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At least 415 records · Page 23

Structure and chemistry of lysinoalanine crosslinking in the spirochaete flagella hook

The flagellar hook protein FlgE from spirochaete bacteria self-catalyzes the formation of an unusual inter-subunit lysinoalanine (Lal) crosslink that is critical for cell motility. Unlike other known examples of Lal biosynthesis, conserved cysteine and lysine residues in FlgE spontaneously react to form Lal without the involvement of additional enzymes. Oligomerization of FlgE via its D0 and Dc domains drives assembly of the crosslinking site at the D1–D2 domain interface. Here, structures of the FlgED2 domain, dehydroalanine (DHA) intermediate and Lal crosslinked FlgE subunits reveal successive snapshots of the reaction. Cys178 flips from a buried configuration to release hydrogen sulfide (H 2 S/HS – ) and produce DHA. Interface residues provide hydrogen bonds to anchor the active site, facilitate β-elimination of Cys178 and polarize the peptide backbone to activate DHA for reaction with Lys165. Cysteine-reactive molecules accelerate DHA formation, whereas nucleophiles can intercept the DHA intermediate, thereby indicating a potential for Lal crosslink inhibitors to combat spirochaetal diseases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

PAVC: The foundation for a Pan-Arctic Vegetation Cover database

Field-measured Arctic vegetation cover data is essential for creating accurate, high-quality vegetation structure and composition maps. Extrapolating field data into high-resolution cover maps provides detailed, function-specific information for use in Earth System Models, vegetation classifications, and monitoring vegetation change over time and space. However, field campaigns that collect plant cover vary substantially in scope, method, and purpose, which makes them difficult to unify across data stores, and they are often not designed to meet remote sensing needs. In this work, we synthesized and harmonized field-based fractional cover data from various data stores to create a high-quality, consistent repository schema for remote sensing-based vegetation cover mapping applications. We developed a reproducible workflow for synthesizing visual estimate and point-intercept fractional cover data. The resultant Pan-Arctic Vegetation Cover (PAVC) database contains synthesized fractional cover at both the species and plant functional type levels. The latter includes absolute foliar cover for deciduous shrubs and trees, evergreen shrubs and trees, forbs, graminoids, lichen, bryophytes, and “other” vegetation, as well as absolute cover for litter and top cover for water and bare ground.

Steckler, Morgan R. [Oak Ridge National Laboratory↗

A clue to unprecedented strategy to HIV eradication: “Lock-in and apoptosis”

Despite the development of antiretroviral therapy against HIV, eradication of the virus from the body, as a means to a cure, remains in progress. A “kick and kill” strategy proposes “kick” of the latent HIV to an active HIV to eventually be “killed”. Latency-reverting agents that can perform the “kick” function are under development and have shown promise. Management of the infected cells not to produce virions after the “kick” step is important to this strategy. Here we show that a newly synthesized compound, L-HIPPO, captures the HIV-1 protein Pr55Gag and intercepts its function to translocate the virus from the cytoplasm to the plasma membrane leading to virion budding. The infecting virus thus “locked-in” subsequently induces apoptosis of the host cells. This “lock-in and apoptosis” approach performed by our novel compound in HIV-infected cells provides a means to bridge the gap between the “kick” and “kill” steps of this eradication strategy. By building upon previous progress in latency reverting agents, our compound appears to provide a promising step toward the goal of HIV eradication from the body

60 APPLIED LIFE SCIENCES↗

Cyclotron resonance in the high mobility GaAs/AlGaAs 2D electron system over the microwave, mm-wave, and terahertz- bands

Abstract The reflected microwave power from the photo-excited high mobility GaAs/AlGaAs 2D device has been measured over the wide frequency band spanning from 30 to 330 GHz simultaneously along with diagonal magnetoresistance as a function of the magnetic field. Easily distinguishable resonances in the reflected power signal are observed at the same magnetic fields as a reduced amplitude in the Shubnikov-de Haas (SdH) oscillations of the diagonal magnetoresistance. The reflection resonances with concurrent amplitude reduction in SdH oscillations are correlated with cyclotron resonance induced by microwave, mm-wave, and terahertz photoexcitation. The magnetoplasma effect was also investigated. The results suggest a finite frequency zero-magnetic-field intercept, providing an estimate for the plasma frequency. The experimentally measured plasma frequency appears to be somewhat lower than the estimated plasma frequency for these Hall bars. The results, in sum, are consistent with an effective mass ratio of m*/m = 0.067, the standard value, even in these high mobility GaAs/AlGaAs devices, at very large filling factors. Preliminary findings from this article have been published as conference proceedings, see Kriisa, A., et al ., J. of Phys. Conf. Ser . 864 , 012057 (2017).

