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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 901 records · Page 50
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Two datasets are better than one: method of double moments for 3D reconstruction in cryo-EM

Cryo-electron microscopy is a powerful imaging technique for reconstructing three-dimensional molecular structures from noisy tomographic projection images of randomly oriented particles. We introduce a new data fusion framework, termed the method of double moments, which reconstructs molecular structures from two instances of the second-order moment of projection images obtained under distinct orientation distributions: one uniform, the other non-uniform and unknown. We prove that these moments generically uniquely determine the underlying structure, up to a global rotation and reflection, and we develop a convex-relaxation-based algorithm that achieves accurate recovery using only second-order statistics. Our results demonstrate the advantage of collecting and modeling multiple datasets under different experimental conditions, illustrating that leveraging dataset diversity can substantially enhance reconstruction quality in computational imaging tasks.

Kam’s method↗
DOE OSTI2024

Enabling Ultralow Volume Analysis with a High-Resolution Ion Mobility Mass Spectrometry Platform

Of all the molecules thought to exist in the universe, it is estimated that researchers only know the chemical structures of 5% of them. Identifying the chemical structures of the remaining 95% has proven extremely challenging because many molecules exhibit low abundance, are contained in small volumes (e.g., <10 nL), do not readily ionize, exhibit similar structures to other molecules, etc. No single analytical technique exists to definitively identify the structure of an unknown molecule, and thus multiple different molecular measurements are typically made (i.e., multi-modal approach). Ion mobility (IMS) and mass spectrometry (MS) are two key tools that researchers use to determine the chemical structures of unknown molecules, and recently high-resolution and ultrahigh resolution IMS-MS instruments have provided greater confidence than ever before. However, HR-IMS-MS instruments typically exhibit low ion utilization efficiency, meaning they require large amounts of sample for an analysis (e.g., >10 µL). Unfortunately, this limitation prohibits the analysis of small volume samples where many unknown molecules exist. Described herein are the efforts made to enable the analysis of ultralow volumes with an HR-IMS-MS platform. A new scanning technique, termed a ‘stuttered traveling wave scan’, was developed as a replacement for the dual-gated scanning technique and works by halting the traveling waves after allowing ions to separate and then repeatedly restarting and stopping the traveling waves to incrementally move ions from the SLIM to the Orbitrap. Ions were stored inside the SLIM while the TWs were stopped, allowing the Orbitrap to perform high-resolution mass analysis. When the Orbitrap was ready, the TWs were restarted for short periods of time (<10 ms) to move ions from the SLIM to the Orbitrap. It was discovered that lower TW amplitudes and speeds than used during IMS separation were required to produce IMS peaks with the highest signal intensities and best resolving powers. The stuttered TW scan was found to produce similar resolutions and signal intensities compared to the dual-gated scanning technique. A new IMS design possessing an intersecting ‘tee’ with a reversible traveling wave was also developed to improve ion utilization efficiency during cyclic operation, which is necessary when only a single IMS spectrum can be acquired, such as when analyzing ultralow volume samples. The new capabilities described in this report lay the groundwork for acquiring HR-IMS-MS spectra of ultralow volume biological samples, such as single cells, where HR-IMS-MS can help elucidate the structures of unknown compounds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Parsec-scale Properties of Steep- and Flat-spectrum Extragalactic Radio Sources from a VLBA Survey of a Complete North Polar Cap Sample

We observed with the Very Long Baseline Array (VLBA) at 2.3 and 8.6 GHz a complete flux-density-limited sample of 482 radio sources with decl. > +75° brighter than 200 mJy at 1.4 GHz drawn from the NVSS catalog. A total of 34% of the sources show parsec-scale emission above the flux density detection limit of 30 mJy; their accurate positions and parsec-scale structure parameters are determined. Among all the sources detected at least at the shortest VLBA baselines, the majority, or 72%, have a steep single-dish spectrum. The fraction of the sources with a detectable parsec-scale structure is above 95% among the flat-spectrum objects and close to 25% among the steep-spectrum objects. We identified 82 compact steep-spectrum source candidates, which make up 17% of the sample; most of them are reported for the first time. The compactness and the brightness temperature of the sources in our sample show a positive correlation with single-dish and VLBA spectral indices. All the sources with a significant 8 GHz variability were detected by the VLBA snapshot observations, which independently confirmed their compactness. We demonstrated that 54% of the sources detected by the VLBA at 2.3 GHz in our sample have a steep VLBA spectrum. The compact radio emission of these sources is likely dominated by optically thin jets or mini-lobes, not by an opaque jet core. These results show that future VLBI surveys aimed at searching for new sources with parsec-scale structure should include not only flat-spectrum sources but also steep-spectrum ones in order to reach an acceptable level of completeness.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Forest structure and solar-induced fluorescence across intact and degraded forests in the Amazon

