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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 1,549 records · Page 86
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Crystal structures of Mycobacterium tuberculosis GlgE and complexes with non-covalent inhibitors

GlgE is a bacterial maltosyltransferase that catalyzes the elongation of a cytosolic, branched α-glucan. In Mycobacterium tuberculosis (M. tb), inactivation of GlgE (Mtb GlgE) results in the rapid death of the organism due to a toxic accumulation of the maltosyl donor, maltose-1-phosphate (M1P), suggesting that GlgE is an intriguing target for inhibitor design. In this study, the crystal structures of the Mtb GlgE in a binary complex with maltose and a ternary complex with maltose and a maltosyl-acceptor molecule, maltohexaose, were solved to 3.3 Å and 4.0 Å, respectively. The maltohexaose structure reveals a dominant site for α-glucan binding. To obtain more detailed interactions between first generation, non-covalent inhibitors and GlgE, a variant Streptomyces coelicolor GlgEI (Sco GlgEI-V279S) was made to better emulate the Mtb GlgE M1P binding site. The structure of Sco GlgEI-V279S complexed with α-maltose-C-phosphonate (MCP), a non-hydrolyzable substrate analogue, was solved to 1.9 Å resolution, and the structure of Sco GlgEI-V279S complexed with 2,5-dideoxy-3-O-α-D-glucopyranosyl-2,5-imino-D-mannitol (DDGIM), an oxocarbenium mimic, was solved to 2.5 Å resolution. These structures detail important interactions that contribute to the inhibitory activity of these compounds, and provide information on future designs that may be exploited to improve upon these first generation GlgE inhibitors.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Highly efficient photoinduced desorption of N{sub 2}O and CO from porous silicon

Photoinduced desorption (PID) of N{sub 2}O and CO from porous silicon (PSi) samples is reported. Both adsorbates exhibit unusually large cross sections for PID at 193 nm, up to 10{sup -15} cm{sup 2}, 2-3 orders of magnitude larger than the literature values for similar processes on flat Si. Under this UV irradiation, N{sub 2}O molecules undergo photodissociation (a competing process leading to surface oxidation) with a cross section that is 2 orders of magnitude smaller than photodesorption. In the case of CO desorption is the exclusive photodepletion mechanism. PID efficiency decreases with increasing CO coverage suggesting PID hindrance by interactions among the desorbing CO molecules leading to re-adsorption at higher coverage. The wavelength and fluence dependence measurements exclude the possibility of laser induced thermal desorption for both adsorbates. The proposed mechanism for this phenomenon is desorption induced by hot electron transfer from the substrate to the adsorbate. Enhanced lifetime of transient negative adsorbate due to stabilization by localized holes on PSi nanotips can explain the observed abnormally large PID efficiency on top of porous silicon.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Simulation insights into wetting properties of hydrogen-brine-clay for hydrogen geo-storage

Hydrogen geo-storage is attracting substantial interdisciplinary interest as a cost-effective and sustainable option for medium- and long-term storage. Hydrogen can be stored underground in diverse formations, including aquifers, salt caverns, and depleted oil and gas reservoirs. The wetting dynamics of the hydrogen-brine-rock system are critical for assessing both structural and residual storage capacities, and ensuring containment safety. Through molecular dynamics simulations, we explore how varying concentrations of cushion gases (CO 2 or CH 4 ) influence the wetting properties of hydrogen-brine-clay systems under geological conditions (15 MPa and 333 K). We employed models of talc and the hydroxylated basal face of kaolinite (kaoOH) as clay substrates. Our findings reveal that the effect of cushion gases on hydrogen-brine-clay wettability is strongly dependent on the clay-brine interactions. Notably, CO 2 and CH 4 reduce the water wettability of talc in hydrogen-brine-talc systems, while exerting no influence on the wettability of hydrogen-brine-kaoOH systems. Detailed analysis of free energy of cavity formation near clay surfaces, clay-brine interfacial tensions, and the Willard-Chandler surface for gas-brine interfaces elucidate the molecular mechanisms underlying wettability changes. Our simulations identify empirical correlations between wetting properties and the average free energy required to perturb a flat interface when clay-brine interactions are less dominant. Here, our thorough thermodynamic analysis of rock-fluid and fluid-fluid interactions, aligning with key experimental observations, underscores the utility of simulated interfacial properties in refining contact angle measurements and predicting experimentally relevant properties. These insights significantly enhance the assessment of gas geo-storage potential. Prospectively, the approaches and findings obtained from this study could form a basis for more advanced multiscale simulations that consider a range of geological and operational variables, potentially guiding the development and improvement of geo-storage systems in general, with a particular focus on hydrogen storage.

