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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 1,117 records · Page 62
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

30S subunit recognition and G1405 modification by the aminoglycoside-resistance 16S ribosomal RNA methyltransferase RmtC

Acquired ribosomal RNA (rRNA) methylation has emerged as a significant mechanism of aminoglycoside resistance in pathogenic bacterial infections. Modification of a single nucleotide in the ribosome decoding center by the aminoglycoside-resistance 16S rRNA (m 7 G1405) methyltransferases effectively blocks the action of all 4,6-deoxystreptamine ring-containing aminoglycosides, including the latest generation of drugs. To define the molecular basis of 30S subunit recognition and G1405 modification by these enzymes, we used a S-adenosyl-L-methionine analog to trap the complex in a postcatalytic state to enable determination of a global 3.0 Å cryo-electron microscopy structure of the m 7 G1405 methyltransferase RmtC bound to the mature Escherichia coli 30S ribosomal subunit. This structure, together with functional analyses of RmtC variants, identifies the RmtC N-terminal domain as critical for recognition and docking of the enzyme on a conserved 16S rRNA tertiary surface adjacent to G1405 in 16S rRNA helix 44 (h44). To access the G1405 N7 position for modification, a collection of residues across one surface of RmtC, including a loop that undergoes a disorder-to order transition upon 30S subunit binding, induces significant distortion of h44. This distortion flips G1405 into the enzyme active site where it is positioned for modification by two almost universally conserved RmtC residues. Further, these studies expand our understanding of ribosome recognition by rRNA modification enzymes and present a more complete structural basis for future development of strategies to inhibit m 7 G1405 modification to resensitize bacterial pathogens to aminoglycosides.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Structure and optical properties of cubic gallium oxynitride synthesized by solvothermal route

Cubic gallium oxynitride was synthesized using a solvothermal processing route. Crystal structure, chemical composition, optical properties and the influence of heat treatment in either reactive or inert atmospheres have been investigated. Despite a strongly distorted lattice revealed using X-ray diffraction, the Raman active modes of a cubic gallium oxynitride structure could be observed. With diffusive reflectance UV–Vis spectroscopy a band gap at around 4.8 eV has been observed. Additionally, cathodoluminescence spectroscopy exhibited observable luminescence caused by defect-related transitions within the optical gap. Cathodoluminescence and photoluminescence spectra collected after heat treatments showed significant changes in the defect structure. In particular, for annealing in ammonia the main spectral modifications were related to the substitution of oxygen by nitrogen on anion sites. - Graphical abstract: CL spectra of gallium oxynitride: As-prepared and heat-treated at temperatures of 500 °C in different atmospheres. Highlights: ► Raman spectrum of cubic gallium oxynitride. ► Experimental determination of optical band gap. ► Shift of band gap energy due to heat treatment. ► Nitrogen incorporation leads to deep level acceptor states. ► Red shifted luminescence spectrum.

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

Confronting Domain Shift in Trained Neural Networks

Neural networks (NNs) are known as universal function approximators and can interpolate nonlinear functions between observed data points. However, when the target domain for deployment shifts from the training domain and NNs must extrapolate, the results are notoriously poor. Prior work Martinez et al. (2019) has shown that NN uncertainty estimates can be used to correct binary predictions in shifted domains without retraining the model. We hypothesize that this approach can be extended to correct real-valued time series predictions. As an exemplar, we consider two mechanical systems with nonlinear dynamics. The first system consists of a spring-mass system where the stiffness changes abruptly, and the second is a real experimental system with a frictional joint that is an open challenge for structural dynamicists to model efficiently. Our experiments will test whether 1) NN uncertainty estimates can identify when the input domain has shifted from the training domain and 2) whether the information used to calculate uncertainty estimates can be used to correct the NN’s time series predictions. While the method as proposed did not significantly improve predictions, our results did show potential for modifications that could improve models’ predictions and play a role in structural health monitoring systems that directly impact public safety.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

