Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Structure Determination”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 847 records · Page 47
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Crystallographic characterization of (C 5 H 4 SiMe 3 ) 3 U(BH 4 )

New syntheses have been developed for the synthesis of (borohydrido-κ 3 H)tris­[η 5 -(tri­methyl­sil­yl)cyclo­penta­dien­yl]uranium(IV), [U(BH 4 )(C 8 H 13 Si) 3 ] or Cp' 3 U(BH 4 ) (Cp' = C 5 H 4 SiMe 3 ) and its structure has been determined by single-crystal X-ray crystallography. This compound crystallized in the space group P1¯ and the structure features three η 5 -coordinated Cp' rings and a κ 3 -coordinated (BH 4 ) – ligand.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Effect of the Electric Field Strength on the Energy Resolution of Cr/CdTe/Pt Detectors

The electrical and spectrometric characteristics of the Cr/cadmium telluride (CdTe)/Pt structure with a metal-semiconductor type rectifying contact, used in X/γ-ray detectors, are investigated. For the detectors fabrication, chlorine-doped CdTe crystals with a resistivity of (3-6) × 10 9 Ω cm at 293 K were used. 137Cs spectra and their modification by applied voltage change were obtained. The reverse bias voltage corresponding to the best energy resolution of the Cr/CdTe/Pt structure is experimentally determined. The concentration of impurities N in the crystal, which determines the thickness of the space-charge region, is estimated. Finally, an energy resolution deterioration of the Cr/CdTe/Pt structure with increasing voltage is explained due to the Gunn effect.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses

Influenza A viruses (IAV) initiate infection by binding to glycans with terminal sialic acids on the cell surface. Hosts of IAV variably express two major forms of sialic acid, N-acetylneuraminic acid (NeuAc) and N-glycolylneuraminic acid (NeuGc). NeuGc is produced in most mammals, including horses and pigs, but is absent in humans, ferrets, and birds. The only known naturally occurring IAV that exclusively bind NeuGc are extinct highly pathogenic equine H7N7 viruses. We determined the crystal structure of a representative equine H7 hemagglutinin (HA) in complex with NeuGc and observed high similarity in the receptor-binding domain with an avian H7 HA. To determine the molecular basis for NeuAc and NeuGc specificity, we performed systematic mutational analyses, based on the structural insights, on two distant avian H7 HAs and an H15 HA. We found that the A135E mutation is key for binding α2,3-linked NeuGc but does not abolish NeuAc binding. The additional mutations S128T, I130V, T189A, and K193R converted the specificity from NeuAc to NeuGc. We investigated the residues at positions 128, 130, 135, 189, and 193 in a phylogenetic analysis of avian and equine H7 HAs. This analysis revealed a clear distinction between equine and avian residues. The highest variability was observed at key position 135, of which only the equine glutamic acid led to NeuGc binding. These results demonstrate that genetically distinct H7 and H15 HAs can be switched from NeuAc to NeuGc binding and vice versa after the introduction of several mutations, providing insights into the adaptation of H7 viruses to NeuGc receptors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structural and dynamic effects of paraoxon binding to human acetylcholinesterase by X-ray crystallography and inelastic neutron scattering

Organophosphorus (OP) compounds, including nerve agents and some pesticides, covalently bind to the catalytic serine of human acetylcholinesterase (hAChE), thereby inhibiting acetylcholine hydrolysis necessary for efficient neurotransmission. Oxime antidotes can reactivate the OP-conjugated hAChE, but reactivation efficiency can be low for pesticides, such as paraoxon (POX). Understanding structural and dynamic determinants of OP inhibition and reactivation can provide insights to design improved reactivators. Here, in this study, X-ray structures of hAChE with unaged POX, with POX and oximes MMB4 and RS170B, and with MMB4 are reported. A significant conformational distortion of the acyl loop was observed upon POX binding, being partially restored to the native conformation by oximes. Neutron vibrational spectroscopy combined with molecular dynamics simulations showed that picosecond vibrational dynamics of the acyl loop soften in the ~20–50 cm –1 frequency range. The acyl loop structural perturbations may be correlated with its picosecond vibrational dynamics to yield more comprehensive template for structure-based reactivator design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Quasi-particle interference of the van Hove singularity in Sr2RuO4

Abstract The single-layered ruthenate Sr 2 RuO 4 is one of the most enigmatic unconventional superconductors. While for many years it was thought to be the best candidate for a chiral p -wave superconducting ground state, desirable for topological quantum computations, recent experiments suggest a singlet state, ruling out the original p -wave scenario. The superconductivity as well as the properties of the multi-layered compounds of the ruthenate perovskites are strongly influenced by a van Hove singularity in proximity of the Fermi energy. Tiny structural distortions move the van Hove singularity across the Fermi energy with dramatic consequences for the physical properties. Here, we determine the electronic structure of the van Hove singularity in the surface layer of Sr 2 RuO 4 by quasi-particle interference imaging. We trace its dispersion and demonstrate from a model calculation accounting for the full vacuum overlap of the wave functions that its detection is facilitated through the octahedral rotations in the surface layer.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Structure of saguaro cactus virus 3′ translational enhancer mimics 5′ cap for eIF4E binding