25 ENERGY STORAGE↗
DOE OSTI2017

Minor Impact of Ligand Shell Steric Profile on Colloidal Nanocarbon Catalysis

The catalytic activity of a colloidal nanoparticle is typically inhibited by the very capping agents that are required to maintain colloidal stability and catalyst dispersion. Yet, the relative importance of steric contributions to the observed attenuation in catalytic activity is poorly understood. In this work, we prepare colloidal graphitic carbon nanoparticles featuring covalent amide linkages to aliphatic surface capping agents of varying length. Using aerobic benzylamine oxidation as a test reaction, we find that the steric profile of the ligand shell plays a negligible role in suppressing catalytic activity relative to chemisorption interactions that alter the surface chemistry of the catalyst. The work indicates that heterostructured nanoparticles that provide distinct surface sites for ligand binding and substrate activation should allow for high colloidal stability and robust catalytic activity.

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

Adsorption Behavior of Organic Molecules: A Study of Benzotriazole on Cu(111) with Spectroscopic and Theoretical Methods

The adsorption of organic molecules on solid substrates is important to applications in fields such as catalysis, photovoltaics, corrosion inhibition, adhesion, and sensors. The molecular level description of the surface–molecule interaction and of the adsorption structures in these complex systems is crucial to understand their properties and function. Here, we present an investigation of one such system, benzotriazole (BTAH) on single-crystal Cu(111) in vacuum conditions. BTAH is the most widely used corrosion inhibitor for copper and thus a molecule of great industrial relevance. We show that the co-application of a wide range of spectroscopic techniques with theoretical methods provides unique insight in the description of the atomistic details of the adsorbed structures. Specifically, spectroscopic photoemission, absorption, and standing wave experiments combined with ab initio computational modeling allowed us to identify that benzotriazole forms overlayers of intact BTAH when deposited at low temperature, and it dissociates into BTA and H at room temperature and above. The dissociated molecule then forms complex structures of mixed chains and dimers of BTA bound to copper adatoms. Our work also reveals that copper adatoms at low concentrations, such as the theoretically predicted superstructures, cannot be resolved by means of current X-ray photoelectron spectroscopy as the modeled Cu 2p spectra are practically indistinguishable from those for a Cu surface without adatoms. Overall this study significantly deepens understanding of BTAH on Cu, a system studied for more than 50 years, and it highlights the benefits of combining spectroscopic and computational methods to obtain a complete picture of a complex adsorption system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Reduction of Feedback Inhibition in Homoserine Kinase (ThrB) of Corynebacterium glutamicum Enhances L -Threonine Biosynthesis

L -Threonine is an important supplement in the food industry. It is currently produced through fermentation of Escherichia coli but requires additional purification steps to remove E. coli endotoxin. To avoid these steps, it is desirable to use Corynebacterium glutamicum , a microorganism generally regarded as safe. Engineering of C. glutamicum to increase production of l -threonine has mainly focused on gene regulation as well as l -threonine export or carbon flux depletion. In this study, we focus on the negative feedback inhibition produced by L -threonine on the enzyme homoserine kinase (ThrB). Although L -threonine binds to allosteric sites of aspartate kinase (LysC) and homoserine dehydrogenase (Hom), serving as a noncompetitive inhibitor, it acts as a competitive inhibitor on ThrB. This is problematic when attempting to engineer enzymes that are nonresponsive to increasing cellular concentrations of L -threonine. Using primary structure alignment as well as analysis of the Methanocaldococcus jannaschii ThrB ( Mja ThrB) active site in complex with L -threonine (inhibitor of ThrB) and L -homoserine (substrate of ThrB), a conserved active-site alanine residue (A20) in C. glutamicum ThrB ( Cgl ThrB) was predicted to be important for differential interactions with L -threonine and L -homoserine. Through site-directed mutagenesis, we show that one variant of C. glutamicum ThrB, Cgl ThrB-A20G, retains wild-type enzymatic activity, with dramatically decreased feedback inhibition by L -threonine. Additionally, by solving the first Corynebacterium X-ray crystal structure of homoserine kinase, we can confirm that the changes in L -threonine affinity to the Cgl ThrB-A20G active site derive from loss of van der Waals interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Crystal Structure of an Activated Variant of Small Heat Shock Protein Hsp16.5