An Investigation of Process Parameter Modifications on Additively Manufactured Inconel 718 Parts

Additive manufacturing (AM) allows for the fabrication of complex parts via layer-by-layer melting of metal powder. Laser powder-bed AM processes use a variety of process parameters including beam power, beam velocity, and hatch spacing to control melting. Alterations to these parameters have often been attempted to reduce porosity, for example, but less work has been done to on comprehensive effects of process parameter modifications. This study looks at the effects of altering these parameters on microstructure, porosity, and mechanical performance of Inconel 718. The results showed that process parameter modifications that result in porosity formation can significantly reduce fatigue life, while microstructure changes were minimal and had little effect on tensile properties. The precipitate structure was not found to be changed significantly. These results can inform future process parameter modifications, as well as heat treatments to optimize mechanical properties.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Pseudouridinylation of mRNA coding sequences alters translation

Chemical modifications of RNAs have long been established as key modulators of nonprotein-coding RNA structure and function in cells. There is a growing appreciation that messenger RNA (mRNA) sequences responsible for directing protein synthesis can also be posttranscriptionally modified. The enzymatic incorporation of mRNA modifications has many potential outcomes, including changing mRNA stability, protein recruitment, and translation. In this work, we tested how one of the most common modifications present in mRNA coding regions, pseudouridine (Ψ), impacts protein synthesis using a fully reconstituted bacterial translation system and human cells. Our work reveals that replacing a single uridine nucleotide with Ψ in an mRNA codon impedes amino acid addition and EF-Tu GTPase activation. A crystal structure of the Thermus thermophilus 70S ribosome with a tRNA Phe bound to a ΨUU codon in the A site supports these findings. We also find that the presence of Ψ can promote the low-level synthesis of multiple peptide products from a single mRNA sequence in the reconstituted translation system as well as human cells, and increases the rate of near-cognate Val-tRNA Val reacting on a ΨUU codon. The vast majority of Ψ moieties in mRNAs are found in coding regions, and our study suggests that one consequence of the ribosome encountering Ψ can be to modestly alter both translation speed and mRNA decoding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Q{sup 2}-evolution of parton densities at small x values. Combined H1 and ZEUS F2 data

We use the Bessel-inspired behavior of the structure function F{sub 2} at small x, obtained for a flat initial condition in the DGLAP evolution equations, with “frozen” and analytic modifications of the strong coupling constant to study precise combined H1 and ZEUS data for the structure function F{sub 2} published recently.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2017

Neutron stars structure in the context of massive gravity

Motivated by the recent interests in spin−2 massive gravitons, we study the structure of neutron star in the context of massive gravity. The modifications of TOV equation in the presence of massive gravity are explored in 4 and higher dimensions. Next, by considering the modern equation of state for the neutron star matter (which is extracted by the lowest order constrained variational (LOCV) method with the AV18 potential), different physical properties of the neutron star (such as Le Chatelier's principle, stability and energy conditions) are investigated. It is shown that consideration of the massive gravity has specific contributions into the structure of neutron star and introduces new prescriptions for the massive astrophysical objects. The mass-radius relation is examined and the effects of massive gravity on the Schwarzschild radius, average density, compactness, gravitational redshift and dynamical stability are studied. Finally, a relation between mass and radius of neutron star versus the Planck mass is extracted.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Effect of 8 MeV electron beam irradiation on the structural and optical properties of CeO{sub 2} nanoparticles

The effect of 8 MeV electron beam irradiation on the structural and optical properties of cerium oxide nanoparticles was investigated. Ceria nanoparticles were synthesized by chemical precipitation method, and characterized by X-ray diffraction, transmission electron microscopy, ultraviolet–visible, photoluminescence and Raman spectroscopy. Ultraviolet–visible absorption spectra, photoluminescence and Raman spectra of beam irradiated samples were modified, and shifted to blue region, which were attributed to quantum size effect. Systematic observations found that nonstoichiometry, defects and size reduction caused by beam irradiation have great influence on optical band gap, blue shift, photoluminescence and Raman band modifications. Moreover, electron beam irradiation is a suitable technique to enhance the structural and optical properties of nanoceria by controlling the particle size, which may lead to potentially useful technological applications. - Highlights: • Investigated effect of beam irradiation on CeO{sub 2} nanoparticles • Beam irradiation caused size reduction and surface modification. • It increases microstrain, decreases d-spacing and broadens XRD peaks. • It also modifies optical band gap, absorption, PL and Raman bands.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Global structure search for molecules on surfaces: Efficient sampling with curvilinear coordinates

