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At least 1,261 records · Page 70

Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis

Advances in high-throughput sequencing have facilitated remarkable insights into the diversity and functioning of naturally occurring microbes; however, current sequencing strategies are insufficient to reveal physiological states of microbial communities associated with protein translation dynamics. Transfer RNAs (tRNAs) are core components of protein synthesis machinery, present in all living cells, and are phylogenetically tractable, which make them ideal targets to gain physiological insights into environmental microbes. Here we report a direct sequencing approach, tRNA-seq, and a software suite, tRNA-seq-tools, to recover sequences, abundance profiles, and post-transcriptional modifications of microbial tRNA transcripts. Our analysis of cecal samples using tRNA-seq distinguishes high-fat-and low-fat-fed mice in a comparable fashion to 16S ribosomal RNA gene amplicons, and reveals taxon- and diet-dependent variations in tRNA modifications. Our results provide taxon-specific in situ insights into the dynamics of tRNA gene expression and post-transcriptional modifications within complex environmental microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗

Self-Assembly Behavior of an Oligothiophene-Based Conjugated Liquid Crystal and Its Implication for Ionic Conductivity Characteristics

Here, a joint experimental and computational study on the synthesis, selfassembly and ionic conduction characteristics of a new conjugated liquid crystal quaterthiophene/poly(ethylene oxide) (PEO4) consisting of terminal tetraethyleneglycol monomethyl ether groups on both ends of a quaterthiophene core. In agreement with molecular dynamic simulations, temperature-dependent grazing-incidence wide angle X-ray scattering and X-ray diffraction indicate that the molecule spontaneously forms a smectic phase at ambient temperature as characterized both in bulk and thin film configurations. Significantly, this smectic phase is maintained upon blending with bis(trifluoro-methanesulfonyl)imide (LiTFSI) as ion source at a concentration ratio up to r = [Li + ]/[EO] = 0.05. Nanosegregation between oligothiophene and PEO moieties and π-π stacking of thiophene rings led to the formation of efficient 2D pathways for ion transport, resulting in thin film in-plane ionic conductivity as high as 5.2 x 10 -4 S/cm -1 at 70°C and r = 0.05 as measured by electrochemical impedance spectroscopy (EIS). Upon heating the samples above a transition temperature around 95 °C, a less ordered phase forms associated with a pronounced drop in ionic conductivity. Finally, upon cooling, partial and local reordering of the conducting smectic domains leads to an ionic conductivity decrease compared to the as-cast state.

36 MATERIALS SCIENCE↗

Electrically Pumped Epitaxially Regrown GaSb-Based Type-I Quantum-Well Surface-Emitting Lasers with Buried High-Index-Contrast Photonic Crystal Layer

Epitaxially regrown electrically pumped photonic crystal surface-emitting lasers (PCSELs) emitting near 2 and 2.6 μm are designed, fabricated, and characterized. A high-index-contrast photonic crystal layer is incorporated into the GaSb-based laser heterostructure by air-hole-retaining epitaxial regrowth. A square lattice of triangular holes is etched in the top waveguide core layer of the incomplete laser heterostructure. The nanopatterned surface is subsequently cleaned and regrown with AlGaAsSb p-cladding material. Transmission electron microscopy studies demonstrate uniform regrowth over the nanopatterned GaSb surface. The selected regrowth regimes yield a buried 2D array of elongated air-holes. The diode PCSELs based on moderately etched nanopatterns demonstrate band-edge lasing near 2 μm up to room temperatures. The cascade diode PCSELs operate near 2.6 μm with minimum threshold current densities of about 500 A cm -2 achieved at 180 K. The devices generate mW level output in narrow divergence beam emitted from the window in substrate contact. The angle-resolved electroluminescence measurements reveal a four-sub-band band structure with an apparent photonic bandgap corresponding to the buried high-index-contrast square photonic crystal layer. Finally, the PCSELs made of heterostructures supporting two modes in the vertical direction demonstrate two sets of sub-bands showing anti-crossing-like interaction.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Statistical properties of the plasma fluctuations and turbulent cross-field fluxes in the outboard mid-plane scrape-off layer of Alcator C-Mod