How does the sequence of a single small heat shock protein (sHSP) assemble into oligomers of different sizes? To gain insight into the underlying structural mechanism, we determined the crystal structure of an engineered variant of Methanocaldococcus jannaschii Hsp16.5 wherein a 14 amino acid peptide from human heat shock protein 27 (Hsp27) was inserted at the junction of the N-terminal region and the {alpha}-crystallin domain. In response to this insertion, the oligomer shell expands from 24 to 48 subunits while maintaining octahedral symmetry. Oligomer rearrangement does not alter the fold of the conserved {alpha}-crystallin domain nor does it disturb the interface holding the dimeric building block together. Rather, the flexible C-terminal tail of Hsp16.5 changes its orientation relative to the {alpha}-crystallin domain which enables alternative packing of dimers. This change in orientation preserves a peptide-in-groove interaction of the C-terminal tail with an adjacent {beta}-sandwich, thereby holding the assembly together. The interior of the expanded oligomer, where substrates presumably bind, retains its predominantly nonpolar character relative to the outside surface. New large windows in the outer shell provide increased access to these substrate-binding regions, thus accounting for the higher affinity of this variant to substrates. Oligomer polydispersity regulates sHSPs chaperone activity in vitro and has been implicated in their physiological roles. The structural mechanism of Hsp16.5 oligomer flexibility revealed here, which is likely to be highly conserved across the sHSP superfamily, explains the relationship between oligomer expansion observed in disease-linked mutants and changes in chaperone activity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Adsorption geometry of CO versus coverage on TiO2(110) from s- and p-polarized infrared spectroscopy

The adsorption of CO on reduced, rutile TiO2(110) is investigated using IR reflection-absorption spectroscopy and temperature programmed desorption. Experiments using s- and p-polarized IR light incident along the [001] and ]011[ azimuths give detailed information on the adsorption geometry of the CO as a function of the CO coverage, θCO. The results indicate that for 0 < θCO ≤ 1 ML, CO adsorbs oriented normal to the surface at Ti5c sites. For 1 < θCO ≤ 1.5 ML, the bonding geometry of the CO adsorbed at Ti5c sites is unchanged, while the additional CO molecules adsorb at OB sites parallel to the surface and parallel to the ]011[ azimuth. The results do not support previous suggestions that CO at Ti5c sites tilt ~20° from normal to reduce repulsive interactions at high coverages. The results demonstrate the utility of polarization-resolved infrared reflection-adsorption spectroscopy for elucidating adsorption geometries on dielectric substrates.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2023

Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin

The Papain-like protease (PLpro) is a domain of a multi-functional, non-structural protein 3 of coronaviruses. PLpro cleaves viral polyproteins and posttranslational conjugates with poly-ubiquitin and protective ISG15, composed of two ubiquitin-like (UBL) domains. Across coronaviruses, PLpro showed divergent selectivity for recognition and cleavage of posttranslational conjugates despite sequence conservation. We show that SARS-CoV-2 PLpro binds human ISG15 and K48-linked di-ubiquitin (K48-Ub 2 ) with nanomolar affinity and detect alternate weaker-binding modes. Crystal structures of untethered PLpro complexes with ISG15 and K48-Ub 2 combined with solution NMR and cross-linking mass spectrometry revealed how the two domains of ISG15 or K48-Ub 2 are differently utilized in interactions with PLpro. Analysis of protein interface energetics predicted differential binding stabilities of the two UBL/Ub domains that were validated experimentally. We emphasize how substrate recognition can be tuned to cleave specifically ISG15 or K48-Ub 2 modifications while retaining capacity to cleave mono-Ub conjugates. These results highlight alternative druggable surfaces that would inhibit PLpro function.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Design and synthesis of model and practical palladium catalysts using atomic layer deposition

Here, we investigated the “one-batch” synthesis of model and practical palladium catalysts using atomic layer deposition (ALD). Two types of model catalysts and one type of powder-based nanocatalyst were synthesized simultaneously by ALD under viscous flow conditions. In addition, Pd/TiO 2 (110) model catalysts were prepared by the identical ALD process but under ultrahigh vacuum conditions. Because of the self-limiting surface reaction that defines ALD, the local structure of all the Pd catalysts were essentially the same as confirmed by a suite of microscopic and spectroscopic characterization techniques. A comprehensive understanding of the Pd-based catalysts was achieved by applying both surface science probes and advanced synchrotron techniques, and by strategically selecting the catalyst substrate best suited for each characterization. Both X-ray absorption spectroscopy and X-ray resonant photoelectron spectroscopy suggested that Pd only weakly interacted with the TiO 2 support. The one-batch synthesis approach facilitated by ALD can potentially bridge the “synthesis gap” between model catalysts and practical catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

Physical understanding of cryogenic implant benefits for electrical junction stability

