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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 523 records · Page 29
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Structural basis of colibactin activation by the ClbP peptidase

Abstract Colibactin, a DNA cross-linking agent produced by gut bacteria, is implicated in colorectal cancer. Its biosynthesis uses a prodrug resistance mechanism: a non-toxic precursor assembled in the cytoplasm is activated after export to the periplasm. This activation is mediated by ClbP, an inner-membrane peptidase with an N-terminal periplasmic catalytic domain and a C-terminal three-helix transmembrane domain. Although the transmembrane domain is required for colibactin activation, its role in catalysis is unclear. Our structure of full-length ClbP bound to a product analog reveals an interdomain interface important for substrate binding and enzyme stability and interactions that explain the selectivity of ClbP for the N -acyl- d -asparagine prodrug motif. Based on structural and biochemical evidence, we propose that ClbP dimerizes to form an extended substrate-binding site that can accommodate a pseudodimeric precolibactin with its two terminal prodrug motifs in the two ClbP active sites, thus enabling the coordinated activation of both electrophilic warheads.

Biochemistry & Molecular Biology↗
DOE OSTI2017

Recruitment of a SUMO isopeptidase to rDNA stabilizes silencing complexes by opposing SUMO targeted ubiquitin ligase activity

Post-translational modification by SUMO (small ubiquitin-like modifier) plays important but still poorly understood regulatory roles in eukaryotic cells, including as a signal for ubiquitination by SUMO targeted ubiquitin ligases (STUbLs). In this work, we delineate the molecular mechanisms for SUMO-dependent control of ribosomal DNA (rDNA) silencing through the opposing actions of a STUbL (Slx5:Slx8) and a SUMO isopeptidase (Ulp2). We identify a conserved region in the Ulp2 C terminus that mediates its specificity for rDNA-associated proteins and show that this region binds directly to the rDNA-associated protein Csm1. Two crystal structures show that Csm1 interacts with Ulp2 and one of its substrates, the rDNA silencing protein Tof2, through adjacent conserved interfaces in its C-terminal domain. Disrupting Csm1's interaction with either Ulp2 or Tof2 dramatically reduces rDNA silencing and causes a marked drop in Tof2 abundance, suggesting that Ulp2 promotes rDNA silencing by opposing STUbL-mediated degradation of silencing proteins. Tof2 abundance is rescued by deletion of the STUbL SLX5 or disruption of its SUMO-interacting motifs, confirming that Tof2 is targeted for degradation in a SUMO- and STUbL-dependent manner. Overall, our results demonstrate how the opposing actions of a localized SUMO isopeptidase and a STUbL regulate rDNA silencing by controlling the abundance of a key rDNA silencing protein, Tof2.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Imaging chiral symmetry breaking from Kekule bond order in graphene

Chirality—or ‘handedness’—is a symmetry property crucial to fields as diverse as biology, chemistry and high-energy physics. In graphene, chiral symmetry emerges naturally as a consequence of the carbon honeycomb lattice. This symmetry can be broken by interactions that couple electrons with opposite momenta in graphene. Here we directly visualize the formation of Kekulé bond order, one such phase of broken chiral symmetry, in an ultraflat graphene sheet grown epitaxially on a copper substrate. We show that its origin lies in the interactions between individual vacancies in the copper substrate that are mediated electronically by the graphene. We show that this interaction causes the bonds in graphene to distort, creating a phase with broken chiral symmetry. Furthermore, the Kekulé ordering is robust at ambient temperature and atmospheric conditions, indicating that intercalated atoms may be harnessed to drive graphene and other two-dimensional materials towards electronically desirable and exotic collective phases.

