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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 19 records

A transient post-translational modification of active site cysteine alters binding properties of the parkinsonism protein DJ-1

Highlights: • A fraction of bacterially expressed polyhistidine-tagged human DJ-1 tightly binds to Ni-nitrilotriacetate (Ni-NTA) column. • The color of Ni-NTA column changes from light cyan to blue violet upon tight binding to DJ-1. • An active site cysteine is post-translationally modified in the fraction of DJ-1 tightly bound to Ni-NTA. • The modificationconferring tightbinding to Ni-NTA is unstable. • Crystal structure shows the unstable modification converts to S-carboxymethylcysteine upon elution from Ni-NTA. Mutations in the human protein DJ-1 cause early onset of Parkinson's disease. A reactive cysteine residue (Cys{sup 106}) of DJ-1 is crucial for its protective function, although the underlying mechanisms are unclear. Here we show that a fraction of bacterially expressed polyhistidine-tagged human DJ-1 could not be eluted from a Ni-nitrilotriacetate (Ni-NTA) column with 150 mM imidazole. This unusually tight binding was accompanied by the appearance of blue violet color on the Ni-NTA column. We demonstrate by X-ray crystallography that Cys{sup 106} is carboxymethylated in a fraction of DJ-1 tightly bound to Ni-NTA and that the replacement of Cys{sup 106} by serine abrogates the tight binding and the appearance of blue violet color. However, carboxymethylation of purified DJ-1 is insufficient to confer the tight binding to Ni-NTA. Moreover, when eluted protein was re-applied to the Ni-NTA column, no tight binding was observed, indicating that the formation of high affinity complex with Ni-NTA depends on a transient modification of Cys{sup 106} that transforms into a Cys{sup 106}-carboxymethyl adduct upon elution from Ni-NTA. We conclude that an unknown metabolite reacts with Cys{sup 106} of DJ-1 to result in a transient post-translational modification. This modification is distinct from simple oxidation to sulfinic or sulfenic acids and confers altered binding properties to DJ-1 suggesting that it could serve as a signal for sensing oxidant stress.

60 APPLIED LIFE SCIENCES↗

Scalable synthesis and post-modification of a mesoporous metal-organic framework called NU-1000

The synthesis of NU-1000, a highly robust mesoporous (containing pores >2 nm) metal-organic framework (MOF), can be conducted efficiently on a multigram scale from inexpensive starting materials. Tetrabromopyrene and (4-(ethoxycarbonyl)phenyl)boronic acid can easily be coupled to prepare the requisite organic strut with four metal-binding sites in the form of four carboxylic acids, while zirconyl chloride octahydrate is used as a precursor for the well-defined metal oxide clusters. NU-1000 has been reported as an excellent candidate for the separation of gases, and it is a versatile scaffold for heterogeneous catalysis. In particular, it is ideal for the catalytic deactivation of nerve agents, and it shows great promise as a new generic platform for a wide range of applications. Multiple post-synthetic modification protocols have been developed using NU-1000 as the parent material, making it a potentially useful scaffold for several catalytic applications. The procedure for the preparation of NU-1000 can be scaled up reliably, and it is suitable for the production of 50 g of the tetracarboxylic acid containing organic linker and 200 mg–2.5 g of NU-1000. The entire synthesis is performed without purification by column chromatography and can be completed within 10 d.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Towards high-energy and durable lithium-ion batteries via atomic layer deposition: elegantly atomic-scale material design and surface modification

Targeted at fueling future transportation and sustaining smart grids, lithium-ion batteries (LIBs) are undergoing intensive investigation for improved durability and energy density. Atomic layer deposition (ALD), enabling uniform and conformal nanofilms, has recently made possible many new advances for superior LIBs. The progress was summarized by Liu and Sun in their latest review [1], offering many insightful views, covering the design of nanostructured battery components (i.e., electrodes and solid electrolytes), and nanoscale modification of electrode/electrolyte interfaces. This work well informs peers of interesting research conducted and it will also further help boost the applications of ALD in next-generation LIBs and other advanced battery technologies.

