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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 955 records · Page 53
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Heptagraphene: Tunable dirac cones in a graphitic structure

Here, we predict the existence and dynamical stability of heptagraphene, a new graphitic structure formed of rings of 10 carbon atoms bridged by carbene groups yielding seven-membered rings. Despite the rectangular unit cell, the band structure is topologically equivalent to that of strongly distorted graphene. Density-functional-theory calculations demonstrate that heptagraphene has Dirac cones on symmetry lines that are robust against biaxial strain but which open a gap under shear. At high deformation values bond reconstructions lead to different electronic band arrangements in dynamically stable configurations. Within a tight-binding framework this richness of the electronic behavior is identified as a direct consequence of the symmetry breaking within the cell which, unlike other graphitic structures, leads to band gap opening. A combined approach of chemical and physical modification of graphene unit cell unfurls the opportunity to design carbon-based systems in which one aims to tune an electronic band gap.

36 MATERIALS SCIENCE↗
DOE OSTI2026

PARP1-HPF1 structure and dynamics on nicked DNA suggest a mechanism for acute and localized ADP-ribosylation

PARP1 detection of DNA strand breaks allosterically leads to PARP1 synthesis of poly(ADP-ribose) modifications that signal DNA damage. HPF1 engages activated PARP1 to control modification site selection. Understanding of the mechanism of DNA break detection and catalytic activation is incomplete, due largely to limited structural information for full-length PARP1. Here, single-particle cryo-EM provides views of the full complement of PARP1 domains engaging a DNA single-strand break in the presence of HPF1 and a fragment of binding partner Timeless. Cryo-EM, single-molecule DNA dynamics, and small-angle X-ray scattering analysis indicate that PARP1 remains dynamic even when the multi-domain structure is organized on a DNA break, with the minimal catalytic region displaying high mobility relative to domains engaging damage. We propose that the organization of PARP1 domains on a DNA break releases a tethered, constitutively active catalytic region to modify molecules in a radius surrounding the DNA break site.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Thiol redox proteomics: Characterization of thiol-based post-translational modifications

Redox post-translational modifications on cysteine thiols (redox PTMs) have profound effects on protein structure and function, thus enabling regulation of various biological processes. Redox proteomics approaches aim to characterize the landscape of redox PTMs at the systems level. These approaches facilitate studies of condition-specific, dynamic processes implicating redox PTMs and have furthered our understanding of redox signaling and regulation. Mass spectrometry (MS) is a powerful tool for such analyses which has been demonstrated by significant advances in redox proteomics during the last decade. A group of well-established approaches involves the initial blocking of free thiols followed by selective reduction of oxidized PTMs and subsequent enrichment for downstream detection. Alternatively, novel chemoselective probe-based approaches have been developed for various redox PTMs. Direct detection of redox PTMs without any enrichment has also been demonstrated given the sensitivity of contemporary MS instruments. This review discusses the general principles behind different analytical strategies and covers recent advances in redox proteomics. Several applications of redox proteomics are also highlighted to illustrate how large-scale redox proteomics data can lead to novel biological insights.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Probing the Short-Distance Structure of the Quark-Gluon Plasma with Energy Correlators

Energy-energy correlators (EECs) are promising observables to study the dynamics of jet evolution in the quark-gluon plasma (QGP) through its imprint on angular scales in the energy flux of final-state particles. We carry out the first complete calculation of EECs using realistic simulations of high-energy heavy-ion collisions and dissect the different dynamics underlying the final distribution through analyses of jet propagation in a uniform medium. The EECs of γ -jets in heavy-ion collisions are found to be enhanced by the medium response from elastic scatterings instead of induced gluon radiation at large angles. In the meantime, EECs are suppressed at small angles due to energy loss and transverse momentum broadening of jet shower partons. These modifications are further shown to be sensitive to the angular scale of the in-medium interaction, as characterized by the Debye screening mass. Experimental verification and measurement of such modifications will shed light on this scale and the short-distance structure of the QGP in heavy-ion collisions. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

Collisional enhancement of energetic particle Alfvénic resonance width in tokamaks