36 MATERIALS SCIENCE↗
NASA NTRS1998

Substrate Effects on Electronic Properties of Atomic Chains

When the device size is reduced down to 0.07 micrometers, the number of dopant atoms in the channel will no longer be macroscopic, typically less than a hundred. A spatial distribution of these dopant atoms will fluctuate statistically from device to device even in identically designed devices, and this places a serious limitation for integration. It is, however, impractical to control dopant positions within atomic dimension. One fundamental solution to this problem is to create electronics with atomically precise, but preferably simple structures. Atomic chains, precise structures of adatoms created on an atomically regulated surface, are candidates for constituent components in future electronics. All the adatoms will be placed at designated positions on the substrate, and all the device structures will be precise, free from any deviations. It was predicted using the tight-binding calculation with universal parameters that silicon chains were metallic and magnesium chains were semiconducting regardless of the lattice spacing, and a possible doping method was also proposed. In these treatments, the substrate was assumed to serve as a non-interacting template holding the adatoms without a formation of chemical bonding with substrate atoms. However, this scheme may not be easy to implement experimentally. Adatoms will have to be fixed with a van der Waals force on the substrate, but the force is generally weak and an extremely low temperature environment has to be prepared to suppress their unwanted thermal displacement. It may be logical to seek a scheme to allow the adatoms to form chemical bonding with the substrate atoms and secure their positions. The substrate effects are studied in detail.

Yamada, Toshishige↗
NASA NTRS1989

Plasma deposited silicon nitride for indium phosphide encapsulation

The composition and the annealing characteristics of plasma-deposited silicon-nitride encapsulating films on the ion-implanted InP substrates were investigated, using two different substrate-cleaning procedures (organic solvents and HF or HIO3 solutions) prior to encapsulation. The effect of plasma deposition of silicon nitride on the InP substrates was assessed through the current-voltage characteristics of Schottky diodes. Results of XPS analyses showed that the cleaning procedure that employed HF solution left less oxygen on the InP surface than the procedure involving HIO3. No chemical interaction between the film and the substrate was observed before or after annealing.

Valco, G. J.↗
DOE OSTI2019

Exploring Molecular Mechanisms of Cosolvent Enhanced Biomass Deconstruction: An Overview of Recent Progress

In this chapter, we explore the mechanisms driving efficient thermochemical deconstruction and fractionation of lignocellulosic biomass in cosolvent mixtures for the production of biofuels and bioproducts. New approaches that combine molecular dynamics simulations with experimental characterization highlight the important role of cosolvents and their influence on molecular processes relevant to overcoming the natural recalcitrance of lignocellulose. From localized phase behavior on cellulose fibers to changes in lignin conformation, insights into cosolvent effects on biomass deconstruction involve understanding complex interactions between the solvent–solvent, solvent–substrate, and solvent–catalyst. Recently coordinated research efforts at multiple scales using computational tools, nano-scale imaging, and kinetic models have significantly advanced identification of high-performance cosolvents, shedding light on the mechanisms behind solvent-biomass interactions. Specifically, multifunctional cosolvents have been employed in leading biomass “solvolysis” technologies that favorably coordinate with dilute acids to solubilize and depolymerize all three primary biomass fractions of biomass: cellulose, hemicellulose, and lignin. As a result, recent work in studying solvent effects of multifunctional cosolvents has led to a paradigm shift toward the use of first principles to design biomass deconstruction techniques with the aim of maximizing total carbon utilization in biomass. The synergistic pairing of cosolvents with biomass deconstruction will lead scientists and engineers to overcome key technical and economic barriers of biomass processing, enabling a successful transition of the current energy landscape toward a future bioeconomy based on biomass as an alternative to petroleum.

Mostofian, Barmak↗
DOE OSTI2025

Investigation of N 2 /O 2 plasma interaction with Pt-catalyst: effect of metastable adsorbates on product hysteresis

