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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 1,261 records · Page 70
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Influence of intermolecular interactions on the infrared complex indices of refraction for binary liquid mixtures

This paper investigates the accuracy of deriving the composite optical constants of binary mixtures from only the complex indices of refraction of the neat materials. These optical constants enable the reflectance spectra of the binary mixtures to be modeled for multiple scenarios (e.g., different substrates, thicknesses, volume ratios), which is important for contact and standoff chemical detection. Using volume fractions, each mixture's complex index of refraction was approximated via three different mixing rules. To explore the impact of intermolecular interactions, these predictions are tested by experimental measurements for two representative sets of binary mixtures: (1) tributyl phosphate combined with n-dodecane, a non-polar medium, to represent mixtures which primarily interact via dispersion forces and (2) tributyl phosphate and 1-butanol to represent mixtures with polar functional groups that can also interact via dipole–dipole interactions, including hydrogen bonding. The residuals and the root-mean-square error between the experimental and calculated index values are computed and demonstrate that for miscible liquids in which the average geometry of the cross-interactions can be considered isotropic (e.g., dispersion), the refractive indices of the mixtures can be modeled using composite n and k values derived from volume fractions of the neat liquids. Conversely, in spectral regions where the geometry of the cross-interactions is more restricted and anisotropic (e.g., hydrogen bonding), the calculated n and k values vary from the measured values. The impact of these interactions on the reflectance spectra are then compared by modeling a thin film of the binary mixtures on an aluminum substrate using both the measured and the mathematically computed indices of refraction.

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

Gallionellaceae in rice root plaque: metabolic roles in iron oxidation, nutrient cycling, and plant interactions

On the roots of wetland plants such as rice, Fe(II) oxidation forms Fe(III) oxyhydroxide-rich plaques that modulate plant nutrient and metal uptake. The microbial roles in catalyzing this oxidation have been debated and it is unclear if these iron-oxidizers mediate other important biogeochemical and plant interactions. To investigate this, we studied the microbial communities, metagenomes, and geochemistry of iron plaque on field-grown rice, plus the surrounding rhizosphere and bulk soil. Plaque iron content (per mass root) increased over the growing season, showing continuous deposition. Analysis of 16S rRNA genes showed abundant Fe(II)-oxidizing and Fe(III)-reducing bacteria (FeOB and FeRB) in plaque, rhizosphere, and bulk soil. FeOB were enriched in relative abundance in plaque, suggesting FeOB affinity for the root surface. Gallionellaceae FeOB Sideroxydans were enriched during vegetative and early reproductive rice growth stages, while a Gallionella was enriched during reproduction through grain maturity, suggesting distinct FeOB niches over the rice life cycle. FeRB Anaeromyxobacter and Geobacter increased in plaque later, during reproduction and grain ripening, corresponding to increased plaque iron. Metagenome-assembled genomes revealed that Gallionellaceae may grow mixotrophically using both Fe(II) and organics. The Sideroxydans are facultative, able to use non-Fe substrates, which may allow colonization of rice roots early in the season. FeOB genomes suggest adaptations for interacting with plants, including colonization, plant immunity defense, utilization of plant organics, and nitrogen fixation. Taken together, our results strongly suggest that rhizoplane and rhizosphere FeOB can specifically associate with rice roots, catalyzing iron plaque formation, with the potential to contribute to plant growth.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structural and biochemical analyses of selectivity determinants in chimeric Streptococcus Class A sortase enzymes

Abstract Sequence variation in related proteins is an important characteristic that modulates activity and selectivity. An example of a protein family with a large degree of sequence variation is that of bacterial sortases, which are cysteine transpeptidases on the surface of gram‐positive bacteria. Class A sortases are responsible for attachment of diverse proteins to the cell wall to facilitate environmental adaption and interaction. These enzymes are also used in protein engineering applications for sortase‐mediated ligations (SML) or sortagging of protein targets. We previously investigated SrtA from Streptococcus pneumoniae , identifying a number of putative β7–β8 loop‐mediated interactions that affected in vitro enzyme function. We identified residues that contributed to the ability of S. pneumoniae SrtA to recognize several amino acids at the P1′ position of the substrate motif, underlined in LPXT G , in contrast to the strict P1′ Gly recognition of SrtA from Staphylococcus aureus . However, motivated by the lack of a structural model for the active, monomeric form of S. pneumoniae SrtA, here, we expanded our studies to other Streptococcus SrtA proteins. We solved the first monomeric structure of S. agalactiae SrtA which includes the C‐terminus, and three others of β7–β8 loop chimeras from S. pyogenes and S. agalactiae SrtA. These structures and accompanying biochemical data support our previously identified β7–β8 loop‐mediated interactions and provide additional insight into their role in Class A sortase substrate selectivity. A greater understanding of individual SrtA sequence and structural determinants of target selectivity may also facilitate the design or discovery of improved sortagging tools.

