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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 829 records · Page 46
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Structure of maize BZR1-type β-amylase BAM8 provides new insights into its noncatalytic adaptation

Plant β-amylase (BAM) proteins play an essential role in growth, development, stress response, and hormone regulation. Despite their typical (β/α) 8 barrel structure as active catalysts in starch breakdown, catalytically inactive BAMs are implicated in diverse yet elusive functions in plants. Further, the noncatalytic BAM7/8 contain N-terminal BZR1 domains and were shown to be involved in the regulation of brassinosteroid signaling and possibly serve as sensors of yet an uncharacterized metabolic signal. While the structures of several catalytically active BAMs have been reported, structural characterization of the catalytically inactive BZR1-type BAMs remain unknown. Here, we determine the crystal structure of β-amylase domain of Zea mays BAM8/BES1/BZR1-5 and provide comprehensive insights into its noncatalytic adaptation. Using structural-guided comparison combined with biochemical analysis and molecular dynamics simulations, we revealed conformational changes in multiple distinct highly conserved regions resulting in rearrangement of the binding pocket. Altogether, this study adds a new layer of understanding to starch breakdown mechanism and elucidates the acquired adjustments of noncatalytic BZR1-type BAMs as putative regulatory domains and/or metabolic sensors in plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Elucidating the Location of Cd 2+ in Post-synthetically Treated InP Quantum Dots Using Dynamic Nuclear Polarization 31 P and 113 Cd Solid-State NMR Spectroscopy

Indium phosphide quantum dots (InP QD) are a promising alternative to traditional QD materials that contain toxic heavy elements such as lead and cadmium. However, InP QD obtained from colloidal synthesis are often plagued by poor photoluminescence quantum yields (PL-QYs). In order to improve the PL-QY of InP QD, a number of post-synthetic treatments have been devised. Recently, it has been shown that InP post-synthetically treated with Lewis acid metal divalent cations (M-InP) exhibit enhanced PL-QY; however, the molecular structure and mechanism behind the improved PL-QY are not fully understood. Here, to determine the surface structure of M-InP QD, dynamic nuclear polarization surface-enhanced nuclear magnetic resonance spectroscopy (DNP SENS) experiments were employed on a series of InP magic size clusters treated with Cd ions, InP QD, cadmium phosphide (Cd 3 P 2 ) QD, and Cd-treated InP QD (Cd–InP QD). With the use of DNP SENS, we were able to obtain the 1D 31 P and 113 Cd NMR spectra, 113 Cd{ 31 P} rotational-echo double-resonance (REDOR) NMR spectra, and 31 P{ 113 Cd} dipolar heteronuclear multiple quantum correlation (D-HMQC) sequence. Changes in the phosphide 31 P chemical shifts after Cd treatment provide indirect evidence that some Cd alloys into the sub-surface regions of the particle. DNP-enhanced 113 Cd solid-state NMR spectra suggest that most Cd ions are coordinated by oxygen atoms from either carboxylate ligands or surface phosphate groups. 113 Cd{ 31 P} REDOR and 31 P{ 113 Cd} D-HMQC experiments confirm that a subset of Cd ions are located on the surface of Cd–InP QD and coordinated with phosphate groups.

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

The crystal structure of Acinetobacter baumannii bacterioferritin reveals a heteropolymer of bacterioferritin and ferritin subunits