Tropical forest degradation (e.g., anthropogenic disturbances such as selective logging and fires) alters forest structure and function and influences the forest's carbon sink. In this study, we explored structure-function relationships across a variety of degradation levels in the southern Brazilian Amazon by 1) investigating how forest structural properties vary as a function of degradation history using airborne lidar data; 2) assessing the effects of degradation on solar-induced chlorophyll fluorescence (SIF) seasonality using TROPOMI data; and 3) quantifying the contribution of structural variables to SIF using multiple regression models with stepwise selection of lidar metrics. Forest degradation history was obtained through Landsat time-series classification. We found that fire, logging, and time since disturbance were major determinants of forest structure, and that forests affected by fires experienced larger variability in leaf area index (LAI), canopy height and vertical structure relative to logged and intact forests. Moreover, only recently burned forests showed significantly depressed SIF during the dry season compared to intact forests. Canopy height and the vertical distribution of foliage were the best predictors of SIF. Unexpectedly, we found that wet-season SIF was higher in active regenerating forests (~ 4 years after fires or logging) compared with intact forests, despite lower LAI. Furthermore, our findings help to elucidate the mechanisms of carbon accumulation in anthropogenically disturbed tropical forests and indicate that they can capture large amounts of carbon while recovering.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Structural adaptation of oxygen tolerance in 4-hydroxybutyrl-CoA dehydratase, a key enzyme of archaeal carbon fixation

Abstract Autotrophic microorganisms that convert inorganic carbon into organic matter were key players in the evolution of life on Earth. As the early atmosphere became oxygenated, microorganisms needed to develop mechanisms for oxygen protection, especially those relying on enzymes containing oxygen-sensitive metal clusters (e.g., Fe-S). Here we investigated how 4-hydroxybutyryl-CoA dehydratase (4HBD) - the key enzyme of the 3-hydroxypropionate/4-hydroxybutyrate (HP/HB) cycle for CO 2 -fixation - adapted as conditions shifted from anoxic to oxic. 4HBD is found in both anaerobic bacteria and aerobic ammonia-oxidizing archaea (AOA). The oxygen-sensitive bacterial 4HBD and oxygen-tolerant archaeal 4HBD share 59 % amino acid identity. To examine the structural basis of oxygen tolerance in archaeal 4HBD, we determined the atomic resolution structure of the enzyme. Two tunnels providing access to the canonical [4Fe-4S] cluster in oxygen-sensitive bacterial 4HBD were closed with four conserved mutations found in all aerobic AOA and other archaea. Further biochemical experiments and molecular dynamics simulations support our findings that restricting access to the active site is the key to oxygen tolerance, explaining how active site evolution drove a major evolutionary transition. Significance statement Autotrophy (primary production) was the first life strategy on Earth. Before photosynthesis (using solar energy to fix carbon dioxide), life relied on chemical reactions for energy. These chemosynthetic reactions are present in all domains of life, including archaea possessing the most energy-efficient carbon fixation pathway - the 3-hydroxypropionate/4-hydroxybutyrate cycle. This efficiency results from enzyme modifications, including enhanced enzyme stability and catalysis of multiple reactions. We reveal the first structure of aerobic 4-hydroxybutyryl-CoA dehydratase (4HBD) from ammonia-oxidizing archaea. These archaea are among the most abundant organisms on the planet, and their 4HBD active site evolved oxygen tolerance to support aerobic metabolism. This modification can provide further insight into enzyme evolution on early earth, as photosynthesis developed and began oxygenating the atmosphere.