Gao, Melody↗
DOE OSTI2011

Understanding the Role of O-GlcNAc Modifications in Plant Development

This project has contributed towards understanding the role of O-GlcNAc (O-linked N-acetylglucosamine) transferases (OGTs) in plants. Through analyses of single and double mutants, we have investigated the unique and overlapping functions of SECRET AGENT (SEC) and SPINDLY (SPY), the arabidopsis OGTs. This work showed that SEC functions as negative regulators of the long-day flowering pathway. SEC also has a positive role in regulation of rosette. An E. coli co-expression system that allows potential substrates to be co-expressed with and O-GlcNAc modified by SEC was developed. We showed that SEC is a bona fide OGT that modifies itself with single O-linked GlcNAc(s). Using this system, we tested a number of proteins that were hypothesized to be substrates of SEC and identified a number of substrates include GIGANTEA (GI), a component of the long day flowering pathway. The hypothesis that O-GlcNAc modification controls GI activity was tested by first mapping where E. coli-expressed SEC modifies GI and then assessing the activity of a non-modifiable mutant form of GI. The activity of the mutant form of GI was indistinguishable from that of wild type suggesting that either O-GlcNAc does not regulate GI activity or that additional modification sites exist on GI. In collaboration with Dr. Juan Antonio Garcia at Universidad Autónoma de Madrid the role of O-GlcNAc modification of the plum pox virus coat protein (PPV-CP) was investigated. SEC was shown to O-GlcNAc modify PPV-CP and the modification was shown to facilitate the infection process. E. coli-expressed SEC was shown to modify the same PPV-CP sites that are modified in plants. SEC has a large protein interaction domain called the TPR domain that has been hypothesized to have a role in determining the substrate specificity of the enzyme and/or to regulate its activity. A mutational analysis of the TPR domain did not find evidence for a role in substrate specificity but did obtain evidence that the domain regulates enzyme activity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

A new herb–drug interaction of Polygonum cuspidatum, a resveratrol‐rich nutraceutical, with carbamazepine in rats

Carbamazepine (CBZ), an antiepileptic with narrow therapeutic window, is a substrate of CYP 3A which metabolizes CBZ to carbamazepine-10,11-epoxide (CBZE), an active metabolite. This study investigated the acute and chronic effects of Polygonum cuspidatum (PC), a resveratrol‐rich nutraceutical, on the pharmacokinetics of CBZ in rats and the underlying mechanisms. Rats were orally administered CBZ (200 mg/kg) alone and coadministered with a single dose and the 7th dose of PC (2 g/kg) in a crossover design. The concentrations of CBZ and CBZE in serum and various tissues were determined by HPLC method. The results showed that PC significantly increased the AUC{sub 0-t} of CBZ and CBZE, whereas the formation rate of CBZE was decreased. Tissue analysis showed that the concentrations of CBZ and CBZE in brain, liver and kidney were significantly increased by PC. Cell studies indicated that the efflux function of MRP 2 was inhibited by the serum metabolites of PC. In conclusion, PC markedly increased the systemic exposure and brain concentration of CBZ and CBZE through inhibiting the activities of CYP 3A and MRP 2. Highlights: ► Polygonum cuspidatum elevated brain carbamazepine (CBZ) levels. ► Polygonum cuspidatum inhibited the activities of CYP 3A and MRP 2. ► Coadministration of PC with CBZ may enhance efficacy or toxicity.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Sputtering of silicon and glass substrates with polyatomic molecular ion beams generated from ionic liquids

