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At least 1,603 records · Page 89

Using nature’s blueprint to expand catalysis with Earth-abundant metals

Original title changed for publication from; " Using Nature's Blueprint to Enable Catalysis with Earth-Abundant Metals" A diverse array of redox transformations that are essential to life are catalyzed by metalloenzymes that feature an earth-abundant metal. In contrast, platinum-group metals have been the cornerstone of many industrial catalytic reactions for decades, providing high activity, thermal stability and tolerance to chemical poisons. We assert that Nature’s blueprint provides the fundamental principles for vastly expanding the use of abundant metals in catalysis. We highlight the key physical properties of abundant metals that distinguish them from precious metals, and we look to Nature to understand how the inherent attributes of abundant metals can be embraced, leading to unique, highly efficient catalysts, emphasizing reactions crucial to the sustainable production and transformation of fuels and chemicals.

Bullock, Ronald M.↗

Pyrobaculum Yellowstonensis Strain WP30 Respires On Elemental Sulfur And/or Arsenate in Circumneutral Sulfidic Sediments of Yellowstone National Park

Thermoproteales populations (phylum Crenarchaeota) are abundant in high-25 temperature (>70° C) environments of Yellowstone National Park (YNP) and are important in mediating biogeochemical cycles of sulfur, arsenic and carbon. The objectives of this study were to determine specific physiological attributes of the isolate Pyrobaculum yellowstonensis strain WP30, which was obtained from an elemental sulfur sediment (Joseph’s Coat Hot Spring [JCHS]; 80 °C; pH 6.1), and relate this organism to geochemical processes occurring in situ. Strain WP30 is a chemoheterotroph that utilizes organic carbon as a source of carbon and electrons and requires elemental sulfur and/or arsenic as electron acceptors. Growth in the presence of elemental sulfur and arsenate resulted in the production of thioarsenates and polysulfides relative to sterile controls. The complete genome of this organism was sequenced (1.99 Mb, 58 % G+C) and revealed numerous metabolic pathways for the degradation of carbohydrates, amino acids and lipids, multiple dimethylsulfoxide molybdopterin (DMSO-MPT) oxidoreductase genes, which are implicated in the reduction of sulfur and arsenic, and pathways for the de novo synthesis of nearly all required cofactors and metabolites. Comparative genomics of P. yellowstonensis versus assembled metagenome sequence from JCHS showed that this organisms is highly-related (~95% average nucleotide identity) to in situ populations. The physiological attributes and metabolic capabilities of P. yellowstonensis provide importanat information towards understanding the distribution and function of these populations in YNP.

Environmental Molecular Sciences Laboratory↗

Glutathionylation of Yersinia pestis LcrV and Its Effects on Plague Pathogenesis

Glutathionylation, the formation of reversible mixed disulfides between glutathione and protein cysteine residues, is a posttranslational modification previously observed for intracellular proteins of bacteria. Here we show that Yersinia pestis LcrV, a secreted protein capping the type III secretion machine, is glutathionylated at Cys 273 and that this modification promotes association with host ribosomal protein S3 (RPS3), moderates Y. pestis type III effector transport and killing of macrophages, and enhances bubonic plague pathogenesis in mice and rats. Secreted LcrV was purified and analyzed by mass spectrometry to reveal glutathionylation, a modification that is abolished by the codon substitution Cys 273 Ala in lcrV . Moreover, the lcrV C273A mutation enhanced the survival of animals in models of bubonic plague. Investigating the molecular mechanism responsible for these virulence attributes, we identified macrophage RPS3 as a ligand of LcrV, an association that is perturbed by the Cys 273 Ala substitution. Furthermore, macrophages infected by the lcrV C273A variant displayed accelerated apoptotic death and diminished proinflammatory cytokine release. Deletion of gshB , which encodes glutathione synthetase of Y. pestis , resulted in undetectable levels of intracellular glutathione, and we used a Y. pestis Δ gshB mutant to characterize the biochemical pathway of LcrV glutathionylation, establishing that LcrV is modified after its transport to the type III needle via disulfide bond formation with extracellular oxidized glutathione. IMPORTANCE Yersinia pestis , the causative agent of plague, has killed large segments of the human population; however, the molecular bases for the extraordinary virulence attributes of this pathogen are not well understood. We show here that LcrV, the cap protein of bacterial type III secretion needles, is modified by host glutathione and that this modification contributes to the high virulence of Y. pestis in mouse and rat models for bubonic plague. These data suggest that Y. pestis exploits glutathione in host tissues to activate a virulence strategy, thereby accelerating plague pathogenesis.

