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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 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Cryo-EM structure of an extracellular Geobacter OmcE cytochrome filament reveals tetrahaem packing

Electrically conductive appendages from the anaerobic bacterium Geobacter sulfurreducens were first observed two decades ago, with genetic and biochemical data suggesting that conductive fibres were type IV pili. Recently, an extracellular conductive filament of G. sulfurreducens was found to contain polymerized c-type cytochrome OmcS subunits, not pilin subunits. Here we report that G. sulfurreducens also produces a second, thinner appendage comprised of cytochrome OmcE subunits and solve its structure using cryo-electron microscopy at ~4.3 A resolution. Although OmcE and OmcS subunits have no overall sequence or structural similarities, upon polymerization both form filaments that share a conserved haem packing arrangement in which haems are coordinated by histidines in adjacent subunits. Unlike OmcS filaments, OmcE filaments are highly glycosylated. In extracellular fractions from G. sulfurreducens, we detected type IV pili comprising PilA-N and -C chains, along with abundant B-DNA. OmcE is the second cytochrome filament to be characterized using structural and biophysical methods. Here, we propose that there is a broad class of conductive bacterial appendages with conserved haem packing (rather than sequence homology) that enable long-distance electron transport to chemicals or other microbial cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Photoelectron spectroscopy and computational investigations of the electronic structures and noncovalent interactions of cyclodextrin-closo-dodecaborate anion complexes x-CD·B12X122- (x = a, ß, y; X = H, F)

We report a joint negative ion photoelectron spectroscopy (NIPES) and computational study on the electronic structures and noncovalent interactions of a series of cyclodextrin-closo-dodecaborate dianion complexes, ?-CD·B12X122- (? = a, ß, ?; X = H, F). The measured vertical / adiabatic detachment energies (VDEs / ADEs) are 1.15/0.93, 3.55/3.20, 3.90/3.60, and 3.85/3.60 eV for B12H122- and its a-, ß-, ?-CD complexes, respectively; while the corresponding values are 1.90/1.70, 4.00/3.60, 4.33/3.95, and 4.30/3.85 eV for the X = F case. These results show that the inclusion of B12X122- into the CD cavities greatly increase the electronic stability of the dianions. The effect of electronic stabilization for ß-CD is roughly the same as for ?-CD, both being considerably stronger than that for a-CD. Density functional theory (DFT) based geometry optimization reveals that B12X122- are inserted into CDs increasingly deeper from a-CD to ?-CD. The calculated VDEs and ADEs agree with the experiments well, particularly, reproducing the electron binding energy (EBE) trends. The molecular orbital analyses indicate that the most loosely bound photodetached electrons origin from the guest B12X122- moieties. In addition to a shift of all signals to larger EBE, significant changes in the signal patterns are observed. At low EBE, this is due to the splitting of highly degenerate B12X122- orbitals, while at high EBE, photodetachment from CD oxygens contributes to the new bands. The guest B12X122- and host CD nocovalent, size-specific interaction based on the independent gradient model (IGM) and energy decomposition analysis (EDA), is dominated by electrostatic interactions. The analysis further unravels unambiguiously the existence of dihydrogen bonding and how it affects the total energy that stabilizes the host-guest complexes of CDs·B12H122- compared to the general hydrogen bonding interaction in CDs·B12F122-. This work clearly exhibits strong influences on the electronic structures of dodecaborates upon clustering with CDs, with both size (a-, ß-, ?-) and molecular (X = H or F) specificities, thus providing critical molecular-level information on the cyclodextrin-closo-dodecaborate interactions of interest to medical applications, e.g. Boron neutron capature therapy. The NIPES experiments done at PNNL were supported by the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Bioscience (X.-B.W.) and was performed at the EMSL, a national scientific user facility sponsored by DOE’s Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. H.S. and Z.S. acknowledge the funding support of National Natural Science Foundation of China (Nos.11727810, 61720106009 and 21603074), the Science and Technology Commission of Shanghai Municipality (Nos. 19JC1412200), and the Program of Introducing Talents of Discipline to Universities 111 project (B12024). Z. L. thanks the China Scholarship Council (CSC) for financial support. We acknowledge the ECNU Multifunctional Platform for Innovation (001) and HPC Research Computing Team for providing computational and storage resources. J.W. acknowledges support from the Alexander von Humboldt foundation (Feodor Lynen Fellowship and Rückkehrerstipendium), a Freigeist fellowship of the Volkswagenfoundation and Prof. Vladimir A. Azov for helpful discussions.

