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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 1,693 records · Page 94
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

A nucleotide-level coarse-grained model of RNA

We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical, and thermodynamic properties of RNA, and the coarse-graining level aims to retain the relevant physics for RNA hybridization and the structure of single- and double-stranded RNA. In order to explore its strengths and weaknesses, we test the model in a range of nanotechnological and biological settings. Applications explored include the folding thermodynamics of a pseudoknot, the formation of a kissing loop complex, the structure of a hexagonal RNA nanoring, and the unzipping of a hairpin motif. We argue that the model can be used for efficient simulations of the structure of systems with thousands of base pairs, and for the assembly of systems of up to hundreds of base pairs. The source code implementing the model is released for public use.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Manifolds of magnetic ordered states and excitations in the almost Heisenberg pyrochlore antiferromagnet MgCr 2 O 4

In spinels ACr 2 O 4 (A=Mg,Zn), realization of the classical pyrochlore Heisenberg antiferromagnet model is complicated by a strong spin-lattice coupling: the extensive degeneracy of the ground state is lifted by a magneto-structural transition at T N =12.5 K. We study the resulting low-temperature low-symmetry crystal structure by synchrotron x-ray diffraction. The consistent features of x-ray low-temperature patterns are explained by the tetragonal model of Ehrenberg et al. [Pow. Diff. 17, 230 (2002)], while other features depend on sample or cooling protocol. A complex, partially ordered magnetic state is studied by neutron diffraction and spherical neutron polarimetry. Multiple magnetic domains of configuration arms of the propagation vectors k 1 =($\frac{1}{2}$ $\frac{1}{2}$ 0),k 2 =(1 0 $\frac{1}{2}$) appear. The ordered moment reaches 1.94(3) μ B /Cr 3+ for k 1 and 2.08(3) μ B /Cr 3+ for k 2 , if equal amount of the k 1 and k 2 phases is assumed. The magnetic arrangements have the dominant components along the [110] and [1-10] diagonals and a smaller c component. We use inelastic neutron scattering to investigate the spin excitations, which comprise a mixture of dispersive spin waves propagating from the magnetic Bragg peaks and resonance modes centered at equal energy steps of 4.5 meV. We interpret these as acoustic and optical spin wave branches, but show that the neutron scattering cross sections of transitions within a unit of two corner-sharing tetrahedra match the observed intensity distribution of the resonances. Finally, the distinctive fingerprint of clusterlike excitations in the optical spin wave branches suggests that propagating excitations are localized by the complex crystal structure and magnetic orders.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

Models of the Hydrodynamic Histories of Post-AGB Stars. I. Multiflow Shaping of OH 231.8+04.2

We present a detailed hydrodynamic model that matches the present structure of the well-observed preplanetary nebula (“pPN”) OH 231.8+04.2 (“OH231”). The purpose of the model is to present a physically justified and coherent picture of its evolutionary history from about 100 years from the start of the formation of its complex outer structures to the present. We have adopted a set of initial conditions that are heavily constrained by high-quality observations of its present structure and kinematics. The shaping of the nebula occurs while the densities of the flows are “light,” i.e., less than the surrounding AGB-wind environment. The simulations show that pairs of essentially coeval clumps and sprays of the same extent and density, but different outflow speeds, sculpted both the pair of thin axial flow “or spine” and the bulbs. The total ejected mass and momentum in the best-fit model are surprisingly large—3 M {sub ⊙} and 2.2 × 10{sup 41} gm cm s{sup −1}, respectively—however, these values are reduced by up to a factor of 10 in other models that fit the data almost as well. Our ultimate goal is to combine the present model results of masses, momenta, flow speeds, and flow geometries for OH231 with those of other models to be published in the future in order to find common attributes of their ejection histories.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Structural understanding of non-nucleoside inhibition in an elongating herpesvirus polymerase