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Updimensioning strategy derived from synthetic equiaxed grain structures for approximating 3D grain size distributions from 2D visualizations with 1D parameters

We generated synthetic equiaxed grain structures using computer graphics software to explore the relationship between various grain size determination methods and true three-dimensional (3D) grain diameters. Mirroring grain measurement techniques, the synthetic 3D grain structures are imaged as 2D micrographs which are measured to yield 1D grain size parameters. Synthetic grain structures provide data at a mass scale and permit exploration of both polished and fractured surface micrographs, revealing one-to-one correspondence between exposed 2D grain cross-sections and individual 3D grains. Analysis of this correspondence yielded a procedure to approximate 3D equiaxed grain size and volume distributions based on the mode of the 2D fractograph grain size distribution. The 3D approximation procedure is shown to be less susceptible to different imaging conditions that affect small, undiscernible grains compared to the standard planimetric and linear intercept methods, which by design also tend to underestimate the 3D grain diameter. The procedure requires larger sample sizes to lower variance and a deeper analysis which could become more practical with machine learning (ML) models for grain boundary segmentation, which synthetic grain structures can help train. This work lays the foundation for analyzing other grain distributions such as columnar and composite grains in similar depth.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Multi-decadal trends in global terrestrial evapotranspiration and its components

In this study, evapotranspiration (ET) is the process by which liquid water becomes water vapor and energetically this accounts for much of incoming solar radiation. If this ET did not occur temperatures would be higher, so understanding ET trends is crucial to predict future temperatures. Recent studies have reported prolonged declines in ET in recent decades, although these declines may relate to climate variability. Here, we used a well-validated diagnostic model to estimate daily ET during 1981–2012, and its three components: transpiration from vegetation (E t ), direct evaporation from the soil (E s ) and vaporization of intercepted rainfall from vegetation (E i ). During this period, ET over land has increased significantly (p < 0.01), caused by increases in E t and E i , which are partially counteracted by E s decreasing. These contrasting trends are primarily driven by increases in vegetation leaf area index, dominated by greening. The overall increase in E t over land is about twofold of the decrease in E s . These opposing trends are not simulated by most Coupled Model Intercomparison Project phase 5 (CMIP5) models, and highlight the importance of realistically representing vegetation changes in earth system models for predicting future changes in the energy and water cycle.

15 GEOTHERMAL ENERGY↗

A trifunctional multi-walled carbon nanotubes/polyethylene glycol (MWCNT/PEG)-coated separator through a layer-by-layer coating strategy for high-energy Li–S batteries

In this study, a trifunctional separator fabricated by using a light-weight layer-by-layer multi-walled carbon nanotubes/polyethylene glycol (MWCNT/PEG) coating has been explored in lithium–sulfur (Li–S) batteries. The conductive MWCNT/PEG coating serves as (i) an upper current collector for accelerating the electron transport and benefiting the electrochemical reaction kinetics of the cell, (ii) a net-like filter for blocking and intercepting the migrating polysulfides through a synergistic effect including physical and chemical interactions, and (iii) a layered barrier for inhibiting the continuous diffusion and alleviating the volume change of the trapped active material by introducing a “buffer zone” in between the coated layers. The multi-layered MWCNT/PEG coating allows the use of the conventional pure sulfur cathode with a high sulfur content (78 wt%) and high sulfur loading (up to 6.5 mg cm -2 ) to achieve a high initial discharge capacity of 1206 mA h g -1 at C/5 rate, retaining a superior capacity of 630 mA h g -1 after 300 cycles. Lastly, the MWCNT/PEG-coated separator optimized by the facile layer-by-layer coating method provides a promising and feasible option for advanced Li–S batteries with high energy density.

25 ENERGY STORAGE↗

Aromatic and aliphatic hydrocarbon hydroxylation via a formally Ni IV =O oxidant

The reaction of (NMe 4 ) 2 [Ni II (L Ph )(OAc)] (1[OAc], L Ph = 2,2',2''-nitrilo-tris-(N-phenylacetamide); OAc = acetate) with 3-chloroperoxybenzoic acid (m-CPBA) resulted in the formation of a self-hydroxylated Ni III -phenolate complex, 2, where one of the phenyl groups of L Ph underwent hydroxylation. 2 was characterised by UV-Vis, EPR, and XAS spectroscopies and ESI-MS. 2 decayed to yield a previously characterised Ni II -phenolate complex, 3. We postulate that self-hydroxylation was mediated by a formally Ni IV =O oxidant, formed from the reaction of 1[OAc] with m-CPBA, which undergoes electrophilic aromatic substitution to yield 2. This is supported by an analysis of the kinetic and thermodynamic properties of the reaction of 1[OAc] with m-CPBA. Addition of exogenous hydrocarbon substrates intercepted the self-hydroxylation process, producing hydroxylated products, providing further support for the formally Ni IV =O entity. This study demonstrates that the reaction between Ni II salts and m-CPBA can lead to potent metal-based oxidants, in contrast to recent studies demonstrating carboxyl radical is a radical free-chain reaction initiator in Ni II /m-CPBA hydrocarbon oxidation catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular catalyst and co-catalyst systems based on transition metal complexes for the electrochemical oxidation of alcohols

