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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 1,045 records · Page 58
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

A New Graphical Dismantling Process Simulation Technology for Flexible Planning of Nuclear Facility

The dismantling of highly radioactive components of the nuclear facility is one of the most difficult activities in decommissioning. In the planning stage, the dismantling scenario including dismantling equipment and processes has a significant effect on the cost and safety of the whole decommissioning. High level radiation of the dismantling object such as a reactor pressure vessel (RPV) and its internals restricts access by human workers, and makes an accident during the dismantling process more difficult to deal with. Decommissioning of nuclear facilities demand a large scale of budget and high level of safety, and therefore the preliminary verification of dismantling scenarios by graphical simulation has special importance at planning stage. In recent years, the manufacturing industry has aggressively adopted the virtual manufacturing technology to verify the facilities and processes with high efficiency. The virtual manufacturing technology was beginning to be adopted in the area of the nuclear facility decommissioning. The dismantling process of the Rotary Specimen Rack (RSR) in the Korea Research Reactor-1 and 2 was established and it was also applied to replace the steam generators on time and on budget in San Onofre Nuclear Generating Station. Current virtual manufacturing technologies are not sufficient for the area of nuclear facility decommissioning because the object segmenting function absolutely required for graphical simulations over various dismantling scenarios is unavailable. This paper proposes a new technology for graphical decommissioning simulator which is able to simulate various dismantling scenarios over nuclear facilities including repetitive object cuttings of heavy and complex structures by applying flexible cutting algorithm.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

An Accelerated Clip Algorithm for Unstructured Meshes: A Batch-Driven Approach

The clip technique is a popular method for visualizing complex structures and phenomena within 3D unstructured meshes. Meshes can be clipped by specifying a scalar isovalue to produce an output unstructured mesh with its external surface as the isovalue. Similar to isocontouring, the clipping process relies on scalar data associated with the mesh points, including scalar data generated by implicit functions such as planes, boxes, and spheres, which facilitates the visualization of results interior to the grid. In this paper, we introduce a novel batch-driven parallel algorithm based on a sequential clip algorithm designed for high-quality results in partial volume extraction. Our algorithm comprises five passes, each progressively processing data to generate the resulting clipped unstructured mesh. The novelty lies in the use of fixed-size batches of points and cells, which enable rapid workload trimming and parallel processing, leading to a significantly improved memory footprint and run-time performance compared to the original version. On a 32-core CPU, the proposed batch-driven parallel algorithm demonstrates a run-time speed-up of up to 32.6x and a memory footprint reduction of up to 4.37x compared to the existing sequential algorithm. The software is currently available under an open-source license in the VTK visualization system.

Tsalikis, Spiros↗
DOE OSTI2015

Molecular and electronic structure of osmium complexes confined to Au(111) surfaces using a self-assembled molecular bridge

The molecular and electronic structure of Os(II) complexes covalently bonded to self-assembled monolayers (SAMs) on Au(111) surfaces was studied by means of polarization modulation infrared reflection absorption spectroscopy, photoelectron spectroscopies, scanning tunneling microscopy, scanning tunneling spectroscopy, and density functional theory calculations. Attachment of the Os complex to the SAM proceeds via an amide covalent bond with the SAM alkyl chain 40° tilted with respect to the surface normal and a total thickness of 26 Å. The highest occupied molecular orbital of the Os complex is mainly based on the Os(II) center located 2.2 eV below the Fermi edge and the LUMO molecular orbital is mainly based on the bipyridine ligands located 1.5 eV above the Fermi edge.

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

Manufacturing of Complex Silicon–Carbon Structures: Exploring Si x C y Materials

This paper reports on the manufacturing of complex three-dimensional Si/C structures via a chemical vapor deposition method. The structure and properties of the grown materials were characterized using various techniques including scanning electron microscopy, aberration-corrected transmission electron microscopy, confocal Raman spectroscopy, and X-ray photoelectron spectroscopy. The spectroscopy results revealed that the grown materials were composed of micro/nanostructures with various compositions and dimensions. These included two-dimensional silicon carbide (SiC), cubic silicon, and various SiC polytypes. The coexistence of these phases at the nano-level and their interfaces can benefit several Si/C-based applications ranging from ceramics and structural applications to power electronics, aerospace, and high-temperature applications. With an average density of 7 mg/cm 3 , the grown materials can be considered ultralightweight, as they are three orders of magnitude lighter than bulk Si/C materials. This study aims to impact how ceramic materials are manufactured, which may lead to the design of new carbide materials or Si/C-based lightweight structures with additional functionalities and desired properties.