The Alcator C-Mod mirror Langmuir probe diagnostic is used to characterize plasma fluctuations in the outboard mid-plane scrape-off layer (SOL). Ohmically heated L-mode plasmas with Greenwald fractions from 0.1 to 0.45 are analyzed. In plasmas with a low line-averaged core density, the radial profiles of the average electron density and temperature feature a two-scale structure with a strong gradient in the near-SOL and a weak gradient in the far-SOL. The relative fluctuation levels of the electron density are below 25% throughout the entire SOL and the fluctuation driven heat flux is dominated by plasma density fluctuations. In the plasma with the highest line-averaged core density, the radial profiles of the electron density and temperature feature only a single weak gradient length scale across the SOL. The plasma density at the limiter radius is approximately 10 times larger than in low-density discharges. The average electron temperature at the separatrix falls to approximately 30 eV while the magnitude of the relative temperature fluctuations increases with the line-averaged core plasma density. With increasing plasma density, the fluctuation-driven heat fluxes increase by more than one order of magnitude while retaining a relative fluctuation level of approximately 3. Even though the SOL is on average cooler than in low density discharges, large electron temperature fluctuations govern the turbulence driven heat flux towards the wall while contributions from density fluctuations and triple correlations contribute approximately 35% and 15%, respectively.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Power modeling of degraded PV systems: Case studies using a dynamically updated physical model (PV-Pro)

Power modeling, widely applied for health monitoring and power prediction, is crucial for the efficiency and reliability of Photovoltaic (PV) systems. The most common approach for power modeling uses a physical equivalent circuit model, with the core challenge being the estimation of model parameters. Traditional parameter estimation either relies on datasheet information, which does not reflect the system's current health status, especially for degraded PV systems, or requires additional I-V characterization, which is generally unavailable for large-scale PV systems. Thus, we build upon our previously developed tool, PV-Pro (originally proposed for degradation analysis), to enhance its application for power modeling of degraded PV systems. PV-Pro extracts model parameters from production data without requiring I-V characterization. This dynamic model, periodically updated, can closely capture the actual degradation status, enabling precise power modeling. PV-Pro is compared with popular power modeling techniques, including persistence, nominal physical, and various machine learning models. The results indicate that PV-Pro achieves outstanding power modeling performance, with an average nMAE of 1.4 % across four field-degraded PV systems, reducing error by 17.6 % compared to the best alternative technique. Furthermore, PV-Pro demonstrates robustness across different seasons and severities of degradation. The tool is available as a Python package at https://github.com/DuraMAT/pvpro.

14 SOLAR ENERGY↗

X-ray transient absorption reveals the 1Au (nπ*) state of pyrazine in electronic relaxation

Abstract Electronic relaxation in organic chromophores often proceeds via states not directly accessible by photoexcitation. We report on the photoinduced dynamics of pyrazine that involves such states, excited by a 267 nm laser and probed with X-ray transient absorption spectroscopy in a table-top setup. In addition to the previously characterized 1 B 2u (ππ*) (S 2 ) and 1 B 3u (nπ*) (S 1 ) states, the participation of the optically dark 1 A u (nπ*) state is assigned by a combination of experimental X-ray core-to-valence spectroscopy, electronic structure calculations, nonadiabatic dynamics simulations, and X-ray spectral computations. Despite 1 A u (nπ*) and 1 B 3u (nπ*) states having similar energies at relaxed geometry, their X-ray absorption spectra differ largely in transition energy and oscillator strength. The 1 A u (nπ*) state is populated in 200 ± 50 femtoseconds after electronic excitation and plays a key role in the relaxation of pyrazine to the ground state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantification of Thermal Oxidation in Metallic Glass Powder using Ultra-small Angle X-ray Scattering

