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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 1,117 records · Page 62
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

A Frequency Domain Methodology for Quantitative Evaluation of Diffuse Wavefield With Applications to Seismic Imaging

Abstract Ambient Noise Imaging (ANI) of subsurface structures relies on seismic interferometry of diffuse seismic wavefields. However, the lack of effective methods to quantify and identify highly diffuse waves hampers applications of ANI, particularly in evaluating seismic attenuation and monitoring structural changes with high temporal resolution. Conventional ANI approaches require data normalization, which effectively suppresses the non‐diffuse component with large amplitude but also results in significant loss of amplitude and phase information in the continuous seismic records. In this study, we propose a frequency domain method to quantitatively evaluate the degree of diffuseness of seismic wavefields by analyzing their statistical characteristics of modal amplitudes for stationarity and randomness. Tests on synthetic waveform and field nodal records show that the proposed method can effectively distinguish between diffuse and non‐diffuse waveforms for either single‐ or three‐component data. As an application, we identify a 60‐s‐long diffuse coda of a local M 2.2 earthquake recorded by a dense nodal array on the San Jacinto Fault Zone, and successfully extract high‐quality dispersion curve andQ‐value without performing data normalization. These results are consistent with those obtained by conventional methods that assess the correlation between coherency and the Green's function, and by modeling ballistic waves generated by road traffic. Our proposed method can advance the imaging of subsurface velocity and attenuation structures as well as monitoring temporal changes for scientific studies and engineering applications.

Geochemistry & Geophysics↗
DOE OSTI2023

Architecture of the human G-protein-methylmalonyl-CoA mutase nanoassembly for B 12 delivery and repair

G-proteins function as molecular switches to power cofactor translocation and confer fidelity in metal trafficking. The G-protein, MMAA, together with MMAB, an adenosyltransferase, orchestrate cofactor delivery and repair of B 12 -dependent human methylmalonyl-CoA mutase (MMUT). The mechanism by which the complex assembles and moves a >1300 Da cargo, or fails in disease, are poorly understood. Herein, we report the crystal structure of the human MMUT-MMAA nano-assembly, which reveals a dramatic 180° rotation of the B 12 domain, exposing it to solvent. The complex, stabilized by MMAA wedging between two MMUT domains, leads to ordering of the switch I and III loops, revealing the molecular basis of mutase-dependent GTPase activation. The structure explains the biochemical penalties incurred by methylmalonic aciduria-causing mutations that reside at the MMAA-MMUT interfaces we identify here.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

3D imaging of magnetic domains in Nd 2 Fe 14 B using scanning hard X-ray nanotomography

Nanoscale structural and electronic heterogeneities are prevalent in condensed matter physics. Investigating these heterogeneities in 3D has become an important task for understanding material properties. To provide a tool to unravel the connection between nanoscale heterogeneity and macroscopic emergent properties in magnetic materials, scanning transmission X-ray microscopy (STXM) is combined with X-ray magnetic circular dichroism. A vector tomography algorithm has been developed to reconstruct the full 3D magnetic vector field without any prior noise assumptions or knowledge about the sample. Two tomographic scans around the vertical axis are acquired on single-crystalline Nd 2 Fe 14 B pillars tilted at two different angles, with 2D STXM projections recorded using a focused 120 nm X-ray beam with left and right circular polarization. Image alignment and iterative registration have been implemented based on the 2D STXM projections for the two tilts. Dichroic projections obtained from difference images are used for the tomographic reconstruction to obtain the 3D magnetization distribution at the nanoscale.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Cryo-EM structure of AAV2 Rep68 bound to integration site AAVS1: insights into the mechanism of DNA melting