DeMirci, Hasan (ORCID:0000000291355397)↗
DOE OSTI2023

Recognition of centromere‐specific histone Cse4 by the inner kinetochore Okp1‐Ame1 complex

Abstract Successful mitosis depends on the timely establishment of correct chromosomal attachments to microtubules. The kinetochore, a modular multiprotein complex, mediates this connection by recognizing specialized chromatin containing a histone H3 variant called Cse4 in budding yeast and CENP‐A in vertebrates. Structural features of the kinetochore that enable discrimination between Cse4/CENP‐A and H3 have been identified in several species. How and when these contribute to centromere recognition and how they relate to the overall structure of the inner kinetochore are unsettled questions. More generally, this molecular recognition ensures that only one kinetochore is built on each chromatid and that this happens at the right place on the chromatin fiber. We have determined the crystal structure of a Cse4 peptide bound to the essential inner kinetochore Okp1‐Ame1 heterodimer from budding yeast. The structure and related experiments show in detail an essential point of Cse4 contact and provide information about the arrangement of the inner kinetochore.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Lattice Design and Advanced Modeling to Guide the Design of High-Performance Lightweight Structural Materials

Lightweight structural materials are required to increase the mobility of fission batteries. The materials must feature a robust combination of mechanical properties to demonstrate structural resilience. The primary objective of this project is to produce lightweight structural materials whose strength-to-weight ratios exceed those of the current widely used structural materials such as 316L stainless steels (316L SS). To achieve this, advanced modeling and simulation tools were employed to design lattice structures with different lattice parameters and different lattice types. A process was successfully developed for transforming lattice-structures models into Multiphysics Object Oriented Simulation Environment (MOOSE) inputs. Finite element modeling (FEM) was used to simulate the uniaxial tensile testing of the lattice-structured parts to investigate the stress distribution at a given displacement. The preliminary results showed that the lattice-structured sample displayed a lower Young’s modulus in comparison with the solid material and that the unit cell size of the lattice had a minimal effect. The novelty here is to apply up-front modeling to determine the best structure for the application before actually producing the sample. The approach of using modeling as a guiding tool for preliminary material design can significantly save time and cost for material development.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Crystal structures reveal catalytic and regulatory mechanisms of the dual-specificity ubiquitin/FAT10 E1 enzyme Uba6

The E1 enzyme Uba6 initiates signal transduction by activating ubiquitin and the ubiquitin-like protein FAT10 in a two-step process involving sequential catalysis of adenylation and thioester bond formation. To gain mechanistic insights into these processes, we determined the crystal structure of a human Uba6/ubiquitin complex. Two distinct architectures of the complex are observed: one in which Uba6 adopts an open conformation with the active site configured for catalysis of adenylation, and a second drastically different closed conformation in which the adenylation active site is disassembled and reconfigured for catalysis of thioester bond formation. Surprisingly, an inositol hexakisphosphate (InsP6) molecule binds to a previously unidentified allosteric site on Uba6. Our structural, biochemical, and biophysical data indicate that InsP6 allosterically inhibits Uba6 activity by altering interconversion of the open and closed conformations of Uba6 while also enhancing its stability. In addition to revealing the molecular mechanisms of catalysis by Uba6 and allosteric regulation of its activities, our structures provide a framework for developing Uba6-specific inhibitors and raise the possibility of allosteric regulation of other E1s by naturally occurring cellular metabolites.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Atomic structure and Mott nature of the insulating charge density wave phase of 1T-TaS 2

Here, using x-ray pair distribution function (PDF) analysis and computer modeling, we explore structure models for the complex charge density wave (CDW) phases of layered 1T-TaS 2 that both well capture their atomic-level features and are amenable to electronic structure calculations. The models give the most probable position of constituent atoms in terms of 3D repetitive unit cells comprising a minimum number of Ta–S layers. Structure modeling results confirm the emergence of star-of-David (SD) like clusters of Ta atoms in the high-temperature incommensurate (IC) CDW phase and show that, contrary to the suggestions of recent studies, the low-temperature commensurate (C) CDW phase expands upon cooling thus reducing lattice strain. The C-CDW phase is also found to preserve the stacking sequence of Ta–S layers found in the room temperature, nearly commensurate (NC) CDW phase to a large extent. DFT based on the PDF refined model shows that bulk C-CDW 1T-TaS 2 also preserves the insulating state of individual layers of SD clusters, favoring the Mott physics description of the metal-to-insulator (NC-CDW to C-CDW) phase transition in 1T-TaS 2 . Our work highlights the importance of using precise crystal structure models in determining the nature of electronic phases in complex materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Magnetic structure and resistivity minimum in GdCuAs 2