In this paper, the composition, structure, morphology and kinetics of evolution during isothermal oxidation of Fe 48 Cr 15 Mo 14 Y 2 C 15 B 6 metallic glass powder in the supercooled region are investigated by an integrated ex-situ and in-situ characterization and modelling approach. Raman and X-ray diffraction spectra established that oxidation yielded a hierarchical structure across decreasing length scales. At larger scale, Fe 2 O 3 grows as a uniform shell over the powder core. This shell, at smaller scale, consists of multiple grains. Ultra-small angle X-ray scattering intensity acquired during isothermal oxidation of the powder over a wide Q-range delineated direct quantification of oxidation behavior. The hierarchical structure was employed to construct a scattering model that was fitted to the measured intensity distributions to estimate the thickness of the oxide shell. The relative gain in mass during oxidation, computed theoretically from this model, relatively underestimated that measured in practice by a thermogravimetric analyzer due to the distribution in sizes of the particles. As a whole, this paper introduces the first direct quantification of oxidation in metallic glass powder by ultra-small angle X-ray scattering. It establishes novel experimental environments that can potentially unfold new paradigms of research into a wide spectrum of interfacial reactions in powder materials at elevated temperatures.

42 ENGINEERING↗

Photoionization of the I 4d and valence orbitals of methyl iodide

Here, the photoabsorption and photoionization dynamics of the I 4d and valence orbitals in methyl iodide have been studied both experimentally and theoretically. Synchrotron radiation has been employed to measure the total ion yield in the vicinity of the I 4d ionization thresholds. The observed structure, due to excitations into Rydberg or valence states, has been assigned using transition energies and relative intensities computed with time-dependent density functional theory within the Tamm–Dancoff approximation. Photoelectron spectra, recorded with plane polarized radiation in two polarization geometries, have allowed the effect of autoionization on the valence electron angular distributions to be investigated. The spectra obtained at photon energies of 50.62 and 52.34 eV, coinciding respectively with the I 4d 5/2 → σ* and 4d 3/2 → σ* transitions, reveal, in addition to valence shell photoelectron bands, features not associated with simple photoionization of the parent molecule. High resolution photoelectron spectra of the I 4d main-lines display structure resulting from spin–orbit coupling and molecular field splitting. The binding energies of the five states contributing to the (I 4d) -1 ionization have been determined. The iodine (in CH 3 I) N 45 VV Auger spectrum has been measured and the observed structure has been assigned using the core hole binding energies derived in the present work together with established ionization energies of the doubly charged ion. The experimentally determined Auger electron angular distributions have been discussed in relation to the theoretical angular distribution parameter characterizing the spatial alignment of molecular axes in the (I 4d) -1 state.

74 ATOMIC AND MOLECULAR PHYSICS↗

Design and Performance Characterization of RADICAL-Pilot on Leadership-Class Platforms

Many extreme scale scientific applications have workloads comprised of a large number of individual highperformance tasks. The Pilot abstraction decouples workload specification, resource management, and task execution via job placeholders and late-binding. As such, suitable implementations of the Pilot abstraction can support the collective execution of large number of tasks on supercomputers. We introduce RADICAL-Pilot (RP) as a portable, modular and extensible Pilot enabled runtime system. We describe RP's design, architecture and implementation. We characterize its performance and show its ability to scalably execute workloads comprised of tens of thousands heterogeneous tasks on DOE and NSF leadership-class HPC platforms. Specifically, we investigate RP's weak/strong scaling with CPU/GPU, single/multi core, (non)MPI tasks and python functions when using most of ORNL Summit and TACC Frontera. RADICAL-Pilot can be used stand-alone, as well as the runtime for third-party workflow systems.

