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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 757 records · Page 42
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Evaluating Effects of Shear Processing on 2D Crystalline Materials in 3D Metal Matrices: Atomistic Understanding of High Shear Deformation of Copper Graphene Composites

Composites made of copper and graphene demonstrate high strength, lubricity and enhanced electrical and thermal conductivity compared pure copper. However, manufacturing these composites at bulk volumes for industrial applications has been a big challenge. Shear deformation assisted processing is an effective method for manufacturing materials such as copper-graphene composites demonstrating ultra-fine grain structures and compositional homogeneity. Nevertheless, microstructural evolution of the composites and their property development under such conditions is not clearly understood currently. To rectify this gap in literature, high strain shear deformation of copper coated graphene foils was performed using a tribometer pin in this study. Changes in microstructure of the composite as well as the constituent components under shear deformation was correlated to process conditions. A sharp increase in the coefficient of friction attributed to rupture and smearing of graphene layer into copper substrate was observed during the shear processing. The coefficient of friction of the sheared copper/graphene composite was lower than that of pure copper, suggesting that partially worn graphene is effectively lubricious at the macroscale. A multimodal characterization of the processed region further revealed a shear deformation-induced ultrafine two-phase grain-structure consisting of copper and graphitic domains. Shear deformation reduced the copper grain size from around 50 – 100 µm to ~200 nm on an average and ~2 – 5 nm in some locations. The semicrystalline graphene films were observed to fracture into 10 – 50 µm size flakes. Oxygen enrichment was observed in the processed region. Finally, graphitic domain were identified for the first time in the copper matrix and not just at the grain boundaries providing evidence for a metastable composite microstructure as a result of solid phase processing at room temperature.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Cyber Physical Subsystems under Adverse Conditions

The United States power grid is built upon complex cyber-physical systems (CPS), including many distributed energy resources (DERs) and microgrid structures. Due to cross-disciplinary domains that govern the interplay between cyber and physical technologies that sustain DERs, it is difficult to confidently predict how these systems will react under adverse conditions such as faults and cyberattacks. This project utilized power hardware in the loop (PHiL) to gain system behavior knowledge and robust understanding through experimentation and observational science. It also produced a large volume of datasets to feed into other efforts to advance high-fidelity model simulations and to support the design of novel control approaches.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2025

Two-Frequency RF Fields Induced Multipactor in Coaxial Transmission Lines

Multipactor is a nonlinear discharge phenomenon that occurs in vacuum RF systems, potentially leading to signal distortion, power loss, and even permanent damage to high-power components. This study presents a detailed investigation of two-surface multipactor in coaxial transmission lines under two-frequency excitation, using one-dimensional (1D) Monte Carlo simulations validated by three-dimensional (3D) Particle-in-Cell (PIC) results and experimental data. Introducing a second carrier mode is shown to suppress multipactor by reshaping and shrinking the susceptibility region, with the extent and location of suppression strongly dependent on the device aspect ratio and the relative phase of the second mode. Distinct suppression patterns emerge across different frequency–gap distance (fd) regimes, and in certain cases, susceptibility expansion is also observed. The study identifies and distinguishes pure and mixed multipactor modes in coaxial geometry, where analytical mode boundaries are not readily defined. Unlike planar systems, pure-mode regions in coaxial structures overlap with mixed-mode domains, complicating classification. Image charge forces are found to have minimal effect on susceptibility thresholds but do influence electron growth rates. These findings provide new insights into waveform-driven control of multipactor in high-power RF systems.

43 PARTICLE ACCELERATORS↗
DOE OSTI2021

Designing alloys with process-mapping AI pre-trained on empirical knowledge

<span style="font-family: Calibri, sans-serif; font-size: 12pt;">Accelerated materials design should match the recent trends in the product development cycles. Materials data analytics can be used to significantly shorten development time of specialized alloys needed for next generation energy applications. However, it faces a challenge of scarce data available for training ML models. Incorporation of the domain knowledge into deep-learning graph structure via fuzzy pre-training and causal process imitation presents a viable approach to developing accurate data-driven models and reliable alloy design tools, with limited datasets. Artificial Intelligence (AI) was used in this study to incorporate such knowledge in the domain-specific computational tool, pyroMind. The tool provides not only novel design ideas but also their interpretation via physics and engineering concepts.</span>