Abstract The Rep68 protein from Adeno-Associated Virus (AAV) is a multifunctional SF3 helicase that performs most of the DNA transactions necessary for the viral life cycle. During AAV DNA replication, Rep68 assembles at the origin of replication, catalyzing the DNA melting and nicking reactions during the hairpin rolling replication process to complete the second-strand synthesis of the AAV genome. We report the cryo-electron microscopy structures of Rep68 bound to the adeno-associated virus integration site 1 in different nucleotide-bound states. In the nucleotide-free state, Rep68 forms a heptameric complex around DNA, with three origin-binding domains (OBDs) bound to the Rep-binding element sequence, while three remaining OBDs form transient dimers with them. The AAA+ domains form an open ring without interactions between subunits and DNA. We hypothesize that the heptameric structure is crucial for loading Rep68 onto double-stranded DNA. The ATPγS complex shows that only three subunits associate with the nucleotide, leading to a conformational change that promotes the formation of both intersubunit and DNA interactions. Moreover, three phenylalanine residues in the AAA+ domain induce a steric distortion in the DNA. Our study provides insights into how an SF3 helicase assembles on DNA and provides insights into the DNA melting process.

Jaiswal, Rahul↗
DOE OSTI2024

Revealing Mesoscale Ionomer Membrane Structure by Tender Resonant X-ray Scattering

Nafion, a perfluorosulfonic acid ionomer, has been well-studied for decades due to its key role as an ion-conductive membrane in electrochemical energy conversion and storage applications. When hydrated, this membrane phase separates into a complex hierarchical nanostructure with hydrophilic domains that facilitate ion transport. Hard X-ray scattering has been a powerful technique in understanding Nafion due to its capabilities in capturing the ionomer’s nanophase separated structure, which gives rise to contrast between polymer and water domains. More recently, resonant X-ray scattering, which tunes to elemental absorption edges to provide specificity on constituent elements, has been explored to highlight key interactions related to the sulfonic acid groups within its structure. Here, in this work, we study the Nafion nanostructure by combining hard X-ray scattering and tender resonant X-ray scattering (TReXS) at the sulfur K-edge to reveal a mesoscopic feature corresponding to a correlation length of approximately 40 nm that has been challenging to resolve with hard X-ray studies. Additionally, we study the effect of the dispersion solvent composition that plays a key role in the formation of this mesoscale feature. Notably, TReXS can attain high contrast to decipher this mesoscale morphology even for dry polymer membranes under a vacuum, which typically have reduced contrast for hard X-rays. We find that the correlation length of this mesoscale feature decreases with increasing water fraction in the dispersion, which is the opposite trend exhibited by the smaller intercrystalline feature in the same membranes. This study showcases the utility of TReXS to uncover multiscale morphological details in functional polymers that are not always revealed by other methods like hard X-ray scattering. We illustrate this with Nafion, which is a relevant ion-conducting polymer for electrochemical technologies.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Structure and Antigenicity of the Porcine Astrovirus 4 Capsid Spike

Porcine astrovirus 4 (PoAstV4) has been recently associated with respiratory disease in pigs. In order to understand the scope of PoAstV4 infections and to support the development of a vaccine to combat PoAstV4 disease in pigs, we designed and produced a recombinant PoAstV4 capsid spike protein for use as an antigen in serological assays and for potential future use as a vaccine antigen. Structural prediction of the full-length PoAstV4 capsid protein guided the design of the recombinant PoAstV4 capsid spike domain expression plasmid. The recombinant PoAstV4 capsid spike was expressed in Escherichia coli, purified by affinity and size-exclusion chromatography, and its crystal structure was determined at 1.85 Å resolution, enabling structural comparisons to other animal and human astrovirus capsid spike structures. The recombinant PoAstV4 capsid spike protein was also used as an antigen for the successful development of a serological assay to detect PoAstV4 antibodies, demonstrating that the recombinant PoAstV4 capsid spike retains antigenic epitopes found on the native PoAstV4 capsid. These studies lay a foundation for seroprevalence studies and the development of a PoAstV4 vaccine for swine.

Virology↗
DOE OSTI2024

Precise Modulation of CO 2 Sorption in Ti 8 Ce 2 –Oxo Clusters: Elucidating Lewis Acidity of the Ce Metal Sites and Structural Flexibility