Li, Zhipeng↗
DOE OSTI2022

Temperature-dependent behavior in the local structure of BaTiO 3 nanocrystals

Here, we use pair distribution function analysis of synchrotron X-ray total scattering data to inspect the local structure of BaTiO 3 nanocrystals from 253 K < T < 413 K. The local structure consists of ca. r = 35 Å domains in which Ti 4+ displacements have the same coherence length as the overall perovskite structure.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Magnetic structure, excitations and short-range order in honeycomb Na 2 Ni 2 TeO 6

Na 2 Ni 2 TeO 6 has a layered hexagonal structure with a honeycomb lattice constituted by Ni 2+ and a chiral charge distribution of Na + that resides between the Ni layers. In the present work, the antiferromagnetic transition temperature of Na 2 Ni 2 TeO 6 is confirmed at TN˜ 27 K, and further, it is found to be robust up to 8 T magnetic field and 1.2 GPa external pressure; and, without any frequency-dependence. Slight deviations from nominal Na-content (up to 5%) does not seem to influence the magnetic transition temperature, TN. Isothermal magnetization curves remain almost linear up to 13 T. Our analysis of neutron diffraction data shows that the magnetic structure of Na 2 Ni 2 TeO 6 is faithfully described by a model consisting of two phases described by the commensurate wave vectors vec kc, (0.5 0 0) and (0.5 0 0.5), with an additional short-range order component incorporated in to the latter phase. Consequently, a zig-zag long-range ordered magnetic phase of Ni 2+ results in the compound, mixed with a short-range ordered phase, which is supported by our specific heat data. Theoretical computations based on density functional theory (DFT) predict predominantly in-plane magnetic exchange interactions that conform to a J1-J2-J3 model with a strong J3 term. The computationally predicted parameters lead to a reliable estimate for TN and the experimentally observed zig-zag magnetic structure. A spin wave excitation in Na 2 Ni 2 TeO 6 at E ˜ 5 meV at T = 5 K is mapped out through inelastic neutron scattering experiments, which is reproduced by linear spin wave theory calculations using the J values from our computations. Our specific heat data and inelastic neutron scattering data strongly indicate the presence of short-range spin correlations, at T > TN, stemming from incipient antiferromagnetic clusters.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, RCSB.org), the US Worldwide Protein Data Bank (wwPDB, wwPDB.org) data center for the global PDB archive, provides access to the PDB data via its RCSB.org research-focused web portal. We report substantial additions to the tools and visualization features available at RCSB.org, which now delivers more than 227000 experimentally determined atomic-level three-dimensional (3D) biostructures stored in the global PDB archive alongside more than 1 million Computed Structure Models (CSMs) of proteins (including models for human, model organisms, select human pathogens, crop plants and organisms important for addressing climate change). In addition to providing support for 3D structure motif searches with user-provided coordinates, new features highlighted herein include query results organized by redundancy-reduced Groups and summary pages that facilitate exploration of groups of similar proteins. Newly released programmatic tools are also described, as are enhanced training opportunities.

Burley, Stephen K.↗
DOE OSTI2025

Impact of structural distortions on the correlated electronic structure of orbital-selective Mott insulating Na 3 ⁢Co 2 ⁢SbO 6 under strain

Na 3 Co 2 SbO 6 is a promising candidate to realize the Kitaev spin liquid phase since the large Kitaev spin exchange interaction is tunable via the change in electronic structure, such as the trigonal crystal field splitting (Δ TCF ). Here, in this study, we show that the uncorrelated electronic structure of Na 3 Co 2 SbO 6 is rather insensitive to the strain effect due to the low crystal symmetry accompanied by oxygen displacements and the presence of Sb s orbitals. Using density functional theory plus dynamical mean field theory, we find that the correlated electronic structure of Na 3 Co 2 SbO 6 is an orbital-selective Mott insulating state where the trigonal a 1g orbital is insulating due to the nearly full occupation, while other d orbitals behave as typical Mott insulators, resulting in the effective tunability of Δ TCF under the strain effect. The sign change of Δ TCF can occur as the in-plane tensile strain is applied, and the Kitaev spin liquid phase could possibly be realized due to the strongly suppressed Δ TCF under tensile strain. Our results show that the local Co-site symmetry and dynamical correlation effects will play an important role in engineering the novel magnetic phase in this and related materials.