The coupling of catalysts and atmospheric-pressure plasma has the potential to improve the efficiency of certain catalytic reactions. Understanding the changes that the catalyst surface undergoes during exposure to plasma is key to improving plasma–catalytic performance. In this work, long term exposure of Pt–Al 2 O 3 powder catalyst to an Ar/N 2 /O 2 non-equilibrium atmospheric-pressure plasma-jet was investigated. Products produced by the interaction were analyzed downstream with Fourier-transform infrared spectroscopy while surface species were analyzed operandi with diffuse reflectance infrared Fourier transform spectroscopy. During exposure, the catalyst temperature was ramped cyclically between 100 °C and 350 °C to understand how substrate temperature affects the plasma–catalyst interaction. Long-lasting changes were revealed to take place on the catalyst surface during plasma exposure. At low temperatures, Pt–O and Pt–NO accumulate on the surface which react at elevated temperatures to form NO 2 . NO 2 initially appears to spill on to the Al 2 O 3 support as nitrites and nitrates instead of desorbing. Stable surface conditions are only achieved after prolonged plasma exposure, when nitrate sites on the Al 2 O 3 support are filled. By changing the catalyst temperature at various rates, the impact of total plasma species flux to the surface was analyzed. It was found that decreasing the heating rate increased the hysteresis in the pattern of NO 2 formation during thermal cycling. The variation with temperature demonstrates that plasma exposure results in a buildup of surface NO x and oxygen species which react or desorb at high temperatures. The observed changes are discussed from the generic viewpoint that a non-equilibrium plasma interacting with a catalyst at low temperature introduces metastable steady-state surface conditions. Upon heating above a threshold temperature, the introduced surface modifications can change either due to thermal effects, or, for a plasma environment, by additional interaction with the incident plasma species flux. The surface/material changes take place in a highly predictable fashion and after sufficient time above the threshold temperature reach a steady-state condition that is different from the transient behavior that is observed during initial heating. During cooling the plasma-surface interaction exhibits a different behavior than during heating, and this results in hysteresis of diverse observables. The metastability/hysteresis description appears quite generic and analogous to hysteresis behavior seen for different systems. Furthermore, it is expected to be useful for understanding the consequences of plasma–catalyst surface interactions for various systems.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Halogen adsorption at an As-stabilized β2–GaAs (001)–(2 × 4) surface

Halogen (F, Cl, Br, and I) adsorption at an As-stabilized GaAs (001) surface with the β2–(2 × 4) reconstruction is studied using the plane-wave projected-augmented wave method. The effect of halogens on the structural and electronic characteristics of the semiconductor surface is analyzed. The T{sub 2}′ site at the missing row edge is shown to be the energetically most favorable for the adsorption of F, Cl, and Br, whereas I prefers the H{sub 3} site between adjacent arsenic dimers in the third layer from the surface. Ga-halogen bond formation suggests that charge is transferred via the depletion of occupied orbitals of the As-dimer surface atoms, which leads to the weakening of Ga–As bonds in the substrate. The weakening of bonds between substrate-surface atoms due to the interaction of halogens with the surface is estimated.

36 MATERIALS SCIENCE↗
NASA NTRS1979

Development of Mullite Substrates and Containers

The mullite-molten silicon interaction was evaluated through fabrication of a series of bodies made with variations in density, alumina-silica ratio, and glass-crystalline ratio. The materials were tested in a sessile drop technique. None of the variations stood up to extended exposure to molten silicon sufficiently to be recommended as a container material. However, directional solidification experiments suggest that, under proper conditions, contamination of the silicon by mullite containers can be minimized. To improve an already good thermal expansion match between mullite and silicon, compositional variations were studied. Altering of the alumina-silica ratio was determined to give a continuously varying thermal expansion. A standard mullite composition was selected and substrates 40 x 4 x .040 inches were fabricated. Slotted substrates of various configurations and various compositions were also fabricated.

Sibold, J. D.↗
NASA NTRS1998

On Substrate for Atomic Chain Electronics

A substrate for future atomic chain electronics, where adatoms are placed at designated positions and form atomically precise device components, is studied theoretically. The substrate has to serve as a two-dimensional template for adatom mounting with a reasonable confinement barrier and also provide electronic isolation, preventing unwanted coupling between independent adatom structures. However, the two requirements conflict. For excellent electronic isolation, we may seek adatom confinement via van der Waals interaction without chemical bonding to the substrate atoms, but the confinement turns out to be very weak and hence unsatisfactory. An alternative chemical bonding scheme with excellent structural strength is examined, but even fundamental adatom chain properties such as whether chains are semiconducting or metallic are strongly influenced by the nature of the chemical bonding, and electronic isolation is not always achieved. Conditions for obtaining semiconducting chains with well-localized surface-modes, leading to good isolation, are clarified and discussed.