Molecular catalysts allow deeper study of underlying mechanisms relative to heterogeneous systems by offering a discrete active site to monitor. Mechanistic study with knowledge of key intermediates subsequently enables the development of design principles through an understanding of how improved reactivity or selectivity can be achieved through modification of the catalyst structure. The co-catalytic inclusion of redox mediators (RM), which are small molecules that can aid in the transfer of protons and electrons, has been shown to improve product conversion and selectivity in many molecular systems, through intercepting key intermediates to direct reaction pathways. The primary focus for the majority of molecular electrocatalysts has been on optimizing design for reductive reactions, such as the hydrogen evolution reaction (HER), the oxygen reduction reaction (ORR), and the carbon dioxide reduction reaction (CO 2 RR). By comparison, there has been much less focus on key oxidative reactions by molecular species, apart from the oxygen evolution reaction (OER). The focus of this review is to highlight molecular catalyst systems optimized for the electrochemical oxidation of alcohols. The electrochemical alcohol oxidation reaction (AOR) can serve a role in synthesizing value-added chemicals and can serve as the counterpart to the CO 2 RR by releasing electricity from energy-rich molecules. State-of-the-art molecular systems for the AOR are divided between single-site catalysts and co-catalytic systems with redox mediators. The AOR is contextualized as an energy relevant reaction, an overview of the area is provided, foundational improvements in catalyst systems are highlighted, and future development principles for incorporating redox mediators are suggested.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Cross-Layered Distributed Data-Driven Framework for Enhanced Smart Grid Cyber-Physical Security

Smart Grid (SG) research and development has drawn much attention from academia, industry and government due to the great impact it will have on society, economics and the environment. Securing the SG is a considerably significant challenge due the increased dependency on communication networks to assist in physical process control, exposing them to various cyber-threats. In addition to attacks that change measurement values using False Data Injection (FDI) techniques, attacks on the communication network may disrupt the power system's real-time operation by intercepting messages, or by flooding the communication channels with unnecessary data. Addressing these attacks requires a cross-layer approach. In this paper a cross-layered strategy is presented, called Cross-Layer Ensemble CorrDet with Adaptive Statistics(CECD-AS), which integrates the detection of faulty SG measurement data as well as inconsistent network inter-arrival times and transmission delays for more reliable and accurate anomaly detection and attack interpretation. Numerical results show that CECD-AS can detect multiple False Data Injections, Denial of Service (DoS) and Man In The Middle (MITM) attacks with a high F1-score compared to current approaches that only use SG measurement data for detection such as the traditional physics-based State Estimation, Ensemble CorrDet with Adaptive Statistics strategy and other machine learning classification-based detection schemes.

cyber-physical security↗

Continuous Integration Service at Fermilab

This paper describes the current architecture of Continuous Integration (CI) service developed at Fermilab, encountered successes and difficulties, as well as future development plans. The current experiment code has hundreds of contributors that provide new features, bug fixes, and other improvements. Version control systems help developers to collaborate in contributing software for their experiments, while the CI system helps developers keep their code healthy. The Fermilab CI service allows experiments and projects to test and validate their offline production and analysis code on the supported platforms. It is built on top of Jenkins, designed to be set up from a configuration file that provides implementation for each phase of the CI workflow, and able to validate experiment code through grid jobs. This CI service provides a dashboard for easy access to logs and statistical graphs. Since the CI service has been adopted by Fermilab experiments/projects, it proved to be very useful to intercept issues in their code early on and get them fixed before running it in production. Currently the CI service is in use by the ArgoNeuT, DUNE, g-2, LArIAT, MINERvA, mu2e, NOvA, SBND and uBooNE experiments and by the following projects: ART and LArSoft software suites, GENIE, and Glidein-WMS. The CI service is under active development and planning to support code profiling.

