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At least 667 records · Page 37

IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata

Viruses are widely recognized as critical members of all microbiomes. Metagenomics enables large-scale exploration of the global virosphere, progressively revealing the extensive genomic diversity of viruses on Earth and highlighting the myriad of ways by which viruses impact biological processes. IMG/VR provides access to the largest collection of viral sequences obtained from (meta)genomes, along with functional annotation and rich metadata. A web interface enables users to efficiently browse and search viruses based on genome features and/or sequence similarity. Here, for this work, we present the fourth version of IMG/VR, composed of >15 million virus genomes and genome fragments, a ≈6-fold increase in size compared to the previous version. These clustered into 8.7 million viral operational taxonomic units, including 231 408 with at least one high-quality representative. Viral sequences in IMG/VR are now systematically identified from genomes, metagenomes, and metatranscriptomes using a new detection approach (geNomad), and IMG standard annotation are complemented with genome quality estimation using CheckV, taxonomic classification reflecting the latest taxonomic standards, and microbial host taxonomy prediction. IMG/VR v4 is available at https://img.jgi.doe.gov/vr, and the underlying data are available to download at https://genome.jgi.doe.gov/portal/IMG_VR.

59 BASIC BIOLOGICAL SCIENCES↗

Performance Analysis of PIConGPU: Particle-in-Cell on GPUs using NVIDIA’s NSight Systems and NSight Compute

PIConGPU, Particle In Cell on GPUs, is an open source simulations framework for plasma and laser-plasma physics used to develop advanced particle accelerators for radiation therapy of cancer, high energy physics and photon science. While PIConGPU has been optimized for at least 5 years to run well on NVIDIA GPU-based clusters, there has been limited exploration by the development team of potential scalability bottlenecks using recently updated and new tools including NVIDIA’s NVProf tool and the brand-new NVIDIA NSight Suite (Systems and Compute) tools. PIConGPU is a highly optimized application that runs production jobs at scale on a system Oak Ridge Leadership Facility’s (OLCF) Summit supercomputer (using the full machine at 4600 nodes; at 98% of GPU utilization on all ~28000 NVIDIA Volta GPUs). PIConGPU has been selected as one of the the eight applications for OLCF’s coveted Center for Accelerated Application Readiness (CAAR) program aimed at the facility’s Frontier supercomputer (OLCF’s first exascale system to launch in 2021), to partner with our vendors (primary vendors: AMD and Cray/HPE) ensuring that Frontier will be able to perform large-scale science when it opens to users in 2022. To this effect, performance engineers on the PIConGPU team wanted to dive deep into the application to understand at the finest granularity, which portions of the code could be further optimized to exploit the hardware on Summit at it’s maximum potential and also to elucidate which key kernels should be tracked and optimized for the CAAR effort to port this code to Frontier. Any bottlenecks that are observed via performance profiling on Summit are likely to also impact scalability on the Frontier-dev system and the Frontier Early Access (EA) system. Additionally, the engineers wanted to take a closer look at the newest NVIDIA profiling tools which allows us to identify the most useful features on these tools and will provide an opportunity to compare it to new AMD and Cray’s performance analysis tool releases and provide feedback to our vendor partners on what features are most important and mission critical for CAAR efforts. The primary goal of this report is to focus on the evaluation of PIConGPU’s most time-intensive kernels using NVProf and NSight Suite. Three kernels, Current Deposition (also known as Compute Current), Particle Push (Move and Mark), and Shift Particles are known to be some of the most time-consuming kernels in PIConGPU. The Current xi Deposition kernel and Particle Push kernel both set up the particle attributes for running any physics simulation with PIConGPU, so it is crucial to improve the performance of these two kernels. In this report, we measure single GPU metrics for the three kernels, offer high level takeaways from the conducted analysis, and compare the profiling data from NSight Compute to that of NVProf. This analysis was performed using a grid size of 240 x 272 x 224, and 10 time steps with the Mid-November Figure of Merit (FOM) run setup. The Traveling Wave Electron Acceleration (TWEAC) science case used in this run is a representative science case for PIConGPU. This execution can also be used for baseline analysis on AMD MI50/ MI60 systems. As of the time of writing, the PIConGPU application has limited use for features of NSight Systems, so this report will mainly focus on insights garnered from NSight Compute. For this analysis, we run the “full” metric set available in NSight Compute version 2020.1.2 and use NSight Systems version 2020.3.1 to generate the application timeline.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Site Suitability and Air Pollution Impacts of Composting Infrastructure for California’s Organic Waste Diversion Law