The genomes of several plant viruses contain RNA structures at their 3' ends called cap-independent translation enhancers (CITEs) that bind the host protein factors such as mRNA 5' cap-binding protein eIF4E for promoting cap-independent genome translation. However, the structural basis of such 5' cap-binding protein recognition by the uncapped RNA remains largely unknown. Here, we have determined the crystal structure of a 3' CITE, panicum mosaic virus-like translation enhancer (PTE) from the saguaro cactus virus (SCV), using a Fab crystallization chaperone. The PTE RNA folds into a three-way junction architecture with a pseudoknot between the purine-rich R domain and pyrimidine-rich Y domain, which organizes the overall structure to protrude out a specific guanine nucleotide, G18, from the R domain that comprises a major interaction site for the eIF4E binding. The superimposable crystal structures of the wild-type, G18A, G18C, and G18U mutants suggest that the PTE scaffold is preorganized with the flipped-out G18 ready to dock into the eIF4E 5' cap-binding pocket. The binding studies with wheat and human eIF4Es using gel electrophoresis and isothermal titration calorimetry, and molecular docking computation for the PTE–eIF4E complex demonstrated that the PTE structure essentially mimics the mRNA 5' cap for eIF4E binding. Such 5' cap mimicry by the uncapped and structured viral RNA highlights how viruses can exploit RNA structures to mimic the host protein-binding partners and bypass the canonical mechanisms for their genome translation, providing opportunities for a better understanding of virus-host interactions and non-canonical translation mechanisms found in many pathogenic RNA viruses.

3' cap-independent translation enhancers↗
DOE OSTI2020

Automated Design of Neuromorphic Networks for Scientific Applications at the Edge

Designing spiking neural networks for neuromorphic deployment is a non-trivial task. It is further complicated when there are resource constraints for the neuromorphic implementation, such as size or power constraints, that may be present in edge applications. In this work, we utilize a previously presented approach, EONS, to design spiking neural networks for a memristive neuromorphic implementation for scientific data applications. We specifically use a multi-objective approach in EONS to maximize network accuracy on the scientific data application task, but also to minimize network size and energy. We illustrate that EONS determines both the network structure and the parameters, removing the burden from the user on determining the appropriate spiking neural network structure, and we show that the resulting networks are very different from the layered structure of typical neural networks. Finally, we show that the multi-objective approach produces smaller, more energy efficient networks than the original EONS approach and produces comparable accuracy to a back-propagation style training approach.

Schuman, Catherine↗
DOE OSTI2020

Electron Nanocrystallography of Complex Materials and Processes

The proposed work is to develop Scanning CBED (SCBED) for the study of multi element crystals, including multiple principal elements alloys or high entropy alloys and relaxor-ferroelectric crystals. SCBED works like scanning transmission electron microscopy (STEM) but records the whole CBED at each probe position. Since CBED is a highly sensitive electron diffraction technique, SCBED combines the full benefits of CBED and STEM. Specifically, the SCBED based approach enables a quantitative determination of local atomic and electronic structures. The proposed work is thus to take advantage of SCBED for the study of complex multi-element crystals. The results from SCBED are expected to complement the methods of electron energy loss spectroscopy (EELS) near edge fine structure for probing local bonds, and X-ray and neutron scattering using the total scattering approach for probing local structure. Under the DOE BES support, we have developed SCBED to determine the structure of high entropy alloys, and we have coupled the work with in-situ compression study of dislocation dynamics to uncover the fundamental mechanisms of crystal slip.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Needle-Like Ferroelastic Domains in Individual Ferroelectric Nanoparticles

Superior structural, physical and electronic properties make ferroelectric nanocrystals essential in enabling a range of next-generation devices. Ferroelectric responses are determined by crystal structure and domain morphology. The ability to reversibly displace, create and annihilate elastic domains is critical to device applications. Whereas electric-field control has been demonstrated for ferroelectric 180° surface domain walls and vortices, similar control of ferroelastic domains and domain boundaries within individual nanocrystals remains challenging. Using controlled external compressive and tensile axial stress, deterministic and reversible control of highly mobile ferroelastic domains and axial polarization in three dimensions is demonstrated in this study. While many studies exist on ferroelastic domains in thin films and bulk, little is known about ferroelastic interactions at the single nanoparticle level, especially involving domain boundaries. Through combining Bragg coherent X-ray diffractive imaging and Landau theory, strain gradients in individual BaTiO3 nanocrystals are shown to stabilize needle-like ferroelastic twin domains. These domains are highly labile under applied axial stress, producing a locally enhanced electric polarization mediated by a ferroelectric phase transition. The efficacy of Bragg coherent X-ray diffractive imaging in studying in operando domains in three-dimensions is demonstrated, while synergy with theory provides a paradigm for domain boundary engineering and potential for nanoscale functional devices.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Combining computational modeling and experimental library screening to affinity-mature VEEV-neutralizing antibody F5