Atomic Layer Deposition↗

Amorphous transparent conducting oxides in context: Work function survey, trends, and facile modification

The work functions of various amorphous and crystalline transparent conducting oxides (TCO5) were measured using Kelvin probe. The films, made by pulsed laser deposition, exhibited varying work functions dependent on the composition and deposition parameters. Tin oxide showed the largest work functions of the oxides measured, while zinc oxide showed the lowest. Binary and ternary combinations of the basis TCOs showed intermediate work functions dependent on the endpoint components. Amorphous TCO5, important in OPV and other technological applications, exhibited similar work functions to their crystalline counterparts. UV/ozone treatment of TCOs temporarily increased the work function, consistent with proposed defect mechanisms associated with near-surface changes in carrier content and Fermi level. Finally, a method for facile adjustment of the work function of commercial TCOs by atomic layer deposition (ALD) capping layers was presented, illustrated by the growth of zinc oxide layers on commercial crystalline ITO films.

Yeh, T. C.↗

Work Function Modification via Combined Charge-Based Through-Space Interaction and Surface Interaction

Work function modification of electrodes is an important factor to achieve high performance in organic electronics. However, a clear explanation of the origin of work function modification has remained elusive. Here, it is investigated how the work function of electrodes is affected by the charge-based through-space interaction with the well-known surface interaction. The studies reveal that the formation of a surface dipole leads to a work function shift, even when the work function modifying layer and substrate are separated. A work function shift is also demonstrated by electrophoretic deposition of ionic polyelectrolytes while the same polyelectrolytes do not cause any work function shift when they are spin cast. More noteworthy is that a neutral (nonionic) polymer which has no specific surface-interacting functional groups can induce work function shift of its substrate by a charge-based through-space interaction when deposited by electrospraying. These results provide a more comprehensive understanding of work function modification and motivate the design and selection of a wide range of effective work function modifying layers for organic electronics.

36 MATERIALS SCIENCE↗

Modifications to WRF's dynamical core to improve the treatment of moisture for large-eddy simulations: WRF DY-CORE MOISTURE TREATMENT

Yamaguchi and Feingold (2012) note that the cloud fields in their Weather Research and Forecasting (WRF) large-eddy simulations (LESs) of marine stratocumulus exhibit a strong sensitivity to time stepping choices. In this study, we reproduce and analyze this sensitivity issue using two stratocumulus cases, one marine and one continental. Results show that (1) the sensitivity is associated with spurious motions near the moisture jump between the boundary layer and the free atmosphere, and (2) these spurious motions appear to arise from neglecting small variations in water vapor mixing ratio (qv) in the pressure gradient calculation in the acoustic sub­stepping portion of the integration procedure. We show that this issue is remedied in the WRF dynamical core by replacing the prognostic equation for the potential temperature θ with one for the moist potential temperature θm=θ(1+1.61qv), which allows consistent treatment of moisture in the calculation of pressure during the acoustic sub­steps. With this modification, the spurious motions and the sensitivity to the time stepping settings (i.e., the dynamic time step length and number of acoustic sub­steps) are eliminated in both of the example stratocumulus cases. This modification improves the applicability of WRF for LES applications, and possibly other models using similar dynamical core formulations, and also permits the use of longer time steps than in the original code.

Xiao, Heng↗

An Investigation of the Aerodynamic Characteristics of an 0.08-Scale Model of the Chance Vought XF7U-1 Airplane in the Langley High-Speed 7- by 10-Foot Tunnel. Part V - Wing-Alone Tests and Effect of Modifications to the Vertical Fins, Speed Brakes, and Fuselage TED No. NACA DE308: Wing-Alone Tests and Effect of Modifications to the Vertical Fins, Speed Brakes, and Fuselage, TED No. NACA DE308 - Part V

Tests have been conducted in the Langley high-speed 7- by 10-foot tunnel over a Mach number range from 0.40 to 0.91 to determine the stability and control characteristics of an 0.08-scale model of the Chance Vought XF7U-1 airplane. The wing-alone tests and the effect of the various vertical-fin modifications, speed-brake modifications, and fuselage modifications on the aerodynamic characteristics in pitch and yaw are presented in the present paper with a limited analysis of the results. Also included are tuft studies of the flow for some of the modifications tested.

Kuhri, Richard E.↗

Potential Effects of Climate Change and Solar Radiation Modification on Renewable Energy Resources

Solar radiation modification (SRM) is a possible deliberate approach to decrease or reflect incoming solar radiation with the goal of reducing global temperatures, which have increased over the last decades due to high atmospheric greenhouse gas concentrations. Stratospheric aerosol injection, specifically, has shown potential for successfully reducing global temperatures in climate model simulations. Despite the growing literature in the areas of climate change and SRM, their combined effects on renewable energy generation, a climate change mitigation strategy, have not been addressed. In this review paper, we synthesize previous literature on the possible effects of climate change and SRM on renewable energy resources (i.e., wind energy, solar energy, biomass energy, and hydropower), review the status of climate change and SRM research, and explore potential effects of SRM on renewable energy primarily in the Continental United States (CONUS), but with global perspectives as well. We discuss the research challenges and impacts of SRM on renewable energy and conclude by discussing the potential implications of SRM for renewables for SRM governance and policy. This work is not advocating for or against SRM. It is highlighting an important potential impact for future decision makers.