Efficient structure search is a major challenge in computational materials science. Here, we present a modification of the basin hopping global geometry optimization approach that uses a curvilinear coordinate system to describe global trial moves. This approach has recently been shown to be efficient in structure determination of clusters [C. Panosetti et al., Nano Lett. 15, 8044–8048 (2015)] and is here extended for its application to covalent, complex molecules and large adsorbates on surfaces. The employed automatically constructed delocalized internal coordinates are similar to molecular vibrations, which enhances the generation of chemically meaningful trial structures. By introducing flexible constraints and local translation and rotation of independent geometrical subunits, we enable the use of this method for molecules adsorbed on surfaces and interfaces. For two test systems, trans-β -ionylideneacetic acid adsorbed on a Au(111) surface and methane adsorbed on a Ag(111) surface, we obtain superior performance of the method compared to standard optimization moves based on Cartesian coordinates.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Structural Studies of Bacterial Enzymes and their Relation to Antibiotic Resistance Mechanisms (Final Paper)

By using protein crystallography and X-ray diffraction, structures of bacterial enzymes were solved to gain a better understanding of how enzymatic modification acts as an antibacterial resistance mechanism. Aminoglycoside phosphotransferases (APHs) are one of three aminoglycoside modifying enzymes that confer resistance to the aminoglycoside antibiotics via enzymatic modification, rendering many drugs obsolete. Specifically, the APH(2”) family vary in their substrate specificities and also in their preference for the phosphate donor (ADP versus GDP). By solving the structures of members of the APH(2”) family of enzymes, we can see how domain movements are important to their substrate specificity. Our structure of the ternary complex of APH(2”)-IIIa with GDP and kanamycin, when compared to the known structures of APH(2”)-IVa, reveals that there are real physical differences between these two enzymes, a structural finding that explains why the two enzymes differ in their preferences for certain aminoglycosides. Another important group of bacterial resistance enzymes are the Class D β- lactamases. Oxacillinase carbapenemases (OXAs) are part of this enzyme class and have begun to confer resistance to ‘last resort’ drugs, most notably carbapenems. Our structure of OXA-143 shows that the conformational flexibility of a conserved hydrophobic residue in the active site (Val130) serves to control the entry of a transient water molecule responsible for a key step in the enzyme’s mechanism. Our results provide insight into the structural mechanisms of these two different enzymes

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Bacterial Enzymes and Antibiotic Resistance- Oral Presentation [Slides]

By using protein crystallography and X-ray diffraction, structures of bacterial enzymes were solved to gain a better understanding of how enzymatic modification acts as an antibacterial resistance mechanism. Aminoglycoside phosphotransferases (APHs) are one of three aminoglycoside modifying enzymes that confer resistance to the aminoglycoside antibiotics via enzymatic modification, rendering many drugs obsolete. Specifically, the APH(2”) family vary in their substrate specificities and also in their preference for the phosphate donor (ADP versus GDP). By solving the structures of members of the APH(2”) family of enzymes, we can see how domain movements are important to their substrate specificity. Our structure of the ternary complex of APH(2”)-IIIa with GDP and kanamycin, when compared to the known structures of APH(2”)-IVa, reveals that there are real physical differences between these two enzymes, a structural finding that explains why the two enzymes differ in their preferences for certain aminoglycosides. Another important group of bacterial resistance enzymes are the Class D β-lactamases. Oxacillinase carbapenemases (OXAs) are part of this enzyme class and have begun to confer resistance to ‘last resort’ drugs, most notably carbapenems. Our structure of OXA-143 shows that the conformational flexibility of a conserved hydrophobic residue in the active site (Val130) serves to control the entry of a transient water molecule responsible for a key step in the enzyme’s mechanism. Our results provide insight into the structural mechanisms of these two different enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Surfactant-assisted synthesis of mono-dispersed cubic BaTiO{sub 3} nanoparticles