Iron storage proteins, e.g., vertebrate ferritin, and the ferritin-like bacterioferritin (Bfr) and bacterial ferritin (Ftn), are spherical, hollow proteins that catalyze the oxidation of Fe 2+ at binuclear iron ferroxidase centers (FOC) and store the Fe 3+ in their interior, thus protecting cells from unwanted Fe 3+ /Fe 2+ redox cycling and storing iron at concentrations far above the solubility of Fe 3+ . Vertebrate ferritins are heteropolymers of H and L subunits with only the H subunits having FOC. Bfr and Ftn were thought to coexist in bacteria as homopolymers, but recent evidence indicates these molecules are heteropolymers assembled from Bfr and Ftn subunits. Despite the heteropolymeric nature of vertebrate and bacterial ferritins, structures have been determined only for recombinant proteins constituted by a single subunit type. Herein we report the structure of Acinetobacter baumannii bacterioferritin, the first structural example of a heteropolymeric ferritin or ferritin-like molecule, assembled from completely overlapping Ftn homodimers harboring FOC and Bfr homodimers devoid of FOC but binding heme. The Ftn homodimers function by catalyzing the oxidation of Fe 2+ to Fe 3+ , while the Bfr homodimers bind a cognate ferredoxin (Bfd) which reduces the stored Fe 3+ by transferring electrons via the heme, enabling Fe 2+ mobilization to the cytosol for incorporation in metabolism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Millisecond timescale reactions observed via X-ray spectroscopy in a 3D microfabricated fused silica mixer

Determination of electronic structures during chemical reactions remains challenging in studies which involve reactions in the millisecond timescale, toxic chemicals, and/or anaerobic conditions. Here, a three-dimensionally (3D) microfabricated microfluidic mixer platform that is compatible with time-resolved X-ray absorption and emission spectroscopy (XAS and XES, respectively) is presented. This platform, to initiate reactions and study their progression, mixes a high flow rate (0.50–1.5 ml min –1 ) sheath stream with a low-flow-rate (5–90 µl min –1 ) sample stream within a monolithic fused silica chip. The chip geometry enables hydro­dynamic focusing of the sample stream in 3D and sample widths as small as 5 µm. The chip is also connected to a polyimide capillary downstream to enable sample stream deceleration, expansion, and X-ray detection. In this capillary, sample widths of 50 µm are demonstrated. Further, convection–diffusion-reaction models of the mixer are presented. The models are experimentally validated using confocal epifluorescence microscopy and XAS/XES measurements of a ferricyanide and ascorbic acid reaction. The models additionally enable prediction of the residence time and residence time uncertainty of reactive species as well as mixing times. Residence times (from initiation of mixing to the point of X-ray detection) during sample stream expansion as small as 2.1 ± 0.3 ms are also demonstrated. Importantly, an exploration of the mixer operational space reveals a theoretical minimum mixing time of 0.91 ms. The proposed platform is applicable to the determination of the electronic structure of conventionally inaccessible reaction intermediates.

3D microfabrication↗
DOE OSTI2023

Harnessing Neural Networks for Elucidating X-ray Absorption Structure–Spectrum Relationships in Amorphous Carbon

Improved understanding of structural and chemical properties through local experimental probes, such as X-ray absorption near-edge structure (XANES) spectroscopy, is crucial for the understanding and design of functional materials. In recent years, significant advancements have been made in the development of data science approaches for the automated interpretation of XANES structure–spectrum relationships. However, existing studies have primarily focused on crystalline solids and small molecules, while fewer efforts have been devoted to disordered systems. Thus, in this work, we demonstrate the development of neural network models for predicting and interpreting XANES spectra of amorphous carbon (a-C) from local structural descriptors. Comparison between different structural descriptors expectedly shows that the inclusion of both bond length and bond angle information is necessary for an accurate prediction of the spectra. Among the descriptors considered in this work, we find that the local many-body tensor representation yields the highest accuracy and greatest interpretability so that it can be leveraged to understand the importance of structural motifs in determining XANES spectra. Furthermore, we also discuss performance of neural network models for predicting both local structure features, such as bond lengths and bond angles, and global chemical composition, such as the sp:sp 2 :sp 3 ratio.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Room-temperature superconductivity in a carbonaceous sulfur hydride