All herpesviruses encode a conserved DNA polymerase that is required for viral genome replication and serves as an important therapeutic target. Currently available herpesvirus therapies include nucleoside and non-nucleoside inhibitors (NNI) that target the DNA-bound state of herpesvirus polymerase and block replication. Here we report the ternary complex crystal structure of Herpes Simplex Virus 1 DNA polymerase bound to DNA and a 4-oxo-dihydroquinoline NNI, PNU-183792 (PNU), at 3.5 Å resolution. PNU bound at the polymerase active site, displacing the template strand and inducing a conformational shift of the fingers domain into an open state. These results demonstrate that PNU inhibits replication by blocking association of dNTP and stalling the enzyme in a catalytically incompetent conformation, ultimately acting as a nucleotide competing inhibitor (NCI). Sequence conservation of the NCI binding pocket further explains broad-spectrum activity while a direct interaction between PNU and residue V823 rationalizes why mutations at this position result in loss of inhibition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Enhancement of Magneto‐Mechanical Actuation of Micropillar Arrays by Anisotropic Stress Distribution

Abstract Magnetically active shape‐reconfigurable microarrays undergo programmed actuation according to the arrangement of magnetic dipoles within the structures, achieving complex twisting and bending deformations. Cylindrical micropillars have been widely used to date, whose circular cross‐sections lead to identical actuation regardless of the actuating direction. In this study, micropillars with triangular or rectangular cross‐sections are designed and fabricated to introduce preferential actuation directions and explore the limits of their actuation. Using such structures, controlled liquid wetting is demonstrated on micropillar surfaces. Liquid droplets pinned on magnetic micropillar arrays undergo directional spreading when the pillars are actuated as depinning of the droplets is enabled only in certain directions. The enhanced deformation due to direction dependent magneto‐mechanical actuation suggests that micropillar arrays can be fundamentally tailored to possess application specific responses and opens up opportunities to exploit more complex designs such as micropillars with polygonal cross sections. Such tunable wetting of liquids on microarray surfaces has potential to improve printing technologies via contactless reconfiguration of stamp geometry by magnetic field manipulation.

Park, Jeong Eun↗
DOE OSTI2016

ANISOTROPY IN COSMIC-RAY ARRIVAL DIRECTIONS IN THE SOUTHERN HEMISPHERE BASED ON SIX YEARS OF DATA FROM THE ICECUBE DETECTOR

The IceCube Neutrino Observatory accumulated a total of 318 billion cosmic-ray-induced muon events between 2009 May and 2015 May. This data set was used for a detailed analysis of the sidereal anisotropy in the arrival directions of cosmic rays in the TeV to PeV energy range. The observed global sidereal anisotropy features large regions of relative excess and deficit, with amplitudes of the order of 10{sup 3} up to about 100 TeV. A decomposition of the arrival direction distribution into spherical harmonics shows that most of the power is contained in the low-multipole ( ℓ ≤ 4) moments. However, higher multipole components are found to be statistically significant down to an angular scale of less than 10°, approaching the angular resolution of the detector. Above 100 TeV, a change in the morphology of the arrival direction distribution is observed, and the anisotropy is characterized by a wide relative deficit whose amplitude increases with primary energy up to at least 5 PeV, the highest energies currently accessible to IceCube. No time dependence of the large- and small-scale structures is observed in the period of six years covered by this analysis. The high-statistics data set reveals more details of the properties of the anisotropy and is potentially able to shed light on the various physical processes that are responsible for the complex angular structure and energy evolution.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Exploring the Structural Behavior of Hydrophilic Diglycolamide Complexes with the Lanthanides and Actinides