The phase-space structure of resonances between fast ions and an Alfvénic mode and the associated modification of density profiles in tokamaks are studied as a function of particle collisions. Guiding-center simulations in a realistic tokamak equilibrium are employed to address the resonance broadening parametric dependencies with respect to changes in the pitch-angle scattering rate. The rate of collisional replenishment, along with resonance strength, given by the combination of eigenmode and resonance structures and equilibrium parameters, determines saturation amplitudes for a given damping rate. As seen from the distribution function flattening, collisions have an effect of broadening the resonances, while the absolute value of δf decreases with increasing collisionality. It is observed that the collisional broadening can be comparable to the collisionless resonance width due to the mode amplitude alone. The resonance broadening coefficients are compared with the existing theory based on analytically expected saturation levels, showing fair agreement. Furthermore the results can be useful in assisting reduced kinetic models, such as quasilinear models, when prescribing the effective resonance phase-space width, i.e., the mode-particle interaction platform, due to collisional or turbulent processes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

The crystal structure of Grindelia robusta 7,13-copalyl diphosphate synthase reveals active site features controlling catalytic specificity

Diterpenoid natural products serve critical functions in plant development and ecological adaptation and many diterpenoids have economic value as bioproducts. The family of class II diterpene synthases catalyzes the committed reactions in diterpenoid biosynthesis, converting a common geranylgeranyl diphosphate precursor into different bicyclic prenyl diphosphate scaffolds. Enzymatic rearrangement and modification of these precursors generate the diversity of bioactive diterpenoids. We report the crystal structure of Grindelia robusta 7,13-copalyl diphosphate synthase, GrTPS2, at 2.1 Å of resolution. GrTPS2 catalyzes the committed reaction in the biosynthesis of grindelic acid, which represents the signature metabolite in species of gumweed (Grindelia spp., Asteraceae). Grindelic acid has been explored as a potential source for drug leads and biofuel production. The GrTPS2 crystal structure adopts the conserved three-domain fold of class II diterpene synthases featuring a functional active site in the γβ-domain and a vestigial α-domain. Substrate docking into the active site of the GrTPS2 apo protein structure predicted catalytic amino acids. Biochemical characterization of protein variants identified residues with impact on enzyme activity and catalytic specificity. Specifically, mutagenesis of Y457 provided mechanistic insight into the position-specific deprotonation of the intermediary carbocation to form the characteristic 7,13 double bond of 7,13-copalyl diphosphate.

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

Comment on “Breakdown of the expansion of finite-size corrections to the hydrogen Lamb shift in moments of charge distribution”

In a recent study, Hagelstein and Pascalutsa [F. Hagelstein and V. Pascalutsa, Phys. Rev. A 91, 040502 (2015)] examine the error associated with an expansion of proton structure corrections to the Lamb shift in terms of moments of the charge distribution. They propose a small modification to a conventional parametrization of the proton's charge form factor and show that this can resolve the proton radius puzzle. However, while the size of the bump they add to the form factor is small, it is large compared to the total proton structure effects in the initial parametrization, yielding a final form factor that is unphysical. Reducing their modification to the point where the resulting form factor is physical does not allow for a resolution of the radius puzzle.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2017

Significance of a Posttranslational Modification of the PilA Protein of Geobacter sulfurreducens for Surface Attachment, Biofilm Formation, and Growth on Insoluble Extracellular Electron Acceptors

