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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Atomistic Structure, Strength, and Kinetic Properties of Intergranular Films in Ceramics

Intergranular films (IGFs) present in polycrystalline oxide and nitride ceramics provide an excellent example of nanoconfined glasses that occupy only a small volume percentage of the bulk ceramic, but can significantly influence various mechanical, thermal, chemical, and optical properties. By employing molecular dynamics computer simulations, we have been able to predict structures and the locations of atoms at the crystal/IGF interface that were subsequently verified with the newest electron microscopies. Modification of the chemistry of the crystal surface in the simulations provided the necessary mechanism for adsorption of specific rare earth ions from the IGF in the liquid state to the crystal surface. Such results had eluded other computational approaches such as ab-initio calculations because of the need to include not only the modified chemistry of the crystal surfaces but also an accurate description of the adjoining glassy IGF. This segregation of certain ions from the IGF to the crystal caused changes in the local chemistry of the IGF that affected fracture behavior in the simulations. Additional work with the rare earth ions La and Lu in the silicon oxynitride IGFs showed the mechanisms for their different affects on crystal growth, even though both types of ions are seen adhering to a bounding crystal surface that would normally imply equivalent affects on grain growth.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Two-way coupled Lagrangian particles in CTH

A basic two-way coupled discrete Lagrangian particle method has been implemented into CTH as a proof of concept. The approach has applications in modeling dilute multiphase phenomena, such as dust entrainment or explosive dispersion of debris. Only a basic Stokes drag law was implemented, but the framework allows for more advanced physics to be implemented in the future, such as particle-particle interactions or state of the art drag models. This memo outlines the modifications made to the code to implement the method, along with simple verification problems for it. The particle data structure used was designed to be as general as possible to facilitate future particle based methods being pursued in the future. For example the same data structure could be leveraged for Lagrangian notional particles used in Probability Density Function approaches, or the advection of a distribution of states such as a Weibull distribution for mechanics.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2019

STXM-XANES analyses of Murchison meteorite samples captured by aerogel after hypervelocity impacts: A potential implication of organic matter degradation for micrometeoroid collection experiments

The Tanpopo mission is an astrobiology space experiment at the Japanese Experiment Module (JEM) 'Kibo' on the International Space Station (ISS). One of the sub-divided themes of the Tanpopo mission is for the intact capture of organic bearing micrometeoroids in low Earth orbit using ultralow density silica aerogel (0.01 g/cm 3 ). In order to evaluate damage to organic matter in micrometeoroids during hyper velocity impacts into the aerogel, Murchison meteorite powdered samples, analogs of organic bearing micrometeoroids, were fired into flight-grade silica aerogel (0.01 g/cm 3 ) using a two-stage light-gas gun with velocities of 4.4 and 5.9 km/s. The recovered Murchison grains were analyzed using scanning transmission X-ray microscopy/X-ray absorption near edge structure (STXM/XANES), transmission electron microscopy (TEM) and nanoscale secondary ion mass spectrometry (NanoSIMS). TEM observation did not show significant modifications of the recovered Murchison grains. Carbon-XANES spectra, however, showed a large depletion of the organic matter after the 5.9 km/s impact, but no such effects nor any significant hydrogen isotopic fractionation were observed after the 4.4 km/s impact.

58 GEOSCIENCES↗
DOE OSTI2024

Protein N -Glycans in Healthy and Sclerotic Glomeruli in Diabetic Kidney Disease

Diabetes is expected to directly affect renal glycosylation; yet to date, there has not been a comprehensive evaluation of alterations in N-glycan composition in the glomeruli of patients with diabetic kidney disease (DKD). Here, we used untargeted mass spectrometry imaging to identify N-glycan structures in healthy and sclerotic glomeruli in formalin-fixed paraffin-embedded sections from needle biopsies of five patients with DKD and three healthy kidney samples. Regional proteomics was performed on glomeruli from additional biopsies from the same patients to compare the abundances of enzymes involved in glycosylation. Secondary analysis of single-nucleus RNA sequencing (snRNAseq) data were used to inform on transcript levels of glycosylation machinery in different cell types and states. We detected 120 N-glycans, and among them, we identified 12 of these protein post-translated modifications that were significantly increased in glomeruli. All glomeruli-specific N-glycans contained an N-acetyllactosamine epitope. Five N-glycan structures were highly discriminant between sclerotic and healthy glomeruli. Sclerotic glomeruli had an additional set of glycans lacking fucose linked to their core, and they did not show tetra-antennary structures that were common in healthy glomeruli. Orthogonal omics analyses revealed lower protein abundance and lower gene expression involved in synthesizing fucosylated and branched N-glycans in sclerotic podocytes. In snRNAseq and regional proteomics analyses, we observed that genes and/or proteins involved in sialylation and N-acetyllactosamine synthesis were also downregulated in DKD glomeruli, but this alteration remained undetectable by our spatial N-glycomics assay. Integrative spatial glycomics, proteomics, and transcriptomics revealed protein N-glycosylation characteristic of sclerotic glomeruli in DKD.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

