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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 1,261 records · Page 70
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

EM structure of a helicase-loader complex depicting a 6:2 binding sub-stoichiometry from Geobacillus kaustophilus HTA426

During DNA replication, bacterial helicase is recruited as a complex in association with loader proteins to unwind the parental duplex. Previous structural studies have reported saturated 6:6 helicase-loader complexes with different conformations. However, structural information on the sub-stoichiometric conformations of these previously-documented helicase-loader complexes remains elusive. Here, with the aid of single particle electron-microscopy (EM) image reconstruction, we present the Geobacillus kaustophilus HTA426 helicase-loader (DnaC-DnaI) complex with a 6:2 binding stoichiometry in the presence of ATPγS. In the 19 Å resolution EM map, the undistorted and unopened helicase ring holds a robust loader density above the C-terminal RecA-like domain. Meanwhile, the path of the central DNA binding channel appears to be obstructed by the reconstructed loader density, implying its potential role as a checkpoint conformation to prevent the loading of immature complex onto DNA. Our data also reveals that the bound nucleotides and the consequently induced conformational changes in the helicase hexamer are essential for active association with loader proteins. These observations provide fundamental insights into the formation of the helicase-loader complex in bacteria that regulates the DNA replication process. - Highlights: • Helicase-loader complex structure with 6:2 sub-stoichiometry is resolved by EM. • Helicase hexamer in 6:2 sub-stoichiometry is constricted and un-opened. • 6:2 binding ratio of helicase-loader complex could act as a DNA loading checkpoint. • Nucleotides stabilize helicase-loader complex at low protein concentrations.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

The crystal structure of DR6 in complex with the amyloid precursor protein provides insight into death receptor activation

The amyloid precursor protein (APP) has garnered considerable attention due to its genetic links to Alzheimer's disease. Death receptor 6 (DR6) was recently shown to bind APP via the protein extracellular regions, stimulate axonal pruning, and inhibit synapse formation. Here, we report the crystal structure of the DR6 ectodomain in complex with the E2 domain of APP and show that it supports a model for APP-induced dimerization and activation of cell surface DR6.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Crystal Structure of a Nickel(II) Complex with the Macrocyclic Azadibenzo-14-crown-4 Ether Ligand Containing the Embedded Di(α-pyridyl)bispidone Moiety

The crystal structure of the nickel(II) complex with substituted azadibenzo-14-crown-4 ether containing the embedded di(α-pyridyl)bispidone moiety having the formula [L(H{sub 2}O)Ni(NO{sub 3}) Ni(H{sub 2}O)L](ClO{sub 4}){sub 3} · 0.7EtOH was studied by X-ray diffraction (T = 150(2) K, R = 0.0628). In the complex cation two five-coordinate nickel complexes are bridged by the nitrate anion to form a dimer. The distorted octahedral environment of Ni atoms is formed by four nitrogen atoms of the molecule L and the oxygen atoms of the water molecule and the NO{sub 3}{sup -} anion. In the nickel complex, like in the cobalt and copper complexes studied previously, the bispidine moiety of the molecule L adopts a chair-chair conformation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

An asymmetric heterodomain interface stabilizes a response regulator-DNA complex

Two-component signal transduction systems consist of pairs of histidine kinases and response regulators, which mediate adaptive responses to environmental cues. Most activated response regulators regulate transcription by binding tightly to promoter DNA via a phosphorylation-triggered inactive-to-active transition. The molecular basis for formation of stable response regulator–DNA complexes that precede the assembly of RNA polymerases is unclear. Here, we present structures of DNA complexed with the response regulator KdpE, a member of the OmpR/PhoB family. The distinctively asymmetric complex in an active-like conformation reveals a unique intramolecular interface between the receiver domain (RD) and the DNA-binding domain (DBD) of only one of the two response regulators in the complex. Structure–function studies show that this RD–DBD interface is necessary to form stable complexes that support gene expression. The conservation of sequence and structure suggests that these findings extend to a large group of response regulators that act as transcription factors.

Narayanan, Anoop↗
DOE OSTI2018

Studying light-harvesting models with superconducting circuits

The process of photosynthesis, the main source of energy in the living world, converts sunlight into chemical energy. The high efficiency of this process is believed to be enabled by an interplay between the quantum nature of molecular structures in photosynthetic complexes and their interaction with the environment. Investigating these effects in biological samples is challenging due to their complex and disordered structure. Here we experimentally demonstrate a technique for studying photosynthetic models based on superconducting quantum circuits, which complements existing experimental, theoretical, and computational approaches. We demonstrate a high degree of freedom in design and experimental control of our approach based on a simplified three-site model of a pigment protein complex with realistic parameters scaled down in energy by a factor of 10 5 . We show that the excitation transport between quantum-coherent sites disordered in energy can be enabled through the interaction with environmental noise. We also show that the efficiency of the process is maximized for structured noise resembling intramolecular phononic environments found in photosynthetic complexes.