The effect of irradiating 1-ethyl-3-methylimidazolium positive (EMIM{sup +}) or dicyanamide negative (DCA{sup –}) ion beams using an ionic liquid ion source was characterized concerning its sputtering properties for single crystalline Si(100) and nonalkaline borosilicate glass substrates. The irradiation of the DCA{sup –} ion beam onto the Si substrate at an acceleration voltage of 4 and 6 kV exhibited detectable sputtered depths greater than a couple of nanometers with an ion fluence of only 1 × 10{sup 15} ions/cm{sup 2}, while the EMIM{sup +} ion beam produced the same depths with an ion fluence 5 × 10{sup 15} ions/cm{sup 2}. The irradiation of a 4 kV DCA{sup –} ion beam at a fluence of 1 × 10{sup 16} ions/cm{sup 2} also yields large etching depths in Si substrates, corresponding to a sputtering yield of Si/DCA{sup – }= 10, and exhibits a smoothed surface roughness of 0.05 nm. The interaction between DCA{sup –} and Si likely causes a chemical reaction that relates to the high sputtering yield and forms an amorphous C-N capping layer that results in the smooth surface. Moreover, sputtering damage by the DCA{sup –} irradiation, which was estimated by Rutherford backscattering spectroscopy with the channeling technique, was minimal compared to Ar{sup +} irradiation at the same condition. In contrast, the glass substrates exhibited no apparent change in surface roughnesses when sputtered by the DCA{sup –} irradiation compared to the unirradiated glass substrates.

42 ENGINEERING↗
DOE OSTI2016

Reducing extrinsic damping of surface acoustic waves at gigahertz frequencies

High-frequency surface acoustic waves (SAWs) in the gigahertz range can be generated using absorption from an ultrafast laser in a patterned metallic grating on a substrate. Reducing the attenuation at these frequencies can yield better sensors as well as enable them to better probe phonon and electron-phonon interactions near surfaces. It is not clear from existing experiments which mechanisms dominate damping at high frequencies. We calculate damping times of SAWs due to various mechanisms in the 1–100 GHz range to find that mechanical loading of the grating on the substrate dominates dissipation by radiating energy from the surface into the bulk. To overcome this and enable future measurements to probe intrinsic damping, we propose incorporating distributed acoustic Bragg reflectors in the experimental structure. Layers of alternating materials with contrasting acoustic impedances embedded a wavelength away from the surface serve to reflect energy back to the surface. Using numerical simulations, we show that a single Bragg reflector is sufficient to increase the energy density at the surface by more than five times. We quantify the resulting damping time to find that it is longer than the intrinsic damping time. The proposed structure can enable future measurements of intrinsic damping in SAWs at ∼100 GHz.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Effect of mobile ions on the electric field needed to orient charged diblock copolymer thin films

We examine the behavior of lamellar phases of charged/neutral diblock copolymer thin films containing mobile ions in the presence of an external electric field. We employ self-consistent field theory and focus on the aligning effect of the electric field on the lamellae. Of particular interest are the effects of the mobile ions on the critical field, the value required to reorient the lamellae from the parallel configuration favored by the surface interaction to the perpendicular orientation favored by the field. We find that the critical field depends strongly on whether the neutral or charged species is favored by the substrates. In the case in which the neutral species is favored, the addition of charges decreases the critical electric field significantly. The effect is greater when the mobile ions are confined to the charged lamellae. In contrast, when the charged species is favored by the substrate, the addition of mobile ions stabilizes the parallel configuration and thus results in an increase in the critical electric field. The presence of ions in the system introduces a new mixed phase in addition to those reported previously.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Entropy and Enthalpy Mediated Segregation of Bottlebrush Copolymers to Interfaces

The composition of polymer blends near interfaces can differ from the average blend composition because the attraction of each polymer toward surfaces is controlled by its chemistry, size, and architecture. In this work, we studied thin film blends of bottlebrush copolymers and linear homopolymers to understand the enthalpic and entropic effects that drive preferential segregation of one constituent to film interfaces. Bottlebrush copolymers containing polystyrene (PS) and poly(methyl methacrylate) (PMMA) side chains were blended with either linear PS or linear PMMA, and time-of-flight secondary ion mass spectroscopy was used to quantify the distribution of bottlebrushes through the film thickness as a function of homopolymer type, homopolymer molecular weight, and processing conditions. We found that the bottlebrush copolymers segregated to air and substrate interfaces above a critical molecular weight of the linear homopolymer, consistent with an entropic preference for chain ends and shorter chains toward the interfaces. This segregation was used to tailor the surface wettability of blend films using bottlebrush additives as a minority component. Modeling using self-consistent field theory highlighted effects of conformational entropy and enthalpic interactions in driving almost complete segregation from the interior of the films toward interfaces. Furthermore, enthalpic interactions were predicted to cause lateral phase segregation in cases where the homopolymer is preferred over the bottlebrush copolymer at the substrate, an effect that was also observed in experiments. Finally, this study demonstrates that bottlebrush copolymer additives can be designed to spontaneously segregate to surfaces in thermal blends, providing a possible route to decouple surface properties from bulk properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Protein engineering of a ubiquitin-variant inhibitor of APC/C identifies a cryptic K48 ubiquitin chain binding site