Kumler, Andrew [National Renewable Energy Laborato↗

Ion beam modification of topological insulator bismuth selenide

In this study, we demonstrate chemical doping of a topological insulator Bi 2 Se 3 using ion implantation. Ion beam-induced structural damage was characterized using grazing incidence X-ray diffraction and transmission electron microscopy. Ion damage was reversed using a simple thermal annealing step. Carrier-type conversion was achieved using ion implantation followed by an activation anneal in Bi 2 Se 3 thin films. These two sets of experiments establish the feasibility of ion implantation for chemical modification of Bi 2 Se 3 , a prototypical topological insulator. Ion implantation can, in principle, be used for any topological insulator. The direct implantation of dopants should allow better control over carrier concentrations for the purposes of achieving low bulk conductivity. Ion implantation also enables the fabrication of inhomogeneously doped structures, which in turn should make possible new types of device designs.

36 MATERIALS SCIENCE↗

A Printing-Centric Approach to the Electrostatic Modification of Polymer/Clay Composites for Use in 3D Direct-Ink Writing

Polymer/clay composite inks are exceptionally useful materials for fabrication processes based on 3D direct-ink writing, however, there remains an insufficient understanding of how their physiochemical dynamics impact printability. Using a model system, N-isopropylacrylamide/Laponite, the electrostatic interactions between Laponite platelets are modified to tune critical rheological properties in order to improve printability. Rheological measurements and X-ray scattering experiments are carried out to monitor the nano/micro-structural dynamics and complex physicochemical interactions of Laponite as it impacts complex modulus in the linear region, flow behavior, thixotropy, and yield stress of the composite ink. Modification of the electrostatic interactions between platelets reduces the yield stress of the material, while maintaining a complex microstructure that allows for sufficient recovery times upon removal of stress to form stable, and thus printable, filaments. A printing-centric approach is established based on a fundamental understanding of electrostatic inter-particle interactions, harnessing the innate microstructure of Laponite in 3D direct-ink writing of composites.

Rauzan, Brittany M.↗

Measurement of D s + production and nuclear modification factor in Pb-Pb collisions at $ \sqrt{{\mathrm{s}}_{\mathrm{NN}}}=2.76 $

Here, the production of prompt D s + mesons was measured for the first time in collisions of heavy nuclei with the ALICE detector at the LHC. The analysis was performed on a data sample of Pb-Pb collisions at a centre-of-mass energy per nucleon pair, √s NN , of 2.76 TeV in two different centrality classes, namely 0–10% and 20–50%. Ds+ mesons and their antiparticles were reconstructed at mid-rapidity from their hadronic decay channel D s + → Φπ + , with Φ → K – K + , in the transverse momentum intervals 4 < pT < 12GeV/c and 6 < pT < 12 GeV/c for the 0–10% and 20–50% centrality classes, respectively. The nuclear modification factor RAA was computed by comparing the pT-differential production yields in Pb-Pb collisions to those in proton-proton (pp) collisions at the same energy. This pp reference was obtained using the cross section measured at √s = 7 TeV and scaled to √s = 2.76 TeV. The RAA of D s + mesons was compared to that of non-strange D mesons in the 10% most central Pb-Pb collisions. At high p T (8 < p T < 12 GeV/c) a suppression of the D s + -meson yield by a factor of about three, compatible within uncertainties with that of non-strange D mesons, is observed. At lower p T (4 < p T < 8 GeV/c) the values of the D s + -meson R AA are larger than those of non-strange D mesons, although compatible within uncertainties. The production ratios D s + /D 0 and D s + /D + were also measured in Pb-Pb collisions and compared to their values in proton-proton collisions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Rapidity and transverse-momentum dependence of the inclusive J/ψ nuclear modification factor in p-Pb collisions at $ \sqrt{s_{N\ N}} $ = 5.02 TeV

