Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “atomic structure”

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 1,459 records · Page 81
All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

Atomic and electronic structures of lutetium oxide Lu{sub 2}O{sub 3}

The chemical composition, electronic structure, structure, and physical properties a lutetium oxide Lu{sub 2}O{sub 3} film are studied by X-ray photoelectron spectroscopy, ellipsometry, and X-ray absorption spectroscopy. The short-range order in Lu{sub 2}O{sub 3} is found to correspond to its cubic modification. The binding energies of the 1s and 2p levels of oxygen and the 4d{sub 5/2} and 4f{sub 7/2} levels of lutetium are 529.2, 5.0 and 7.4, 195.9 eV, respectively. The energy gap determined from the electron energy loss spectrum of the film is 5.9 eV. The electron energy loss spectra have two peaks at 17.4 and 22.0 eV, which can be attributed to the excitation of bulk plasma oscillations. The dispersion of the refractive index is measured by spectral ellipsometry. The refractive index is shown to increase from 1.82 at 1.5 eV to 2.18 at 5.0 eV, and the high-frequency permittivity of Lu{sub 2}O{sub 3} is 3.31.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2015

Electronic structure investigation of atomic layer deposition ruthenium(oxide) thin films using photoemission spectroscopy

Analyzing and manipulating the electronic band line-up of interfaces in novel micro- and nanoelectronic devices is important to achieve further advancement in this field. Such band alignment modifications can be achieved by introducing thin conformal interfacial dipole layers. Atomic layer deposition (ALD), enabling angstrom-precise control over thin film thickness, is an ideal technique for this challenge. Ruthenium (Ru{sup 0}) and its oxide (RuO{sub 2}) have gained interest in the past decade as interfacial dipole layers because of their favorable properties like metal-equivalent work functions, conductivity, etc. In this study, initial results of the electronic structure investigation of ALD Ru{sup 0} and RuO{sub 2} films via photoemission spectroscopy are presented. These experiments give insight into the band alignment, growth behavior, surface structure termination, and dipole formation. The experiments were performed in an integrated vacuum system attached to a home-built, stop-flow type ALD reactor without exposing the samples to the ambient in between deposition and analysis. Bis(ethylcyclopentadienyl)ruthenium(II) was used as precursor and oxygen as reactant. The analysis chamber was outfitted with X-ray photoemission spectroscopy (LIXPS, XPS). The determined growth modes are consistent with a strong growth inhibition situation with a maximum average growth rate of 0.21 Å/cycle for RuO{sub 2} and 0.04 Å/cycle for Ru.{sup 0} An interface dipole of up to −0.93 eV was observed, supporting the assumption of a strongly physisorbed interface. A separate experiment where the surface of a RuO film was sputtered suggests that the surface is terminated by an intermediate, stable, non-stoichiometric RuO{sub 2}/OH compound whose surface is saturated with hydroxyl groups.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

Potential-specific structure at the hematite-electrolyte interface

The atomic-scale structure of interfaces between metal oxides and aqueous electrolytes controls their catalytic, geochemical, and corrosion behavior. Measurements that probe these interfaces in situ provide important details of ion and solvent arrangements, but atomically precise structural models do not exist for common oxide-electrolyte interfaces far from equilibrium. Using a novel cell, we measured the structure of the hematite (a-Fe 2 O 3 ) (110$\bar{2}$)-electrolyte interface under controlled electrochemical bias using synchrotron crystal truncation rod X ray scattering. At increasingly cathodic potentials, charge-compensating protonation of surface oxygen groups increases the coverage of specifically bound water while adjacent water layers displace outwardly and became disordered. Returning to open circuit potential leaves the surface in a persistent metastable protonation state. The flux of current and ions at applied potential is thus regulated by a unique interfacial electrolyte environment, suggesting that electrical double layer models should be adapted to the dynamically changing interfacial structure far from equilibrium.