Yamada, Toshishige↗
DOE OSTI2019

Electrostatically controlled surface boundary conditions in nematic liquid crystals and colloids

Differing from isotropic fluids, liquid crystals exhibit highly anisotropic interactions with surfaces, which define boundary conditions for the alignment of constituent rod-like molecules at interfaces with colloidal inclusions and confining substrates. We show that surface alignment of the nematic molecules can be controlled by harnessing the competing aligning effects of surface functionalization and electric field arising from surface charging and bulk counterions. The control of ionic content in the bulk and at surfaces allows for tuning orientations of shape-anisotropic particles like platelets within an aligned nematic host and for changing the orientation of director relative to confining substrates. The ensuing anisotropic elastic and electrostatic interactions enable colloidal crystals with reconfigurable symmetries and orientations of inclusions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Simultaneous Decomposition and Dewetting of Nanoscale Alloys: A Comparison of Experiment and Theory

In this work, we consider the coupled process of phase separation and dewetting of metal alloys of nanoscale thickness deposited on solid substrates. The experiments involve applying nanosecond laser pulses that melt the Ag40Ni60 alloy films in two setups: either on thin supporting membranes or on bulk substrates. These two setups allow for extracting both temporal and spatial scales on which the considered processes occur. The theoretical model involves a longwave version of the Cahn–Hilliard formulation used to describe spinodal decomposition, coupled with an asymptotically consistent longwave-based description of dewetting that occurs due to destabilizing interactions between the alloy and the substrate, modeled using the disjoining pressure approach. Careful modeling, combined with linear stability analysis and fully nonlinear simulations, leads to results consistent with the experiments. In particular, we find that the two instability mechanisms occur concurrently, with the phase separation occurring faster and on shorter temporal scales. The modeling results show a strong influence of the temperature dependence of relevant material properties, implying that such a dependence is crucial for the understanding of the experimental findings. The agreement between theory and experiment suggests the utility of the proposed theoretical approach in helping to develop further experiments directed toward formation of metallic alloy nanoparticles of desired properties.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Plasmonic Landau damping in active environments

Optical manipulation of charge on the nanoscale is of fundamental importance to an array of proposed technologies from selective photocatalysis to nanophotonics. Open plasmonic systems where collective electron oscillations release energy and charge to their environments offer a potential means to this end as plasmons can rapidly decay into energetic electron-hole pairs; however, isolating this decay from other plasmon-environment interactions remains a challenge. Here we introduce an analytic theory of noble-metal nanoparticles that quantitatively models plasmon decay into electron-hole pairs, demonstrates that this decay depends significantly on the nanoparticle's dielectric environment, and disentangles this effect from competing decay pathways. Using our method to incorporate embedding material and substrate effects on plasmon-electron interaction, we show that predictions from the model agree with four separate experiments. Finally, examination of coupled nanoparticle-emitter systems further shows that the hybridized in-phase mode more efficiently decays to photons whereas the out-of-phase mode more efficiently decays to electron-hole pairs, offering a strategy to tailor open plasmonic systems for charge manipulation.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Cooperative allostery and structural dynamics of streptavidin at cryogenic- and ambient-temperature

Multimeric protein assemblies are abundant in nature. Streptavidin is an attractive protein that provides a paradigm system to investigate the intra- and intermolecular interactions of multimeric protein complexes. Also, it offers a versatile tool for biotechnological applications. Here, we present two apo-streptavidin structures, the first one is an ambient temperature Serial Femtosecond X-ray crystal (Apo-SFX) structure at 1.7 Å resolution and the second one is a cryogenic crystal structure (Apo-Cryo) at 1.1 Å resolution. These structures are mostly in agreement with previous structural data. Combined with computational analysis, these structures provide invaluable information about structural dynamics of apo streptavidin. Collectively, these data further reveal a novel cooperative allostery of streptavidin which binds to substrate via water molecules that provide a polar interaction network and mimics the substrate biotin which displays one of the strongest affinities found in nature.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Structural determinants and cellular environment define processed actin as the sole substrate of the N-terminal acetyltransferase NAA80