42 ENGINEERING↗
DOE OSTI2022

Monitoring of mechanical changes in a pipe assembly with complex geometry using multi-mode acoustic signals

Guided wave ultrasonic testing has been widely used for nondestructive and long-range evaluation of diverse mechanical structures, such as pipes and plates. In general, a large number of guided wave modes exist even in the simplest geometries, and they exhibit highly dispersive characteristics. Thus, sophisticated excitation methods and elaborate modal analyses need to be implemented to excite, acquire, and process well-defined pure modes as part of such a measurement method. If the interrogated structure has complex geometry, for example, with cross-sectional variations or multiple joints, the utilization of pure modes becomes significantly more difficult. To overcome this difficulty, this paper proposes the use of multi-mode, multi-frequency guided waves for long-range inspection of structures with arbitrarily complex geometries. Furthermore, using broadband chirp signals and multi-mode time–frequency analysis in a prototypical complex pipe assembly that includes multiple pipe diameters, elbows, and flange connections, we experimentally show sensitive detection of mechanical changes (both material addition and loss). In addition, we demonstrate that the complexity of the structure can be modeled in the digital domain with sufficient detail to allow accurate numerical simulation of the acoustic response using this method.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Review on crystal structures and magnetic properties of RTX 3 materials

The structural and compositional diversity of the RTX 3 family of materials offers various magnetic and thermodynamic properties such as complex magnetic structure, vibronic bound states, heavy-fermions, valence fluctuations, metamagnetism, spin glass behavior, quantum criticality, and unconventional superconductivity. In this study we present an overview of the crystal structures, crystal growth and magnetic properties of RTX 3 compounds as well as a discussion of the relevant physics. The magnetic properties of several compounds of the RTX 3 family still remain unexplored. The compounds with a complex magnetic structure could potentially host exotic topological phases. This review article may help explore exotic magnetic properties such as the vibron state and topological spin textures.

quantum materials↗
DOE OSTI2022

Cryo-EM structures of light-harvesting 2 complexes from Rhodopseudomonas palustris reveal the molecular origin of absorption tuning

The genomes of some purple photosynthetic bacteria contain a multigene puc family encoding a series of α- and β-polypeptides that together form a heterogeneous antenna of light-harvesting 2 (LH2) complexes. To unravel this complexity, we generated four sets of puc deletion mutants in Rhodopseudomonas palustris , each encoding a single type of pucBA gene pair and enabling the purification of complexes designated as PucA-LH2, PucB-LH2, PucD-LH2, and PucE-LH2. The structures of all four purified LH2 complexes were determined by cryogenic electron microscopy (cryo-EM) at resolutions ranging from 2.7 to 3.6 Å. Uniquely, each of these complexes contains a hitherto unknown polypeptide, γ, that forms an extended undulating ribbon that lies in the plane of the membrane and that encloses six of the nine LH2 αβ-subunits. The γ-subunit, which is located near to the cytoplasmic side of the complex, breaks the C9 symmetry of the LH2 complex and binds six extra bacteriochlorophylls (BChls) that enhance the 800-nm absorption of each complex. The structures show that all four complexes have two complete rings of BChls, conferring absorption bands centered at 800 and 850 nm on the PucA-LH2, PucB-LH2, and PucE-LH2 complexes, but, unusually, the PucD-LH2 antenna has only a single strong near-infared (NIR) absorption peak at 803 nm. Comparison of the cryo-EM structures of these LH2 complexes reveals altered patterns of hydrogen bonds between LH2 αβ-side chains and the bacteriochlorin rings, further emphasizing the major role that H bonds play in spectral tuning of bacterial antenna complexes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Structure of a Bud6/Actin Complex Reveals a Novel WH2-like Actin Monomer Recruitment Motif

In budding yeast, the actin-binding protein Bud6 cooperates with formins Bni1 and Bnr1 to catalyze the assembly of actin filaments. The nucleation-enhancing activity of Bud6 requires both a “core” domain that binds to the formin and a “flank” domain that binds monomeric actin. Here, we describe the structure of the Bud6 flank domain in complex with actin. Two helices in Bud6 flank interact with actin; one binds in a groove at the barbed end of the actin monomer in a manner closely resembling the helix of WH2 domains, a motif found in many actin nucleation factors. The second helix rises along the face of actin. Mutational analysis verifies the importance of these Bud6-actin contacts for nucleation-enhancing activity. The Bud6 binding site on actin overlaps with that of the formin FH2 domain and is also incompatible with inter-subunit contacts in F-actin, suggesting that Bud6 interacts only transiently with actin monomers during filament nucleation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Structure of the Public Irradiation Dose During Operation of Experimental-Demonstration Power Complex Enterprises