We have studied the transverse-momentum (p T ) dependence of the inclusive J/ψ production in p-Pb collisions at $\sqrt{^sNN}$ = 5.02 TeV, in three center-of-mass rapidity (y cms ) regions, down to zero p T . Results in the forward and backward rapidity ranges (2.03 < y cms < 3.53 and –4.46 < y cms < –2.96) are obtained by studying the J/ψ decay to μ + μ – , while the mid-rapidity region (–1.37 < y cms < 0.43) is investigated by measuring the e + e – decay channel. The p T dependence of the J/ψ production cross section and nuclear modification factor are presented for each of the rapidity intervals, as well as the J/ψ mean p T values. Forward and mid-rapidity results show a suppression of the J/ψ yield, with respect to pp collisions, which decreases with increasing p T . At backward rapidity no significant J/ψ suppression is observed. Theoretical models including a combination of cold nuclear matter effects such as shadowing and partonic energy loss, are in fair agreement with the data, except at forward rapidity and low transverse momentum. The implications of the p-Pb results for the evaluation of cold nuclear matter effects on J/ψ production in Pb-Pb collisions are also discussed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Modification of Salmonella Lipopolysaccharides Prevents the Outer Membrane Penetration of Novobiocin

Small hydrophilic antibiotics traverse the outer membrane of Gram-negative bacteria through porin channels. Large lipophilic agents traverse the outer membrane through its bilayer, containing a majority of lipopolysaccharides in its outer leaflet. Genes controlled by the two-component regulatory system PhoPQ modify lipopolysaccharides. We isolate lipopolysaccharides from isogenic mutants of Salmonella sp., one lacking the modification, the other fully modified. These lipopolysaccharides were reconstituted asmonolayers at the air-water interface, and their properties, aswell as their interaction with a large lipophilic drug, novobiocin, was studied. X-ray reflectivity showed that the drug penetrated the monolayer of the unmodified lipopolysaccharides reaching the hydrophobic region,butwas prevented fromthis penetration intothemodified lipopolysaccharides.Results correlatewith behavior of bacterial cells, which become resistant to antibiotics after PhoPQ-regulated modifications. Grazing incidence x-ray diffraction showed that novobiocin produced a striking increase in crystalline coherence length, and the size of the near-crystalline domains.

60 APPLIED LIFE SCIENCES↗

Improved Annotation of Untargeted Metabolomics Data through Buffer Modifications That Shift Adduct Mass and Intensity

Annotation of untargeted high-resolution full-scan LC-MS metabolomics data remains challenging due to individual metabolites generating multiple LC-MS peaks arising from isotopes, adducts and fragments. Adduct annotation is a particular challenge, as the same mass difference between peaks can arise from adduct formation, fragmentation, or different biological species. To address this, here we describe a Buffer Modification Workflow (BMW), in which the same sample is run by LC-MS in both liquid chromatography solvent with 14 NH 3 -acetate buffer, and in solvent with the buffer modified with 15 NH 3 -formate. Buffer switching results in characteristic mass and signal intensity changes for adduct peaks, facilitating their annotation. This relatively simple and convenient chromatography modification annotated yeast metabolomics data with similar effectiveness to growing the yeast in isotope-labeled media. Application to mouse liver data annotated both known metabolite and known adduct peaks with 95% accuracy. Altogether, it identified 26% of ~ 27,000 liver LC-MS features as putative metabolites, of which ~ 2600 showed HMDB or KEGG database formula match. This workflow is well-suited to biological samples that cannot be readily isotope labeled, including plants, mammalian tissues, and tumors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Prediction of histone post-translational modifications using deep learning

Abstract Motivation Histone post-translational modifications (PTMs) are involved in a variety of essential regulatory processes in the cell, including transcription control. Recent studies have shown that histone PTMs can be accurately predicted from the knowledge of transcription factor binding or DNase hypersensitivity data. Similarly, it has been shown that one can predict PTMs from the underlying DNA primary sequence. Results In this study, we introduce a deep learning architecture called DeepPTM for predicting histone PTMs from transcription factor binding data and the primary DNA sequence. Extensive experimental results show that our deep learning model outperforms the prediction accuracy of the model proposed in Benveniste et al. (PNAS 2014) and DeepHistone (BMC Genomics 2019). The competitive advantage of our framework lies in the synergistic use of deep learning combined with an effective pre-processing step. Our classification framework has also enabled the discovery that the knowledge of a small subset of transcription factors (which are histone-PTM and cell-type-specific) can provide almost the same prediction accuracy that can be obtained using all the transcription factors data. Availabilityand implementation https://github.com/dDipankar/DeepPTM. Supplementary information Supplementary data are available at Bioinformatics online.

Baisya, Dipankar Ranjan (ORCID:0000000267847359)↗