Geobacter sulfurreducens , an anaerobic metal-reducing bacterium, possesses type IV pili. These pili are intrinsic structural elements in biofilm formation and, together with a number of c -type cytochromes, are thought to serve as conductive nanowires enabling long-range electron transfer (ET) to metal oxides and graphite anodes. Here, we report that a posttranslational modification of a nonconserved amino acid residue within the PilA protein, the structural subunit of the type IV pili, is crucial for growth on insoluble extracellular electron acceptors. Matrix-assisted laser desorption ionization (MALDI) mass spectrometry of the secreted PilA protein revealed a posttranslational modification of tyrosine-32 with a moiety of a mass consistent with a glycerophosphate group. Mutating this tyrosine into a phenylalanine inhibited cell growth with Fe(III) oxides as the sole electron acceptor. In addition, this amino acid substitution severely diminished biofilm formation on graphite surfaces and impaired current output in microbial fuel cells. These results demonstrate that the capability to attach to insoluble electron acceptors plays a crucial role for the cells' ability to utilize them. The work suggests that glycerophosphate modification of Y32 is a key factor contributing to the surface charge of type IV pili, influencing the adhesion of Geobacter to specific surfaces. Type IV pili are bacterial appendages that function in cell adhesion, virulence, twitching motility, and long-range electron transfer (ET) from bacterial cells to insoluble extracellular electron acceptors. The mechanism and role of type IV pili for ET in Geobacter sulfurreducens is still a subject of research. In this study, we identified a posttranslational modification of the major G. sulfurreducens type IV pilin, suggested to be a glycerophosphate moiety. We show that a mutant in which the glycerophosphate-modified tyrosine-32 is replaced with a phenylalanine has reduced abilities for ET and biofilm formation compared with those of the wild type. The results show the importance of the glycerophosphate-modified tyrosine for surface attachment and electron transfer in electrode- or Fe(III)-respiring G. sulfurreducens cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Surface Modification of Rock-Forming Minerals of Diamond-Bearing Kimberlites under Interaction with Wastewater and Electrochemically Treated Water

The structural and chemical surface transformation of basic kimberlite-forming minerals (calcite, olivine, serpentine) under the contact with natural and waste mineralized water and products of electrochemical treatment of the water are studied using X-ray photoelectronic spectroscopy, scanning electron microscopy and X-ray spectral micro-analysis, and atomic force microscopy. It is found that contact with kimberlite extract and recycling water induces chemical modification of calcite surface, which consists in adsorption of hydrocarbon impurities, and chlorine- and silica-bearing compounds, majority of which are removed during interaction with the product of electrochemical treatment of recycling water. The change in the structural and chemical surface properties of rock-forming silicates, aside from adsorption–desorption of organic compound, is also connected with the distortion of nano-size layer structure after leaching of Mg, Fe and Si, and with the carbonatization of the surface.

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

Structures of N-terminally processed KRAS provide insight into the role of N-acetylation

Although post-translational modification of the C-terminus of RAS has been studied extensively, little is known about N-terminal processing. Mass spectrometric characterization of KRAS expressed in mammalian cells showed cleavage of the initiator methionine (iMet) and N-acetylation of the nascent N-terminus. Interestingly, structural studies on GDP- and GMPPNP-bound KRAS lacking the iMet and N-acetylation resulted in Mg 2+ -free structures of KRAS with flexible N-termini. In the Mg 2+ -free KRAS-GDP structure, the flexible N-terminus causes conformational changes in the interswitch region resulting in a fully open conformation of switch I. In the Mg 2+ -free KRAS-GMPPNP structure, the flexible N-terminus causes conformational changes around residue A59 resulting in the loss of Mg 2+ and switch I in the inactive state 1 conformation. Structural studies on N-acetylated KRAS-GDP lacking the iMet revealed the presence of Mg 2+ and a conformation of switch regions also observed in the structure of GDP-bound unprocessed KRAS with the iMet. In the absence of the iMet, the N-acetyl group interacts with the central beta-sheet and stabilizes the N-terminus and the switch regions. These results suggest there is crosstalk between the N-terminus and the Mg 2+ binding site, and that N-acetylation plays an important role by stabilizing the N-terminus of RAS upon excision of the iMet.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Possible reason for the numerical value of the fine-structure constant

A simple picture of the electron emerges if there is a cross section of πλ 2 for vacuum virtual photons to stimulate an isolated electron to emit an additional virtual photon. This reaction mechanism leads to the storage of the rest-mass energy in the surrounding cloud of virtual photons. The Lamb shift can be obtained if one out of every 1/α of the stimulated emissions is preceded by the absorption and re-emission of the incident vacuum virtual photon including the corresponding electron recoil. This suggests a “doorway” cross section of απλ 2 plays a key role in some QED processes. Additional support for this suggestion is obtained via a simple semi-classical picture of Compton scattering. Several speculative semi-classical reaction mechanism choices, including near-field effects, give the anomalous magnetic moment of the free electron. These choices are partially justified by their ability to give the magnetic moment of electrons in hydrogen-like atoms as a function of the atomic number of the corresponding nucleus, close to the correct result. The stimulated-emission process used to obtain the rest-mass energy allows for the possibility that stimulated virtual photons can be exchanged between an electron pair. This exchange can be used to estimate a repulsive force between electrons, and thus allows for a calculation of the fine-structure constant. A result near to the experimental value is obtained with minor modifications to the assumptions that give the rest mass, Lamb shift, and anomalous magnetic moment of the electron. Additional studies are required to confirm or negate the suggestions made here.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Structure of AadA from Salmonella enterica: a monomeric aminoglycoside (3′′)(9) adenyltransferase