Engineered monoclonal antibodies have proven to be highly effective therapeutics in recent viral outbreaks. However, despite technical advancements, an ability to rapidly adapt or increase antibody affinity and by extension, therapeutic efficacy, has yet to be fully realized. We endeavored to stand-up such a pipeline using molecular modeling combined with experimental library screening to increase the affinity of F5, a monoclonal antibody with potent neutralizing activity against Venezuelan Equine Encephalitis Virus (VEEV), to recombinant VEEV (IAB) E1E2 antigen. We modeled the F5/E1E2 binding interface and generated predictions for mutations to improve binding using a Rosetta-based approach and dTERMen, an informatics approach. The modeling was complicated by the fact that a high-resolution structure of F5 is not available and the H3 loop of F5 exceeds the length for which current modeling approaches can determine a unique structure. A subset of the predicted mutations from both methods were incorporated into a phage display library of scFvs. This library and a library generated by error-prone PCR were screened for binding affinity to the recombinant antigen. Results from the screens identified favorable mutations which were incorporated into 12 human-IgG1 variants. The best variant, containing eight mutations, improved KD from 0.63 nM (parental) to 0.01 nM. While this did not improve neutralization or therapeutic potency of F5 against IAB, it did increase cross-reactivity to other closely related VEEV epizootic and enzootic strains, demonstrating the potential of this method to rapidly adapt existing therapeutics to emerging viral strains.

affinity-maturation↗
DOE OSTI2026

Structural interactions of TLP18.3 and Psb27-H1 to the luminal CP43 and Rubredoxin-ENH1 to the stromal side of Photosystem II in higher plants

TLP18.3 and Psb27 are known proteins on the luminal side of photosystem II. The structural locations of these two proteins are still absent in the currently available higher plant photosystem II cryo-EM structures. We interrogated the structural locations of these proteins using chemical cross-linking followed by liquid chromatography/tandem MS analysis. Structural mass spectrometry results then provided chemical restrains to direct structural modelling to determine the collective binding/stabilization of these two proteins to the luminal PSII CP43 protein. Using this pipeline, we also found the structural location of a Rubredoxin protein on the stromal side of PSII. Discovery of this redox active iron-sulfur protein in the vicinity of PSII subunit D1/D2 proteins, greatly showcases the importance of the redox processes that are potentially involved in PSII assembly or less known steady state functionality or photoprotection. This structural mass spectrometry platform high-lights its powerful applicability in protein complex discovery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Vascular K ATP channel structural dynamics reveal regulatory mechanism by Mg-nucleotides

Vascular tone is dependent on smooth muscle K ATP channels comprising pore-forming Kir6.1 and regulatory SUR2B subunits, in which mutations cause Cantú syndrome. Unique among K ATP isoforms, they lack spontaneous activity and require Mg-nucleotides for activation. Structural mechanisms underlying these properties are unknown. Here, we determined cryogenic electron microscopy structures of vascular K ATP channels bound to inhibitory ATP and glibenclamide, which differ informatively from similarly determined pancreatic K ATP channel isoform (Kir6.2/SUR1). Unlike SUR1, SUR2B subunits adopt distinct rotational “propeller” and “quatrefoil” geometries surrounding their Kir6.1 core. The glutamate/aspartate-rich linker connecting the two halves of the SUR-ABC core is observed in a quatrefoil-like conformation. Molecular dynamics simulations reveal MgADP-dependent dynamic tripartite interactions between this linker, SUR2B, and Kir6.1. The structures captured implicate a progression of intermediate states between MgADP-free inactivated, and MgADP-bound activated conformations wherein the glutamate/aspartate-rich linker participates as mobile autoinhibitory domain, suggesting a conformational pathway toward K ATP channel activation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Detection, monitoring, and determination of location of changes in metallic structures using multimode acoustic signals

Acoustic transducers generate and receive acoustic signals at multiple locations along a surface of rigid structure, wherein longitudinal spacing between transducer locations define measurement zones. Acoustic signals with chosen amplitude-time-frequency characteristics excite multiple vibration modes in the structure within each zone. Small mechanical changes in inspection zones lead to scattering and attenuation of broadband acoustic signals, which are detectable as changes in received signal characteristics as part of a through-transmission technique. Additional use of short, narrowband pulse acoustic signals as part of a pulse-echo technique allows determination of the relative location of the mechanical change within each zone based on the differential delay profiles. For accurate acoustic modeling and simulation, the mesh size, time step, time delay, and time-window size are optimized. Frequency normalization of the Short-Time Fourier Transform of acoustic response output improves experiment-simulation cross-validation. Applications of the method to structures with arbitrarily complex geometries are also demonstrated.