Mono-dispersed BaTiO{sub 3} nanoparticles have been prepared via the assistance of capping agent poly(vinylpyrrolidone) (PVP). - Highlights: • BaTiO{sub 3} nanoparticles with single cubic crystal structure. • Poor dispersibility of nanoparticles has been overcome by in situ modification way. • Growth competition between BaTiO3 core and polymer shell. - Abstract: In this study, poly(vinylpyrrolidone)-assisted synthesis of mono-dispersed BaTiO{sub 3} nanoparticles have been reported. The various processing parameters, namely, refluxing temperature, KOH concentration, and poly(vinylpyrrolidone) concentration, have been varied, and the effects on the growth of BaTiO{sub 3} particles have been analyzed systematically. X-ray diffraction studies indicated that poly(vinylpyrrolidone) did not affect the crystal structure, but rather influenced the crystal lattice structure. In addition, the use of surfactant poly(vinylpyrrolidone) hindered the agglomeration of the nanoparticles, and facilitated the formation of mono-dispersed core–shell organic/inorganic hybrid nanocomposite. Furthermore, the mineralizer KOH promoted the dissolution of reactants and promoted the crystallization of BaTiO{sub 3} particles. Accordingly, the dissolution-precipitation scheme was believed to be the mechanism underlying the formation of BaTiO{sub 3} particles. This was further substantiated by the experimental observations, which indicated that the nucleation and crystallization of the particles was affected by the KOH concentration in the reaction system. Finally, the formation of mono-dispersed core–shell nanocomposites proceeded via reaction limited cluster aggregation. We believe that the method proposed in this study could be extended for the synthesis of mono-dispersed nanoparticles for industrial applications.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Novel Amorphous Carbons for the Adsorption of Phosphate: Part I. Elucidation of Chemical Structure of N-Metal-Doped Chars

Due to phosphate’s necessity in agriculture and its danger to the environment, the development of adsorbents for its removal has been the subject of intensive research activity. Although the introduction of nitrogen functionality to chars and modification of biochar with metals have proven to change the character of the char structure, making it more active toward nutrients, there is no study regarding the doping of biochar with metals and nitrogen simultaneously for the adsorption of phosphates. This paper is the first of two in which we report the production, characterization, and evaluation of N-metal-doped biochars from cellulose for phosphate removal from liquid effluents. In this part, we describe the production and characterization of N-Ca-, N-Fe-, and N-Mg-doped biochars. The elemental composition and surface area of each of the materials produced is reported. Elemental and surface characterization of the chars are reported with the largest N content appearing at a temperature of 800 °C (12.5 wt %) and a maximum surface area for biochar produced at 900 °C (1314 m2/g). All of the adsorbents were visualized by scanning electron microscope (SEM), confirming that although there are some crystals on the surface of the biochar produced, most of the N, Mg, and Ca are part of the polyaromatic ring structure. Transmission electron microscope (TEM) images clearly show the formation of nanoclusters with the metals in the case of N-Fe and N-Ca biochars. The N-Mg biochars show a uniform distribution of the Mg through the carbon surface. X-ray photoelectron spectroscopy (XPS) studies of the biochars produced with metals and varying nitrogen levels clearly show Mg and Ca peaks shifting their position in the presence of N, suggesting the formation of stable structures between metals and N in the carbon polyaromatic ring system. To elucidate the nature of these structures, we conducted DFT-based calculations on different configurations of the nitrogenated structures. The calculated binding energy shifts were found to closely match the XPS experimental binding energy, confirming the likelihood of these structures in biochar. Finally, based on our experimental and modeling results, we hypothesize that an important fraction of the Mg and Ca is introduced to these biochars at the edges. Another fraction of Mg and Ca is in the form of phthalocyanine-like internal structures. More experimental studies are needed to confirm the formation of these very interesting structures and their potential use as adsorbents or catalysts.