The emerging field of polaritonic chemistry explores the behavior of molecules under strong coupling with cavity modes. Despite recent developments in ab initio polaritonic methods for simulating polaritonic chemistry under electronic strong coupling, their capabilities are limited, especially in cases where the molecule also features strong electronic correlation. To bridge this gap, we have developed a novel method for cavity QED calculations utilizing the Density Matrix Renormalization Group (DMRG) algorithm in conjunction with the Pauli–Fierz Hamiltonian. Our approach is applied to investigate the effect of the cavity on the S0–S1 transition of n-oligoacenes, with n ranging from 2 to 5, encompassing 22 fully correlated π orbitals in the largest pentacene molecule. Our findings indicate that the influence of the cavity intensifies with larger acenes. Additionally, we demonstrate that, unlike the full determinantal representation, DMRG efficiently optimizes and eliminates excess photonic degrees of freedom, resulting in an asymptotically constant computational cost as the photonic basis increases.

54 ENVIRONMENTAL SCIENCES↗

X-ray verification of sol-gel resist shrinkage in substrate-conformal imprint lithography for a replicated blazed reflection grating

Surface-relief gratings fabricated through nanoimprint lithography (NIL) are prone to topographic distortion induced by resist shrinkage. Characterizing the impact of this effect on blazed diffraction efficiency is particularly important for applications in astrophysical spectroscopy at soft x-ray wavelengths ( λ ≈ 0.5 − 5 nm) that call for the mass-production of large-area grating replicas with sub-micron, sawtooth surface-relief profiles. A variant of NIL that lends itself well for this task is substrate-conformal imprint lithography (SCIL), which uses a flexible, composite stamp formed from a rigid master template to imprint nanoscale features in an inorganic resist that cures thermodynamically through a silica sol-gel process. While SCIL enables the production of several hundred imprints before stamp degradation and avoids many of the detriments associated with large-area imprinting in NIL, the sol-gel resist suffers shrinkage dependent on the post-imprint cure temperature. Through atomic force microscopy and diffraction-efficiency testing at beamline 6.3.2 of the Advanced Light Source, the impact of this effect on blaze response is constrained for a ∼160-nm-period grating replica cured at 90 ° C. Results demonstrate a ∼2 ° reduction in blaze angle relative to the master grating, which was fabricated by anisotropic wet etching in 〈311〉-oriented silicon to yield a facet angle close to 30 ° .

McCoy, Jake A. (ORCID:0000000216057517)↗

A review of the fabrication methods and mechanical behavior of continuous thermoplastic polymer fiber–thermoplastic polymer matrix composites