The regulation of the cell wall by glycosylphosphatidylinositol-anchored proteins in Arabidopsis

A polysaccharides-based cell wall covers the plant cell, shaping it and protecting it from the harsh environment. Cellulose microfibrils constitute the cell wall backbone and are embedded in a matrix of pectic and hemicellulosic polysaccharides and glycoproteins. Various environmental and developmental cues can regulate the plant cell wall, and diverse glycosylphosphatidylinositol (GPI)-anchored proteins participate in these regulations. GPI is a common lipid modification on eukaryotic proteins, which covalently tethers the proteins to the membrane lipid bilayer. Catalyzed by a series of enzymic complexes, protein precursors are post-translationally modified at their hydrophobic carboxyl-terminus in the endomembrane system and anchored to the lipid bilayer through an oligosaccharidic GPI modification. Ultimately, mature proteins reach the plasma membrane via the secretory pathway facing toward the apoplast and cell wall in plants. In Arabidopsis, more than three hundred GPI-anchored proteins (GPI-APs) have been predicted, and many are reported to be involved in diverse regulations of the cell wall. In this review, we summarize GPI-APs involved in cell wall regulation. GPI-APs are proposed to act as structural components of the cell wall, organize cellulose microfibrils at the cell surface, and during cell wall integrity signaling transduction. Besides regulating protein trafficking, the GPI modification is potentially governed by a GPI shedding system that cleaves and releases the GPI-anchored proteins from the plasma membrane into the cell wall.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Enzymes in 3D: Synthesis, remodelling, and hydrolysis of cell wall (1,3;1,4)-β-glucans

Abstract Recent breakthroughs in structural biology have provided valuable new insights into enzymes involved in plant cell wall metabolism. More specifically, the molecular mechanism of synthesis of (1,3;1,4)-β-glucans, which are widespread in cell walls of commercially important cereals and grasses, has been the topic of debate and intense research activity for decades. However, an inability to purify these integral membrane enzymes or apply transgenic approaches without interpretative problems associated with pleiotropic effects has presented barriers to attempts to define their synthetic mechanisms. Following the demonstration that some members of the CslF sub-family of GT2 family enzymes mediate (1,3;1,4)-β-glucan synthesis, the expression of the corresponding genes in a heterologous system that is free of background complications has now been achieved. Biochemical analyses of the (1,3;1,4)-β-glucan synthesized in vitro, combined with 3-dimensional (3D) cryogenic-electron microscopy and AlphaFold protein structure predictions, have demonstrated how a single CslF6 enzyme, without exogenous primers, can incorporate both (1,3)- and (1,4)-β-linkages into the nascent polysaccharide chain. Similarly, 3D structures of xyloglucan endo-transglycosylases and (1,3;1,4)-β-glucan endo- and exohydrolases have allowed the mechanisms of (1,3;1,4)-β-glucan modification and degradation to be defined. X-ray crystallography and multi-scale modeling of a broad specificity GH3 β-glucan exohydrolase recently revealed a previously unknown and remarkable molecular mechanism with reactant trajectories through which a polysaccharide exohydrolase can act with a processive action pattern. The availability of high-quality protein 3D structural predictions should prove invaluable for defining structures, dynamics, and functions of other enzymes involved in plant cell wall metabolism in the immediate future.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Structural and Optical Interplay of Palladium-Modified TiO 2 Nanoheterostructure

The electronic structure and optical properties of Pd-modified TiO 2 nanotubes (NTs) with a vertically aligned nanotubular structure grown by a two-step electrochemical anodization method have been studied using X-ray spectroscopy. X-ray absorption near-edge structure (XANES) at the Ti L 3,2 - and O K-edges was used to investigate the TiO 2 NTs before and after Pd modification. It was found that Pd nanoparticles (NPs) are uniformly coated on the NT surface. The Pd L 3 -edge of the deposited Pd NPs shows a more intense whiteline and a blue shift for the Pd L 3 -edge absorption threshold relative to Pd metal, indicating charge depletion from the Pd 4d orbital as a result NP formation. The lattice of Pd is slightly contracted upon NP formation, although it remains fcc as revealed by extended X-ray absorption fine structure (EXAFS) analysis at the Pd K-edge. X-ray-excited optical luminescence (XEOL) together with XANES with element and site specificity was used to study the optical luminescence from TiO 2 NTs. It was found that the defect-originated XEOL intensity dropped noticeably in the Pd NP-coated NTs, suggesting a Pd NP–TiO 2 -interaction-mediated reduction in the radiative recombination of electrons and holes. Finally, further evidence is provided by Ti 2 p resonant inelastic X-ray scattering (RIXS), in which no low-energy loss features (d–d transitions) were observed. The implications of these results are discussed.