In the ongoing effort to meet the anticipated rise in energy demand while maintaining the full-scale abandonment of natural gas and coal, a substantial shift in our considerations of green energy is required through the wider adoption of nuclear power. However, the advantages of nuclear power are hindered by the challenges of safely managing nuclear waste. Hydrophilic diglycolamides (DGA) ligands have been explored for use as stripping agents in various lanthanide and actinide partitioning processes. Additionally, the separation of lanthanide fission products and transplutonic actinides can serve multifaceted advantages in that the separation neutron poisoning rare earth element (REE) fission products from minor actinides from used nuclear fuel (UNF) can be mutually beneficial to the fundamental research behind REE separations and UNF separations. With this in mind, understanding the bonding differences between the Ln3+ and An3+ ions as a function of DGA structure, such as varying the alkyl groups on each of the amide functional groups, has an influence on the molecule’s selectivity and solubility and whose changes in molecular architecture also impact the radiolytic behavior of these molecules. As such, crystal structures of (Y3+, La-Lu3+, excl. Pm, Pu3+/4+, Am3+, Bk3+, and Cf3+) with hydrophilic diglycolamides show the systematic progression, and changes in coordination habits, as a function of a f-element ions. These coordination complexes see a consistent decrease in bond lengths and changes in the coordination environment while traversing across the f-elements, owing to the effects of the lanthanide contraction as well as local geometry around the metal centers. Direct comparisons of lanthanide with actinide DGA structures display both striking similarities in coordination with earlier actinides of Pu and Am, while later actinides of Bk and Cf display a complete breakdown of these observed trends. This work has also presented the rare opportunity to study homoleptic DGA compounds across multiple oxidation states have provided insight into their nuanced differences in structural chemistry.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2013

The structure of the SBP-Tag–streptavidin complex reveals a novel helical scaffold bridging binding pockets on separate subunits

The structure of the SBP-Tag–streptavidin complex reveals a novel mode of peptide recognition in which a single peptide binds simultaneously to biotin-binding pockets from adjacent subunits of streptavidin. The molecular details of peptide recognition suggest how the SBP-Tag can be further modified to become an even more useful tag for a wider range of biotechnological applications. The 38-residue SBP-Tag binds to streptavidin more tightly (K{sub d} ≃ 2.5–4.9 nM) than most if not all other known peptide sequences. Crystallographic analysis at 1.75 Å resolution shows that the SBP-Tag binds to streptavidin in an unprecedented manner by simultaneously interacting with biotin-binding pockets from two separate subunits. An N-terminal HVV peptide sequence (residues 12–14) and a C-terminal HPQ sequence (residues 31–33) form the bulk of the direct interactions between the SBP-Tag and the two biotin-binding pockets. Surprisingly, most of the peptide spanning these two sites (residues 17–28) adopts a regular α-helical structure that projects three leucine side chains into a groove formed at the interface between two streptavidin protomers. The crystal structure shows that residues 1–10 and 35–38 of the original SBP-Tag identified through in vitro selection and deletion analysis do not appear to contact streptavidin and thus may not be important for binding. A 25-residue peptide comprising residues 11–34 (SBP-Tag2) was synthesized and shown using surface plasmon resonance to bind streptavidin with very similar affinity and kinetics when compared with the SBP-Tag. The SBP-Tag2 was also added to the C-terminus of β-lactamase and was shown to be just as effective as the full-length SBP-Tag in affinity purification. These results validate the molecular structure of the SBP-Tag–streptavidin complex and establish a minimal bivalent streptavidin-binding tag from which further rational design and optimization can proceed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

X-ray Intermolecular Structure Factor (XISF): separation of intra- and intermolecular interactions from total X-ray scattering data

XISF is a MATLAB program developed to separate intermolecular structure factors from total X-ray scattering structure factors for molecular liquids and amorphous solids. The program is built on a trust-region-reflective optimization routine with the r.m.s. deviations of atoms physically constrained. XISF has been optimized for performance and can separate intermolecular structure factors of complex molecules.