36 MATERIALS SCIENCE↗
DOE OSTI2016

X-ray Emission Spectroscopy of Mn Coordination Complexes Toward Interpreting the Electronic Structure of the Oxygen-Evolving Complex of Photosystem II

X-ray emission (XES) spectroscopy is an attractive technique for analysis of the electronic structure of molecules, materials, and metalloproteins. However, a better understanding of XES results is required. Using a combination of experiment and ground-state density functional theory analysis, we rationalize differences in the X-ray emission spectra of multinuclear Mn complexes. Model compounds, including dinuclear [Mn 2 O 2 L' 4 ](ClO 4 ) 3 (L'= 2,2'-bipyridyl, [1]) and two examples from the Mn 4 O 4 L 6 “cubane” family of model compounds (L = (p-R-C 6 H 4 )PO 2 – , R = OCH 3 [2], CH3 [3] ), were compared with the Oxygen Evolving Complex of Photosystem II. Our analysis demonstrates that changes in the structure of the Mn complexes, resulting in changes to the spin polarization, can introduce significant spectral shifts in compounds of the same formal redox state. The implications of changes in spin polarization for understanding photosynthetic water-splitting catalysis is discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Structure of Crenezumab Complex with Aβ Shows Loss of β-Hairpin

Accumulation of amyloid-β (Aβ) peptides and amyloid plaque deposition in brain is postulated as a cause of Alzheimer’s disease (AD). The precise pathological species of Aβ remains elusive although evidence suggests soluble oligomers may be primarily responsible for neurotoxicity. Crenezumab is a humanized anti-Aβ monoclonal IgG4 that binds multiple forms of Aβ, with higher affinity for aggregated forms, and that blocks Aβ aggregation, and promotes disaggregation. To understand the structural basis for this binding profile and activity, we determined the crystal structure of crenezumab in complex with Aβ. The structure reveals a sequential epitope and conformational requirements for epitope recognition, which include a subtle but critical element that is likely the basis for crenezumab’s versatile binding profile. We find interactions consistent with high affinity for multiple forms of Aβ, particularly oligomers. Of note, crenezumab also sequesters the hydrophobic core of Aβ and breaks an essential salt-bridge characteristic of the β-hairpin conformation, eliminating features characteristic of the basic organization in Aβ oligomers and fibrils, and explains crenezumab’s inhibition of aggregation and promotion of disaggregation. These insights highlight crenezumab’s unique mechanism of action, particularly regarding Aβ oligomers, and provide a strong rationale for the evaluation of crenezumab as a potential AD therapy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

A mononuclear nonheme {FeNO} 6 complex: synthesis and structural and spectroscopic characterization

While the synthesis and characterization of {FeNO} 7,8,9 complexes have been well documented in heme and nonheme iron models, {FeNO} 6 complexes have been less clearly understood. Herein, we report the synthesis and structural and spectroscopic characterization of mononuclear nonheme {FeNO} 6 and iron(III)–nitrito complexes bearing a tetraamido macrocyclic ligand (TAML), such as [(TAML)Fe III (NO)] - and [(TAML)Fe III (NO 2 )] 2- , respectively. First, direct addition of NO (g) to [Fe III (TAML)] - results in the formation of [(TAML)Fe III (NO)] - , which is sensitive to moisture and air. The spectroscopic data of [(TAML)Fe III (NO)] - , such as 1 H nuclear magnetic resonance and X-ray absorption spectroscopies, combined with computational study suggest the neutral nature of nitric oxide with a diamagnetic Fe center (S = 0). We also provide alternative pathways for the generation of [(TAML)Fe III (NO)] - , such as the iron–nitrite reduction triggered by protonation in the presence of ferrocene, which acts as an electron donor, and the photochemical iron–nitrite reduction. To the best of our knowledge, the present study reports the first photochemical nitrite reduction in nonheme iron models.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Structural dynamics of a thermally silent triiron( II ) spin crossover defect grid complex

The structural evolution of spin crossover (SCO) complexes during their spin transition at equilibrium and out-of-equilibrium conditions needs to be understood to enable their successful utilisation in displays, actuators and memory components. In this study, diffraction techniques were employed to study the structural changes accompanying the temperature increase and the light irradiation of a defect [2 × 2] triiron(II) metallogrid of the form [Fe II 3 L H 2 (HL H ) 2 ](BF 4 ) 4 ·4MeCN (FE3), L H = 3,5-bis{6-(2,2'-bipyridyl)}pyrazole. Although a multi-temperature crystallographic investigation on single crystals evidenced that the compound does not exhibit a thermal spin transition, the structural analysis of the defect grid suggests that the flexibility of the grid, provided by a metal-devoid vertex, leads to interesting characteristics that can be used for intermolecular cooperativity in related thermally responsive systems. Time-resolved photocrystallography results reveal that upon excitation with a ps laser pulse, the defect grid shows the first two steps of the out-of-equilibrium process, namely the photoinduced and elastic steps, occurring at the ps and ns time scales, respectively. Similar to a previously reported [2 × 2] tetrairon(II) metallogrid, FE3 exhibits a local distortion of the entire grid during the photoinduced step and a long-range distortion of the lattice during the elastic step. Although the lifetime of the pure photoinduced high spin (HS) state is longer in the tetranuclear grid than in the defect grid, suggesting that the global nuclearity plays a crucial role for the lifetime of the photoinduced species, the influence of the co-crystalising solvent on the lifetime of the photoinduced HS state remains unknown. This study sheds light on the out-of-equilibrium dynamics of a thermally silent defect triiron SCO metallogrid.