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

Structure of aryl O -demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism

Significance Modern industrial and agricultural practices generate large quantities of aromatic pollutants; however, these waste products can be converted into fine chemicals, fuels, and plastics through biocatalytic pathways. The bacterial world can inform such utilization strategies as certain strains of soil and marine bacteria metabolize environmentally derived aromatics. Many of these metabolic pathways involve aryl intermediates that require demethylation to facilitate modification and ring opening for assimilation into the tricarboxylic acid (TCA) cycle. Aryl demethylases, which catalyze this reaction, are poorly understood, making their utilization in biotechnology difficult. We provide the structural and mechanistic characterization of a single-domain aryl demethylase, LigM, which employs a tyrosine-dependent mechanism. Insights from this work will inform synthetic biology approaches to convert underutilized aromatics into higher value compounds.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Structural basis of divergent cyclin-dependent kinase activation by Spy1/RINGO proteins

Cyclin-dependent kinases (Cdks) are principal drivers of cell division and are an important therapeutic target to inhibit aberrant proliferation. Cdk enzymatic activity is tightly controlled through cyclin interactions, posttranslational modifications, and binding of inhibitors such as the p27 tumor suppressor protein. Spy1/RINGO (Spy1) proteins bind and activate Cdk but are resistant to canonical regulatory mechanisms that establish cell-cycle checkpoints. Cancer cells exploit Spy1 to stimulate proliferation through inappropriate activation of Cdks, yet the mechanism is unknown. We have determined crystal structures of the Cdk2-Spy1 and p27-Cdk2-Spy1 complexes that reveal how Spy1 activates Cdk. We find that Spy1 confers structural changes to Cdk2 that obviate the requirement of Cdk activation loop phosphorylation. Spy1 lacks the cyclin-binding site that mediates p27 and substrate affinity, explaining why Cdk-Spy1 is poorly inhibited by p27 and lacks specificity for substrates with cyclin-docking sites. We identify mutations in Spy1 that ablate its ability to activate Cdk2 and to proliferate cells. Our structural description of Spy1 provides important mechanistic insights that may be utilized for targeting upregulated Spy1 in cancer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Radiation-Induced Modifications in Copper Oxide Growth

Radiation-induced effects and their influence on oxidation processes were evaluated for their use as a forensic tool for special nuclear material (SNM). A beam of 10 MeV Au³⁺ ions was used to mimic the accumulation of microstructural damage from self-irradiation through the decay of radionuclides. Several copper samples were irradiated as suitable surrogate materials at 200 °C with a flux of 1x10¹² ions/cm·s to damage levels of 5, 10, and 15 displacements per atom (dpa). This corresponds to about 50, 100, and 150 years, respectively, of accumulated α-decay damage in a PuGa alloy assuming a damage rate of 0.1 dpa/year. After irradiation, all samples were exposed to an accelerated aging process induced by thermal treatment at 350 °C for 1 hour in air. This resulted in the growth of a mixed oxide layer (Cu₂O and CuO) which was characterized in detail using several complementary analytical techniques: Scanning Electron Microscopy, Raman spectroscopy, Synchrotron X-ray diffraction (transmission mode), and Grazing Incidence X-ray diffraction. The oxide layer growth of irradiated Cu at 350°C is distinctly modified as a result of the ion irradiation. Most notably, the growth of the CuO phase is suppressed with increasing radiation damage on the Cu substrate, and structural changes occurred in the Cu₂O phase. These results indicate that damage from self-irradiation over time can cause quantifiable modifications in the oxidation process of metals that could be harnessed for their use as a novel forensic tool.