We investigate the effect of cryogenic temperature implants on electrical junction stability for ultra shallow junction applications for sub-32 nm technology nodes and beyond. A comprehensive study was conducted to gain physical understanding of the impact of cryogenic temperature implants on dopant-defect interactions. Carborane (C{sub 2}B{sub 10}H{sub 12}) molecule, a potential alternative to monomer boron was implanted in carbon preamorphized silicon substrates at cryogenic implant temperatures. Results indicate implants at cryogenic temperatures increase dopant activation with reduced diffusion, resulting in lower sheet resistance for a lower junction depth. Further, this study emphasizes the benefits of co-implants performed at cryogenic temperatures as alternative to traditional preamorphizing implants.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Molecular dynamics simulation of graphene growth at initial stage on Ni(100) facet for low flux C energy by CVD

In this study, atomic simulation for graphene growth on Ni (100) at initial stage via chemical vapor deposition method has been developed. The C-C atoms interaction was performed by Terasoff potential mean while Ni-Ni interaction was specified by EAM (Embedded Atom Modified). On the other hand, we used very simple interatomic potential to describe Ni-C interaction during deposition process. From this simulation, it shows that the formation of graphene is not occurs through a combined deposition mechanism on Ni substrate but via C segregation. It means, Ni-C amorphous is source for graphene growth when cooling down of Ni substrate. This result is appropriate with experiments, tight binding and quantum mechanics simulation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Structural basis for the tRNA-dependent activation of the terminal complex of selenocysteine synthesis in humans

Abstract O-Phosphoseryl-tRNASec selenium transferase (SepSecS) catalyzes the terminal step of selenocysteine (Sec) synthesis in archaea and eukaryotes. How the Sec synthetic machinery recognizes and discriminates tRNASec from the tRNA pool is essential to the integrity of the selenoproteome. Previously, we suggested that SepSecS adopts a competent conformation that is pre-ordered for catalysis. Herein, using high-resolution X-ray crystallography, we visualized tRNA-dependent conformational changes in human SepSecS that may be a prerequisite for achieving catalytic competency. We show that tRNASec binding organizes the active sites of the catalytic protomer, while stabilizing the N- and C-termini of the non-catalytic protomer. Binding of large anions to the catalytic groove may further optimize the catalytic site for substrate binding and catalysis. Our biochemical and mutational analyses demonstrate that productive SepSecS•tRNASec complex formation is enthalpically driven and primarily governed by electrostatic interactions between the acceptor-, TΨC-, and variable arms of tRNASec and helices α1 and α14 of SepSecS. The detailed visualization of the tRNA-dependent activation of SepSecS provides a structural basis for a revised model of the terminal reaction of Sec formation in archaea and eukaryotes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Picoscale structural insight into superconductivity of monolayer FeSe/SrTiO 3

Remarkable enhancement of the superconducting transition temperature ( c ) has been observed for monolayer (ML) FeSe films grown on SrTiO 3 substrates. The atomic-scale structure of the FeSe/SrTiO 3 interface is an important determinant of both the magnetic and interfacial electron-phonon interactions and is a key ingredient to understanding its high- T c superconductivity. We resolve the atomic-scale structure of the FeSe/SrTiO 3 interface through a complementary analysis of scanning transmission electron microscopy and in situ surface x-ray diffraction. We find that the interface is more strongly bonded for a particular registration, which leads to a coherently strained ML. We also determine structural parameters, such as the distance between ML FeSe and the oxide, Se-Fe-Se bond angles, layer-resolved distances between Fe-Se, and registry of the FeSe lattice relative to the oxide. This picoscale structure determination provides an explicit structural framework and constraint for theoretical approaches addressing the high- T c mechanism in FeSe/SrTiO 3 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

A dynamic protein interactome drives energy conservation and electron flux in Thermococcus kodakarensis