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

Pathway structure determination in complex stochastic networks with non-exponential dwell times

Analysis of complex networks has been widely used as a powerful tool for investigating various physical, chemical, and biological processes. To understand the emergent properties of these complex systems, one of the most basic issues is to determine the structure and topology of the underlying networks. Recently, a new theoretical approach based on first-passage analysis has been developed for investigating the relationship between structure and dynamic properties for network systems with exponential dwell time distributions. However, many real phenomena involve transitions with non-exponential waiting times. We extend the first-passage method to uncover the structure of distinct pathways in complex networks with non-exponential dwell time distributions. It is found that the analysis of early time dynamics provides explicit information on the length of the pathways associated to their dynamic properties. It reveals a universal relationship that we have condensed in one general equation, which relates the number of intermediate states on the shortest path to the early time behavior of the first-passage distributions. Our theoretical predictions are confirmed by extensive Monte Carlo simulations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Crystal Structure of CYP3A4 Complexed with Fluorol Identifies the Substrate Access Channel as a High-Affinity Ligand Binding Site

Cytochrome P450 3A4 (CYP3A4) is a major human drug-metabolizing enzyme, notoriously known for its extreme substrate promiscuity, allosteric behavior, and implications in drug–drug interactions. Despite extensive investigations, the mechanism of ligand binding to CYP3A4 is not fully understood. We determined the crystal structure of CYP3A4 complexed with fluorol, a small fluorescent dye that can undergo hydroxylation. In the structure, fluorol associates to the substrate channel, well suited for the binding of planar polyaromatic molecules bearing polar groups, through which stabilizing H-bonds with the polar channel residues, such as Thr224 and Arg372, can be established. Mutagenesis, spectral, kinetic, and functional data confirmed the involvement but not strict requirement of Thr224 for the association of fluorol. Collectively, our data identify the substrate channel as a high-affinity ligand binding site and support the notion that hydrophobic ligands first dock to the nearby peripheral surface, before migrating to the channel and, subsequently, into the active site.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Na-Montmorillonite Edge Structure and Surface Complexes: An Atomistic Perspective

The edges of montmorillonite (MMT) react strongly with metals and organic matter, but the atomic structure of the edge and its surface complexes are not unambiguous since the experimental isolation of the edge is challenging. In this study, we introduce an atomistic model of a Na MMT edge that is suitable for classical molecular dynamics (MD) simulations, in particular for the B edge, a representative edge surface of 2:1 phyllosilicates. Our model possesses the surface groups identified through density functional theory (DFT) geometry optimizations performed with variation in the structural charge deficit and Mg substitution sites. The edge structure of the classical MD simulations agreed well with previous DFT-based MD simulation results. Our MD simulations revealed an extensive H-bond network stabilizing the Na-MMT edge surface, which required an extensive simulation trajectory. Some Na counter ions formed inner-sphere complexes at two edge sites. The stronger edge site coincided with the exposed vacancy in the dioctahedral sheet; a weaker site was associated with the cleaved hexagonal cavity of the tetrahedral sheet. The six-coordinate Na complexes were not directly associated with the Mg edge site. Our simulations have demonstrated the heterogeneous surface structures, the distribution of edge surface groups, and the reactivity of the MMT edge.

58 GEOSCIENCES↗
DOE OSTI2017

Synthesis and structure of ruthenium complexes [Ph{sub 3}PCH{sub 2}C{sub 6}H{sub 4}F-4]{sub 2}[RuCl{sub 6}] and [Ph{sub 3}PCH{sub 2}C{sub 6}H{sub 4}F-4][trans-RuCl{sub 4}(dmso-S){sub 2}]

The reaction of (4-fluorobenzyl)triphenylphosphonium chloride with ruthenium(III) chloride hydrate in the presence of hydrochloric acid in dimethyl sulfoxide affords the complex [Ph{sub 3}PCH{sub 2}C{sub 6}H{sub 4}F-4]{sub 2}[RuCl{sub 6}]. In the absence of hydrochloric acid, the reaction gives the complex [Ph{sub 3}PCH{sub 2}C{sub 6}H{sub 4}F-4][trans-RuCl{sub 4}(dmso-S){sub 2}]. The structures of the complexes were studied by {sup 1}H, {sup 19}F, and {sup 31}P NMR spectroscopy and X-ray diffraction.