Abstract Thermoplastic polymer fiber–thermoplastic polymer matrix composites (PPCs or PRFPs), often recognized as self‐reinforced or single polymer composites, are potential candidates for future advanced polymer composites because of various advantages ( e.g., recyclability, formability, low‐cost, ultra‐lightweight, environmental friendliness, etc.). The manufacturability and mechanical behavior of these composites compared to conventional carbon‐/glass‐/aramid‐fiber‐reinforced polymers is of great interest to the composites community, but there are a limited number of studies in this area. To this end, this paper reviewed fabrication methods with different processing parameters and mechanical behavior of uni‐/multi‐directional thermoplastic PPCs featuring continuous thermoplastic polymer fibers from limited data in the literature. It was shown that most specific behaviors (normalized by density) of these materials in various loading conditions (e.g., quasi‐static tension/shear/flexure, tension‐tension fatigue, and out‐of‐plane impacting, etc.) are comparable to or better than glass‐/aramid‐fiber‐reinforced polymers. Particularly, the specific ductility in the foregoing conditions outperforms all the carbon‐/glass‐/aramid‐fiber‐reinforced polymers. Thermoplastic PPCs with remarkable performance can be achieved through several uncomplicated methods (e.g., film stacking, hot compaction, powder and solution impregnations, matrix infusion and injection molding, additive manufacturing, etc.), which have some similarities to the methods used for carbon‐/glass‐/aramid‐fiber‐reinforced polymers. Moreover, several opportunities and challenging problems of thermoplastic PPCs were summarized at the end of this review paper. Efficient solutions may require countless efforts in the composites community to further strengthen the performance and understanding of thermoplastic PPCs for wide applications in various engineering fields in the future.

36 MATERIALS SCIENCE↗

Use of Transmission Electron Microscopy for Analysis of Aerosol Particles and Strategies for Imaging Fragile Particles

For over 25 years, transmission electron microscopy (TEM) has provided a method for the study of aerosol particles with sizes from below the optical diffraction limit to several microns, resolving the particles as well as smaller features. The wide use of this technique to study aerosol particles has contributed important insights about environmental aerosol particle samples and model atmospheric systems. TEM produces an image that is a 2D projection of aerosol particles that have been impacted onto grids and, through associated techniques and spectroscopies, can contribute additional information such as the determination of elemental composition, crystal structure, and 3D particle structures. Soot, mineral dust, and organic/inorganic particles have all been analyzed using TEM and spectroscopic techniques. TEM, however, has limitations that are important to understand when interpreting data including the ability of the electron beam to damage and thereby change the structure and shape of particles, especially in the case of particles composed of organic compounds and salts. In this paper, we concentrate on the breadth of studies that have used TEM as the primary analysis technique. Another focus is on common issues with TEM and cryogenic-TEM. Insights for new users on best practices for fragile particles, that is, particles that are easily susceptible to damage from the electron beam, with this technique are discussed. Tips for readers on interpreting and evaluating the quality and accuracy of TEM data in the literature are also provided and explained.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Engineered Living Materials For Sustainability

Recent advances in synthetic biology and materials science have given rise to a new form of materials, namely engineered living materials (ELMs), which are composed of living matter or cell communities embedded in self-regenerating matrices of their own or artificial scaffolds. Like natural materials such as bone, wood, and skin, ELMs, which possess the functional capabilities of living organisms, can grow, self-organize, and self-repair when needed. They also spontaneously perform programmed biological functions upon sensing external cues. Currently, ELMs show promise for green energy production, bioremediation, disease treatment, and fabricating advanced smart materials. This review first introduces the dynamic features of natural living systems and their potential for developing novel materials. We then summarize the recent research progress on living materials and emerging design strategies from both synthetic biology and materials science perspectives. Lastly, we discuss the positive impacts of living materials on promoting sustainability and key future research directions.

36 MATERIALS SCIENCE↗

Seismic Tremors From Sea‐Landfast Ice Interactions Near Utqiaġvik, Alaska

The mechanical state of Arctic landfast sea ice remains poorly constrained due to limited observations. This study investigates interactions between drifting sea ice and the coastal landfast ice near Utqiaġvik, Alaska by integrating data from broadband seismometer, Distributed Acoustic Sensing, and marine radar. We find that decreases in sea ice velocity, marking transitions from drift to compressive contact, coincide with increased seismic energy. Tremor characteristics vary seasonally with ice conditions. In January, dense ice packs produced sustained harmonic tremors with gliding and U-shaped spectral features, consistent with repetitive stick-slip motion at the ice–ice or ice–ground interface under velocity-weakening friction. In April, smaller fragmented floes generated short-lived, chaotic tremors linked to brittle failure and spatially dispersed impacts. These findings demonstrate that seismic tremors encode the mechanical properties of interacting ice, offering a new tool to distinguish ice regimes and monitor evolving Arctic coastal dynamics under climate change.