Romanov, Vyacheslav↗
DOE OSTI2020

Hierarchical morphologies in co-sputter deposited thin films

Co-depositions of immiscible alloy films at specific processing conditions have yielded hierarchical microstructures which consist of distinct features at multiple length scales, often agglomerates and concentration modulations on the sub-micrometer-scale and fine nanoprecipitates in a matrix on the nanoscale. The present work examined a series of immiscible alloy systems: Cu-Mo, Cu-Ag, Cu-Fe, Cu-Ta, Mo-Ag, Cu-Mo-Ag, to determine the kinetic conditions favorable for hierarchical organization and the formation mechanism of such structures. Thin films of six immiscible systems were sputter co-deposited over a range of deposition rates from 0.12 to 2 nm/s and various temperatures from 400 to 800°C. The resulting microstructures indicate that hierarchical structures form with sufficient disparity in kinetic energy between the constituent atoms, one species being highly mobile (A) and the other relatively immobile (B). This condition arises typically at elevated deposition temperatures and reduced deposition rates but is also alloy dependent. The hierarchical structures form during deposition via phase separation and self-organization processes across the multiple length scales. The adatoms diffuse on the film surface with the highly mobile species swiftly agglomerating into A-rich domains within which B-rich nanoprecipitates form, often self-organizing into periodic arrays. The smallest B-rich nanoprecipitates in the A-rich domains are found to be coherent and in a metastable crystal structure (B taking the structure of A), but coarser precipitates that exhibit the equilibrium structure of B element. The A-rich domains are surrounded by a B-rich matrix that phase-separates into a concentration modulated structure. In conclusion, the observations are interpreted via a model incorporating material properties and process parameters.

36 MATERIALS SCIENCE↗
DOE OSTI2022

A Surface Exposed, Two-Domain Lipoprotein Cargo of a Type XI Secretion System Promotes Colonization of Host Intestinal Epithelia Expressing Glycans

The only known required component of the newly described Type XI secretion system (TXISS) is an outer membrane protein (OMP) of the DUF560 family. TXISS OMPs are broadly distributed across proteobacteria, but properties of the cargo proteins they secrete are largely unexplored. We report biophysical, histochemical, and phenotypic evidence that Xenorhabdus nematophila NilC is surface exposed. Biophysical data and structure predictions indicate that NilC is a two-domain protein with a C-terminal, 8-stranded β-barrel. This structure has been noted as a common feature of TXISS effectors and may be important for interactions with the TXISS OMP . The NilC N-terminal domain is more enigmatic, but our results indicate it is ordered and forms a β-sheet structure, and bioinformatics suggest structural similarities to carbohydrate-binding proteins. X. nematophila NilC and its presumptive TXISS OMP partner NilB are required for colonizing the anterior intestine of Steinernema carpocapsae nematodes: the receptacle of free-living, infective juveniles and the anterior intestinal cecum (AIC) in juveniles and adults. We show that, in adult nematodes, the AIC expresses a Wheat Germ Agglutinin (WGA)-reactive material, indicating the presence of N-acetylglucosamine or N-acetylneuraminic acid sugars on the AIC surface. A role for this material in colonization is supported by the fact that exogenous addition of WGA can inhibit AIC colonization by X. nematophila. Conversely, the addition of exogenous purified NilC increases the frequency with which X. nematophila is observed at the AIC, demonstrating that abundant extracellular NilC can enhance colonization. NilC may facilitate X. nematophila adherence to the nematode intestinal surface by binding to host glycans, it might support X. nematophila nutrition by cleaving sugars from the host surface, or it might help protect X. nematophila from nematode host immunity. Proteomic and metabolomic analyses of wild type X. nematophila compared to those lacking nilB and nilC revealed differences in cell wall and secreted polysaccharide metabolic pathways. Additionally, purified NilC is capable of binding peptidoglycan, suggesting that periplasmic NilC may interact with the bacterial cell wall. Overall, these findings support a model that NilB-regulated surface exposure of NilC mediates interactions between X. nematophila and host surface glycans during colonization. This is a previously unknown function for a TXISS.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

How Distinct Structural Flexibility within SARS-CoV-2 Spike Protein Reveals Potential Therapeutic Targets

The emergence and rapid worldwide spread of the novel coronavirus disease, COVID-19, has prompted concerted efforts to find successful treatments. The causative virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), uses its spike (S) protein to gain entry into host cells. Therefore, the S protein presents a viable target to develop a directed therapy. Here, we deployed an integrated artificial intelligence with all-atom molecular dynamics simulation approach to provide new details of the S protein structure. Based on a comprehensive structural analysis of S proteins from SARS-CoV-2 and previous human coronaviruses, we found that the protomer state of S proteins is structurally flexible. Without the presence of a stabilizing beta sheet from another protomer chain, two regions in the S2 domain and the hinge connecting the S1 and S2 subunits lose their secondary structures. Interestingly, the region in the S2 domain was previously identified as an immunodominant site in the SARS-CoV-1 S protein. We anticipate that the molecular details elucidated here will assist in effective therapeutic development for COVID-19.