Ubiquitin (Ub)-mediated proteolysis is a fundamental mechanism used by eukaryotic cells to maintain homeostasis and protein quality, and to control timing in biological processes. Two essential aspects of Ub regulation are conjugation through E1-E2-E3 enzymatic cascades and recognition by Ub-binding domains. An emerging theme in the Ub field is that these 2 properties are often amalgamated in conjugation enzymes. In addition to covalent thioester linkage to Ub’s C terminus for Ub transfer reactions, conjugation enzymes often bind noncovalently and weakly to Ub at “exosites.” However, identification of such sites is typically empirical and particularly challenging in large molecular machines. In this work, studying the 1.2-MDa E3 ligase anaphase-promoting complex/cyclosome (APC/C), which controls cell division and many aspects of neurobiology, we discover a method for identifying unexpected Ub-binding sites. Using a panel of Ub variants (UbVs), we identify a protein-based inhibitor that blocks Ub ligation to APC/C substrates in vitro and ex vivo. Biochemistry, NMR, and cryo-electron microscopy (cryo-EM) structurally define the UbV interaction, explain its inhibitory activity through binding the surface on the APC2 subunit that recruits the E2 enzyme UBE2C, and ultimately reveal that this APC2 surface is also a Ub-binding exosite with preference for K48-linked chains. The results provide a tool for probing APC/C activity, have implications for the coordination of K48-linked Ub chain binding by APC/C with the multistep process of substrate polyubiquitylation, and demonstrate the power of UbV technology for identifying cryptic Ub-binding sites within large multiprotein complexes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Predicting proton titration in cationic micelle and bilayer environments

Knowledge of the protonation behavior of pH-sensitive molecules in micelles and bilayers has significant implications in consumer product development and biomedical applications. However, the calculation of pK{sub a}’s in such environments proves challenging using traditional structure-based calculations. Here we apply all-atom constant pH molecular dynamics with explicit ions and titratable water to calculate the pK{sub a} of a fatty acid molecule in a micelle of dodecyl trimethylammonium chloride and liquid as well as gel-phase bilayers of diethyl ester dimethylammonium chloride. Interestingly, the pK{sub a} of the fatty acid in the gel bilayer is 5.4, 0.4 units lower than that in the analogous liquid bilayer or micelle, despite the fact that the protonated carboxylic group is significantly more desolvated in the gel bilayer. This work illustrates the capability of all-atom constant pH molecular dynamics in capturing the delicate balance in the free energies of desolvation and Coulombic interactions. It also shows the importance of the explicit treatment of ions in sampling the protonation states. The ability to model dynamics of pH-responsive substrates in a bilayer environment is useful for improving fabric care products as well as our understanding of the side effects of anti-inflammatory drugs.

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

Effect of the stresses caused by substrate on the electrical conductivity of ferromagnetic manganite lanthanum–barium films

This is a complex study of the electrophysical and magnetic characteristics of epitaxial manganite La{sub 0.7}Ba{sub 0.3}MnO{sub 3} (LBMO) films under conditions of crystal structure stresses caused by misfit in the lattice parameters of the LBMO crystal and a substrate. The substrate used had the lattice parameter smaller than that in the LBMO crystal. It is shown that the temperature dependence of the electrical resistance of the films at low temperatures is not dependent on the existence of stresses in the film and agrees well with the calculation with allowance made for the interaction of carriers with magnetic excitations in the presence of strongly correlated electronic states. The study of the ferromagnetic resonance line indicates an inhomogeneity of the ferromagnetic phase in the LBMO films and the increase in the ferromagnetic resonance line width with decreasing temperature.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

CO oxidation on gold-supported iron oxides: New insights into strong oxide–metal interactions

Very active FeO x –Au catalysts for CO oxidation are obtained after depositing nanoparticles of FeO, Fe 3 O 4 , and Fe 2 O 3 on a Au(111) substrate. Neither FeO nor Fe 2 O 3 is stable under the reaction conditions. Under an environment of CO/O 2 , they undergo oxidation (FeO) or reduction (Fe 2 O 3 ) to yield nanoparticles of Fe 3 O 4 that are not formed in a bulk phase. Using a combined experimental and theoretical approach, we show a strong oxide–metal interaction (SOMI) between Fe 3 O 4 nanostructures and Au(111), which gives the oxide special properties, allows the formation of an active phase, and provides a unique interface to facilitate a catalytic reaction. This work highlights the important role that the SOMI can play in enhancing the catalytic performance of the oxide component in metal–oxide catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Strongly Interacting, Two-Dimensional, Dipolar Spin Ensembles in (111)-Oriented Diamond