58 GEOSCIENCES↗

Magnetic character of the low-energy enhancement in 70 Zn

The transition of an atomic nucleus from an excited state to a state of lower energy is typically accompanied by the emission of photons. The likelihood of photon emission is a function of the photon energy and of properties of the initial and final nuclear states and is known as the photon (or γ-ray) strength function (γSF). Of the features present in the γSF, an enhancement in the low-energy region has been observed in some nuclei, but the electromagnetic nature of this enhancement remains an open question. This low-energy enhancement in the γSF significantly impacts our understanding of how elements are created in stars and the structure of the nucleus. Here we present the results from an experiment on the γSF of 70 Zn that show that the enhancement in the γSF of this nucleus is of magnetic nature. This observation helps address a long-open question about γSFs in atomic nuclei and directly impacts our predictive capabilities in nuclear science.

Physics - Nuclear physics and radiation physics↗

High-energy ballistic electrons in low-pressure radio-frequency plasmas

This study demonstrates the presence of a small number of high-energy ballistic electrons (HEBEs) that originate from secondary electrons in low-pressure radio-frequency (rf) plasmas. The kinetic behaviors of the HEBEs are illustrated through electron energy probability functions from the fully kinetic particle-in-cell simulations, showing two wavy high-energy tails and two bifurcations during one rf cycle. Test-particle simulations and a semi-analytical method associated with nonlocal electron kinetics are performed to characterize the HEBE trajectories, which reveal the ballistic nature of the HEBEs and their typical bouncing features between the rf sheaths. Parameter dependence of the HEBEs on the discharge conditions (e.g., gas pressure, gap distance, and rf frequency) are identified, which is relevant to the plasma collisionality. With a pronounced presence of HEBEs, the overall impacts of the secondary electron emission on discharge parameters, such as electron power absorption and ionization rate, are also illustrated.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Thermal Probes of Phonon-Coupled Kitaev Spin Liquids: From Accurate Extraction of Quantized Edge Transport to Anyon Interferometry

Recent theoretical studies inspired by experiments on the Kitaev magnet α-RuCl 3 highlight the nontrivial impact of phonons on the thermal Hall conductivity of chiral topological phases. Here, we introduce mixed mesoscopic-macroscopic devices that allow refined thermal-transport probes of non-Abelian spin liquids with Ising topological order. These devices feature a quantum-coherent region with quantized or negligible phonon conductance, flanked by macroscopic lobes that facilitate efficient thermalization between chiral Majorana edge modes and bulk phonons. We show that our devices enable (i) accurate determination of the quantized thermal Hall conductivity, (ii) identification of non-Abelian Ising anyons via the temperature dependence of the thermal conductance, and, most interestingly, (iii) single-anyon detection through heat-based anyon interferometry. Analogous results apply broadly to phonon-coupled chiral topological orders.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Grid-Ready Flexible Transformers for Resilient Transmission Networks

Today’s transmission networks extend for hundreds of kilometers, transferring significant amounts of electrical energy. For every country, there are sort of “back- bone” lines, where a massive failure of transformers would create serious challenges to sustain a reliable energy supply. Natural phenomena and human driven actions could be triggers of such catastrophic events. For large utilities, or groups of utilities, it would be highly convenient to count with “flexible transformers”, which could be used as replacements for different voltage levels and with impedance adjustable to match optimum local requirements of impacted substations. Currently applied “emergency transformers” are fixed-impedance devices. In this contribution, a new concept of flexible, “future-grid ready” type of power transformers, specially devised for transmission networks is explained. This transformer has adjustable impedance features, which could be on-line operated. The concept has been proven to be functional and stable in the factory lab and in the field, by means of a prototype autotransformer of of 100 MVA, 165/69 Kv.