Chen, Serena↗
DOE OSTI2022

An auto-inhibited state of protein kinase G and implications for selective activation

Cyclic GMP-dependent protein kinases (PKGs) are key mediators of the nitric oxide/cyclic guanosine monophosphate (cGMP) signaling pathway that regulates biological functions as diverse as smooth muscle contraction, cardiac function, and axon guidance. Understanding how cGMP differentially triggers mammalian PKG isoforms could lead to new therapeutics that inhibit or activate PKGs, complementing drugs that target nitric oxide synthases and cyclic nucleotide phosphodiesterases in this signaling axis. Alternate splicing of PRKG1 transcripts confers distinct leucine zippers, linkers, and auto-inhibitory (AI) pseudo-substrate sequences to PKG Iα and Iβ that result in isoform-specific activation properties, but the mechanism of enzyme auto-inhibition and its alleviation by cGMP is not well understood. Here, we present a crystal structure of PKG Iβ in which the AI sequence and the cyclic nucleotide-binding (CNB) domains are bound to the catalytic domain, providing a snapshot of the auto-inhibited state. Specific contacts between the PKG Iβ AI sequence and the enzyme active site help explain isoform-specific activation constants and the effects of phosphorylation in the linker. We also present a crystal structure of a PKG I CNB domain with an activating mutation linked to Thoracic Aortic Aneurysms and Dissections. Similarity of this structure to wildtype cGMP-bound domains and differences with the auto-inhibited enzyme provide a mechanistic basis for constitutive activation. We show that PKG Iβ auto-inhibition is mediated by contacts within each monomer of the native full-length dimeric protein, and using the available structural and biochemical data we develop a model for the regulation and cooperative activation of PKGs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

The crystal structure of methanogen McrD , a methyl‐coenzyme M reductase‐associated protein

Methyl‐coenzyme M reductase (MCR) is a multi‐subunit (α 2 β 2 γ 2 ) enzyme responsible for methane formation via its unique F 430 cofactor. The genes responsible for producing MCR ( mcrA , mcrB and mcrG ) are typically colocated with two other highly conserved genes mcrC and mcrD . We present here the high‐resolution crystal structure for McrD from a human gut methanogen Methanomassiliicoccus luminyensis strain B10. The structure reveals that McrD comprises a ferredoxin‐like domain assembled into an α + β barrel‐like dimer with conformational flexibility exhibited by a functional loop. The description of the M. luminyensis McrD crystal structure contributes to our understanding of this key conserved methanogen protein typically responsible for promoting MCR activity and the production of methane, a greenhouse gas.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

The C2 domain augments Ras GTPase-activating protein catalytic activity

Regulation of Ras GTPases by GTPase-activating proteins (GAPs) is essential for their normal signaling. Nine of the ten GAPs for Ras contain a C2 domain immediately proximal to their canonical GAP domain, and in RasGAP (p120GAP, p120RasGAP;RASA1) mutation of this domain is associated with vascular malformations in humans. Here, we show that the C2 domain of RasGAP is required for full catalytic activity toward Ras. Analyses of the RasGAP C2-GAP crystal structure, AlphaFold models, and sequence conservation reveal direct C2 domain interaction with the Ras allosteric lobe. This is achieved by an evolutionarily conserved surface centered around RasGAP residue R707, point mutation of which impairs the catalytic advantage conferred by the C2 domain in vitro. In mice,R707Cmutation phenocopies the vascular and signaling defects resulting from constitutive disruption of theRASA1gene. In SynGAP, mutation of the equivalent conserved C2 domain surface impairs catalytic activity. Our results indicate that the C2 domain is required to achieve full catalytic activity of GAPs for Ras.

Science & Technology - Other Topics↗
DOE OSTI2023

Energy coupling and stoichiometry of Zn 2+ /H + antiport by the prokaryotic cation diffusion facilitator YiiP