Findikoglu, Alp Tugrul↗
DOE OSTI2021

Candidate structure for the H 2 -PRE phase of solid hydrogen

Experimental progress finally reached the metallic solid hydrogen phase, which was predicted by Wigner and Huntington over 80 years ago. However, the different structures in the phase diagram are still being debated due to the difficulty of diffraction experiments for high-pressured hydrogen. The determination of crystal structures under extreme condition is both of the basic condensed matter physics, and in planetary science: the behavior of giant gaseous planets (e.g., Jupiter and Saturn) strongly depends on the properties of inner high-pressured hydrogen. This work describes possible structures appearing under high pressures of 400~600 GPa. We applied a structural search using particle swarm optimization with density functional theory (DFT) to propose several candidate structures. For these structures, we performed fixed-node diffusion Monte Carlo simulations combined with DFT zero-point energy corrections to confirm their relative stability. We found P2 1 /c-8 as a promising candidate structure for the H 2 -PRE phase. P2 1 /c-8 is predicted the most stable at 400 and 500 GPa. P2 1 /c-8 reproduces qualitatively the IR spectrum peaks observed in the H 2 -PRE phase.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Embedded acoustic sensing and monitoring techniques for small modular reactors

The goal of this project was to study the applicability of specific innovative instrumentation techniques for assessing parameters needed for safe small modular reactor operation and safeguarding of nuclear material. Small modular reactor core designs are currently being developed to provide energy more effectively and efficiently than in the past because they can be built as modules at fabrication sites and then transported to a power-producing facility. However, these modules and/or the final core will often be sealed and not accessible again until disposal. Instead of instruments that access the core directly, during and after operation, to monitor flux/dose and structural integrity, as current power plants use, new sensors need to be designed that can be built into the reactor initially to determine operating history, structural integrity through operation of the system, and nuclear material accountancy after shutdown and before disposition of the core. Embedded sensors already exist that can provide neutron flux, gamma dose, and temperatures, but techniques to expand upon these for assessing structural health and material inventory in the system over time need to be developed. Structural health assessments include the detection and imaging of cracks in the components that could eventually cause radioactive fission products to be released.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

Experimental Investigation of Thermodynamic Stabilization in Boron Imidazolate Frameworks (BIFs) Synthesized by Mechanochemistry

This study experimentally explores the energetics for the formation of boron–imidazolate frameworks (BIFs), which are synthesized by mechanochemistry. The topologically similar frameworks employ the same tetratopic linker based on tetrakis(imidazolyl)boric acid but differ in the monovalent cation metal nodes. This permits assessment of the stabilizing effect of metal nodes in frameworks with sodalite (SOD) and diamondoid (dia) topologies. The enthalpy of formation from endmembers (metal oxide and linker), which define thermodynamic stability of the structures, has been determined by use of acid solution calorimetry. The results show that heavier metal atoms in the node promote greater energetic stabilization of denser structures. Overall, in BIFs the relation between cation descriptors (ionic radius and electronegativity) and thermodynamic stability depends on framework topology. Thermodynamic stability increases with the metallic character of the cation employed as the metal node, independent of the framework topology. In conclusion, the results suggest unifying aspects for thermodynamic stabilization across MOF systems.

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

Structural basis for SARS-CoV-2 envelope protein recognition of human cell junction protein PALS1

The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has created global health and economic emergencies. SARS-CoV-2 viruses promote their own spread and virulence by hijacking human proteins, which occurs through viral protein recognition of human targets. To understand the structural basis for SARS-CoV-2 viral-host protein recognition, here we use cryo-electron microscopy (cryo-EM) to determine a complex structure of the human cell junction protein PALS1 and SARS-CoV-2 viral envelope (E) protein. Our reported structure shows that the E protein C-terminal DLLV motif recognizes a pocket formed exclusively by hydrophobic residues from the PDZ and SH3 domains of PALS1. Our structural analysis provides an explanation for the observation that the viral E protein recruits PALS1 from lung epithelial cell junctions. In addition, our structure provides novel targets for peptide- and small-molecule inhibitors that could block the PALS1-E interactions to reduce E-mediated virulence.

59 BASIC BIOLOGICAL SCIENCES↗