Di benedetto, Vito↗

Stable isotopes composition of precipitation fallen over Cluj-Napoca, Romania, between 2009-2012

The paper presents the deuterium and oxygen 18 content from All precipitations events, which have occured over Cluj-Napoca, Romania from 2009 until 2012. Time series for δ{sup 2}H and δ{sup 18}O values point out both the seasonal variation that has increased amplitude reflecting the continental character of the local climate as well as dramatic variations of isotopic content of successive precipitation events, emphasizing the anomalous values. These fluctuations are the footprint of the variations and trends in climate events. Local Meteoric Water Line (LMWL), reflecting the δ{sup 2}H - δ{sup 18}O correlation, has the slop and the intercept slightly deviated from the GMWL, indicating that the dominant process affecting local precipitations are close to the equilibrium condition. LMWL has a slope smaller then that of the GMWL in the warm season due to lower humidity and a slope closest to the slop of GMWL in cold season with high humidity. The δ{sup 2}H and δ{sup 18}O values both for the precipitation events and monthly mean values are positively correlated with the temperature values with a very good correlation factor. The values of δ{sup 2}H and δ{sup 18}O are not correlated with amount of precipitation, the 'amount effect' of isotopic composition of precipitation is not observed for this site.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Motion of a virtual cathode in a cylindrical channel with electron beam transport in the “compressed” state

This paper studies the motion of a virtual cathode in a two-section drift tube with the formation and breakup of the “compressed” state of an electron beam. Experimental arrangements to intercept part of the injected current during the voltage pulse and to provide virtual cathode motion toward the collector are proposed. The arrangements were implemented on the SINUS-7 high-current electron accelerator. Theoretical and experimental dependences of the virtual cathode velocity on the injected current and cathode voltage are presented. The experimental data on virtual cathode motion agree with its theoretical model based on analytical solutions of equations assisted by computer simulation with the PIC code KARAT. The results of the work demonstrate the feasibility of controlling the virtual cathode motion which can be used in collective ion acceleration and microwave generation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Measurements of an expanding surface flashover plasma

A better understanding of vacuum surface flashover and the plasma produced by it is of importance for electron and ion sources, as well as advanced accelerators and other vacuum electronic devices. This article describes time-of-flight and biased-probe measurements made on the expanding plasma generated from a vacuum surface flashover discharge. The plasma expanded at velocities of 1.2–6.5 cm/μs, and had typical densities of 10{sup 10}–10{sup 12} cm{sup −3}. The expansion velocity of the plasma leading edge often exhibited a sharp increase at distances of about 50 mm from the discharge site. Comparison with biased-probe data suggests that, under most conditions, the plasma leading edge was dominated by negative ions, with the apparent increase in velocity being due to fast H{sup −} overtaking slower, heavier ions. In some cases, biased-probe data also showed abrupt discontinuities in the plasma energy distribution co-located with large changes in the intercepted plasma current, suggesting the presence of a shock in the leading edge of the expanding plasma.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A non-invasive beam profile monitor for charged particle beams

Non-interceptive beam profile monitors are highly desirable in almost all particle accelerators. Such techniques are especially valuable in applications where real time monitoring of the beam properties is required while beam preservation and minimal influence on the vacuum are of the greatest importance. This applies to many kinds of accelerators such as high energy machines where the normal diagnostics cannot withstand the beam's power, medical machines where treatment time is valuable and cannot be allocated to diagnostics and also low energy, low intensity accelerators where the beam's properties are difficult to measure. This paper presents the design of a gas-jet based beam profile monitor which was developed and commissioned at the Cockcroft Institute and can operate in a very large background pressure range from 10{sup −7} down to below 10{sup −11} millibars. The functioning principle of the monitor is described and the first experimental results obtained using a 5 keV electron beam are discussed.

43 PARTICLE ACCELERATORS↗

Directional gamma sensing from covariance processing of inter-detector Compton crosstalk energy asymmetries

Energy asymmetry of inter-detector crosstalk from Compton scattering can be exploited to infer the direction to a gamma source. A covariance approach extracts the correlated crosstalk from data streams to estimate matched signals from Compton gammas split over two detectors. On a covariance map the signal appears as an asymmetric cross diagonal band with axes intercepts at the full photo-peak energy of the original gamma. The asymmetry of the crosstalk band can be processed to determine the direction to the radiation source. The technique does not require detector shadowing, masking, or coded apertures, thus sensitivity is not sacrificed to obtain the directional information. An angular precision of better than 1° of arc is possible, and processing of data streams can be done in real time with very modest computing hardware.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

An ion mobility mass spectrometer for investigating photoisomerization and photodissociation of molecular ions

An ion mobility mass spectrometry apparatus for investigating the photoisomerization and photodissociation of electrosprayed molecular ions in the gas phase is described. The device consists of a drift tube mobility spectrometer, with access for a laser beam that intercepts the drifting ion packet either coaxially or transversely, followed by a quadrupole mass filter. An ion gate halfway along the drift region allows the instrument to be used as a tandem ion mobility spectrometer, enabling mobility selection of ions prior to irradiation, with the photoisomer ions being separated over the second half of the drift tube. The utility of the device is illustrated with photoisomerization and photodissociation action spectra of carbocyanine molecular cations. The mobility resolution of the device for singly charged ions is typically 80 and it has a mass range of 100-440 Da, with the lower limit determined by the drive frequency for the ion funnels, and the upper limit by the quadrupole mass filter.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