Microbiology↗

Large Blooms of Bacillales ( Firmicutes ) Underlie the Response to Wetting of Cyanobacterial Biocrusts at Various Stages of Maturity

Biological soil crusts (biocrusts) account for a substantial portion of primary production in dryland ecosystems. They successionally mature to deliver a suite of ecosystem services, such as carbon sequestration, water retention and nutrient cycling, and climate regulation. Biocrust assemblages are extremely well adapted to survive desiccation and to rapidly take advantage of the periodic precipitation events typical of arid ecosystems. Here we focus on the wetting response of incipient cyanobacterial crusts as they mature from “light” to “dark.” We sampled a cyanobacterial biocrust chronosequence before (dry) and temporally following a controlled wetting event and used high-throughput 16S rRNA and rRNA gene sequencing to monitor the dynamics of microbial response. Overall, shorter-term changes in phylogenetic beta diversity attributable to periodic wetting were as large as those attributable to biocrust successional stage. Notably, more mature crusts showed significantly higher resistance to precipitation disturbance. A large bloom of a few taxa within the Firmicutes , primarily in the order Bacillales , emerged 18 h after wetting, while filamentous crust-forming cyanobacteria showed variable responses to wet-up across the successional gradient, with populations collapsing in less-developed light crusts but increasing in later-successional-stage dark crusts. Overall, the consistent Bacillales bloom accompanied by the variable collapse of pioneer cyanobacteria of the Oscillatoriales order across the successional gradient suggests that the strong response of few organisms to a hydration pulse with the mortality of the autotroph might have important implications for carbon (C) balance in semiarid ecosystems. IMPORTANCE Desert biological soil crusts are terrestrial topsoil microbial communities common to arid regions that comprise 40% of Earth’s terrestrial surface. They successionally develop over years to decades to deliver a suite of ecosystem services of local and global significance. Ecosystem succession toward maturity has been associated with both resistance and resilience to disturbance. Recent work has shown that the impacts of both climate change and physical disturbance on biocrusts increase the potential for successional resetting. A larger proportion of biocrusts are expected to be at an early developmental stage, hence increasing susceptibility to changes in precipitation frequencies. Therefore, it is essential to characterize how biocrusts respond to wetting across early developmental stages. In this study, we document the wetting response of microbial communities from a biocrust chronosequence. Overall, our results suggest that the cumulative effects of altered precipitation frequencies on the stability of biocrusts will depend on biocrust maturity.

59 BASIC BIOLOGICAL SCIENCES↗

Pangenomes suggest ecological-evolutionary responses to experimental soil warming