electrochemistry↗
DOE OSTI2015

Chemical reactivity of twin-modified copper nanowire surfaces

Effect of twin boundary (TB) spacing on atomic surface structure and chemical reactivity of nanotwinned Cu nanowires (NWs) is investigated. Post-etching surface structure and wire diameter of Cu NWs were examined by transmission electron microscopy. When TB spacing is less than 10 nm, the Cu NWs remain almost intact after chemical attack and show faceted surface structures with low atomic step density. A mechanism based on surface tension torque acting on TB/surface triple junctions is proposed to explain the faceted structure formation and enhanced corrosion resistance of nanotwinned Cu NWs.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Ordering and dimensional crossovers in metallic glasses and liquids

The atomic-level structures of liquids and glasses are amorphous, lacking long-range order. We characterize the atomic structures by integrating radial distribution functions (RDF) from molecular dynamics (MD) simulations for several metallic liquids and glasses: Cu 46 Zr 54 , Ni 80 Al 20 , Ni 33.3 Zr 66.7 , and Pd 82 Si 18 . Resulting cumulative coordination numbers (CN) show that metallic liquids have a dimension of d = 2.55 ± 0.06 from the center atom to the first coordination shell and metallic glasses have d = 2.71 ± 0.04, both less than 3. Between the first and second coordination shells, both phases crossover to a dimension of d = 3, as for a crystal. Observations from discrete atom center-of-mass position counting are corroborated by continuously counting Cu glass- and liquid-phase atoms on an artificial grid, which accounts for the occupied atomic volume. Results from Cu grid analysis show short-range d = 2.65 for Cu liquid and d = 2.76 for Cu glass. Cu grid structures crossover to d = 3 at ξ ~ 8 Å (~3 atomic diameters). We study the evolution of local structural dimensions during quenching and discuss its correlation with the glass transition phenomenon.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Nitrogenase MoFe protein from Clostridium pasteurianum at 1.08 Å resolution: comparison with the Azotobacter vinelandii MoFe protein

Determination of the nitrogenase MoFe protein from C. pasteurianum at 1.08 Å resolution and comparison to its distinct ortholog from A. vinelandii at atomic resolution reveals conserved structural arrangements that are significant to the function of nitrogenase. The X-ray crystal structure of the nitrogenase MoFe protein from Clostridium pasteurianum (Cp1) has been determined at 1.08 Å resolution by multiwavelength anomalous diffraction phasing. Cp1 and the ortholog from Azotobacter vinelandii (Av1) represent two distinct families of nitrogenases, differing primarily by a long insertion in the α-subunit and a deletion in the β-subunit of Cp1 relative to Av1. Comparison of these two MoFe protein structures at atomic resolution reveals conserved structural arrangements that are significant to the function of nitrogenase. The FeMo cofactors defining the active sites of the MoFe protein are essentially identical between the two proteins. The surrounding environment is also highly conserved, suggesting that this structural arrangement is crucial for nitrogen reduction. The P clusters are likewise similar, although the surrounding protein and solvent environment is less conserved relative to that of the FeMo cofactor. The P cluster and FeMo cofactor in Av1 and Cp1 are connected through a conserved water tunnel surrounded by similar secondary-structure elements. The long α-subunit insertion loop occludes the presumed Fe protein docking surface on Cp1 with few contacts to the remainder of the protein. This makes it plausible that this loop is repositioned to open up the Fe protein docking surface for complex formation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Atomic resolution crystal structure of VcLMWPTP-1 from Vibrio cholerae O395: Insights into a novel mode of dimerization in the low molecular weight protein tyrosine phosphatase family

