous studies have shown that fluid models with anomalous scattering can describe the electron transport in hollow cathode generated plasmas. An improved theory of the hollow cathode plasmas is developed and computational results using the theory are compared with laboratory experiments. Numerical predictions for a hollow cathode plasma source of the type considered for use on the Shuttle are presented, as are three-dimensional NASCAP/LEO calculations of the emitted ion trajectories and the resulting potentials in the vicinity of the Orbiter. The computer calculations show that the hollow cathode plasma source makes vastly superior contact with the ionospheric plasma compared with either an electron gun or passive ion collection by the Orbiter.

Davis, V. A.↗
NASA NTRS1993

Model of superthermal ions in the Venus ionosphere

A model is presented that simulates the behavior of superthermal ions previously reported in the dayside ionosphere of Venus. The model considers effects of ExB and gradient drifts, charge exchange and collisions with the ambient neutral atmosphere and the possible effects of a wave-particle (anomalous) scattering process. Results indicate that scattering processes are required if superthermal ions are the explanation for the observed 'missing pressure' component in the day-side Venus ionosphere. The scattering scale length required to match the 'missing pressure' distribution is similar to the scale length previously predicted for growth of a lower hybrid beam instability.

Kramer, Leonard↗
DOE OSTI2020

Inelastic neutron scattering evidence for anomalous H–H distances in metal hydrides

Hydrogen-containing materials are of basic as well as technological interest. An outstanding question for both is the amount of hydrogen that can be incorporated in such materials, because that determines dramatically their physical properties such as electronic and crystalline structure. The number of hydrogen atoms in a metal is controlled by the interaction of hydrogens with the metal and by the hydrogen–hydrogen interactions. It is well established that the minimal possible hydrogen–hydrogen distances in conventional metal hydrides are around 2.1 Å under ambient conditions, although closer H–H distances are possible for materials under high pressure. We introduce inelastic neutron scattering measurements on hydrogen in Z r V 2 H x showing nonexpected scattering at low-energy transfer. The analysis of the spectra reveals that these spectral features in part originate from hydrogen vibrations confined by neighboring hydrogen at distances as short as 1.6 Å. These distances are much smaller than those found in related hydrides, thereby violating the so-called Switendick criterion. The results have implications for the design and creation of hydrides with additional properties and applications.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Anomalous X-Ray Scattering and Extended X-Ray Absorption Fine Structure Study of the Local Structure of CrFeCoNiMo x (x = 0.11, 0.18, and 0.23) High-Entropy Alloys

Anomalous x-ray scattering (AXS) and extended x-ray absorption fine structure (EXAFS) were used to determine the local structure of Mo in CrFeCoNiMo x (x = 0.11, 0.18, and 0.23), a high-entropy alloy with a face-centered cubic (FCC) lattice. No superlattice peaks were observed down to the 10 -4 intensity level. This observation along with the nearly constant decrease of the FCC diffraction peaks above the Mo K absorption edge suggests that Mo atoms have no preferred site occupancy in the FCC lattice. Modeling of the EXAFS data suggests a local chemical order in CrFeCoNiMo x , where in Mo-rich samples (e.g., x = 0.23), Mo atoms are preferably surrounded by lighter atoms, such as Cr.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

Anomalous neutron nuclear-magnetic interference spectroscopy

The electron–phonon interaction plays a critical role in materials’ electrical, thermal, optical, and superconducting properties. However, measuring the phonon mode-resolved electron–phonon interaction has been challenging. Here we propose neutron-scattering-based Anomalous Neutron nUclear-Magnetic Interference Spectroscopy (ANUBIS), where the co-existence of neutron nuclear scattering and magnetic scattering leads to anomalous dynamical structure factor under the presence of the electron–phonon interaction. Such anomalous structure factor is linear in electron–phonon coupling constant at the phonon wavevector, and is directly proportional to the momentum and energy-resolved dielectric function. The experimental configuration can be achieved using existing polarized inelastic neutron scattering setup, and an order-of-magnitude estimate shows the viability to observe the anomalous scattering signal is around to 10 –4 to 10 –3 relative to phonon scattering, which is examined through the preliminary experiments and achievable at emerging neutron facilities. As a result, our proposal offers an alternative neutron-based metrology to probe the crucial electronic properties.

Electron-phonon interactions↗
DOE OSTI2022

Lattice dynamics of high-pressure hydrides studied by inelastic neutron scattering

Due to the small mass and anomalously large neutron scattering cross-section of proton (about 80 barns compared to a few barns for other nuclei), inelastic neutron scattering is considered as one of the most effective tools in studying optical vibrations of hydrogen atoms in metal hydrides. The current review is focused on the binary hydrides of 3d- and 4d-metals of groups VI–VIII, which were produced at high hydrogen pressures of several gigapascals in relatively large quantities of hundreds of mg, quenched to low temperature and studied by INS ex situ at ambient pressure with high statistical accuracy. One of the unusual effects revealed by INS is a strong increase in the strength of the metal-hydrogen interactions with decreasing atomic number of the d-metal accompanied by an increase in the Me-H distance. Based on the available experimental results, the spectra g(E) of the phonon density of states and temperature dependencies CV(T) of the heat capacity at constant volume at T up to 1000 K have been derived in this paper and presented both in the figures and in digital form. This provides the reference data for the theoretical investigations of the crystal structures and compositions of new practically important hydrides giving the opportunity to validate calculation methods by comparing the calculated g(E) and CV(T) with the accurate experimental dependencies for the binary hydrides. Recent INS studies showed [R.A. Klein et al., J. Alloy. Compd. 894 (2022) 162381] that the fingerprints of anomalously short H-H separations of 1.6 Å violating the “2 Å rule” can be easily and unambiguously identified in the complex INS spectra of quaternary hydrides (La,Ce)NiInH 1+x . This makes neutron spectroscopy an attractive means for obtaining valuable data in the search for novel hydrides with a record high hydrogen capacity.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2024

Anomalous frequency and temperature dependent scattering in the dilute metallic phase in lightly doped-SrTiO 3

The mechanism of superconductivity in materials with aborted ferroelectricity and its emergence out of a dilute metallic phase in systems like doped-SrTiO 3 is an outstanding issue in condensed matter physics. This dilute metal has anomalous properties that are both similar and different to those found in the normal state of other unconventional superconductors. For instance, T 2 resistivity can be found at densities that are too small to allow current decay through electronelectron scattering. We have investigated the optical properties of the dilute metallic phase in doped-SrTiO 3 using THz time-domain spectroscopy. At low frequencies the THz response exhibits a Drude-like form as expected for typical metal-like conductivity. We observed the frequency and temperature dependencies to the low energy scattering rate Γ(ω, T) ∝ (¯hω) 2 + (pπk B T) 2 expected in a conventional Fermi liquid. However we find the lowest known p values of 0.39-0.72. As p is 2 in a canonical Fermi liquid and existing models based on energy dependent elastic scattering bound p from below to 1, our observation lies outside current explanation. Our data also gives insight into the high temperature regime and shows that the temperature dependence of the resistivity derives in part from strong T dependent mass renormalizations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