Nguyen, Nam [Univ. of Illinois, Chicago, IL (Unite↗
DOE OSTI2020

Site-Specific Structure at Multiple Length Scales in Kagome Quantum Spin Liquid Candidates

Realizing a quantum spin liquid (QSL) ground state in a real material is a leading issue in condensed matter physics research. In this pursuit, it is crucial to fully characterize the structure and influence of defects, as these can significantly affect the fragile QSL physics. In this work, we perform a variety of cutting-edge synchrotron x-ray scattering and spectroscopy techniques, and we advance new methodologies for site-specific diffraction and L-edge Zn absorption spectroscopy. The experimental results along with our first-principles calculations address outstanding questions about the local and long-range structures of the two leading kagome QSL candidates, Zn-substituted barlowite Cu 3 Zn x Cu 1-x (OH) 6 FBr and herbertsmithite Cu 3 Zn(OH) 6 Cl 2 . On all length scales probed, there is no evidence that Zn substitutes onto the kagome layers, thereby preserving the QSL physics of the kagome lattice. Our calculations show that antisite disorder is not energetically favorable and is even less favorable in Zn-barlowite compared to herbertsmithite. Site-specific x-ray diffraction measurements of Zn-barlowite reveal that Cu 2+ and Zn 2+ selectively occupy distinct interlayer sites, in contrast to herbertsmithite. Using the first measured Zn L-edge inelastic x-ray absorption spectra combined with calculations, we discover a systematic correlation between the loss of inversion symmetry from pseudo-octahedral (herbertsmithite) to trigonal prismatic coordination (Zn-barlowite) with the emergence of a new peak. Overall, our measurements suggest that Zn-barlowite has structural advantages over herbertsmithite that make its magnetic properties closer to an ideal QSL candidate: its kagome layers are highly resistant to nonmagnetic defects while the interlayers can accommodate a higher amount of Zn substitution.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Nanometer-scale structure differences in the myofilament lattice spacing of two cockroach leg muscles correspond to their different functions

ABSTRACT Muscle is highly organized across multiple length scales. Consequently, small changes in the arrangement of myofilaments can influence macroscopic mechanical function. Two leg muscles of a cockroach have identical innervation, mass, twitch responses, length–tension curves and force–velocity relationships. However, during running, one muscle is dissipative (a ‘brake’), while the other dissipates and produces significant positive mechanical work (bifunctional). Using time-resolved X-ray diffraction in intact, contracting muscle, we simultaneously measured the myofilament lattice spacing, packing structure and macroscopic force production of these muscles to test whether structural differences in the myofilament lattice might correspond to the muscles' different mechanical functions. While the packing patterns are the same, one muscle has 1 nm smaller lattice spacing at rest. Under isometric stimulation, the difference in lattice spacing disappeared, consistent with the two muscles' identical steady-state behavior. During periodic contractions, one muscle undergoes a 1 nm greater change in lattice spacing, which correlates with force. This is the first identified structural feature in the myofilament lattice of these two muscles that shares their whole-muscle dynamic differences and quasi-static similarities.

Tune, Travis Carver↗
DOE OSTI2021

Structural and genetic convergence of HIV-1 neutralizing antibodies in vaccinated non-human primates