Highlights: • VcLMWPTP-1 forms dimer in solution. • The dimer is catalytically active unlike other reported dimeric LMWPTPs. • The formation of extended dimeric surface excludes the active site pocket. • The surface bears closer resemblance to eukaryotic LMWPTPs. - Abstract: Low molecular weight protein tyrosine phosphatase (LMWPTP) is a group of phosphotyrosine phosphatase ubiquitously found in a wide range of organisms ranging from bacteria to mammals. Dimerization in the LMWPTP family has been reported earlier which follows a common mechanism involving active site residues leading to an enzymatically inactive species. Here we report a novel form of dimerization in a LMWPTP from Vibrio cholera 0395 (VcLMWPTP-1). Studies in solution reveal the existence of the dimer in solution while kinetic study depicts the active form of the enzyme. This indicates that the mode of dimerization in VcLMWPTP-1 is different from others where active site residues are not involved in the process. A high resolution (1.45 Å) crystal structure of VcLMWPTP-1 confirms a different mode of dimerization where the active site is catalytically accessible as evident by a tightly bound substrate mimicking ligand, MOPS at the active site pocket. Although being a member of a prokaryotic protein family, VcLMWPTP-1 structure resembles very closely to LMWPTP from a eukaryote, Entamoeba histolytica. It also delineates the diverse surface properties around the active site of the enzyme.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

All-Atom Simulations Uncover Structural and Dynamical Properties of STING Proteins in the Membrane System

Recent studies have shown that the stimulator of interferon gene (STING) protein plays a central role in the immune system by facilitating the production of type I interferons in cells. The STING signaling pathway is also a prominent activator of cancer-killing T cells that initiate a powerful adaptive immune response. Since biomolecular signaling pathways are complicated and not easily identified through traditional experiments, molecular dynamics (MD) has often been used to study structural and dynamical responses of biological pathways. In this work, we carried out MD simulations for full-length chicken and human STING (chSTING and hSTING) proteins. Specifically, we investigated ligand-bound closed (holo) and ligand-unbound open (apo) forms of STING in the membrane system by comparing their conformational and dynamical differences. Our research provides clues for understanding the mechanism of the STING signaling pathway by uncovering detailed insights for the examined systems: the residues from each chain in the binding pocket are strongly correlated to one another in the open STING structure compared with those in the closed STING structure. Ligand-bound closed STING displays ~174° rotation of the ligand-binding domain (LBD) relative to the open STING structure. The dynamical analysis of residue Cys148 located in the linker region of hSTING does not support the earlier hypothesis that Cys148 can form disulfide bonds between adjacent STING dimers. We also demonstrate that using the full-length proteins is critical, since the MD simulations of the LBD portion alone cannot properly describe the global conformational properties of STING.

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

Energetics and Structure of Nickel Atoms and Nanoparticles on MgO(100)

The growth morphology and interfacial energetics of vapor deposited Ni on the MgO(100) surface at 300 and 100 K have been studied using single crystal adsorption calorimetry (SCAC), He + low-energy ion scattering spectroscopy (LEIS), X-ray photoelectron spectroscopy (XPS), and low-energy electron diffraction (LEED). At 300 K, the Ni atoms grow as three-dimensional nanoparticles with a saturation number density of 5 × 10 16 particles/m 2 . The differential heat of adsorption at 300 K increases rapidly with coverage, from 276 (initially) to 311 kJ/mol by 0.4 ML. Thereafter, it slowly increases asymptotically to the sublimation enthalpy of bulk Ni (430 kJ/ml) by 9 ML. The Ni 2p 3/2 XPS peak binding energy at 300 K is initially (i.e., at 0.16 ML) 1.4 eV higher than that for bulk Ni(solid), but it decreases to that value at high coverage. The Ni atoms form a metastable phase at 300 K when in nanoparticles with diameter <2.5 nm, and the adhesion energy of such Ni nanoparticles to MgO(100) was found to be 3.05 J/m 2 . At 100 K, the Ni atoms form single adatoms and then 0.17 nm thick 2D islands at low coverage with fewer Ni-Ni bonds compared to the Ni nanoparticles formed at 300 K. Thus, the initial heat (i.e., for the first ~0.03 ML) is 148 kJ/mol at 100 K, 128 kJ/mol lower than at 300 K, and remains lower for the 2D islands. With increasing coverage at 100 K, the tiny 2D Ni islands grow in size to cover nearly the entire surface before thickening. Lastly, the XPS Ni 2p 3/2 peak binding energy for 0.21 ML Ni on MgO(100) at 100 K is 2.2 eV higher than that for bulk Ni(solid), suggesting charge transfer from Ni to MgO(100) and formation of Ni 2+ at very low coverage.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