ABSTRACT Below-ground carbon transformations that contribute to healthy soils represent a natural climate change mitigation, but newly acquired traits adaptive to climate stress may alter microbial feedback mechanisms. To better define microbial evolutionary responses to long-term climate warming, we study microorganisms from an ongoing in situ soil warming experiment where, for over three decades, temperate forest soils are continuously heated at 5°C above ambient. We hypothesize that across generations of chronic warming, genomic signatures within diverse bacterial lineages reflect adaptations related to growth and carbon utilization. From our bacterial culture collection isolated from experimental heated and control plots, we sequenced genomes representing dominant taxa sensitive to warming, including lineages of Actinobacteria, Alphaproteobacteria, and Betaproteobacteria. We investigated genomic attributes and functional gene content to identify signatures of adaptation. Comparative pangenomics revealed accessory gene clusters related to central metabolism, competition, and carbon substrate degradation, with few functional annotations explicitly associated with long-term warming. Trends in functional gene patterns suggest genomes from heated plots were relatively enriched in central carbohydrate and nitrogen metabolism pathways, while genomes from control plots were relatively enriched in amino acid and fatty acid metabolism pathways. We observed that genomes from heated plots had less codon bias, suggesting potential adaptive traits related to growth or growth efficiency. Codon usage bias varied for organisms with similar 16S rrn operon copy number, suggesting that these organisms experience different selective pressures on growth efficiency. Our work suggests the emergence of lineage-specific trends as well as common ecological-evolutionary microbial responses to climate change. IMPORTANCE Anthropogenic climate change threatens soil ecosystem health in part by altering below-ground carbon cycling carried out by microbes. Microbial evolutionary responses are often overshadowed by community-level ecological responses, but adaptive responses represent potential changes in traits and functional potential that may alter ecosystem function. We predict that microbes are adapting to climate change stressors like soil warming. To test this, we analyzed the genomes of bacteria from a soil warming experiment where soil plots have been experimentally heated 5°C above ambient for over 30 years. While genomic attributes were unchanged by long-term warming, we observed trends in functional gene content related to carbon and nitrogen usage and genomic indicators of growth efficiency. These responses may represent new parameters in how soil ecosystems feedback to the climate system.

Choudoir, Mallory J. (ORCID:0000000291175150)↗

pH-Dependent Single-Step Rapid Synthesis of CuO Nanoparticles and Their Optical Behavior

This paper reports the pH-dependent growth of copper oxide (CuO) nanoparticles by wet chemical precipitation method using pH value of the samples as the only variable parameter. The phase purity, morphology, optical behavior, and elemental analysis of synthesized nanoparticles are shown to be critically dependent on the pH of the samples. Scanning electron microscope (SEM) results shows that a higher pH results well-defined CuO nanoflakes. X-ray powder diffraction (XRD) results disclosed that the growth of pure CuO with monoclinic structure at higher pH 8, whereas mixed phase was formed at lower pH 7. The average crystallite size of samples prepared at pH 8 to 10 was varying from 23.36 to 25.78 nm. The infrared spectroscopy showed that the O–H stretching peaks become narrow with an increase in the pH value. Optical results revealed the existence of the sharp absorption edges with precise excitonic features and photoluminescence bands both located at visible and near infrared spectral region attributed to the excellent optical behavior and narrow size distribution of particles. The additional near infrared band in photoluminescence spectrum located at 860 nm is attributed the defect-related luminescence. The growth mechanism of CuO nanostructures was discussed in the light of our findings.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

The role of AlGaN buffers and channel thickness in the electronic transport properties of Al{sub x}In{sub 1–x}N/AlN/GaN heterostructures

We try to theoretically analyze the reported experimental data of the Al{sub x}In{sub 1–x}N/AlN/GaN heterostructures grown by MOCVD and quantitatively investigate the effects of AlGaN buffers and the GaNchannel thickness on the electrical transport properties of these systems. Also, we obtain the most important effective parameters of the temperature-dependent mobility in the range 35–300 K. Our results show that inserting a 1.1 μm thick Al{sub 0.04}Ga{sub 0.96}N buffer enhances electron mobility by decreasing the effect of phonons, the interface roughness, and dislocation and crystal defect scattering mechanisms. Also, as the channel thickness increases from 20 nm to 40 nm, the electron mobility increases from 2200 to 2540 cm{sup 2}/(V s) and from 870 to 1000 cm{sup 2}/(V s) at 35 and 300 K respectively, which is attributed to the reduction in the dislocation density and the strain-induced field. Finally, the reported experimental data show that inserting a 450 nm graded AlGaN layer before an Al{sub 0.04}Ga{sub 0.96}N buffer causes a decrease in the electron mobility, which is attributed to the enhancement of the lateral size of roughness, the dislocation density, and the strain-induced field in this sample.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