A primary goal of HIV-1 vaccine development is the consistent elicitation of protective, neutralizing antibodies. While highly similar neutralizing antibodies (nAbs) have been isolated from multiple HIV-infected individuals, it is unclear whether vaccination can consistently elicit highly similar nAbs in genetically diverse primates. Here, we show in three outbred rhesus macaques that immunization with Env elicits a genotypically and phenotypically conserved nAb response. From these vaccinated macaques, we isolated four antibody lineages that had commonalities in immunoglobulin variable, diversity, and joining gene segment usage. Atomic-level structures of the antigen binding fragments of the two most similar antibodies showed nearly identical paratopes. The Env binding modes of each of the four vaccine-induced nAbs were distinct from previously known monoclonal HIV-1 neutralizing antibodies, but were nearly identical to each other. The similarities of these antibodies show that the immune system in outbred primates can respond to HIV-1 Env vaccination with a similar structural and genotypic solution for recognizing a particular neutralizing epitope. These results support rational vaccine design for HIV-1 that aims to reproducibly elicit, in genetically diverse primates, nAbs with specific paratope structures capable of binding conserved epitopes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural response of 3D-printed rubber lattice structures under compressive fatigue

In this work, a new direct UV curing, polyurethane-like, highly stretchable rubber, Elastic ToughRubber 90™ (ETR 90), is demonstrated for 3D printing via photocuring with Texas Instruments DLP® optical systems. An array of test specimens, comprising a sandwich structure with a body-centered cubic lattice core, are 3D printed from ETR 90. The compressive behavior of these specimens is characterized up to 10 k and up to 100 k fatigue-loading cycles. The internal, visually obstructed, structures under loads are visualized using in situ X-ray tomography. All lattice structures remain intact and full recovery is observed, indicating the cyclic durability of the 3D-printed rubber.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Marshall Islands Dose Assessment and Radioecology Program: Report on the (i) 2018 Visual Study of Exterior Concrete of the Cactus Crater Containment Structure (ii) Periodic Monitoring of Groundwater on Runit Island and (iii) Initial Health Risk Assessment from Contaminants in the Cactus Crater Containment Structure

In 2012, Congress passed P.L. 112-149, Insular Areas Act of 2011, which amended the Compact of Free Association Amendments Act of 2003 by assigning Cactus Crater containment monitoring and reporting requirements to the Secretary of Energy (Secretary). Effective January 1, 2012, the Secretary was required to “periodically (but not less frequently than every 4 years) conduct -- (I) a visual study of the concrete exterior of the Cactus Crater Containment Structure on Runit Island; and (II) a radiochemical analysis of the groundwater surrounding and in the Cactus Crater Containment Structure on Runit Island.” 48 U.S.C. 1921b(f)(1)(B)(i). The Secretary was also directed to submit to Congress a report describing the results of each visual survey and the radiochemical analysis and “a determination on whether the surveys and analyses indicate any significant change in the health risks to the people of Enewetak from the contaminants within the Cactus Crater Containment Structure.” 48 U.S.C. 1921b(f)(1)(B)(ii)(II).

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2021

Accurate Thermochemistry of Complex Lignin Structures via Density Functional Theory, Group Additivity, and Machine Learning

A molecular-level understanding of lignin structures and bond dissociation energies could facilitate depolymerization technologies. Still, this information is currently limited due to the lack of databases and the simplification of surrogate models. Here, substitution effects on seven common linkages in lignin polymers are systematically investigated. An automated reaction network generator is employed to create a database of structures. A new group additivity (GA) model based on principal component analysis (PCA) descriptors is introduced and trained on gas-phase density functional theory data of 4100 species at the M06-2X/6-311++G(d,p) level. Hydrogen bonds, local steric, and nonaromatic ring contributions are also incorporated. Lastly, we improve the accuracy of the group additivity model to reach the G4 theory by computing a data set of 770 species at this level and using a data fusion approach.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Recent Developments in the General Atomic and Molecular Electronic Structure System

A discussion of many of the recently implemented features of GAMESS (General Atomic and Molecular Electronic Structure System) and LibCChem (the C++ CPU/GPU library associated with GAMESS) is presented. These features include fragmentation methods like the fragment molecular orbital, effective fragment potential and effective fragment molecular orbital methods, hybrid MPI/OpenMP approaches to Hartree-Fock and resolution of the identity second order perturbation theory. Many new coupled cluster theory methods have been implemented in GAMESS, as have multiple levels of density functional/tight binding theory. The role of accelerators, especially graphical processing units, is discussed in the context of the new features of LibCChem, as is the associated problem of power consumption as the power of computers increases dramatically. The process by which a complex program suite like GAMESS is maintained and developed is considered. Future developments are briefly summarized.

74 ATOMIC AND MOLECULAR PHYSICS↗