36 MATERIALS SCIENCE↗
DOE OSTI2014

60 keV Ar⁺-ion induced modification of microstructural, compositional, and vibrational properties of InSb

Room temperature irradiation of InSb(111) by 60 keV Ar⁺-ions at normal (0°) and oblique (60°) angles of incidence led to the formation of nanoporous structure in the high fluence regime of 1×10¹⁷ to 3×10¹⁸ ions cm⁻². While a porous layer comprising of a network of interconnected nanofibers was generated by normal ion incidence, evolution of plate-like structures was observed for obliquely incident ions. Systematic studies of composition and structure using energy dispersive x-ray spectroscopy, Raman spectroscopy, x-ray photoelectron spectroscopy, Raman mapping, grazing incidence x-ray diffraction, and cross-sectional transmission electron microscopy revealed a high degree of oxidation of the ion-induced microstructures with the presence of In₂O₃ and Sb₂O₃ phases and presence of nanocrystallites within the nanoporous structures. The observed structural evolution was understood in terms of processes driven by ion-induced defect accumulation within InSb.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2012

The E3 Ubiquitin Ligase- and Protein Phosphatase 2A (PP2A)-binding Domains of the Alpha4 Protein Are Both Required for Alpha4 to Inhibit PP2A Degradation

Protein phosphatase 2A (PP2A) is regulated through a variety of mechanisms, including post-translational modifications and association with regulatory proteins. Alpha4 is one such regulatory protein that binds the PP2A catalytic subunit (PP2Ac) and protects it from polyubiquitination and degradation. Alpha4 is a multidomain protein with a C-terminal domain that binds Mid1, a putative E3 ubiquitin ligase, and an N-terminal domain containing the PP2Ac-binding site. In this work, we present the structure of the N-terminal domain of mammalian Alpha4 determined by x-ray crystallography and use double electron-electron resonance spectroscopy to show that it is a flexible tetratricopeptide repeat-like protein. Structurally, Alpha4 differs from its yeast homolog, Tap42, in two important ways: (1) the position of the helix containing the PP2Ac-binding residues is in a more open conformation, showing flexibility in this region; and (2) Alpha4 contains a ubiquitin-interacting motif. The effects of wild-type and mutant Alpha4 on PP2Ac ubiquitination and stability were examined in mammalian cells by performing tandem ubiquitin-binding entity precipitations and cycloheximide chase experiments. Our results reveal that both the C-terminal Mid1-binding domain and the PP2Ac-binding determinants are required for Alpha4-mediated protection of PP2Ac from polyubiquitination and degradation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Structural Basis for Metastability in Amorphous Calcium Barium Carbonate (ACBC)

Metastable amorphous precursors are emerging as valuable intermediates for the synthesis of materials with compositions and structures far from equilibrium. Recently, it was found that amorphous calcium barium carbonate (ACBC) can be converted into highly barium-substituted “balcite,” a metastable high temperature modification of calcite with exceptional hardness. A systematic analysis ACBC (Ca 1-x Ba x CO 3 ·1.2H 2 O) in the range from x = 0–0.5 is presented. Combining techniques that independently probe the local environment from the perspective of calcium, barium, and carbonate ions, with total X-ray scattering and a new molecular dynamics/density functional theory simulations approach, provides a holistic picture of ACBC structure as a function of composition. With increasing barium content, ACBC becomes more ordered at short and medium range, and increasingly similar to crystalline balcite, without developing long-range order. This is not accompanied by a change in the water content and does not carry a significant energy penalty, but is associated with differences in cation coordination resulting from changing carbonate anion orientation. Therefore, the local order imprinted in ACBC may increasingly lower the kinetic barrier to subsequent transformations as it becomes more pronounced. This pathway offers clues to the design of metastable materials by tuning coordination numbers in the amorphous solid state.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Characterization of Oxidative Modifications to Short Peptides Using Low Dose Rate X-Rays

The method of X-ray footprinting and mass spectrometry (XFMS) using high flux synchrotron X-ray sources has become an established method in structural biology and is based on the radiolytic production of hydroxyl radicals, which oxidatively modify protein sidechains. While other methods of producing hydroxyl radicals are available, one benefit of using high flux density sources is that hydroxyl radical scavenging reactions can be minimized, and exposure times kept short to minimize secondary reactions. Here we present an application of the XFMS method using low dose rate X-rays from a commercial instrument. We demonstrate the feasibility of the approach using short peptides, characterizing the oxidative modifications +14, +16, and +32 Da under both aerobic and low oxygen conditions, and we additionally quantify the hydrogen peroxide production for various doses using the low dose rate source. These results provide fundamental information on the oxidative damage to peptides due to hydroxyl radicals using a low dose rate X-ray source.