One of the long-standing challenges in experimental physics is the observation of room-temperature superconductivity (RTSC). Recently, high temperature conventional superconductivity in hydrogen-rich materials has been reported in several systems under high pressure. The most significant discovery in reaching RTSC is the pressure-driven disproportionation of hydrogen sulfide (H 2 S) to H 3 S with a confirmed Tc of 203 kelvin at 155 gigapascals. As H 2 S readily mixes with hydrogen to form guest-host structures at lower pressures, the comparable size of methane to H 2 S should allow molecular exchange within a large assemblage of van der Waals solids that are (highly) hydrogen-rich with H 2 inclusions that are then the building blocks for novel superconducting compounds at extreme conditions. Here, we report superconductivity in a photochemically transformed carbonaceous sulfur hydride system with a maximum superconducting transition temperature of 287.7 ± 1.2 kelvin (~15° celsius) achieved at 267 ± 10 gigapascals. The superconducting state is observed over a broad pressure range from 140 to 275 gigapascals, with a dramatic upturn in Tc above 220 gigapascals. Superconductivity is established by the observation of zero resistance, magnetic susceptibility up to 190 gigapascals, and reduction of Tc under an external magnetic field up to 9 tesla, with an upper critical magnetic field of ~62 tesla based on Ginzburg–Landau (GL) model at zero temperature. The light, quantum nature of hydrogen limits structural and stoichiometric determination using x-ray scattering techniques. Raman spectroscopy is used to probe the chemical and structural transformations pre-metallization. In conclusion, the introduction of chemical tuning within our reported ternary system could be the path forward to lowering the pressure while preserving the RTSC properties.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Conjugation- and Aggregation-Directed Design of Covalent Organic Frameworks as White-Light-Emitting Diodes

2D covalent organic frameworks (COFs) have emerged as a promising class of organic luminescent materials due to their structural diversity, which allows the systematic tuning of organic building blocks to optimize emitting properties. However, a significant knowledge gap exists between the design strategy and the fundamental understanding of the key structural parameters that determine their photophysical properties. Here, in this work, we report two highly emissive sp 2 -C-COFs and the direct correlation of the structure (conjugation and aggregation) with their light absorption/emission, charge transfer (CT), and exciton dynamics, the key properties that determine their function as luminescent materials. We show that white light can be obtained by simply coating COFs on an LED strip or mixing the two COFs. Using the combination of time-resolved absorption and emission spectroscopy as well as computational prediction, we show that the planarity, conjugation, orientation of the dipole moment, and interlayer aggregation not only determine the light-harvesting ability of COFs but also control the exciton relaxation pathway and photoluminescent quantum yield.

14 SOLAR ENERGY↗
DOE OSTI2020

Auxetic two-dimensional transition metal selenides and halides

Abstract Auxetic two-dimensional (2D) materials provide a promising platform for biomedicine, sensors, and many other applications at the nanoscale. In this work, utilizing a hypothesis-based data-driven approache, we identify multiple materials with remarkable in-plane auxetic behavior in a family of buckled monolayer 2D materials. These materials are transition metal selenides and transition metal halides with the stoichiometry MX (M = V, Cr, Mn, Fe, Co, Cu, Zn, Ag, and X = Se, Cl, Br, I). First-principles calculations reveal that the desirable auxetic behavior of these 2D compounds originates from the interplay between the buckled 2D structure and the weak metal–metal interaction determined by their electronic structures. We observe that the Poisson’s ratio is sensitive to magnetic order and the amount of uniaxial stress applied. A transition from positive Poisson’s ratio (PPR) to negative Poisson’s ratio (NPR) for a subgroup of MX compounds under large uniaxial stress is predicted. The work provides a guideline for the future design of 2D auxetic materials at the nanoscale.