YiiP from Shewanella oneidensis is a prokaryotic Zn 2+ /H + antiporter that serves as a model for the Cation Diffusion Facilitator (CDF) superfamily, members of which are generally responsible for homeostasis of transition metal ions. Previous studies of YiiP as well as related CDF transporters have established a homodimeric architecture and the presence of three distinct Zn 2+ binding sites named A, B, and C. In this study, we use cryo-EM, microscale thermophoresis and molecular dynamics simulations to address the structural and functional roles of individual sites as well as the interplay between Zn 2+ binding and protonation. Structural studies indicate that site C in the cytoplasmic domain is primarily responsible for stabilizing the dimer and that site B at the cytoplasmic membrane surface controls the structural transition from an inward facing conformation to an occluded conformation. Binding data show that intramembrane site A, which is directly responsible for transport, has a dramatic pH dependence consistent with coupling to the proton motive force. A comprehensive thermodynamic model encompassing Zn 2+ binding and protonation states of individual residues indicates a transport stoichiometry of 1 Zn 2+ to 2–3 H + depending on the external pH. This stoichiometry would be favorable in a physiological context, allowing the cell to use the proton gradient as well as the membrane potential to drive the export of Zn 2+ .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Magnetism in the axion insulator candidate Eu 5 In 2 Sb 6

Eu 5 In 2 Sb 6 is a member of a family of orthorhombic nonsymmorphic rare-earth intermetallics that combines large localized magnetic moments and itinerant exchange with a low carrier density and perpendicular glide planes. This may result in special topological crystalline (wallpaper fermion) or axion insulating phases. Recent studies of Eu 5 In 2 Sb 6 single crystals have revealed colossal negative magnetoresistance and multiple magnetic phase transitions. Here, we clarify this ordering process using neutron scattering, resonant elastic x-ray scattering, muon spin-rotation, and magnetometry. The nonsymmorphic and multisite character of Eu 5 In 2 Sb 6 results in coplanar noncollinear magnetic structures with an Ising-like net magnetization along the a axis. A reordering transition, attributable to competing ferro- and antiferromagnetic couplings, manifests as the onset of a second commensurate Fourier component. In the absence of spatially resolved probes, the experimental evidence for this low-temperature state can be interpreted either as an unusual double- q structure or in a phase separation scenario. The net magnetization produces variable anisotropic hysteretic effects which also couple to charge transport. The implied potential for functional domain physics and topological transport suggests that this structural family may be a promising platform to implement concepts of topological antiferromagnetic spintronics. Published by the American Physical Society 2024

Rahn, M. C. (ORCID:0000000174038288)↗
DOE OSTI2023

Crystal structure of a highly conserved enteroviral 5' cloverleaf RNA replication element

The extreme 5'-end of the enterovirus RNA genome contains a conserved cloverleaf-like domain that recruits 3CD and PCBP proteins required for initiating genome replication. Here, we report the crystal structure at 1.9 Å resolution of this domain from the CVB3 genome in complex with an antibody chaperone. The RNA folds into an antiparallel H-type four-way junction comprising four subdomains with co-axially stacked sA-sD and sB-sC helices. Long-range interactions between a conserved A40 in the sC-loop and Py-Py helix within the sD subdomain organize near-parallel orientations of the sA-sB and sC-sD helices. Our NMR studies confirm that these long-range interactions occur in solution and without the chaperone. The phylogenetic analyses indicate that our crystal structure represents a conserved architecture of enteroviral cloverleaf-like domains, including the A40 and Py-Py interactions. The protein binding studies further suggest that the H-shape architecture provides a ready-made platform to recruit 3CD and PCBP2 for viral replication.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Evidence for Plant-Conserved Region Mediated Trimeric CESAs in Plant Cellulose Synthase Complexes

Higher plants synthesize cellulose using membrane-bound, six-lobed cellulose synthase complexes, each lobe containing trimeric cellulose synthases (CESAs). Although molecular biology reports support heteromeric trimers composed of different isoforms, a homomeric trimer was reported for in vitro studies of the catalytic domain of CESA1 of Arabidopsis (AtCESA1CatD) and confirmed in cryoEM structures of full-length CESA8 and CESA7 of poplar and cotton, respectively. In both structures, a small portion of the plant-conserved region (P-CR) forms the only contacts between catalytic domains of the monomers. Here, we report inter-subunit lysine-crosslinks that localize to the small P-CR, negative-stain EM structure, and modeling data for homotrimers of AtCESA1CatD. Molecular dynamics simulations for AtCESA1CatD trimers based on the CESA8 cryoEM structure were stable and dependent upon a small set of residue contacts. The results suggest that homomeric CESA trimers may be important for the synthesis of primary and secondary cell walls and identify key residues for future mutagenic studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Peptidoglycan Contribution to the B Cell Superantigen Activity of Staphylococcal Protein A