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

A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra

Motivation: Although proteomics has rapidly developed in the past decade, researchers are still in the early stage of exploring the world of complex proteoforms, which are protein products with various primary structure alterations resulting from gene mutations, alternative splicing, post-translational modifications, and other biological processes. Proteoform identification is essential to mapping proteoforms to their biological functions as well as discovering novel proteoforms and new protein functions. Top-down mass spectrometry is the method of choice for identifying complex proteoforms because it provides a “bird’s eye view” of intact proteoforms. The combinatorial explosion of various alterations on a protein may result in billions of possible proteoforms, making proteoform identification a challenging computational problem. Results: We propose a new data structure, called the mass graph, for efficient representation of proteoforms and design mass graph alignment algorithms. We developed TopMG, a mass graph-based software tool for proteoform identification by top-down mass spectrometry. Experiments on top-down mass spectrometry data sets showed that TopMG outperformed existing methods in identifying complex proteoforms.

Dynamic Programming↗
DOE OSTI2026

A divergent synthetic route to functional copolymer libraries via modular polymers

High-throughput polymer synthesis enables rapid exploration of chemical space but remains limited by batch-to-batch inconsistencies that can obscure structure–property relationship trends. To address this challenge, we developed a synthetic approach to produce multifunctional copolymers using post-polymerization modification of activated ester modular polymers with commercially available amines. Easily derivitized parent polymers—poly(tetrafluorophenyl acrylate) and poly(tetrafluorophenyl styrene sulfonate)—were synthesized by RAFT polymerization to yield single polymer batches containing highly reactive tetrafluorophenyl esters or sulfonate esters on each repeat unit. Tuning post-polymerization modification reaction conditions enabled the addition of sub-stoichiometric amounts of amines (relative to the repeat unit) to yield partially functionalized intermediates that could then be further derivatized. Reaction monitoring by 19 F NMR spectroscopy confirmed good control over these sequential post-polymerization modifications. This synthetic route produced a variety of copolymers with defined comonomer ratios while preserving the underlying polymer structure (degree of polymerization, dispersity, tacticity) for both the acrylate and styrene sulfonate backbones. We further applied this approach in a divergent manner to create a small library of structurally distinct copolymers from a single parent batch in three synthetic steps. This modular, divergent synthesis demonstrates a general route to structurally consistent copolymer libraries that enable systematic studies of structure–property relationships and can accelerate functional materials discovery.

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

Initial Studies on Development of High-Performance Nano-structured Fe{sub 2}O{sub 3} Catalysts for Solid Rocket Propellants

Space launch vehicles and strategic military vehicles commonly employ composite solid rocket propellants containing Fe{sub 2}O{sub 3} as ballistic modifier. Nanoscale catalysts, including nanoscale Fe{sub 2}O{sub 3}, have been reported to exhibit superior activity in the thermal decomposition and combustion of composite rocket propellants. However, scalable methods to prepare such nano-structured catalysts with high performance as ballistic modifiers and systematic studies relating the synthesis parameters to the catalyst characteristics and consequently to the thermal and combustion properties of the composite propellant are scarce. In this paper, we report a novel and facile route to prepare nano-structured Fe{sub 2}O{sub 3} with enhanced catalytic activity in the ballistic modification of ammonium perchlorate (AP)-based composite solid rocket propellant. A submerged spray precipitation method using air-assisted liquid-centered coaxial atomization has been developed to prepare these nano-structured Fe{sub 2}O{sub 3} catalysts. The prepared Fe{sub 2}O{sub 3} catalysts possess higher surface area and exhibit superior activity in the thermal sensitization of AP, leading to an 88% increase in the burning rate of AP-based composite solid rocket propellants, than the Fe{sub 2}O{sub 3} catalyst prepared via traditional precipitation method. Merits of the developed preparatory route, influence of the atomization process on the nano-structure morphology and subsequent benefits of these nano-structured catalysts on the ballistic properties of AP-based propellants are demonstrated and discussed in this paper.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Structure and regulation of ZCCHC4 in m 6 A-methylation of 28S rRNA