2d materials↗
DOE OSTI2020

Human XPG nuclease structure, assembly, and activities with insights for neurodegeneration and cancer from pathogenic mutations

Xeroderma pigmentosum group G (XPG) protein is both a functional partner in multiple DNA damage responses (DDR) and a pathway coordinator and structure-specific endonuclease in nucleotide excision repair (NER). Different mutations in the XPG gene ERCC5 lead to either of two distinct human diseases: Cancer-prone xeroderma pigmentosum (XP-G) or the fatal neurodevelopmental disorder Cockayne syndrome (XP-G/CS). To address the enigmatic structural mechanism for these differing disease phenotypes and for XPG’s role in multiple DDRs, here we determined the crystal structure of human XPG catalytic domain (XPGcat), revealing XPG-specific features for its activities and regulation. Furthermore, XPG DNA binding elements conserved with FEN1 superfamily members enable insights on DNA interactions. Notably, all but one of the known pathogenic point mutations map to XPGcat, and both XP-G and XP-G/CS mutations destabilize XPG and reduce its cellular protein levels. Mapping the distinct mutation classes provides structure-based predictions for disease phenotypes: Residues mutated in XP-G are positioned to reduce local stability and NER activity, whereas residues mutated in XP-G/CS have implied long-range structural defects that would likely disrupt stability of the whole protein, and thus interfere with its functional interactions. Combined data from crystallography, biochemistry, small angle X-ray scattering, and electron microscopy unveil an XPG homodimer that binds, unstacks, and sculpts duplex DNA at internal unpaired regions (bubbles) into strongly bent structures, and suggest how XPG complexes may bind both NER bubble junctions and replication forks. Collective results support XPG scaffolding and DNA sculpting functions in multiple DDR processes to maintain genome stability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Biophysical and biochemical evidence for the role of acetate kinases (AckAs) in an acetogenic pathway in pathogenic spirochetes

Unraveling the metabolism of Treponema pallidum is a key component to understanding the pathogenesis of the human disease that it causes, syphilis. For decades, it was assumed that glucose was the sole carbon/energy source for this parasitic spirochete. But the lack of citric-acid-cycle enzymes suggested that alternative sources could be utilized, especially in microaerophilic host environments where glycolysis should not be robust. Recent bioinformatic, biophysical, and biochemical evidence supports the existence of an acetogenic energy-conservation pathway in T . pallidum and related treponemal species. In this hypothetical pathway, exogenous D-lactate can be utilized by the bacterium as an alternative energy source. Herein, we examined the final enzyme in this pathway, acetate kinase (named TP0476), which ostensibly catalyzes the generation of ATP from ADP and acetyl-phosphate. We found that TP0476 was able to carry out this reaction, but the protein was not suitable for biophysical and structural characterization. We thus performed additional studies on the homologous enzyme (75% amino-acid sequence identity) from the oral pathogen Treponema vincentii , TV0924. This protein also exhibited acetate kinase activity, and it was amenable to structural and biophysical studies. We established that the enzyme exists as a dimer in solution, and then determined its crystal structure at a resolution of 1.36 Å, showing that the protein has a similar fold to other known acetate kinases. Mutation of residues in the putative active site drastically altered its enzymatic activity. A second crystal structure of TV0924 in the presence of AMP (at 1.3 Å resolution) provided insight into the binding of one of the enzyme’s substrates. On balance, this evidence strongly supported the roles of TP0476 and TV0924 as acetate kinases, reinforcing the hypothesis of an acetogenic pathway in pathogenic treponemes.

Deka, Ranjit K.↗
DOE OSTI2025

Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study

The easiest and often most useful way to work with experimentally determined or computationally predicted structures of biomolecules is by viewing their three-dimensional (3D) shapes using a molecular visualization tool. Mol* was collaboratively developed by RCSB Protein Data Bank (RCSB PDB, RCSB.org) and Protein Data Bank in Europe (PDBe, PDBe.org) as an open-source, web-based, 3D visualization software suite for examination and analyses of biostructures. It is capable of displaying atomic coordinates and related experimental data of biomolecular structures together with a variety of annotations, facilitating basic and applied research, training, education, and information dissemination. Across RCSB.org, the RCSB PDB research-focused web portal, Mol* has been implemented to support single-mouse-click atomic-level visualization of biomolecules (e.g., proteins, nucleic acids, carbohydrates) with bound cofactors, small-molecule ligands, ions, water molecules, or other macromolecules. RCSB.org Mol* can seamlessly display 3D structures from various sources, allowing structure interrogation, superimposition, and comparison. Using influenza A H5N1 virus as a topical case study of an important pathogen, we exemplify how Mol* has been embedded within various RCSB.org tools—allowing users to view polymer sequence and structure-based annotations integrated from trusted bioinformatics data resources, assess patterns and trends in groups of structures, and view structures of any size and compositional complexity. In addition to being linked to every experimentally determined biostructure and Computed Structure Model made available at RCSB.org, Standalone Mol* is freely available for visualizing any atomic-level or multi-scale biostructure at rcsb.org/3d-view.