The electrical resistivity of GdCuAs 2 single crystals exhibits an anomalous Kondo-like resistivity minimum above the antiferromagnetic ordering temperature T N 1 approximate to 10.6 K, which is unusual for a highly localized 4f-moment (Gd 3+ ) system. Using x-ray resonant magnetic scattering, we determined the magnetic structure of GdCuAs 2 , where Gd moments are antiferromagnetically aligned along the crystallographic a axis and in the (+ + --) arrangement in the c direction and ferromagnetically arranged in the b direction. The antiferromagnetic order appears first at q = (δ, 0, 0.5) below 10 K, with an incommensurate modulation along the a axis and locks into a commensurate position at q = (1/3, 0, 0.5) below T N 2 approximate to 6 K. Our high-resolution x-ray diffraction measurements show a two-peak structure at Q = (2, 0, 6) above the resistivity minimum, suggesting a lower-symmetry crystal structure than the reported tetragonal structure, and the Q = (2, 0, 6) peak becomes a sharp one-peak structure below the resistivity minimum, implying a magnetoelastic coupling above T N . In conclusion, our findings suggest a complex interplay between the crystal structure and antiferromagnetic structure through a magnetoelastic coupling, associated with the anomalous resistivity minimum above T N 1 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Influence of topology optimization parameters on the mechanical response of an additively manufactured test structure

Topology Optimization (TO) determines a material distribution within a domain under given conditions and design constraints, and generally generates complex geometries as a result. Complementary to TO, Additive Manufacturing (AM) offers the ability to fabricate complex geometries which may be difficult to manufacture using traditional techniques such as milling. AM has been used in multiple industries including the medical devices area. Hence, TO may be used to create patient-matched devices where the mechanical response is catered to a particular patient. Furthermore, during a medical device regulatory 510(k) pathway, demonstrating that worst-cases are known and tested is critical to the review process. Using TO and AM to predict worst-case designs for subsequent performance testing may be challenging and does not appear to have been thoroughly explored. Investigating the effects of TO input parameters when AM is employed may be the first step in determining the feasibility of predicting these worst-cases.

36 MATERIALS SCIENCE↗
DOE OSTI2020

The crystal structures of Fe-bearing MgCO 3 sp 2 - and sp 3 -carbonates at 98 GPa from single-crystal X-ray diffraction using synchrotron radiation

The crystal structure of MgCO 3 -II has long been discussed in the literature where DFT-based model calculations predict a pressure-induced transition of the carbon atom from the sp 2 to the sp 3 type of bonding. We have now determined the crystal structure of iron-bearing MgCO 3 -II based on single-crystal X-ray diffraction measurements using synchrotron radiation. We laser-heated a synthetic (Mg 0.85 Fe 0.15 )CO 3 single crystal at 2500 K and 98 GPa and observed the formation of a monoclinic phase with composition (Mg 2.53 Fe 0.47 )C 3 O 9 in the space group C 2/ m that contains tetrahedrally coordinated carbon, where CO 4 4- tetrahedra are linked by corner-sharing oxygen atoms to form three-membered C 3 O 9 6- ring anions. The crystal structure of (Mg 0.85 Fe 0.15 )CO 3 (magnesium iron carbonate) at 98 GPa and 300 K is reported here as well. In comparison with previous structure-prediction calculations and powder X-ray diffraction data, our structural data provide reliable information from experiments regarding atomic positions, bond lengths, and bond angles.

Chariton, Stella (ORCID:0000000155220498)↗
DOE OSTI2022

Crystal Structure of CYP3A4 Complexed with Fluorol Identifies the Substrate Access Channel as a High-Affinity Ligand Binding Site

Cytochrome P450 3A4 (CYP3A4) is a major human drug-metabolizing enzyme, notoriously known for its extreme substrate promiscuity, allosteric behavior, and implications in drug–drug interactions. Despite extensive investigations, the mechanism of ligand binding to CYP3A4 is not fully understood. We determined the crystal structure of CYP3A4 complexed with fluorol, a small fluorescent dye that can undergo hydroxylation. In the structure, fluorol associates to the substrate channel, well suited for the binding of planar polyaromatic molecules bearing polar groups, through which stabilizing H-bonds with the polar channel residues, such as Thr224 and Arg372, can be established. Mutagenesis, spectral, kinetic, and functional data confirmed the involvement but not strict requirement of Thr224 for the association of fluorol. Collectively, our data identify the substrate channel as a high-affinity ligand binding site and support the notion that hydrophobic ligands first dock to the nearby peripheral surface, before migrating to the channel and, subsequently, into the active site.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structure of the antenna complex expressed during far-red light photoacclimation in Synechococcus sp. PCC 7335