97 MATHEMATICS AND COMPUTING↗

Novel Polyoxovanadate K{sub 2}ZnV{sub 5}O{sub 14}: Crystal Structure and Peculiarities of Crystal Chemistry

A novel structure type has been established as a result of studying a non-merohedral microtwin of polyoxovanadate (K{sub 2}ZnV{sub 5}O{sub 14}) by X-ray diffractometry (R = 0.0595). The new compound, synthesized under hydrothermal conditions in the ZnCl{sub 2}–K{sub 2}CO{sub 3}–V{sub 2}O{sub 5}–H{sub 2}O system, is characterized as follows: a = 8.066(5) Å, b = 8.117(5) Å, c = 9.236(5) Å, β = 105.287(5)°, sp. P2{sub 1}/m, Z = 2, ρ{sub calcd} = 3.54 g/cm{sup 3}. Edge-shared five-core “clusters” consisting of vanadium octahedra, between which ZnO{sub 4} tetrahedra (sharing vertices with octahedra) are located, form two-dimensional two-layer anion packets of the (ZnV{sub 5}O{sub 14}){sup 2–} composition, alternating along the c axis with layers of potassium atoms. Structural peculiarities determine the morphology and color of new-phase crystals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spatial soft sweeps: Patterns of adaptation in populations with long-range dispersal

Adaptation in extended populations often occurs through multiple independent mutations responding in parallel to a common selection pressure. As the mutations spread concurrently through the population, they leave behind characteristic patterns of polymorphism near selected loci—so-called soft sweeps—which remain visible after adaptation is complete. These patterns are well-understood in two limits of the spreading dynamics of beneficial mutations: the panmictic case with complete absence of spatial structure, and spreading via short-ranged or diffusive dispersal events, which tessellates space into distinct compact regions each descended from a unique mutation. However, spreading behaviour in most natural populations is not exclusively panmictic or diffusive, but incorporates both short-range and long-range dispersal events. Here, we characterize the spatial patterns of soft sweeps driven by dispersal events whose jump distances are broadly distributed, using lattice-based simulations and scaling arguments. We find that mutant clones adopt a distinctive structure consisting of compact cores surrounded by fragmented “haloes” which mingle with haloes from other clones. As long-range dispersal becomes more prominent, the progression from diffusive to panmictic behaviour is marked by two transitions separating regimes with differing relative sizes of halo to core. We analyze the implications of the core-halo structure for the statistics of soft sweep detection in small genomic samples from the population, and find opposing effects of long-range dispersal on the expected diversity in global samples compared to local samples from geographic subregions of the range. We also discuss consequences of the standing genetic variation induced by the soft sweep on future adaptation and mixing.

Genetics & Heredity↗

The Young Supernova Experiment Data Release 1 (YSE DR1): Light Curves and Photometric Classification of 1975 Supernovae

We present the Young Supernova Experiment Data Release 1 (YSE DR1), comprised of processed multicolor PanSTARRS1 griz and Zwicky Transient Facility (ZTF) gr photometry of 1975 transients with host–galaxy associations, redshifts, spectroscopic and/or photometric classifications, and additional data products from 2019 November 24 to 2021 December 20. YSE DR1 spans discoveries and observations from young and fast-rising supernovae (SNe) to transients that persist for over a year, with a redshift distribution reaching z ≈ 0.5. We present relative SN rates from YSE's magnitude- and volume-limited surveys, which are consistent with previously published values within estimated uncertainties for untargeted surveys. We combine YSE and ZTF data, and create multisurvey SN simulations to train the ParSNIP and SuperRAENN photometric classification algorithms; when validating our ParSNIP classifier on 472 spectroscopically classified YSE DR1 SNe, we achieve 82% accuracy across three SN classes (SNe Ia, II, Ib/Ic) and 90% accuracy across two SN classes (SNe Ia, core-collapse SNe). Our classifier performs particularly well on SNe Ia, with high (>90%) individual completeness and purity, which will help build an anchor photometric SNe Ia sample for cosmology. We then use our photometric classifier to characterize our photometric sample of 1483 SNe, labeling 1048 (~71%) SNe Ia, 339 (~23%) SNe II, and 96 (~6%) SNe Ib/Ic. YSE DR1 provides a training ground for building discovery, anomaly detection, and classification algorithms, performing cosmological analyses, understanding the nature of red and rare transients, exploring tidal disruption events and nuclear variability, and preparing for the forthcoming Vera C. Rubin Observatory Legacy Survey of Space and Time.