The structure of the public radiation dose resulting from gas aerosol emissions of the experimental-demonstration energy complex incorporating the BREST-OD-300 reactor and fuel fabrication and reprocessing modules is determined. The yearly radiation dose to humans at the point of maximum ground concentration of radionuclides from design basis emissions of the energy complex is formed primarily by {sup 3}H,{sup 14}C, and fission products (0.73, 1.2 2, and 0.9 μSv, respectively) through the peroral pathway as a result of the fallout during the running year of operation of the enterprises. The largest contribution to the irradiation dose is due to the emissions from the spent fuel reprocessing module – 2.33 μSv/yr – and 50% is due to {sup 14}C. The radiation dose from the emissions of the BREST-OD-300 reactor is almost completely due to {sup 3}H and {sup 210}Po (0.73 and 0.17 μSv/yr, respectively). The emissions from the fuel fabrication module have the smallest effect on the public. The dose from fission products is produced by emissions from the reprocessing module approximately in equal amounts in terms of external and internal pathways (0.47 and 0.43 μSv).

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2019

Hydrothermal synthesis and structural characterization of several complex rare earth tantalates: Ln 2 TaO 5 (OH) (Ln = La, Pr) and Ln 3 Ta 2 O 9 (OH) (Ln = Pr, Nd)

Reactions are reported of early rare earth oxides, RE 2 O 3 (RE = La, Pr, Nd) with Ta 2 O 5 under hydrothermal conditions (650 °C, 1.5 kbar) in concentrated aqueous hydroxide (20–30 M KOH) as a mineralizer. Under various stoichiometries several members of two new structure types were isolated, Ln 2 TaO 5 (OH) (Ln = La, Pr) and Ln 3 Ta 2 O 9 (OH) (Ln = Pr, Nd). The analogous niobate La 2 NbO 5 (OH) was also obtained. Both structure types were characterized by single crystal X-ray diffraction and contain pentavalent tantalatum oxide octahedra and complex rare earth oxide frameworks. The Ln 2 TaO 5 (OH) structure type contains Ln–O 8 and Ln–O 9 building blocks and TaO 6 octahedra in a 3-D framework. It contains a 3-D rare earth oxide framework formed by from zig-zag chains of rare earth oxides linking sheets of rare earth oxides. The tantalates form edge-shared Ta 2 O 10 dimers occupying gaps in the rare earth oxide frameworks. The structure of Ln 3 Ta 2 O 9 (OH) contains two types of 2-D rare earth oxide slabs built of seven and eight coordinate rare earth metals. The tantalate units form 2-D slabs through a multiple corner-sharing scheme of TaO 6 octahedra. The Ln 3 Ta 2 O 9 (OH) structure type has an interesting close structural relationship to the previously reported rare earth titanate La 5 Ti 4 O 15 (OH), which is discussed. The presence of hydroxide in the lattice is confirmed by IR spectroscopy and the H atom locations are assigned unambiguously using bond valence sums.

36 MATERIALS SCIENCE↗
DOE OSTI2017

The introspective may achieve more: Enhancing existing Geoscientific models with native-language emulated structural reflection

Geoscientific models manage myriad and increasingly complex data structures as trans -disciplinary models are integrated. They often incur significant redundancy with cross-cutting tasks. Reflection, the ability of a program to inspect and modify its structure and behavior at runtime, is known as a powerful tool to improve code reusability, abstraction, and separation of concerns. Reflection is rarely adopted in high-performance Geoscientific models, especially with Fortran, where it was previously deemed implausible. Practical constraints of language and legacy often limit us to feather-weight, native-language solutions. We demonstrate the usefulness of a structural-reflection-emulating, dynamically-linked metaObjects, gd . We show real-world examples including data structure self-assembly, effortless save/restart and upgrade to parallel I/O, recursive actions and batch operations. We share gd and a derived module that reproduces MATLAB-like structure in Fortran and C++. We suggest that both a gd representation and a Fortran-native representation are maintained to access the data, each for separate purposes. In conclusion, embracing emulated reflection allows generically-written codes that are highly re-usable across projects.