impedance of transformers↗

Resilience Metrics Framework for Solar Photovoltaics

This presentation was given at the Photovoltaic Specialist Conference (PVSC) 54 in New Orleans, Louisiana. Photovoltaic (PV) systems are routinely exposed to extreme weather, including wind and hail storms. Historically, most systems have proven to be resilient to such events, but some storms have damaged PV systems, leading to physical and financial loss. Storm hardening measures and specific system attributes can reduce this risk. This work introduces a set of resilience metrics and a framework for quantifying, comparing, and predicting PV system resilience. The framework is divided into two parts: 1) predictive, attribute metrics based on site and component characteristics, and 2) impact metrics that assess post-storm performance. Metrics are weighted and aggregated, producing hazard-specific resilience scores. We derive damage functions from storm-impacted PV systems, establishing a baseline against which post-storm performance can be compared. This damage was widely variable across hail and wind intensities, and field hail damage was less than predicted by laboratory tests, suggesting that system features - in addition to storm conditions - influence damage likelihood. Finally, the metrics framework is demonstrated using three case studies of storm damaged PV systems. Although additional data are needed to create attribute specific damage functions and establish metric weights, this study presents a methodology for evaluating PV resilience and contributes new damage functions to the literature.

14 SOLAR ENERGY↗

SEI formation mechanisms and Li + dissolution in lithium metal anodes: Impact of the electrolyte composition and the electrolyte-to-anode ratio

The lithium metal battery is one of today's most promising high-energy-density storage devices. Its full-scale implementation depends on solving operational and safety issues intrinsic to the Li metal high reactivity leading to uncontrolled electrolyte decomposition and uneven Li deposition. In this work, we study the spontaneous formation of the solid electrolyte interphase (SEI) upon contact of Li metal with the electrolyte and describe the heterogeneous SEI morphological features. Multiple electrolyte formulations based on lithium bis(fluorosulfonyl)imide (LiFSI), dimethoxyethane (DME), dimethyl carbonate (DMC), 1,2,2-tetrafluoroethyl-2,2,3,3-tetrafluoropropyl ether (TTE) and bis(2,2,2-trifluoroethyl) ether (BTFE) are used. Findings include the description of the SEI evolution from dispersed LiO, LiS, LiN, and LiF clusters to a continuous and compact inorganic phase in which the LiO and LiF content depend on the presence of fluorine diluents. Further, the role of the DME ether solvent helping the growth of a “wet-SEI” is compared to that of the highly unstable carbonate DMC, which decomposes into complex radical oligomers that might contribute to further electrolyte decomposition. The impact of the electrolyte-to-anode ratio on LiFSI decomposition is highlighted. Finally, we suggest the existence of a critical LiFSI concentration and electrolyte-to-anode ratio that could potentially balance the rate of electrolyte depletion and lithium consumption.

25 ENERGY STORAGE↗

Impact of Tiny Fermi Pockets with Extremely High Mobility on the Hall Anomaly in the Kagome Metal CsV 3 ⁢Sb 5

The kagome metal CsV 3 ⁢Sb 5 exhibits an unusual charge-density-wave (CDW) order, where the emergence of loop current order that breaks time-reversal symmetry (TRS) has been proposed. A key feature of this CDW phase is a nonmonotonic Hall effect at low fields, often attributed to TRS breaking. However, its origin remains unclear. Here, we conduct comprehensive magnetotransport measurements on CsV 3 ⁢Sb 5 and, through mobility spectrum analysis, identify the formation of tiny Fermi pockets with extremely high mobility below the CDW transition. Furthermore, electron irradiation experiments reveal that the nonmonotonic Hall effect is significantly suppressed in samples with reduced mobility, despite no substantial change in the electronic structure. In conclusion, these results indicate that the nonmonotonic Hall effect originates from these tiny Fermi pockets with high mobility carriers rather than anomalous Hall mechanisms, providing new insights into understanding the Hall anomaly in this kagome system.