Investigating the structure-property correlation in porous materials is a fundamental and consistent focus in various scientific domains, especially within sorption research. Metal oxide clusters with capping ligands, characterized by intrinsic cavities formed through specific solid-state packing, demonstrate significant potential as versatile platforms for sorption investigations due to their precisely tunable atomic structures and inherent long-range order. This study presents a series of Ti 8 Ce 2 -oxo clusters with subtle variations in coordinated linkers and explores their sorption behavior. Notably, Ti 8 Ce 2 -BA (BA denotes benzoic acid) manifests a distinctive two-step profile during CO 2 adsorption, accompanied by a hysteresis loop. This observation marks a new instance within the metal oxide cluster field. Of intrigue, the presence of unsaturated Ce(IV) sites was found to be correlated with the stepped sorption property. Moreover, the introduction of an electrophilic fluorine atom, positioned ortho or para to the benzoic acid, facilitated precise control over gate pressure and stepped sorption quantities. Advanced in-situ techniques systematically unraveled the underlying mechanism behind this unique sorption behavior. The findings elucidate that robust Lewis base-acid interactions are established between CO 2 molecules and Ce ions, consequently altering the conformation of coordinated linkers. Conversely, the F atoms primarily contribute to gate pressure variation by influencing the Lewis acidity of the Ce sites. This research advances the understanding in fabricating metal-oxo clusters with structural flexibility and provides profound insights into their host-guest interaction motifs. Furthermore, these insights hold substantial promise across diverse fields and offer valuable guidance for future adsorbent designs grounded in fundamental theories of structure-property relationships.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Primordial black hole dark matter: A quantitative parameter sensitivity comparison across formation mechanisms and particle candidates

Primordial black holes (PBHs) in the asteroid-mass window ( 10 17 – 10 22 g ) can account for all of the dark matter without violating any observational constraint, yet are routinely dismissed as fine-tuned. I put that dismissal to the test by applying three complementary sensitivity measures uniformly across a broad landscape: three noninflationary PBH production mechanisms, six classes of inflationary PBH models, and seven particle dark matter benchmarks, all evaluated against the same observable target. Three distinct naturalness universality classes emerge, determined entirely by the analytic structure of the abundance map rather than by the nature of the dark matter candidate. Biased-domain-wall PBHs, in their least model-dependent (free- V b ) form, have the same low sensitivity, Δ = 4.5 , as off-resonance weakly interacting massive particles and freeze-in particles ( Δ = 2 ), a sensitivity that, because it is constant over the entire parameter space of the construction, also coincides trivially with its own Wilson-normalized average within that parameter space (Section Definition and conventions), an equivalence that concerns only the space over which Δ is computed and is not a naturalness statement about the construction as a whole; a further reduction to Δ = 2 is possible only under the additional, independently motivated but not required, assumption that the domain-wall bias is generated by Planck-suppressed operators; early matter-domination PBHs occupy an intermediate tier alongside coannihilating weakly interacting massive particles (WIMPs), unified by a structural identity in which the sensitivity measure equals the logarithm of the ratio of the formation scale to the matter–radiation equality scale; first-order phase transition PBHs, once the more accurate super-exponential collapse probability is used in place of the single-exponential approximation, instead belong to the same highly sensitive tier as resonant WIMP annihilation and single-field inflationary collapse, for a structurally distinct reason; single-field ultraslow-roll inflationary collapse is severely tuned for a distinct reason: a double exponential in which the power spectrum amplitude is itself exponentially sensitive to the inflaton potential coefficients, on top of the exponential collapse sensitivity of the abundance map. My main conclusion is that the claim that PBH dark matter is generically fine-tuned conflates the worst case with a landscape spanning every naturalness tier. The Barbieri-Giudice sensitivity computed here and the Wilson-normalized measure of Iovino and Riotto answer distinct and mutually consistent questions about the same construction, a distinction I clarify within the two-layer decomposition.

Profumo, Stefano [University of California, Santa ↗
DOE OSTI2022

Competing magnetic and nonmagnetic states in monolayer VSe 2 with charge density wave