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

Experimental Structures of Antibody/MHC-I Complexes Reveal Details of Epitopes Overlooked by Computational Prediction

Abstract mAbs to MHC class I (MHC-I) molecules have proved to be crucial reagents for tissue typing and fundamental studies of immune recognition. To augment our understanding of epitopic sites seen by a set of anti–MHC-I mAb, we determined X-ray crystal structures of four complexes of anti–MHC-I Fabs bound to peptide/MHC-I/β2-microglobulin (pMHC-I). An anti–H2-Dd mAb, two anti–MHC-I α3 domain mAbs, and an anti–β2-microglobulin mAb bind pMHC-I at sites consistent with earlier mutational and functional experiments, and the structures explain allelomorph specificity. Comparison of the experimentally determined structures with computationally derived models using AlphaFold Multimer showed that although predictions of the individual pMHC-I heterodimers were quite acceptable, the computational models failed to properly identify the docking sites of the mAb on pMHC-I. The experimental and predicted structures provide insight into strengths and weaknesses of purely computational approaches and suggest areas that merit additional attention.

Immunology↗
DOE OSTI2021

Heterogeneous Composition of Oxygen-Evolving Complexes in Crystal Structures of Dark-Adapted Photosystem II

Photosystem II (PSII) is a homodimeric protein complex that catalyzes water oxidation at the oxygen-evolving complex (OEC), a heterocubanoid calcium-tetra-manganese cluster. Here, we analyze the omit electron-density peaks of the OEC’s metal ions in five X-ray free-electron laser PSII structures at a resolution between 2.15 Å and 1.95 Å. The omit peaks can be described by the total number of electrons and approximated by the variance of electron density distribution when the distributions are spherically symmetric. We show that the number of electrons of metal centers are different in the two OECs of PSII dimers, implying that either the oxidation states and/or occupancies of individual metal ions are different in the two monomers. In either case, we find that the two OECs of dark-adapted PSII dimers in crystals are not fully synchronized in the same expected S 1 state. Differences in redox states of the OEC in PSII only partially account for the observation that the electron densities integrate to a smaller number of electrons than expected. Differences between the determined and expected relative electron numbers are much larger than the estimated errors, indicating heterogeneity in the OEC composition. Here, the reported findings suggest that two OECs of dark-adapted PSII crystals are typically not fully synchronized in the S 1 state and likely generate heterogeneity in the crystallographical data of PSII intermediate structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Perspective: Explicitly correlated electronic structure theory for complex systems

The explicitly correlated approach is one of the most important breakthroughs in ab initio electronic structure theory, providing arguably the most compact, accurate, and efficient ansatz for describing the correlated motion of electrons. Since Hylleraas first used an explicitly correlated wave function for the He atom in 1929, numerous attempts have been made to tackle the significant challenges involved in constructing practical explicitly correlated methods that are applicable to larger systems. These include identifying suitable mathematical forms of a correlated wave function and an efficient evaluation of many-electron integrals. R12 theory, which employs the resolution of the identity approximation, emerged in 1985, followed by the introduction of novel correlation factors and wave function ansätze, leading to the establishment of F12 theory in the 2000s. Rapid progress in recent years has significantly extended the application range of explicitly correlated theory, offering the potential of an accurate wave-function treatment of complex systems such as photosystems and semiconductors. In conclusion, this perspective surveys explicitly correlated electronic structure theory, with an emphasis on recent stochastic and deterministic approaches that hold significant promise for applications to large and complex systems including solids.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Computing virtual dark-field X-ray microscopy images of complex discrete dislocation structures from large-scale molecular dynamics simulations

Dark-field X-ray microscopy (DFXM) is a novel diffraction-based imaging technique that non-destructively maps the local deformation from crystalline defects in bulk materials. While studies have demonstrated that DFXM can spatially map 3D defect geometries, it is still challenging to interpret DFXM images of the high-dislocation-density systems relevant to macroscopic crystal plasticity. This work develops a scalable forward model to calculate virtual DFXM images for complex discrete dislocation structure(s) (DDS) obtained from atomistic simulations. Our new DDS-DFXM model integrates a non-singular formulation for calculating the local strain from the DDS and an efficient geometrical optics algorithm for computing the DFXM image from the strain field. We apply the model to complex DDS obtained from a large-scale mol­ecular dynamics simulation of compressive loading on single-crystal silicon. Simulated DFXM images exhibit prominent contrast for dislocation features between the multiple slip systems, demonstrating the potential of DFXM to resolve features from dislocation multiplication. In conclusion, the integrated DDS-DFXM model provides a toolbox for DFXM experimental design and image interpretation in the context of bulk crystal plasticity for a range of measurements across shock plasticity and the broader materials science community.

X-ray imaging↗