79 ASTRONOMY AND ASTROPHYSICS↗

The structure of jet turbulence producing jet noise

The structure of the turbulence in the mixing region for the first few diameters downstream from the outlet of a circular subsonic jet is characterized at three Mach numbers, 0.3, 0.5, and 0.7, with most of the measurements taken at M = 0.3. Profiles of turbulence intensity showed that downstream of the lip intensity is independent of axial distance, while in the core intensity varies by a factor of eight between the jet outlet and the end of the core. A digital data reduction program was used to calculate the auto- and cross-correlations of axial velocity fluctuations and the power spectral densities. Convection velocities were measured using broadband, hot wire signals and signals that were digitally filtered for band-passes about center frequencies of 0.8, 1.3, 1.6, and 3.2 kHz. The center frequency of 1.3 kHz corresponded to the peak energy in the core spectrum. The results support the hypothesis that the coherent pressure field is driven by the intermittent fluctuations at the core boundary, which in turn are related to the large (low frequency) eddies.

Wooldridge, C. E.↗

Probing the presently tenuous link between comets and the origin of life

The possibilities of using millimeter-wave technology to probe the subsurface processes of comets to investigate links between cometary materials and the origins of life are explored. It is noted that current theories hold that the necessities for life to begin comprise a fairly uniform temperature, the presence of a solvent to give materials mobility, and the presence of atoms which can form long chains of molecules. Consideration is given to two cometary nuclei models: a core with an equal amount of liquid water and lunar material, and a nucleus with equal amounts of frozen water ice and lunar material. Solutions to the radiative transfer equation for the two models are presented to characterize identifiable emissions using radiometric spectrometer instrumentation on a spacecraft. Particular species such as OH, CN, HCN, and glycine are expected to be detectable if present.

Hobbs, R. W.↗

Observations of plasmas associated with the magnetic signature of a plasmoid in the distant magnetotail

The three-dimensional electron and positive ion velocity distributions were examined for four events for which the magnetic signature of plasmoids occurred at the Geotail spacecraft position in Earth's distant magnetotail. The proton bulk parameters and the electron velocity distributions for one of the events are presented in order to characterize the qualitative character of the set of events. The north-to-south turnings of the magnetic field that were taken for evidence of the passage of a plasmoid were often accompanied by a significant strong core of B(sub y) that was centered on the transition of B(sub z) from north to south. The magnetic signatures thus appeared to be more indicative of flux ropes than of classical plasmoids with weak core fields. The proton and electron bulk velocities in these magnetic structures are not equal, a situation that provides an earthward current. The plasma beta was typically one or greater. Counterstreaming of low-energy electrons was often found on the magnetic field lines around the central magnetic core and suggested the existence of a closed field line topology in these regions. These events appeared to be the tailward flowing debris from acceleration processes occuring in the vicinity of a separator positioned nearer to Earth.

Frank, L. A.↗

High Water Contents in the Siberian Cratonic Mantle: An FTIR Study of Udachnaya Peridotite Xenoliths