The crystal structure of the aminoglycoside-adenylating enzyme AadA is reported together with functional experiments providing insights into its oligomeric state, ligand binding and catalysis. Aminoglycoside resistance is commonly conferred by enzymatic modification of drugs by aminoglycoside-modifying enzymes such as aminoglycoside nucleotidyltransferases (ANTs). Here, the first crystal structure of an ANT(3′′)(9) adenyltransferase, AadA from Salmonella enterica, is presented. AadA catalyses the magnesium-dependent transfer of adenosine monophosphate from ATP to the two chemically dissimilar drugs streptomycin and spectinomycin. The structure was solved using selenium SAD phasing and refined to 2.5 Å resolution. AadA consists of a nucleotidyltransferase domain and an α-helical bundle domain. AadA crystallizes as a monomer and is a monomer in solution as confirmed by small-angle X-ray scattering, in contrast to structurally similar homodimeric adenylating enzymes such as kanamycin nucleotidyltransferase. Isothermal titration calorimetry experiments show that ATP binding has to occur before binding of the aminoglycoside substrate, and structure analysis suggests that ATP binding repositions the two domains for aminoglycoside binding in the interdomain cleft. Candidate residues for ligand binding and catalysis were subjected to site-directed mutagenesis. In vivo resistance and in vitro binding assays support the role of Glu87 as the catalytic base in adenylation, while Arg192 and Lys205 are shown to be critical for ATP binding.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Strongly Modified Scaling of CO Hydrogenation in Metal Supported TiO Nanostripes

The boundary between a metal-oxide and its metal support (metal-oxide|support) provides an intriguing structural interface for heterogeneous catalysis. The hydrogenation of CO is a reaction step believed to be rate limiting in electro-chemical CO2 reduction. Density functional theory (DFT) calculations were performed to study this reaction step for a class of catalytic material: metal supported TiO nanostripe. The most stable adsorption sites were identified for all metal supports which showed a striking difference in adsorbate geometry between the strong and weak binding metal supports. The modified CO hydrogenation scaling shows a significant strengthening over (111) and (211) transition metal surfaces. Such enhancement can be attributed to a combination of geometrical effects and metal-oxide|support electronic interactions. A correlation analysis was performed to identify the key features needed to accurately predict *CO and *CHO adsorption energies on the TiO nanostripes and to further validate our physical analysis of the results. This structural motif seems to be a promising avenue to explore scaling modification in other metal-oxide materials and reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Dynamics of pectic homogalacturonan in cellular morphogenesis and adhesion, wall integrity sensing and plant development

Homogalacturonan (HG) is the most abundant pectin subtype in plant cell walls. Although it is a linear homopolymer, its modification states allow for complex molecular encoding. HG metabolism affects its structure, chemical properties, mobility and binding capacity, allowing it to interact dynamically with other polymers during wall assembly and remodelling and to facilitate anisotropic cell growth, cell adhesion and separation, and organ morphogenesis. HGs have also recently been found to function as signalling molecules that transmit information about wall integrity to the cell. Here we highlight recent advances in our understanding of the dual functions of HG as a dynamic structural component of the cell wall and an initiator of intrinsic and environmental signalling. Here, we also predict how HG might interconnect the cell wall, plasma membrane and intracellular components with transcriptional networks to regulate plant growth and development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Single-particle detection of enhanced polarizability in Au-decorated semiconducting nanorods via scanning dielectric microscopy