X-ray methods↗
DOE OSTI2016

Modifications of band gap in Si/Ge multilayers through vacuum annealing

In the present paper, important experimental findings and their impact on physical properties of Si/Ge systems are presented with the focus on structural and electronic properties investigations also covering band gap engineering. The use of synchrotron radiation based valence band photoemission spectroscopy technique has been demonstrated which provides the variation in bandgap values as a function of annealing on [Si/Ge]{sub x10} multilayers structure. For this purpose, the required VB offsets are obtained by considering the corresponding VB maximum of as prepared sample as a reference. The bandgap values thus obtained show a gradually decreasing pattern with increasing temperature, which is discussed in terms of the effect of various factors such as: (i) quantum confinement effect normally observed in confined systems (ii) change in the annealing induced intermixing leading to the formation of SiGe alloy and (iii) roughness at the surface/interface.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Doping evolution of the Mott–Hubbard landscape in infinite-layer nickelates

The recent observation of superconductivity in N d 0.8 S r 0.2 N i O 2 has raised fundamental questions about the hierarchy of the underlying electronic structure. Calculations suggest that this system falls in the Mott–Hubbard regime, rather than the charge-transfer configuration of other nickel oxides and the superconducting cuprates. Here, we use state-of-the-art, locally resolved electron energy-loss spectroscopy to directly probe the Mott–Hubbard character of N d 1 − x S r x N i O 2 . Upon doping, we observe emergent hybridization reminiscent of the Zhang–Rice singlet via the oxygen-projected states, modification of the Nd 5d states, and the systematic evolution of Ni 3d hybridization and filling. These experimental data provide direct evidence for the multiband electronic structure of the superconducting infinite-layer nickelates, particularly via the effects of hole doping on not only the oxygen but also nickel and rare-earth bands.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Tunable allosteric library of caspase-3 identifies coupling between conserved water molecules and conformational selection

The native ensemble of caspases is described globally by a complex energy landscape where the binding of substrate selects for the active conformation, whereas targeting an allosteric site in the dimer interface selects an inactive conformation that contains disordered active-site loops. Mutations and posttranslational modifications stabilize high-energy inactive conformations, with mostly formed, but distorted, active sites. To examine the interconversion of active and inactive states in the ensemble, we used detection of related solvent positions to analyze 4,995 waters in 15 high-resolution (<2.0 Å) structures of wild-type caspase-3, resulting in 450 clusters with the most highly conserved set containing 145 water molecules. The data show that regions of the protein that contact the conserved waters also correspond to sites of posttranslational modifications, suggesting that the conserved waters are an integral part of allosteric mechanisms. To test this hypothesis, we created a library of 19 caspase-3 variants through saturation mutagenesis in a single position of the allosteric site of the dimer interface, and we show that the enzyme activity varies by more than four orders of magnitude. Altogether, our database consists of 37 high-resolution structures of caspase-3 variants, and we demonstrate that the decrease in activity correlates with a loss of conserved water molecules. Furthermore, the data show that the activity of caspase-3 can be fine-tuned through globally desolvating the active conformation within the native ensemble, providing a mechanism for cells to repartition the ensemble and thus fine-tune activity through conformational selection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Surface modification of sol–gel synthesized TiO{sub 2} nanoparticles induced by La-doping

The influence of La-doping in the range of 0.5–6.0 mol% on structural and morphological properties of TiO{sub 2} nanopowders synthesized by sol–gel routine has been investigated by XRPD, AFM, EDS and BET measurements, as well as Raman spectroscopy. The XRPD and Raman measurements have revealed the anatase phase as dominant in all nanopowders, with crystallite size decreasing from ∼ 15 nm in pure TiO{sub 2} to ∼ 12 nm in La-doped samples. The BET data suggest that all samples are fully mesoporous, with mean pore diameters in the range of ∼ 6–8 nm. The specific surface area and the complexity of pore structure are greater in doped samples than in pure TiO{sub 2} sample. The spectroscopic ellipsometry has apparently shown that the band gap has been gradually increased with the increase of La content. The STM and STS techniques have been used successfully to evaluate the surface morphology and electronic properties of La-doped nanopowders. All investigated properties have been related to photocatalytic activity, tested in degradation of a metoprolol tartrate salt (0.05 mM), and induced by UV-radiation. All doped samples showed increased photocatalytic activity compared to pure TiO{sub 2}, among which the 0.65 mol% La-doped sample appeared to be the most efficient. - Highlights: • Effects of La-doping on structural, morphological and electronic properties of TiO{sub 2} nanopowders. • Surface morphology and electronic properties of La-doped nanopowders evaluated by STM/STS. • Spectroscopic ellipsometry shown gradual increase of bandgap with the increase of La content. • Photocatalytic activity of samples was tested in degradation of MET under UV light.

36 MATERIALS SCIENCE↗