36 MATERIALS SCIENCE↗

The crystal structure of Grindelia robusta 7,13-copalyl diphosphate synthase reveals active site features controlling catalytic specificity

Diterpenoid natural products serve critical functions in plant development and ecological adaptation and many diterpenoids have economic value as bioproducts. The family of class II diterpene synthases catalyzes the committed reactions in diterpenoid biosynthesis, converting a common geranylgeranyl diphosphate precursor into different bicyclic prenyl diphosphate scaffolds. Enzymatic rearrangement and modification of these precursors generate the diversity of bioactive diterpenoids. We report the crystal structure of Grindelia robusta 7,13-copalyl diphosphate synthase, GrTPS2, at 2.1 Å of resolution. GrTPS2 catalyzes the committed reaction in the biosynthesis of grindelic acid, which represents the signature metabolite in species of gumweed (Grindelia spp., Asteraceae). Grindelic acid has been explored as a potential source for drug leads and biofuel production. The GrTPS2 crystal structure adopts the conserved three-domain fold of class II diterpene synthases featuring a functional active site in the γβ-domain and a vestigial α-domain. Substrate docking into the active site of the GrTPS2 apo protein structure predicted catalytic amino acids. Biochemical characterization of protein variants identified residues with impact on enzyme activity and catalytic specificity. Specifically, mutagenesis of Y457 provided mechanistic insight into the position-specific deprotonation of the intermediary carbocation to form the characteristic 7,13 double bond of 7,13-copalyl diphosphate.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

How structural differences influence cross-model consistency: An electric sector case study

Multiple models are often employed to describe a range of possible outcomes for one or more scenarios, yielding insights into causal relationships and their uncertainties. Electric sector capacity expansion scenarios are a common topic of such efforts due to the economic influence of the electric sector, but model results typically span a broad solution space despite efforts to harmonize input assumptions, making decision implications difficult to discern. This study investigates the relationship between input harmonization and cross-model scenario consistency under disparate electric sector scenarios. We compare cross-model consistency between two state-of-the-art electric sector capacity expansion models (GCAM-USA and ReEDS) for six electric sector scenarios comprising alternate assumptions about fossil fuel resource availability, technology innovation, and long-term economy-wide transitions under four harmonization configurations varying model representations of electricity demand, fuel prices, renewable resources, and capacity retirements. These comparisons reveal that cross-model consistency can vary across scenarios under a given harmonization configuration, suggesting that harmonization efforts must often be scenario-specific if comparable cross-model consistency is desired. Model structural differences can hinder consistency, and the impact of these differences can depend on the scenario. Ultimately, thorough harmonization can reveal insights into cross-model consistency, which can be used to tighten uncertainty bounds and improve the decision-making implications of multi-model activities.

Cohen, Stuart↗

Nanoscale Polarization-Dependent Young’s Modulus of Ferroelectric BaTiO 3 Single Crystals

Flexoelectric fields produced by strong strain gradients at the nanoscale couple to ferroelectric polarization, promoting changes in the mechanical properties of ferroelectric materials as a function of the direction of the ferroelectric polarization. In this work, we calculate the asymmetry in the Young’s modulus found in oppositely polarized out-of-plane domains of BaTiO 3 single crystals by means of contact resonance AFM, and we evaluate its impact on the electromechanical response as measured by piezoresponse force microscopy, both using band excitation modes. Furthermore, we analyze the electromechanical response of the different BaTiO 3 domains using k-means to build up their mean elastic and electromechanical features and quantify the flexoelectrically induced modulation of the Young’s modulus. Finally, we discuss the use of contact Kelvin probe force microscope measurements to decouple electrostatic artifacts from purely piezoelectric ones when flexoelectric coupling appears.

BaTiO 3 single crystals↗