The effect of zero Langmuir oscillations of an electromagnetic field on the transverse dielectric permittivity of a degenerate electron–ion plasma

It is shown theoretically that the electromagnetic background of longitudinal zero oscillations of a temperature-degenerate electron–ion plasma in a thermodynamic equilibrium state resonantly distorts the wave functions of its electrons. This gives rise to a characteristic quantum frequency that nonanalytically depends on Planck’s constant ℏ. Vacuum phenomena in plasma attributed to zero oscillations turn out to be anomalously large. Quantum corrections to the transverse dielectric permittivity of a degenerate electron–ion plasma, which are nonanalytic with respect to ℏ and are attributed to the zero-point oscillations of the plasma, are determined.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Bimodality in Arrays of In{sub 0.4}Ga{sub 0.6}As Hybrid Quantum-Confined Heterostructures Grown on GaAs Substrates

Hybrid quantum-confined heterostructures grown by metal-organic vapor-phase epitaxy (MOVPE) via the deposition of In{sub 0.4}Ga{sub 0.6}As layers with various nominal thicknesses onto vicinal GaAs substrates are studied by photoluminescence spectroscopy and transmission electron microscopy. The photoluminescence spectra of these structures show the superposition of two spectral lines, which is indicative of the bimodal distribution of the size and/or shape of light-emitting objects in an array. The dominant spectral line is attributed to the luminescence of hybrid “quantum well–dot” nanostructures in the form of a dense array of relatively small quantum dots (QDs) with weak electron and hole localization. The second, lower intensity line is attributed to luminescence from a less dense array of comparatively larger QDs. Analysis of the behavior of the spectral line intensities at various temperatures showed that the density of larger QDs grows with increasing thickness of the InGaAs layer.

36 MATERIALS SCIENCE↗

Plasmon Resonance Induced Photoconductivity in the Yttria Stabilized Zirconia Films with Embedded Au Nanoclusters

We report on the investigation of the photoconductivity (PC) in the yttria stabilized zirconia (YSZ) films with embedded Au nanoclusters (NCs). A peak in the PC spectrum corresponding to the plasmon optical absorption resonance in the Au NCs was observed. The temperature dependence of PC near 300 K obeyed Mott law. In this case, the PC was attributed to the heating of the YSZ matrix due to the plasmon optical absorption in the Au NCs (bolometric effect). Near 77 K, the PC did not depend on temperature and was attributed to plasmon-assisted electron transport between the NCs via the vacancy α-band in YSZ.

36 MATERIALS SCIENCE↗

Effect of thermochemical treatments on laser-induced luminescence spectra from strontium titanate: comparison with swift ion-beam irradiation experiments

Results recently reported on the effect of thermochemical treatments on the (He-Cd) laser-excited emission spectra of strontium titanate (STO) are re-analyzed here and compared with results obtained under ion-beam irradiation. Contributing bands centered at 2.4 eV and 2.8 eV, which appear under laser excitation, present intensities dependent upon previous thermal treatments in oxidizing (O 2 ) or reducing atmosphere (H 2 ). As a key result, the emission band centered at 2.8 eV is clearly enhanced in samples exposed to a reducing atmosphere. From a comparison with the ionoluminescence data, it is concluded that the laser-excited experiments can be rationalized within a framework developed from ion-beam excitation studies. In particular, the band at 2.8 eV, sometimes attributed to oxygen vacancies, behaves as expected for optical transitions from conduction-band (CB) states to the ground state level of the self-trapped exciton center. The band at 2.0 eV reported in ion-beam irradiated STO, and attributed to oxygen vacancies, is not observed in laser-excited crystals. As a consequence of our analysis, a consistent scheme of electronic energy levels and optical transitions can now be reliably offered for strontium titanate.