Hybrid nanostructures that combine semiconducting and metallic components offer great potential for photothermal therapy, optoelectronics, and sensing, by integrating tunable optical properties with enhanced light absorption and charge transport. Boosting the integrated performance of these hybrid systems demands techniques capable of probing local variations of the physical properties inaccessible to bulk analysis. Here, we report the single-particle dielectric characterization of hybrid, semiconducting bismuth sulfide (Bi 2 S 3 ) nanorods (NR) decorated with metallic Au nanoparticles (NP), employing scanning dielectric microscopy, which uses electrostatic force microscopy in combination with finite-element numerical simulations. We reveal a pronounced enhancement in the local dielectric response of Bi2S3 upon Au decoration, attributed to interfacial polarization and electron transfer from Au to the Bi 2 S 3 matrix, thus suggesting a enhanced metallic-like polarizability at the single-particle level. Numerical simulations show that the response is dominated by the vertical component of the permittivity and that the decorating metallic Au NP produce only moderate shielding of the semiconductor Bi 2 S 3 NR core, indicating that the large increase in the dielectric response originates primarily from intrinsic modifications within the NR. Overall, these findings provide direct insight into structure–property relationships at the single-particle level, supporting the rational design of advanced hybrid nanostructures with tailored electronic functionalities.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Impact of La{sub 2}O{sub 3} interfacial layers on InGaAs metal-oxide-semiconductor interface properties in Al{sub 2}O{sub 3}/La{sub 2}O{sub 3}/InGaAs gate stacks deposited by atomic-layer-deposition

We examine the electrical properties of atomic layer deposition (ALD) La{sub 2}O{sub 3}/InGaAs and Al{sub 2}O{sub 3}/La{sub 2}O{sub 3}/InGaAs metal-oxide-semiconductor (MOS) capacitors. It is found that the thick ALD La{sub 2}O{sub 3}/InGaAs interface provides low interface state density (D{sub it}) with the minimum value of ∼3 × 10{sup 11} cm{sup −2} eV{sup −1}, which is attributable to the excellent La{sub 2}O{sub 3} passivation effect for InGaAs surfaces. It is observed, on the other hand, that there are a large amount of slow traps and border traps in La{sub 2}O{sub 3}. In order to simultaneously satisfy low D{sub it} and small hysteresis, the effectiveness of Al{sub 2}O{sub 3}/La{sub 2}O{sub 3}/InGaAs gate stacks with ultrathin La{sub 2}O{sub 3} interfacial layers is in addition evaluated. The reduction of the La{sub 2}O{sub 3} thickness to 0.4 nm in Al{sub 2}O{sub 3}/La{sub 2}O{sub 3}/InGaAs gate stacks leads to the decrease in hysteresis. On the other hand, D{sub it} of the Al{sub 2}O{sub 3}/La{sub 2}O{sub 3}/InGaAs interfaces becomes higher than that of the La{sub 2}O{sub 3}/InGaAs ones, attributable to the diffusion of Al{sub 2}O{sub 3} through La{sub 2}O{sub 3} into InGaAs and resulting modification of the La{sub 2}O{sub 3}/InGaAs interface structure. As a result of the effective passivation effect of La{sub 2}O{sub 3} on InGaAs, however, the Al{sub 2}O{sub 3}/10 cycle (0.4 nm) La{sub 2}O{sub 3}/InGaAs gate stacks can realize still lower D{sub it} with maintaining small hysteresis and low leakage current than the conventional Al{sub 2}O{sub 3}/InGaAs MOS interfaces.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Laser material processing with tightly focused cylindrical vector beams

We demonstrate a comprehensive modification study of silica glass, crystalline silicon, and amorphous silicon film, irradiated by tightly focused cylindrical vector beams with azimuthal and radial polarizations. The evidence of the longitudinal field associated with radial polarization is revealed by second harmonic generation in z-cut lithium niobate crystal. Despite the lower threshold of ring-shaped modification of silicon materials, the modification in the center of single pulse radially polarized beam is not observed. The phenomenon is interpreted in terms of the enhanced reflection of longitudinal component at the interface with high-index contrast, demonstrating that the longitudinal component is inefficient for the flat surface modification. Enhanced interaction of the longitudinal light field with silicon nanopillar structures produced by the first pulse of double-pulse irradiation is also demonstrated.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