58 GEOSCIENCES↗
DOE OSTI2015

Structure of FcγRI in complex with Fc reveals the importance of glycan recognition for high-affinity IgG binding

Fc gamma receptor I (FcγRI) contributes to protective immunity against bacterial infections, but exacerbates certain autoimmune diseases. The sole high-affinity IgG receptor, FcγRI plays a significant role in immunotherapy. To elucidate the molecular mechanism of its high-affinity IgG binding, we determined the crystal structure of the extracellular domains of human FcγRI in complex with the Fc domain of human IgG 1 . FcγRI binds to the Fc in a similar mode as the low-affinity FcγRII and FcγRIII receptors. In addition to many conserved contacts, FcγRI forms additional hydrogen bonds and salt bridges with the lower hinge region of Fc. Unique to the high-affinity receptor-Fc complex, however, is the conformation of the receptor D2 domain FG loop, which enables a charged KHR motif to interact with proximal carbohydrate units of the Fc glycans. Both the length and the charge of the FcγRI FG loop are well conserved among mammalian species. Ala and Glu mutations of the FG loop KHR residues showed significant contributions of His-174 and Arg-175 to antibody binding, and the loss of the FG loop–glycan interaction resulted in an ~20- to 30-fold decrease in FcγRI affinity to all three subclasses of IgGs. Furthermore, deglycosylation of IgG 1 resulted in a 40-fold loss in FcγRI binding, demonstrating involvement of the receptor FG loop in glycan recognition. Here, these results highlight a unique glycan recognition in FcγRI function and open potential therapeutic avenues based on antibody glycan engineering or small molecular glycan mimics to target FcγRI for certain autoimmune diseases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Classification of Intensity Distributions of Transmission Eigenchannels of Disordered Nanophotonic Structures Using Machine Learning

Light-matter interaction optimization in complex nanophotonic structures is a critical step towards the tailored performance of photonic devices. The increasing complexity of such systems requires new optimization strategies beyond intuitive methods. For example, in disordered photonic structures, the spatial distribution of energy densities has large random fluctuations due to the interference of multiply scattered electromagnetic waves, even though the statistically averaged spatial profiles of the transmission eigenchannels are universal. Classification of these eigenchannels for a single configuration based on visualization of intensity distributions is difficult. However, successful classification could provide vital information about disordered nanophotonic structures. Emerging methods in machine learning have enabled new investigations into optimized photonic structures. In this work, we combine intensity distributions of the transmission eigenchannels and the transmitted speckle-like intensity patterns to classify the eigenchannels of a single configuration of disordered photonic structures using machine learning techniques. Specifically, we leverage supervised learning methods, such as decision trees and fully connected neural networks, to achieve classification of these transmission eigenchannels based on their intensity distributions with an accuracy greater than 99%, even with a dataset including photonic devices of various disorder strengths. Simultaneous classification of the transmission eigenchannels and the relative disorder strength of the nanophotonic structure is also possible. Our results open new directions for machine learning assisted speckle-based metrology and demonstrate a novel approach to classifying nanophotonic structures based on their electromagnetic field distributions. These insights can be of paramount importance for optimizing light-matter interactions at the nanoscale.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Redox-active dinuclear oxorhenium(V) pyrazolate complexes

Four new structurally similar dinuclear oxorhenium(V) complexes, [{Re(O)X(PPh 3 )} 2 (μ-O)(μ-4-x'-pz) 2 ], where pz = pyrazolate anion, X = X' = Cl (1) and Br (4), X = Cl, X' = Br (2), and X = Br, X' = Cl (3), have been synthesized and characterized. Little variation in spectroscopic features – 1 H NMR, IR, UV–Vis – exists among the four complexes. All complexes possess a bent Re-O-Re core as well as distorted octahedral coordination geometry around the rhenium centers. Finally, a reversible one-electron electrochemical process is observed at approximately 0.84 V vs. Fc + /Fc in all four complexes; however, changing the terminal halide from chloride to bromide slightly destabilizes the oxidized Re(VI) center.

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

Complex Dirac-like Electronic Structure in Atomic Site-Ordered Rh 3 In 3.4 Ge 3.6

We report the synthesis via an indium flux method of a novel single-crystalline compound Rh 3 In 3.4 Ge 3.6 that belongs to the cubic Ir 3 Ge 7 structure type. In Rh 3 In 3.4 Ge 3.6 , the In and Ge atoms preferentially occupy, respectively, the 12d and 16f sites of the Im3¯m space group, thus creating a colored variant of the Ir 3 Ge 7 structure. Like the other compounds of the Ir 3 Ge 7 family, Rh 3 In 3.4 Ge 3.6 shows potential as a thermoelectric, displaying a relatively large power factor, PF ~ 2 mW/cm K 2 , at a temperature T ~ 225 K, albeit showing a modest figure of merit, ZT = 8 x 10 -4 , because of the lack of a finite band gap. These figures might improve through a use of chemical substitution strategies to achieve band gap opening. Remarkably, electronic band structure calculations reveal that this compound displays a complex Dirac-like electronic structure relatively close to the Fermi level. The electronic structure is composed of several Dirac type-I and type-II nodes, and even Dirac type-III nodes that result from the touching between a flat band and a linearly dispersing band. Here, this rich Dirac-like electronic dispersion suggests the possibility to observe experimentally Dirac type-III nodes and study their role in the physical properties of Rh 3 In 3.4 Ge 3.6 and related Ir 3 Ge 7 -type materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