Staphylococcus aureus causes reiterative and chronic persistent infections. This can be explained by the formidable ability of this pathogen to escape immune surveillance mechanisms. Cells of S. aureus display the abundant staphylococcal protein A (SpA). SpA binds to immunoglobulin (Ig) molecules and coats the bacterial surface to prevent phagocytic uptake. SpA also binds and cross-links variable heavy 3 (V H 3) idiotype (IgM) B cell receptors, promoting B cell expansion and the secretion of nonspecific V H 3-IgM via a mechanism requiring CD4 + T cell help. SpA binding to antibodies is mediated by the N-terminal Ig-binding domains (IgBDs). The so-called region X, uncharacterized LysM domain, and C-terminal LPXTG sorting signal for peptidoglycan attachment complete the linear structure of the protein. Here, we report that both the LysM domain and the LPXTG motif sorting signal are required for the B cell superantigen activity of SpA in a mouse model of infection. SpA molecules purified from staphylococcal cultures are sufficient to exert B cell superantigen activity and promote immunoglobulin secretion as long as they carry intact LysM and LPXTG motif domains with bound peptidoglycan fragments. The LysM domain binds the glycan chains of peptidoglycan fragments, whereas the LPXTG motif is covalently linked to wall peptides lacking glycan. These findings emphasize the complexity of SpA interactions with B cell receptors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Interplay between Cation “Coloring” and Stereochemically Active Lone Pairs in AgBiS 2 Thin Films

Solution-processed AgBiS 2 thin films were fabricated using novel thiol− amine precursor inks to investigate the stereochemical activity of Bi 3+ 6s 2 lone pairs and their impact on the structure. A dual-space analysis combining Bragg diffraction and hard X-ray photoelectron spectroscopy (HAXPES) revealed a rock salt-like average structure with local distortions linked to cation coloring. Density functional theory (DFT) and crystal orbital Hamilton population (COHP) analyses confirmed that local Bi-rich and Ag-rich nanodomains amplify stereochemical activity, whereas more mixed and cation-order nanodomains are less stereochemically active. This local, nanoscopic mixing of segregated and ordered domains would indeed explain an average Fm3̅m structure that is rock salt-like and that does not manifest the full anharmonicity and noncentrosymmetry evidenced in canonical structures with stereochemical expression. These findings provide insights into the local structural and electronic complexities governing the optoelectronic properties of AgBiS 2 thin films.

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

Multi-layered heterochromatin interaction as a switch for DIM2-mediated DNA methylation

Functional crosstalk between DNA methylation, histone H3 lysine-9 trimethylation (H3K9me3) and heterochromatin protein 1 (HP1) is essential for proper heterochromatin assembly and genome stability. However, how repressive chromatin cues guide DNA methyltransferases for region-specific DNA methylation remains largely unknown. Here, we report structure-function characterizations of DNA methyltransferase Defective-In-Methylation-2 (DIM2) in Neurospora . The DNA methylation activity of DIM2 requires the presence of both H3K9me3 and HP1. Our structural study reveals a bipartite DIM2-HP1 interaction, leading to a disorder-to-order transition of the DIM2 target-recognition domain that is essential for substrate binding. Furthermore, the structure of DIM2-HP1-H3K9me3-DNA complex reveals a substrate-binding mechanism distinct from that for its mammalian orthologue DNMT1. In addition, the dual recognition of H3K9me3 peptide by the DIM2 RFTS and BAH1 domains allosterically impacts the DIM2-substrate binding, thereby controlling DIM2-mediated DNA methylation. Together, this study uncovers how multiple heterochromatin factors coordinately orchestrate an activity-switching mechanism for region-specific DNA methylation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Autoprocessing and oxyanion loop reorganization upon GC373 and nirmatrelvir binding of monomeric SARS-CoV-2 main protease catalytic domain

The monomeric catalytic domain (residues 1–199) of SARS-CoV-2 main protease (MPro 1-199 ) fused to 25 amino acids of its flanking nsp4 region mediates its autoprocessing at the nsp4-MPro 1-199 junction. We report the catalytic activity and the dissociation constants of MPro 1-199 and its analogs with the covalent inhibitors GC373 and nirmatrelvir (NMV), and the estimated monomer-dimer equilibrium constants of these complexes. Mass spectrometry indicates the presence of the accumulated adduct of NMV bound to MPro WT and MPro 1-199 and not of GC373. A room temperature crystal structure reveals a native-like fold of the catalytic domain with an unwound oxyanion loop (E state). In contrast, the structure of a covalent complex of the catalytic domain-GC373 or NMV shows an oxyanion loop conformation (E* state) resembling the full-length mature dimer. These results suggest that the E-E* equilibrium modulates autoprocessing of the main protease when converting from a monomeric polyprotein precursor to the mature dimer.

59 BASIC BIOLOGICAL SCIENCES↗