N 6 -methyladenosine (m 6 A) modification provides an important epitranscriptomic mechanism that critically regulates RNA metabolism and function. However, how m 6 A writers attain substrate specificities remains unclear. We report the 3.1 Å-resolution crystal structure of human CCHC zinc finger-containing protein ZCCHC4, a 28S rRNA-specific m 6 A methyltransferase, bound to S-adenosyl-L-homocysteine. The methyltransferase (MTase) domain of ZCCHC4 is packed against N-terminal GRF-type and C2H2 zinc finger domains and a Cterminal CCHC domain, creating an integrated RNA-binding surface. Strikingly, the MTase domain adopts an autoinhibitory conformation, with a self-occluded catalytic site and a fullyclosed cofactor pocket. Mutational and enzymatic analyses further substantiate the molecular basis for ZCCHC4-RNA recognition and a role of the stem-loop structure within substrate in governing the substrate specificity. Overall, this study unveils unique structural and enzymatic characteristics of ZCCHC4, distinctive from what was seen with the METTL family of m 6 A writers, providing the mechanistic basis for ZCCHC4 modulation of m 6 A RNA methylation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Hollow-structured Ni-N-C catalysts for highly selective CO 2 electroreduction

Atomically dispersed single-atom catalysts have emerged as promising non-precious catalyst alternatives to expensive Ag and Au catalysts for electrochemical CO 2 reduction reaction (CO 2 RR). In particular, nickel-nitrogen-carbon (Ni-N-C) catalysts have demonstrated a high faradaic efficiency (FE) toward CO formation at low overpotentials. Nonetheless, the exact nature of Ni active sites under CO 2 RR remains elusive and conventional Ni-N-C catalysts are limited by microporosity and low density of Ni single atoms, hindering performance in CO 2 electrolyzers. Here, we report the synthesis of hollow-structured Ni-N-C ( hs -Ni-N-C) catalysts via a post-synthesis modification (PSM) strategy using partial ligand exchange of 2-methylimidazole with 3-amino-1,2,4-triazole. This approach enables the formation of a hollow structure, resulting in more than a twofold increase in Ni atom density compared to regular Ni-N-C (r-Ni-N-C). In a zero-gap CO 2 electrolyzer, the optimized hs -Ni-N-C allows for achieving an FE CO of 97% at a current density of > 100 mA cm⁻ 2 , while maintaining high CO selectivity with stable performance over 100 h at 2.5 V. hs-Ni-N-C shows a more than sevenfold increase in the CO partial current density relative to r-Ni-N-C resulting from the combined effects of a higher density of Ni single-atom sites, improved kinetics, and lower transport resistance under the operating conditions, as indicated by electrochemical impedance spectra and distribution of relaxation times analysis. Operando high energy-resolution X-ray absorption spectroscopy (XAS) reveals that atop-bonded CO on Ni single sites induces dynamic transformations of the Ni–N coordination environment, leading to a symmetric coordination structure of hs -Ni-N-C. Under CO 2 RR, the catalysts undergo a more pronounced structural change and form a minor fraction of Ni nanoparticles. Density functional theory calculations are consistent with the XAS results and provide molecular insights showing that the interplay between protonation and CO adsorption leads to adsorbate-induced restructuring of the Ni single atom. This work demonstrates the synergistic role of hollow structure and high-density Ni atoms in governing CO 2 RR selectivity and provides mechanistic insights into the structural dynamics of single-atom catalysts under operating conditions.

36 MATERIALS SCIENCE↗