Water is believed to be a key factor controlling the long-term stability of cratonic lithosphere, but mechanisms responsible for the water content distribution in the mantle remain poorly constrained. Water contents were obtained by FTIR in olivine, pyroxene and garnet for 20 well-characterized peridotite xenoliths from the Udachnaya kimberlite (central Siberian craton) and equilibrated at 2-7 GPa. Water contents in minerals do not appear to be related to interaction with the host kimberlite. Diffusion modeling indicates that the core of olivines preserved their original water contents. The Udachnaya peridotites show a broad range of water contents in olivine (6.5 +/- 1.1 to 323 +- 65 ppm H2O (2 sigma)), and garnet (0 - 23 +/- 6 ppm H2O). The water contents of olivine and garnet are positively correlated with modal clinopyroxene, garnet and FeO in olivine. Water-rich garnets are also rich in middle rare earth elements. This is interpreted as the result of interaction between residual peridotites and water rich-melts, consistent with modal and cryptic metasomatism evidenced in the Siberian cratonic mantle. The most water-rich Udachnaya minerals contain 2 to 3 times more water than those from the Kaapvaal craton, the only craton with an intact mantle root for which water data is available. The highest water contents in olivine and orthopyroxene in this study (>= 300 ppm) are found at the bottom of the lithosphere (> 6.5 GPa). This is in contrast with the Kaapvaal craton where the olivines of peridotites equilibrated at > 6.4 GPa have < 1 ppm H2O. The latter "dry" olivine may make the base of the Kaapvaal cratonic root strong and thus protects it from erosion by the convective mantle The calculated viscosity for water-rich Udachnaya peridotites at > 6 GPa is lower or similar (8.4× 10(exp 16) to 8.0× 10(exp 18) Pa./s) to that of the asthenosphere (<= 3.7x10(exp 18) Pa./s ). Such lithologies would not be able to resist delamination by the convecting asthenosphere. However, seismology studies as well as the high equilibration pressures of our samples indicate that the Udachnaya cratonic lithosphere is 220-250 km thick. Consequently, the water-rich peridotites are likely not representative of the overall Siberian cratonic lithosphere. Their composition is linked to spatially limited melt metasomatism in mantle regions above asthenospheric upwellings responsible for the kimberlite magmatism prior to their ascent and eruption.

Doucet, Luc S.↗

Direct Imaging of a Cold Jovian Exoplanet in Orbit around the Sun-Like Star GJ 504

Several exoplanets have recently been imaged at wide separations of >10 AU from their parent stars. These span a limited range of ages (<50 Myr) and atmospheric properties, with temperatures of 800-1800 K and very red colors (J −H > 0.5 mag), implying thick cloud covers. Furthermore, substantial model uncertainties exist at these young ages due to the unknown initial conditions at formation, which can lead to an order of magnitude of uncertainty in the modeled planet mass. Here, we report the direct imaging discovery of a Jovian exoplanet around the Sun-like star GJ 504, detected as part of the SEEDS survey. The system is older than all other known directly-imaged planets; as a result, its estimated mass remains in the planetary regime independent of uncertainties related to choices of initial conditions in the exoplanet modeling. Using the most common exoplanet cooling model, and given the system age of 160(+350/−60) Myr, GJ 504 b has an estimated mass of 4(+4.5/−1.0) Jupiter masses, among the lowest of directly imaged planets. Its projected separation of 43.5 AU exceeds the typical outer boundary of approx.. 30 AU predicted for the core accretion mechanism. GJ 504 b is also significantly cooler (510(+30/−20) K)) and has a bluer color (J − H = −0.23 mag) than previously imaged exoplanets, suggesting a largely cloud-free atmosphere accessible to spectroscopic characterization. Thus, it has the potential of providing novel insights into the origins of giant planets, as well as their atmospheric properties.

exoplanets↗

Chemistry Characterization of Jet Aircraft Engine Particulate by XPS: Results from APEX III

This paper reports XPS analysis of jet exhaust particulate from a B737, Lear, ERJ, and A300 aircraft during the APEX III NASA led field campaign. Carbon hybridization and bonding chemistry are identified by high-resolution scans about the C1s core-shell region. Significant organic content as gauged by the sp3/sp2 ratio is found across engines and platforms. Polar oxygen functional groups include carboxylic, carbonyl and phenol with combined content of 20 percent or more. By lower resolution survey scans various elements including transition metals are identified along with lighter elements such as S, N, and O in the form of oxides. Burning additives within lubricants are probable sources of Na, Ba, Ca, Zn, P and possibly Sn. Elements present and their percentages varied significantly across all engines, not revealing any trend or identifiable cause for the differences, though the origin is likely the same for the same element when observed. This finding suggests that their presence can be used as a tracer for identifying soots from aircraft engines as well as diagnostic for monitoring engine performance and wear.

soot↗