Far-red light photoacclimation, or FaRLiP, is a facultative response exhibited by some cyanobacteria that allows them to absorb and utilize lower energy light (700–800 nm) than the wavelengths typically used for oxygenic photosynthesis (400–700 nm). During this process, three essential components of the photosynthetic apparatus are altered: photosystem I, photosystem II, and the phycobilisome. In all three cases, at least some of the chromophores found in these pigment–protein complexes are replaced by chromophores that have red-shifted absorbance relative to the analogous complexes produced in visible light. Recent structural and spectroscopic studies have elucidated important features of the two photosystems when altered to absorb and utilize far-red light, but much less is understood about the modified phycobiliproteins made during FaRLiP. We used single-particle, cryo-EM to determine the molecular structure of a phycobiliprotein core complex comprising allophycocyanin variants that absorb far-red light during FaRLiP in the marine cyanobacterium Synechococcus sp. PCC 7335. The structure reveals the arrangement of the numerous red-shifted allophycocyanin variants and the probable locations of the chromophores that serve as the terminal emitters in this complex. It also suggests how energy is transferred to the photosystem II complexes produced during FaRLiP. The structure additionally allows comparisons with other previously studied allophycocyanins to gain insights into how phycocyanobilin chromophores can be tuned to absorb far-red light. These studies provide new insights into how far-red light is harvested and utilized during FaRLiP, a widespread cyanobacterial photoacclimation mechanism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Nanometer Resolution Structure‐Emission Correlation of Individual Quantum Emitters via Enhanced Cathodoluminescence in Twisted Hexagonal Boron Nitride

Understanding the atomic structure of quantum emitters, often originating from point defects or impuritie, is essential for designing and optimizing materials for quantum technologies such as quantum computing, communication, and sensing. Despite the availability of atomic-resolution scanning transmission electron microscopy and nanoscale cathodoluminescence microscopy, experimentally determining the atomic structure of individual emitters is challenging due to the conflicting needs for thick samples to generate strong cathodoluminescence signals and thin samples for structural analysis. To overcome this challenge, significantly enhanced cathodoluminescence at twisted interfaces is leveraged to achieve sub-nanometer localization precision for the first time in mapping individual quantum emitters in carbon-implanted hexagonal boron nitride. This unprecedent spatial sensitivity, together with correlative electron energy loss spectroscopy quantitative scanning transmission electron microscopy imaging, and first principles density functional theory calculations, enables the identification of the atomic structure of the 440 nm blue emitter in hexagonal boron nitride as a substituted vertical carbon dimer. Building on the atomic structure insights, nanoscale spatially precise creation of blue emitters is demonstrated by electron beam irradiation of carbon-coated hexagonal boron nitride. This advancement in correlating atomic structures with optical properties lays the foundation for a deeper understanding and precise engineering of quantum emitters, significantly advancing the development of cutting-edge quantum information technologies.

2D material↗
DOE OSTI2023

Crystal structure of the kinase domain of a receptor tyrosine kinase from a choanoflagellate, Monosiga brevicollis

Genomic analysis of the unicellular choanoflagellate, Monosiga brevicollis (MB), revealed the remarkable presence of cell signaling and adhesion protein domains that are characteristically associated with metazoans. Strikingly, receptor tyrosine kinases, one of the most critical elements of signal transduction and communication in metazoans, are present in choanoflagellates. We determined the crystal structure at 1.95 Å resolution of the kinase domain of the M . brevicollis receptor tyrosine kinase C8 (RTKC8, a member of the choanoflagellate receptor tyrosine kinase C family) bound to the kinase inhibitor staurospaurine. The chonanoflagellate kinase domain is closely related in sequence to mammalian tyrosine kinases (~ 40% sequence identity to the human Ephrin kinase domain EphA3) and, as expected, has the canonical protein kinase fold. The kinase is structurally most similar to human Ephrin (EphA5), even though the extracellular sensor domain is completely different from that of Ephrin. The RTKC8 kinase domain is in an active conformation, with two staurosporine molecules bound to the kinase, one at the active site and another at the peptide-substrate binding site. To our knowledge this is the first example of staurospaurine binding in the Aurora A activation segment (AAS). We also show that the RTKC8 kinase domain can phosphorylate tyrosine residues in peptides from its C-terminal tail segment which is presumably the mechanism by which it transmits the extracellular stimuli to alter cellular function.

59 BASIC BIOLOGICAL SCIENCES↗