3D biostructure↗
DOE OSTI2022

Chemical crystallography by serial femtosecond X-ray diffraction

Abstract Inorganic–organic hybrid materials represent a large share of newly reported structures, owing to their simple synthetic routes and customizable properties 1 . This proliferation has led to a characterization bottleneck: many hybrid materials are obligate microcrystals with low symmetry and severe radiation sensitivity, interfering with the standard techniques of single-crystal X-ray diffraction 2,3 and electron microdiffraction 4–11 . Here we demonstrate small-molecule serial femtosecond X-ray crystallography (smSFX) for the determination of material crystal structures from microcrystals. We subjected microcrystalline suspensions to X-ray free-electron laser radiation 12,13 and obtained thousands of randomly oriented diffraction patterns. We determined unit cells by aggregating spot-finding results into high-resolution powder diffractograms. After indexing the sparse serial patterns by a graph theory approach 14 , the resulting datasets can be solved and refined using standard tools for single-crystal diffraction data 15–17 . We describe the ab initio structure solutions of mithrene (AgSePh) 18–20 , thiorene (AgSPh) and tethrene (AgTePh), of which the latter two were previously unknown structures. In thiorene, we identify a geometric change in the silver–silver bonding network that is linked to its divergent optoelectronic properties 20 . We demonstrate that smSFX can be applied as a general technique for structure determination of beam-sensitive microcrystalline materials at near-ambient temperature and pressure.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Systems and methods for generating phase diagrams for metastable material states

A system can include one or more processors configured to access at least one parameter of a material, generate a plurality of structures of the material using the at least one parameter, determine a state of each structure of the plurality of structures using the at least one parameter, determine a difference between the state of each structure of the plurality of structures and a ground state value, evaluate a convergence condition responsive to determining the difference between the state of each structure of the plurality of structures and the ground state value, and output at least one structure of the plurality of structures responsive to the convergence condition being satisfied.

Sankaranarayanan, Subramanian↗
DOE OSTI2020

Electron Paramagnetic Resonance Characteristics and Crystal Structure of a Tutton Salt Analogue: Copper-Doped Cadmium Creatininium Sulfate

Electron paramagnetic resonance and crystallographic studies on copper-doped cadmium creatininium sulfate (CdCrnS) were undertaken to study the characteristics of a copper-hexahydrate complex in an organic analogue of Tutton's salt. X-ray diffraction experiments determined the crystal structure of CdCrnS at both 100 and 298 K. CdCrnS, like Tutton salt, crystallizes in the monoclinic space group P2 1 /n. The unit cell contains two cadmium hexahydrate complexes, four creatininium ions, four sulfates, and four additional solvation waters. Both crystallography and EPR find that the doped copper replaces the cadmium in the structure. Single-crystal EPR measurements at room temperature determined the g and copper hyperfine (A Cu ) tensors (principal values: g = 2.437, 2.134, and 2.080 and A Cu = -327, -84.8, and 7.33 MHz). EPR spectra of the powder at room temperature gave g = 2.448, 2.125, and 2.085 and A Cu = -315, -75.0, and 35.0 MHz and at 110 K gave g = 2.462, 2.116, and 2.077 and A Cu = -340, -30.0, and 35.0 MHz. The room-temperature tensors are close to the "rigid lattice limit" values found in copper-doped Tutton salts but with a higher gmin and weaker A Cu x coupling than average. A small but measurable temperature dependency of the tensors indicated the presence of a dynamic Jahn-Teller (JT) effect. In addition, the EPR line width changed dramatically with temperature, which is like that found in all copper-doped Tutton crystals. Utilizing the model of Silver-Getz for the g-value variation gave an estimate for the energy difference (δ 12 = 640 cm -1 ) between the ground and next highest JT configurations. An empirical correlation appears to exist between δ 12 and g min and A Cu x for the copper hexahydrates studied in similar crystals. Finally, this suggests a relationship between the amount of unpaired spins in the copper d-orbital x lobe and the gap between wells of the adiabatic potential surface.