ABSTRACT Life is supported by energy gains fueled by catabolism of a wide range of substrates, each reliant on the selective partitioning of electrons through redox ( red uction and ox idation) reactions. Electron flux through tunable and regulated protein interactions provides dynamic routes for energy conservation, but how electron flux is regulated in vivo , particularly for archaeal metabolisms that support rapid growth at the thermodynamic limits of life, is poorly understood. Identification of bona fide in vivo protein assemblies and how such assemblies dictate the totality of electron flux is critical to our understanding of the regulation imposed on metabolism, energy production, and energy conservation. Here, 25 key proteins in central metabolic redox pathways in the model, genetically accessible, hyperthermophilic archaeon Thermococcus kodakarensis , were purified to reveal an extensive, dynamic, and tightly interconnected network of protein interactions that responds to environmental cues (such as the availability of various reductive sinks) to direct electron flux to maximize energetic gains. Interactions connecting disparate functions suggest many catabolic and anabolic activities occur in spatial proximity in vivo , and while protein complexes have been historically defined under optimal conditions, many of these complexes appear to maintain alternative partnerships in changing conditions. The totality of the results obtained redefines our understanding of in vivo assemblies driving ancient metabolic strategies supporting the growth of modern Archaea. IMPORTANCE Given the potential for rational genetic manipulations of biofuel- and biotech-promising archaea to yield transformative results for major markets, it is a priority to define how the metabolisms of such species are controlled, at least in part, by in vivo protein assemblies, and from such, define routes of energy flux that can be most efficiently altered toward biofuel or biotechnological gains. Proteinaceous electron carriers (PECs, such as ferredoxins) offer the potential for specific protein–protein interactions to coordinate selective reductive flow. Employing the model, genetically accessible, hyperthermophilic archaeon, Thermococcus kodakarensis , we establish the metabolic protein interactome of 25 key redox proteins, revealing that each redox active protein has a dynamic partnership profile, suggesting catabolic and anabolic activities may occur in concert and in temporal and spatial proximity in vivo . These results reveal critical importance in evaluating the newly identified partnerships and their role and utility in providing regulated redox flux in T. kodakarensis .

Williams, Sere A. (ORCID:0000000235509590)↗
DOE OSTI2019

Structure and mechanism of TagA, a novel membrane-associated glycosyltransferase that produces wall teichoic acids in pathogenic bacteria

Staphylococcus aureus and other bacterial pathogens affix wall teichoic acids (WTAs) to their surface. These highly abundant anionic glycopolymers have critical functions in bacterial physiology and their susceptibility to β-lactam antibiotics. The membrane-associated TagA glycosyltransferase (GT) catalyzes the first-committed step in WTA biosynthesis and is a founding member of the WecB/TagA/CpsF GT family, more than 6,000 enzymes that synthesize a range of extracellular polysaccharides through a poorly understood mechanism. Crystal structures of TagA from T. italicus in its apo- and UDP-bound states reveal a novel GT fold, and coupled with biochemical and cellular data define the mechanism of catalysis. We propose that enzyme activity is regulated by interactions with the bilayer, which trigger a structural change that facilitates proper active site formation and recognition of the enzyme’s lipid-linked substrate. These findings inform upon the molecular basis of WecB/TagA/CpsF activity and could guide the development of new anti-microbial drugs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

NSTX-U liquid metal core-edge facility (LMCE)

NSTX-U/LMCE will provide a unique and world-leading research facility to address the primary challenge to delivering economic and timely magnetic fusion energy, namely the need to develop a power and particle exhaust and first-wall system that can withstand very high edge heat fluxes, maximize energy confinement, and avoid the production of large masses of solid eroded first-wall material. The NSTX-U/LMCE facility will assess the ability of liquid metals (LMs) – especially liquid lithium – to provide a new boundary condition for magnetic fusion systems, to extend the lifetime of the plasma facing components (PFCs) and improve core plasma confinement. Such capability is needed to establish the basis for next-step fusion facilities including fusion pilot plants, and to maintain U.S. world leadership in core-edge integration research. NSTX-U/LMCE will leverage the ability to generate very high divertor perpendicular heat flux q⊥ ~ 100MW/m 2 , extensive diagnostics, and liquid-metal-applicable infrastructure of NSTX-U. NSTX-U/LMCE will provide access to a high-confinement plasma core with majority self-driven plasma current, the flexibility to test a range of liquid metal divertor concepts, access to a range of separatrix collisionalities (from high to very low), and the ability to controllably vary the first-wall temperature to vary the plasma- wall interaction physics on liquid lithium components. Further, NSTX-U/LMCE will utilize more reactor-relevant high-Z refractory-metal PFC substrates. With these capabilities the NSTX-U/LMCE facility will explore the full continuum of core-edge solutions ranging from high core radiated power, to conditions with radiative losses concentrated in the scrape-off layer (SOL), and ultimately low recycling conditions. The low collisionality SOL that may be accessible in the low recycling regime is relatively unexplored and will require a kinetic treatment of the edge, which can be addressed theoretically, and with experiments in LTX-β. Additional smaller-scale preparatory R&D facilities will be required to reduce the risk of premature technical/engineering failure of liquid metal systems implemented in NSTX-U. The NSTX-U/LMCE facility aligns very well with recommendations in the FESAC Long-Range Plan and NASEM Pilot Plant reports and the Bold Decadal Vision, will be unique in the world program throughout the next decade, and is garnering private company interest in utilizing NSTX-U/LMCE for development of LM PFCs.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