MATLAB↗
DOE OSTI2016

Tunneling magnetoresistance and electroresistance in Fe/PbTiO{sub 3}/Fe multiferroic tunnel junctions

We perform first-principles electronic structure and spin-dependent transport calculations for a Fe/PbTiO{sub 3}/Fe multiferroic tunnel junction with asymmetric TiO{sub 2}- and PbO-terminated interfaces. We demonstrate that the interfacial electronic reconstruction driven by the in situ screening of ferroelectric polarization, in conjunction with the intricate complex band structure of barrier, play a decisive role in controlling the spin-dependent tunneling. Reversal of ferroelectric polarization results in a transition from insulating to half-metal-like conducting state for the interfacial Pb 6p{sub z} orbitals, which acts as an atomic-scale spin-valve by releasing the tunneling current in antiparallel magnetization configuration as the ferroelectric polarization pointing to the PbO-terminated interface. This effect produces large change in tunneling conductance. Our results open an attractive avenue in designing multiferroic tunnel junctions with excellent performance by exploiting the interfacial electronic reconstruction originated from the in situ screening of ferroelectric polarization.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

A discretized representation for Monte Carlo simulation of deformed semiflexible chains

In this study, we present a novel orientation discretization approach based on the rhombic triacontahedron for Monte Carlo simulations of semiflexible polymer chains, aiming at enhancing structural analysis through rheo-small-angle scattering (rheo-SAS). Our approach provides a more accurate representation of the geometric features of semiflexible chains under deformation, surpassing the capabilities of traditional lattice structures. Validation against the Kratky–Porod chain system demonstrated superior consistency, underscoring its potential to significantly improve the precision of uncovering geometric details from rheo-SAS data. Further, this approach opens new avenues for investigating the conformations of semiflexible polymers and mechanically induced phase transitions in more complex polymer structures, offering deeper insights into their behavior under various conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Ab Initio Simulation of Structure and Properties in Ni-Based Superalloys: Haynes282 and Inconel740

The electronic structure, interatomic bonding, and mechanical properties of two supercell models of Ni-based superalloys are calculated using ab initio density functional theory methods. The alloys, Haynes282 and Inconel740, are face-centered cubic lattices with 864 atoms and eleven elements. These multi-component alloys have very complex electronic structure, bonding and partial-charge distributions depending on the composition and strength of the local bonding environment. We employ the novel concept of total bond order density (TBOD) and its partial components (PBOD) to ascertain the internal cohesion that controls the intricate balance between the propensity of metallic bonding between Ni, Cr and Co, and the strong bonds with C and Al. We find Inconel740 has slightly stronger mechanical properties than Haynes282. Both Inconel740 and Haynes282 show ductile natures based on Poisson’s ratio. Poisson’s ratio shows marginal correlation with the TBOD. Comparison with more conventional high entropy alloys with equal components are discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Effect of a por-Si Buffer Layer on the Structure and Morphology of Epitaxial In{sub x}Ga{sub 1 – x}N/Si(111) Heterostructures

Integrated heterostructures exhibiting nanocolumnar morphology of the In{sub x}Ga{sub 1 – x}N/Si(111) film are grown on a single-crystal silicon substrate (c-Si(111)) and a substrate with a nanoporous buffer sublayer (por-Si) by molecular-beam epitaxy with the plasma activation of nitrogen. Using a complex of structural and microscopic methods of analysis, it is shown that the growth of In{sub x}Ga{sub 1 – x}N nanocolumns on a nanoporous buffer layer offers a number of advantages over growth on c-Si. The por-Si substrate predetermines the preferential orientation of the growth of In{sub x}Ga{sub 1 – x}N nanocolumns closer to the Si(111) orientation direction and makes it possible to produce In{sub x}Ga{sub 1 – x}N nanocolumns with a higher degree of crystallographic uniformity and with a nanocolumn lateral size of ~40 nm unified over the entire surface. The growth of In{sub x}Ga{sub 1 – x}N nanocolumns on a por-Si layer yields a decrease in the strain components ε{sub xx} and ε{sub zz} and in the density of edge and screw dislocations compared to the corresponding parameters for In{sub x}Ga{sub 1 – x}N nanocolumns grown on c-Si. The In{sub x}Ga{sub 1 – x}N nanocolumnar layer fabricated on por-Si exhibits a 20% higher charge-carrier concentration compared to the layer grown on c-Si as well as a higher intensity of the photoluminescence quantum yield (+25%).