The field of two-dimensional ferromagnets has been reinvigorated by the discovery of VSe 2 monolayer grown on van der Waals substrates, which is reported to be ferromagnetic with a Curie point higher than 330 K. However, the ferromagnetic and nonmagnetic states of pristine monolayer VSe 2 are highly debated. Here, employing density functional theory, Wannier function calculations, and the band unfolding method, we explore the electronic structure of monolayer VSe 2 with a $\sqrt{3} × \sqrt{7}$ charge density wave (CDW). Certain qualitative aspects of the calculated unfolded band dispersion and unfolded Fermi surface of monolayer VSe 2 with the $\sqrt{3} × \sqrt{7}$ CDW in the nonmagnetic state agree well with previous angle-resolved photoemission spectroscopy results, albeit with uncertainty about whether these experiments probed single or multiple domains. Specifically, we find that an isolated CDW domain naturally induces a strong breaking of the threefold symmetry of the electronic structure. In addition we find that, relative to the undistorted structure, the CDW structure shows a strong competition between nonmagnetic and various magnetic states, with an energy difference less than 5 meV/f.u. For the CDW structure in the antiferromagnetic state, the band dispersions and Fermi surface are similar to those in the nonmagnetic state, while the unfolded bands of the ferromagnetic CDW state display a sizable exchange splitting. These results indicate the possibility of various antiferromagnetic fluctuations in VSe 2 to coexist and compete with ferromagnetic order and the experimentally reported CDW order. In this work, our calculations build insights for exploring the interplay between magnetism and CDW behaviors more generally in transition metal dichalcogenides.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Deconvolution of X-ray natural and magnetic circular dichroism in chiral Dy-ferroborate

Structural chirality and magnetism, when intertwined, can have profound implications on materials properties. Using X-ray imaging and spectroscopic measurements that leverage the natural and magnetic circular dichroic effects present in magnetized chiral crystal structures, we probe the interplay between chirality and magnetism across the field-induced spin-flop transition of Dy ferroborate, DyFe 3 (BO 3 ) 4 . Deconvolution of natural and magnetic circular dichroic signals at the Fe K and Dy L 2,3 absorption edges of the non-centrosymmetric structure was enabled by use of tunable temperature and magnetic field, providing access to element-specific magnetic information across the spin-flop transition. The magnetic response of Fe and Dy sublattices was found to be independent of domain chirality. The chiral domains were robust against both the (chirality preserving) R32 to P3 1 21/P3 2 21 structural phase transition at 280 K, and application of magnetic field up to 4 Tesla. A third flavor of X-ray dichroism, magneto-chiral dichroism, was not detected within the accuracy of our measurements. The absence of significant Fe magnetization along the screw, c-axis for the magnetic field strength used in this study, together with non-linear coupling of magnetic field to electric polarization across the spin-flop transition, may hinder observation of magneto-chiral dichroic effects in this system.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Local atomic structure and Ni nanophase segregation in Zn 1-x Ni x S thin films

Here, the local atomic structure of Zn 1-x Ni x S thin films was investigated using X-ray absorption spectroscopy. The films were grown using RF-sputtering at atomic concentrations x = 0.00, x = 0.04, x = 0.08 and x = 0.14. X-ray diffraction shows that the lattice parameter contracts with increasing Ni concentration, consistent with the smaller atomic radii of Ni compared to that one of Zn. Optical absorption reveals a reduction of the bandgap as Ni concentration increases, except for sample x = 0.14 where a complex behavior is observed. Results from X-ray absorption near edge structure (XANES) spectroscopy indicate a shift in the valence state of Ni for the x = 0.14 sample. The analysis of the extended X-ray absorption fine structure (EXAFS) spectra indicate a contraction of ~0.7 Å in the Ni–S bond distance when compared to the Zn–S bond length, which generates local lattice distortions and an increment of the static disorder as the Ni concentration increases. The EXAFS results for sample x = 0.14 show the presence of a Zn 1-x Ni x S phase and a nanoscopic metallic Ni phase with domain sizes below the diffraction limit. These results reveal that the local atomic structure differs in a significant manner from the average crystalline structure, implying its importance for the determination of the electronic properties of this material.