N-terminal (Nt) acetylation is a major protein modification catalyzed by N-terminal acetyltransferases (NATs). Methionine acidic N termini, including actin, are cotranslationally Nt acetylated by NatB in all eukaryotes, but animal actins containing acidic N termini, are additionally posttranslationally Nt acetylated by NAA80. Actin Nt acetylation was found to regulate cytoskeletal dynamics and motility, thus making NAA80 a potential target for cell migration regulation. In this work, we developed potent and selective bisubstrate inhibitors for NAA80 and determined the crystal structure of NAA80 in complex with such an inhibitor, revealing that NAA80 adopts a fold similar to other NAT enzymes but with a more open substrate binding region. Furthermore, in contrast to most other NATs, the substrate specificity of NAA80 is mainly derived through interactions between the enzyme and the acidic amino acids at positions 2 and 3 of the actin substrate and not residues 1 and 2. A yeast model revealed that ectopic expression of NAA80 in a strain lacking NatB activity partially restored Nt acetylation of NatB substrates, including yeast actin. Thus, NAA80 holds intrinsic capacity to posttranslationally Nt acetylate NatB-type substrates in vivo. In sum, the presence of a dominant cotranslational NatB in all eukaryotes, the specific posttranslational actin methionine removal in animals, and finally, the unique structural features of NAA80 leave only the processed actins as in vivo substrates of NAA80. Together, this study reveals the molecular and cellular basis of NAA80 Nt acetylation and provides a scaffold for development of inhibitors for the regulation of cytoskeletal properties.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Trophic interactions shape the spatial organization of medium-chain carboxylic acid producing granular biofilm communities

Abstract Granular biofilms producing medium-chain carboxylic acids (MCCA) from carbohydrate-rich industrial feedstocks harbor highly streamlined communities converting sugars to MCCA either directly or via lactic acid as intermediate. We investigated the spatial organization and growth activity patterns of MCCA producing granular biofilms grown on an industrial side stream to test (i) whether key functional guilds (lactic acid producing Olsenella and MCCA producing Oscillospiraceae) stratified in the biofilm based on substrate usage, and (ii) whether spatial patterns of growth activity shaped the unique, lenticular morphology of these biofilms. First, three novel isolates (one Olsenella and two Oscillospiraceae species) representing over half of the granular biofilm community were obtained and used to develop FISH probes, revealing that key functional guilds were not stratified. Instead, the outer 150–500 µm of the granular biofilm consisted of a well-mixed community of Olsenella and Oscillospiraceae, while deeper layers were made up of other bacteria with lower activities. Second, nanoSIMS analysis of 15N incorporation in biofilms grown in normal and lactic acid amended conditions suggested Oscillospiraceae switched from sugars to lactic acid as substrate. This suggests competitive-cooperative interactions may govern the spatial organization of these biofilms, and suggests that optimizing biofilm size may be a suitable process engineering strategy. Third, growth activities were similar in the polar and equatorial biofilm peripheries, leaving the mechanism behind the lenticular biofilm morphology unexplained. Physical processes (e.g., shear hydrodynamics, biofilm life cycles) may have contributed to lenticular biofilm development. Together, this study develops an ecological framework of MCCA-producing granular biofilms that informs bioprocess development.

09 BIOMASS FUELS↗
DOE OSTI2017

Solvent Entropy Contributions to Catalytic Activity in Designed and Optimized Kemp Eliminases

This work reports on the role of solvation for enzymatic catalysis in two distinct, artificially designed Kemp Eliminases, KE07 and KE70, and mutated variants that were optimized by laboratory directed evolution. Using a spatially resolved analysis of hydration patterns, intermolecular vibrations, and local solvent entropies, we identify distinct classes of hydration water and follow their changes upon substrate binding and transition state formation for the designed KE07 and KE70 enzymes and their evolved variants. We observe that differences in hydration of the enzymatic systems are concentrated in the active site and undergo significant changes during substrate recruitment. For KE07, directed evolution reduces variations in the hydration of the polar catalytic center upon substrate binding, preserving strong protein-water interactions, while the evolved enzyme variant of KE70 features a more hydrophobic reaction center for which the expulsion of low-entropy water molecules upon substrate binding is substantially enhanced. While our analysis suggests a system-dependent role of solvation for the substrate binding process, we identify more subtle changes in solvation for the transition state formation, which are less affected by directed evolution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2017

Micromechanical Devices for Control of Cell-Cell Interaction, and Methods of Use Thereof

The development and function of living tissues depends largely on interactions between cells that can vary in both time and space; however, temporal control of cell-cell interaction is experimentally challenging. By employing a micromachined silicon substrate with moving parts, herein is disclosed the dynamic regulation of cell-cell interactions via direct manipulation of adherent cells with micron-scale precision. The inventive devices and methods allow mechanical control of both tissue composition and spatial organization. The inventive device and methods enable the investigation of dynamic cell-cell interaction in a multitude of applications, such as intercellular communication, spanning embryogenesis, homeostasis, and pathogenic processes.

Bhatia, Sangeeta N.↗