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

Jacobian sparsity detection using Bloom filters

Determining Jacobian sparsity structure is an important step in the efficient computation of sparse Jacobians. We introduce a new method for determining Jacobian sparsity patterns by combining bit vector probing with Bloom filters. In conclusion, we further refine Bloom filter probing by combining it with hierarchical probing to yield a highly effective strategy for Jacobian sparsity pattern determination.

Bloom filter↗
DOE OSTI2026

First CLAS12 Double-Pion (Npp) Electroproduction Analysis

The N* program aims to explore strong interaction dynamics of the three-valence quark distance-dependent structure. The electroproduction and photoproduction studies provide insight into the nucleon resonance structure. One of the primary objectives of N* is to extract the electroexcitation amplitudes, which are crucial in determining the inner structure of various nucleon excitation states and their underlying degrees of freedom. Studying them on the nucleon length scale reveals also parts of the complex nature of the universe and its origin at their most fundamental level. The extraction of these amplitudes is mostly based on the single-pion, and particularly at higher invariant masses W, on the double-pion electroproduction channels, because nucleon resonance dominantly couple to them. CLAS has produced mostly all of the world data on charged double-pion electroproduction in the nucleon resonance region for photon virtualities Q2 up to 5 GeV2. The kinematic range can be extended with CLAS12, which can explore these amplitudes in the still almost unexplored range of Q2 > 5.0 GeV2. This will offer opportunities to understand the resonance structure at distances where the three-bound quark degree of freedom dominates and pave the way towards perturbative Quantum Chromodynamics (pQCD). This dissertation presents new double-pion electroproduction cross sections in the W range [1.4, 2.10] GeV and the Q2 range [2.0, 8.0] GeV2, using the Run Group A Fall-2018 dataset. This data was taken with the CLAS12 detector in Hall B at Thomas Jefferson National Laboratory (JLab) at an electron beam energy of 10.6 GeV. These cross sections are the basis for the extraction of resonance electroexcitation amplitudes using the phenomenological JLab- Moscow State University (JM) model.

Neupane, Krishna↗
DOE OSTI2021

Structure of ice confined in silica nanopores

Observed anomalous thermodynamic properties of confined water such as deviations in the melting point and freezing point motivate the determination of the structure of confined water as a function of pore size and temperature. Here, we investigate the dynamic evolution of the structure of confined ice in SBA-15 porous materials with pore diameters of 4 nm, 6 nm, and 8 nm at temperatures ranging from 183 K to 300 K using in operando Wide-Angle X-Ray Scattering (WAXS) measurements, X-Ray Partial Distribution Function (PDF) measurements, and classical Molecular Dynamics (MD) simulations. Formation of hexagonal ice structures is noted in all the three pore sizes. In silica nanopores with diameters of 4 nm, cubic ice formation is noted in addition to hexagonal ice. Longer lasting hydrogen bonds and longer residence times of the water molecules in the first coordination shell contribute to observed crystalline organization of ice in confinement. Self-diffusion coefficients of confined liquid water, predicted from classical MD simulations, are four orders of magnitude higher compared to ice formed in confinement. These experimental and simulation results provide comprehensive insights underlying the organization of confined water and ice in silica nanopores and the underlying physico-chemical interactions that contribute to the observed structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