Systems of spins with strong dipolar interactions and controlled dimensionality enable new explorations in quantum sensing and simulation. In this work, we investigate the creation of strong dipolar interactions in a two-dimensional ensemble of nitrogen-vacancy (NV) centers generated via plasma-enhanced chemical vapor deposition on (111)-oriented diamond substrates. We find that diamond growth on the (111) plane yields high incorporation of spins, both nitrogen and NV centers, where the density of the latter is tunable via the miscut of the diamond substrate. Our process allows us to form dense, preferentially aligned, 2D NV ensembles with volume-normalized ac sensitivity down to η ac = 810 pT μ m 3 / 2 Hz − 1 / 2 . Furthermore, we show that (111) affords maximally positive dipolar interactions among a 2D NV ensemble, which is crucial for leveraging dipolar-driven entanglement schemes and exploring new interacting spin physics. Published by the American Physical Society 2025

Hughes, Lillian B. (ORCID:0000000210201661)↗
DOE OSTI2014

Kohn-Luttinger superconductivity in monolayer and bilayer semimetals with the Dirac spectrum

The effect of Coulomb interaction in an ensemble of Dirac fermions on the formation of superconducting pairing in monolayer and bilayer doped graphene is studied using the Kohn-Luttinger mechanism disregarding the Van der Waals potential of the substrate and impurities. The electronic structure of graphene is described using the Shubin-Vonsovsky model taking into account the intratomic, interatomic, and interlayer (in the case of bilayer graphene) Coulomb interactions between electrons. The Cooper instability is determined by solving the Bethe-Saltpeter integral equation. The renormalized scattering amplitude is obtained with allowance for the Kohn-Luttinger polarization contributions up to the second order of perturbation theory in the Coulomb interaction. It plays the role of effective interaction in the Bethe-Salpeter integral equation. It is shown that the allowance for the Kohn-Luttinger renormalizations as well as intersite Coulomb interaction noticeably affects the competition between the superconducting phases with the f-wave and d + id-wave symmetries of the order parameter. It is demonstrated that the superconducting transition temperature for an idealized graphene bilayer with significant interlayer Coulomb interaction between electrons is noticeably higher than in the monolayer case.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Tight-Binding Theoretical Study of the Tunneling Conductance in Ferromagnetically Ordered Graphene-on-Substrate

We report here a tight-binding theoretical study of the tunneling conductance and temperature dependent specific heat of graphene-on-substrate. The Hamiltonian consists of the electron hoppings up to third nearest neighbors in the presence of doping and on-site Coulomb interactions at two sub-lattices of honey-comb lattice. The total Hamiltonian is solved by Zubarev Green’s functions technique. Then, the sub-lattice magnetizations, tunneling conductance, and specific heat are calculated from the Green’s functions and are computed numerically. The effect of impurity, substrate induced gap, and repulsive Coulomb potential on tunneling conductance is discussed. The anomaly in specific heat at low temperatures is described.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2013

Recognition of SUMO-modified PCNA requires tandem receptor motifs in Srs2

Ubiquitin (Ub) and ubiquitin-like (Ubl) modifiers such as SUMO (also known as Smt3 in Saccharomyces cerevisiae) mediate signal transduction through post-translational modification of substrate proteins in pathways that control differentiation, apoptosis and the cell cycle, and responses to stress such as the DNA damage response. In yeast, the proliferating cell nuclear antigen PCNA (also known as Pol30) is modified by ubiquitin in response to DNA damage and by SUMO during S phase. Whereas Ub-PCNA can signal for recruitment of translesion DNA polymerases, SUMO-PCNA signals for recruitment of the anti-recombinogenic DNA helicase Srs2. It remains unclear how receptors such as Srs2 specifically recognize substrates after conjugation to Ub and Ubls. Here we show, through structural, biochemical and functional studies, that the Srs2 carboxy-terminal domain harbors tandem receptor motifs that interact independently with PCNA and SUMO and that both motifs are required to recognize SUMO-PCNA specifically. The mechanism presented is pertinent to understanding how other receptors specifically recognize Ub- and Ubl-modified substrates to facilitate signal transduction.

59 BASIC BIOLOGICAL SCIENCES↗