36 MATERIALS SCIENCE↗
DOE OSTI2023

tRNA shape is an identity element for an archaeal pyrrolysyl-tRNA synthetase from the human gut

Protein translation is orchestrated through tRNA aminoacylation and ribosomal elongation. Among the highly conserved structure of tRNAs, they have distinguishing features which promote interaction with their cognate aminoacyl tRNA synthetase (aaRS). These key features are referred to as identity elements. In our study, we investigated the tRNA:aaRS pair that installs the 22nd amino acid, pyrrolysine (tRNAPyl:PylRS). Pyrrolysyl-tRNA synthetases (PylRSs) are naturally encoded in some archaeal and bacterial genomes to acylate tRNAPyl with pyrrolysine. Their large amino acid binding pocket and poor recognition of the tRNA anticodon have been instrumental in incorporating > 200 noncanonical amino acids. PylRS enzymes can be divided into three classes based on their genomic structure. Two classes contain both an N-terminal and C-terminal domain, however the third class (ΔpylSn) lacks the N-terminal domain. In this study we explored the tRNA identity elements for a ΔpylSn tRNAPyl from Candidatus Methanomethylophilus alvus which drives the orthogonality seen with its cognate PylRS (MaPylRS). From aminoacylation and translation assays we identified five key elements in ΔpylSn tRNAPyl necessary for MaPylRS activity. The absence of a base (position 8) and a G–U wobble pair (G28:U42) were found to affect the high-resolution structure of the tRNA, while molecular dynamic simulations led us to acknowledge the rigidity imparted from the G–C base pairs (G3:C70 and G5:C68).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers

Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. In this study, we aim to develop a reliable methodology for a rational aptamer in silico et vitro design. The new approach combines multiple steps: (1) Molecular design, based on screening in a DNA aptamer library and directed mutagenesis to fit the protein tertiary structure; (2) 3D molecular modeling of the target; (3) Molecular docking of an aptamer with the protein; (4) Molecular dynamics (MD) simulations of the complexes; (5) Quantum-mechanical (QM) evaluation of the interactions between aptamer and target with further analysis; (6) Experimental verification at each cycle for structure and binding affinity by using small-angle X-ray scattering, cytometry, and fluorescence polarization. By using a new iterative design procedure, structure- and interaction-based drug design (SIBDD), a highly specific aptamer to the receptor-binding domain of the SARS-CoV-2 spike protein, was developed and validated. The SIBDD approach enhances speed of the high-affinity aptamers development from scratch, using a target protein structure. The method could be used to improve existing aptamers for stronger binding. This approach brings to an advanced level the development of novel affinity probes, functional nucleic acids. It offers a blueprint for the straightforward design of targeting molecules for new pathogen agents and emerging variants.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Heterophilic and homophilic cadherin interactions in intestinal intermicrovillar links are species dependent

Enterocytes are specialized epithelial cells lining the luminal surface of the small intestine that build densely packed arrays of microvilli known as brush borders. These microvilli drive nutrient absorption and are arranged in a hexagonal pattern maintained by intermicrovillar links formed by 2 nonclassical members of the cadherin superfamily of calcium-dependent cell adhesion proteins: protocadherin-24 (PCDH24, also known as CDHR2) and the mucin-like protocadherin (CDHR5). The extracellular domains of these proteins are involved in heterophilic and homophilic interactions important for intermicrovillar function, yet the structural determinants of these interactions remain unresolved. Here, we present X-ray crystal structures of the PCDH24 and CDHR5 extracellular tips and analyze their species-specific features relevant for adhesive interactions. In parallel, we use binding assays to identify the PCDH24 and CDHR5 domains involved in both heterophilic and homophilic adhesion for human and mouse proteins. Our results suggest that homophilic and heterophilic interactions involving PCDH24 and CDHR5 are species dependent with unique and distinct minimal adhesive units.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Biased localization of actin binding proteins by actin filament conformation

The assembly of actin filaments into distinct cytoskeletal structures plays a critical role in cell physiology, but how proteins localize differentially to these structures within a shared cytoplasm remains unclear. Here, we show that the actin-binding domains of accessory proteins can be sensitive to filament conformational changes. Using a combination of live cell imaging and in vitro single molecule binding measurements, we show that tandem calponin homology domains (CH1–CH2) can be mutated to preferentially bind actin networks at the front or rear of motile cells. We demonstrate that the binding kinetics of CH1–CH2 domain mutants varies as actin filament conformation is altered by perturbations that include stabilizing drugs and other binding proteins. These findings suggest that conformational changes of actin filaments in cells could help to direct accessory binding proteins to different actin cytoskeletal structures through a biophysical feedback loop.

42 ENGINEERING↗