74 ATOMIC AND MOLECULAR PHYSICS↗

IRNet: A General Purpose Deep Risidual Regression Framework for Materials Discovery

Materials discovery is crucial for making scientific advances in many domains. Collections of data from experiments and first-principle computations have spurred interest in applying machine learning methods to create predictive models capable of mapping from composition and crystal structures to materials properties. Generally, these are regression problems with the input being a 1D vector composed of numerical attributes representing the material composition and/or crystal structure. While neural networks consisting of fully connected layers have been applied to such problems, their performance often suffers from the vanishing gradient problem when network depth is increased. Hence, predictive modeling for such tasks has been mainly limited to traditional machine learning techniques such as Random Forest. In this paper, we study and propose design principles for building deep regression networks composed of fully connected layers with numerical vectors as input. We introduce a novel deep regression network with individual residual learning, IRNet, that places shortcut connections after each layer so that each layer learns the residual mapping between its output and input. We use the problem of learning properties of inorganic materials from numerical attributes derived from material composition and/or crystal structure to compare IRNet’s performance against that of other machine learning techniques. Using multiple datasets from the Open Quantum Materials Database (OQMD) and Materials Project for training and evaluation, we show that IRNet provides significantly better prediction performance than the state-of-the-art machine learning approaches currently used by domain scientists. We also show that IRNet’s use of individual residual learning leads to better convergence during the training phase than when shortcut connections are between multi-layer stacks while maintaining the same number of parameters.

deep learning↗

Wattchmen: Watching the Wattchers – High Fidelity, Flexible GPU Energy Modeling

Modern GPU-rich HPC systems are increasingly becoming energy-constrained. Thus, understanding an application’s energy consumption becomes essential. Unfortunately, current GPU energy attribution techniques are either inaccurate, inflexible, or outdated. Therefore, we propose Wattchmen, a flexible methodology for measuring, attributing, and predicting GPU energy consumption. We construct a per-instruction energy model using a diverse set of microbenchmarks to systematically quantify the energy consumption of GPU instructions, enabling finer-grain prediction and energy consumption breakdowns for applications. Compared with the state-of-the-art systems like AccelWattch (32%) and Guser (25%), across 16 popular GPGPU, graph analytics, HPC, and ML workloads, Wattchmen reduces the mean absolute percent error (MAPE) to 14% on V100 GPUs. Furthermore, we show that Wattchmen provides similar MAPEs for water-cooled V100s (15%) and extends to later architectures, including air-cooled A100 (11%) and H100 (12%) GPUs. Finally, to further demonstrate Wattchmen ’s value, we apply it to applications such as Backprop and QMCPACK, where Wattchmen ’s insights enable energy reductions of up to 35%.

Tran, Brandon [University of Wisconsin, Madison] (↗

Synthesis and Characterization of Perfluorinated Anion Exchange Membranes

Anion exchange membranes (AEMs) are of high interest for a number of electrochemical device applications including fuel cells, electrolyzers, and flow batteries. Perfluorinated sulfonic acid polymers have been the standard polymer used in the much more established area of proton exchange membrane based devices due to specific advantageous attributes including chemical stability, high conductivity, high water mobility, and the ability to create high performance electrodes. These attributes would make for desirable AEMs, but synthesizing perfluorinated AEMs has been limited and has significant challenges. Here, we report our efforts to develop novel synthesis routes to sulfonamide-linked alkyl ammonium perfluorinated AEMs. We have demonstrated the ability to achieve both high levels of ion exchange and membrane conductivity. We have achieved improved durability by extending the length of the alkyl tether from 3 to 6 carbons, and we have demonstrated the ability to process these polymers into membranes, ionomer solutions/dispersions, and fuel cells with reasonable performance.