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Accurate Prediction of HSE06 Band Structures for a Diverse Set of Materials Using Δ-Learning

Here we used machine learning (ML) to accurately predict eigenvalues of the hybrid HSE06 functional using eigenvalues computed by the less computationally expensive PBE functional and associated electronic features based on the k-point resolved atomic band character. The ML model was trained by using eigenvalues from only one k-point for each of the 168 compounds in the training set. The HSE06 eigenvalues across all k-points were then predicted for a separate set of 169 compounds with a mean absolute error (MAE) of 0.13 eV, representing a significant improvement over the error of PBE-computed eigenvalues relative to that of HSE06 (MAE = 0.96 eV). These accurately predicted eigenvalues result in remarkably accurate predictions for the band structures, projected density of states, and band gaps, even though the model was not explicitly trained on these other properties. Finally, we demonstrate that our ML model has a similar accuracy for both ternary and quaternary compounds well outside the initial training set and on systems with 112 and 160 atoms, demonstrating its potential to rapidly predict HSE06-quality electronic structures of complex materials that are practically unfeasible for HSE06.

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

Crystal and Magnetic Structures of the Ternary Ho 2 Ni 0.8 Si 1.2 and Ho 2 Ni 0.8 Ge 1.2 Compounds: An Example of Intermetallics Crystallizing with the Zr 2 Ni 1–x P Prototype

We report two new rare-earth (R) ternary intermetallic compounds—Ho 2 Ni 0.8 T 1.2 with T = Si and Ge—that correspond to the R 5 Ni 2 T 3 phase earlier reported to form in Dy–Ni–T and Ho–Ni–T ternary systems. The compounds crystallize in a filled version of the orthorhombic Zr 2 Ni 1–x P-type structure with x = 0.52; their stoichiometry, determined from both single-crystal and powder X-ray diffraction data, is centered on Ho 2 Ni 0.8 T 1.2 with a narrow solid solubility range for the silicide, while the germanide appears to be a line phase. In addition to R = Dy and Ho, R 2 Ni 0.8 T 1.2 compounds also form for R = Y and Tb, representing the first examples of rare-earth-based compounds adopting the Zr 2 Ni 1–x P structural prototype. Bulk magnetization data reveal the main transitions of the ferrimagnetic or ferromagnetic type at TC = 38 K for Ho 2 Ni 0.8 Si 1.2 and TC = 37 K for Ho 2 Ni 0.8 Ge 1.2 , which are followed by subsequent magnetic reordering at lower temperatures. Neutron diffraction shows complex magnetic structures below T C with both ferromagnetic and antiferromagnetic components and magnetic propagation vector κ 1 = [0, 0, 0]. Below T N ≅ 24 K (22 K) for the silicide (germanide), an additional antiferromagnetic coupling following an incommensurate magnetic propagation vector κ 2 = [κ x , 0, 0] appears to coexist with the first magnetic structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Electronic structure of magnetic semiconductor CdCr{sub 2}Te{sub 4}: A possible spin-dependent symmetry filter

We present a theoretical investigation of the electronic and magnetic structure of spinel CdCr{sub 2}Te{sub 4} using density functional theory, its extensions via onsite Hubbard U interactions, and a screened-hybrid-functional exchange potential. We find that the ground state is semiconducting within the latter approach, and within this magnetic-semiconducting system, we compute the complex band structure, finding a slowly decaying evanescent Δ{sup ~}{sub 1} state possibly suitable for realizing a spin-dependent symmetry filter effect.

36 MATERIALS SCIENCE↗