30 DIRECT ENERGY CONVERSION↗

Understanding Li-Ion Cell Internal Short Circuit and Thermal Runaway through Small, Slow and In Situ Sensing Nail Penetration

Here we report a small, slow and in situ sensing (3S) nail penetration test method to understand Li-ion cell internal short circuit (ISC) and thermal runaway. The method not only keeps conventional nail penetration's advantage of simple implementation, but also enhances its relevance to field failures and enables detailed in situ diagnosis. It was applied to 3-Ah pouch cells and revealed insights that could not be captured by conventional methods. Most interestingly, multiple in situ temperature peaks were observed during a period of over 100 s before thermal runaway. These initial peaks exceeded safety limit but the temperature rapidly decreased after each peak instead of causing immediate thermal runaway. Further investigation suggested that the initial temperature peaks occurred when nail tip reached aluminum foil current collector to form a low resistance ISC between anode and aluminum foil. The rapid temperature decrease after each peak can be attributed to sudden drop of ISC current, which can be further attributed to rupture of aluminum foil and increase of contact resistance. The findings show that 3S nail penetration test can separate processes of ISC from thermal runaway and provide details of ISC at the level of individual electrode and current collector.

25 ENERGY STORAGE↗

Manipulating Water in High-Performance Hydroxide Exchange Membrane Fuel Cells through Asymmetric Humidification and Wetproofing

Hydroxide exchange membrane fuel cells (HEMFCs) are an emerging low-cost alternative to conventional proton exchange membrane fuel cells. In addition to producing water at the anode, HEMFCs consume water at the cathode, leading to distinctive water transport behavior. We report that gas diffusion layer (GDL) wetproofing strictly lowers cell performance, but that the penalty is much higher when the anode side is wetproofed compared to the cathode side. We attribute this penalty primarily to mass transport losses from anode flooding, suggesting that cathode humidification may be more beneficial than anode humidification for this device. GDLs with little or no wetproofing perform best, yielding a competitive peak power density of 737 mW cm(-2). (C) The Author(s) 2015. Published by ECS. This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 License (CC BY, hup://creativecommons.orgilicenses/by/4.0/), which permits unrestricted reuse of the work in any medium, provided the original work is properly cited. All rights reserved.

Kaspar, RB↗

Capacity Fading Mechanisms of Silicon Nanoparticle Negative Electrodes for Lithium Ion Batteries

A thorough analysis of the evolution of the voltage profiles of silicon nanoparticle electrodes upon cycling has been conducted. The largest changes to the voltage profiles occur at the earlier stages (> 0.16 V vs Li/Li + ) of lithiation of the silicon nanoparticles. The changes in the voltage profiles suggest that the predominant failure mechanism of the silicon electrode is related to incomplete delithiation of the silicon electrode during cycling. The incomplete delithiation is attributed to resistance increases during delithiation, which are predominantly contact and solid electrolyte interface (SEI) resistance. The capacity retention can be significantly improved by lowering delithiation cutoff voltage or by introducing electrolyte additives, which generate a superior SEI. The improved capacity retention is attributed to the reduction of the contact and SEI resistance.

25 ENERGY STORAGE↗

Direct Observation of Sulfur Radicals as Reaction Media in Lithium Sulfur Batteries

Lithium sulfur (Li-S) battery has been regaining tremendous interest in recent years because of its attractive attributes such as high gravimetric energy, low cost and environmental benignity. However, it is still not conclusively known how polysulfide ring/chain participates in the whole cycling and whether the discharge and charge processes follow the same pathway. Herein, we demonstrate the direct observation of sulfur radicals by using in situ electron paramagnetic resonance (EPR) technique. Based on the concentration changes of sulfur radicals at different potentials and the electrochemical characteristics of the cell, it is revealed that the chemical and electrochemical reactions in Li-S cell are driving each other to proceed through sulfur radicals, leading to two completely different reaction pathways during discharge and charge. The proposed radical mechanism may provide new perspectives to investigate the interactions between sulfur species and the electrolyte, inspiring novel strategies to develop Li-S battery technology.

25 ENERGY STORAGE↗