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At least 1,405 records · Page 78

Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton

ABSTRACT Metagenomics is a powerful method for interpreting the ecological roles and physiological capabilities of mixed microbial communities. Yet, many tools for processing metagenomic data are neither designed to consider eukaryotes nor are they built for an increasing amount of sequence data. EukHeist is an automated pipeline to retrieve eukaryotic and prokaryotic metagenome-assembled genomes (MAGs) from large-scale metagenomic sequence data sets. We developed the EukHeist workflow to specifically process large amounts of both metagenomic and/or metatranscriptomic sequence data in an automated and reproducible fashion. Here, we applied EukHeist to the large-size fraction data (0.8–2,000 µm) from Tara Oceans to recover both eukaryotic and prokaryotic MAGs, which we refer to as TOPAZ (Tara Oceans Particle-Associated MAGs). The TOPAZ MAGs consisted of >900 environmentally relevant eukaryotic MAGs and >4,000 bacterial and archaeal MAGs. The bacterial and archaeal TOPAZ MAGs expand upon the phylogenetic diversity of likely particle- and host-associated taxa. We use these MAGs to demonstrate an approach to infer the putative trophic mode of the recovered eukaryotic MAGs. We also identify ecological cohorts of co-occurring MAGs, which are driven by specific environmental factors and putative host-microbe associations. These data together add to a number of growing resources of environmentally relevant eukaryotic genomic information. Complementary and expanded databases of MAGs, such as those provided through scalable pipelines like EukHeist, stand to advance our understanding of eukaryotic diversity through increased coverage of genomic representatives across the tree of life. IMPORTANCE Single-celled eukaryotes play ecologically significant roles in the marine environment, yet fundamental questions about their biodiversity, ecological function, and interactions remain. Environmental sequencing enables researchers to document naturally occurring protistan communities, without culturing bias, yet metagenomic and metatranscriptomic sequencing approaches cannot separate individual species from communities. To more completely capture the genomic content of mixed protistan populations, we can create bins of sequences that represent the same organism (metagenome-assembled genomes [MAGs]). We developed the EukHeist pipeline, which automates the binning of population-level eukaryotic and prokaryotic genomes from metagenomic reads. We show exciting insight into what protistan communities are present and their trophic roles in the ocean. Scalable computational tools, like EukHeist, may accelerate the identification of meaningful genetic signatures from large data sets and complement researchers’ efforts to leverage MAG databases for addressing ecological questions, resolving evolutionary relationships, and discovering potentially novel biodiversity.

59 BASIC BIOLOGICAL SCIENCES↗

Laboratory Investigations of Aerosol-Cloud Interactions in an Entraining, Turbulent Environment (Final Technical Report)

The effects that aerosol particles have on clouds in Earth’s atmosphere and the role that clouds play in determining the fate of aerosol particles play a crucial role in determining the human experience on this planet. These interwoven interactions can determine whether it rains or snows, is comfortable, hot or cold, or whether the cloud you gaze at in the sky looks like a tiger or a lump of porridge. How clouds mix with the air surrounding them, a process known as entrainment, further affects these processes. We conducted laboratory experiments of aerosol-cloud interactions in a setting in which we can measure the effects of entrainment – the first laboratory experiments since the pioneering work of Latham and Reed in 1977. We measured the effects of entrainment on aerosol-cloud interactions in the Pi Chamber and also used a state-of-the-art large eddy simulation (LES) to investigate processes in fine detail.

54 ENVIRONMENTAL SCIENCES↗

Resource-Efficient Chemistry on Quantum Computers with the Variational Quantum Eigensolver and The Double Unitary Coupled-Cluster approach

Applications of quantum simulation algorithms to obtain electronic energies of molecules on noisy intermediate-scale quantum (NISQ) devices require careful consideration of resources describing the complex electron correlation effects. In modeling second-quantized problems, the biggest challenge confronted is that the number of qubits scales linearly with the size of molecular basis. This poses a significant limitation on the size of the basis sets and the number of correlated electrons included in quantum simulations of chemical processes. To address this issue and to enable more realistic simulations on NISQ computers, we employ the double unitary coupled-cluster (DUCC) method to effectively downfold correlation effects into the reduced-size orbital space, commonly referred to as the active space. Using downfolding techniques, we demonstrate that properly constructed effective Hamiltonians can capture the effect of the whole orbital space in small-size active spaces. Combining the downfolding pre-processing technique with the Variational Quantum Eigensolver, we solve for the ground-state energy of H2 and Li2 in the cc-pVTZ basis using the DUCC-reduced active spaces. We compare these results to full configuration-interaction and high-level coupled-cluster reference calculations.

quantum computing, variational quantum solver, cou↗

Studies on Workability of Geopolymer Solidification - 18171

In Japan, intermediate-level radioactive waste, such as spent resin, is solidified and set in sealed containers without venting. To reduce the amount of hydrogen generated due to water radiolysis in stored intermediate-level waste, geopolymer solidification has been studied. Geopolymer solidification is an excellent method for conditioning intermediate-level waste from the viewpoint of its high thermal stability and low processing cost. However, it has a problem that the apparent viscosity increases drastically a few minutes after the onset of setting. This may cause some trouble in the process of pouring the geopolymer into drums and mixing it with waste. In this study, in order to control the workability of a geopolymer mixture, we investigated the effects of the compounding ratio and the kinds of chemical agents used. We confirmed that the geopolymer reaction was slowed down by reducing the amount of calcium and adding boron. The uniaxial compressive strength of the geopolymer was 3-80 MPa. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

WPTO Comprehensive References [Poster]

Protecting hydroelectric plants from incidents that adversely impact their cyber-physical systems presents unique challenges due to the plants’ widely dispersed geographic locations and varied configurations as well as the relative nascent nature of the cyberattacks targeting these facilities. To help hydroelectric plants better respond to and mitigate cybersecurity incidents, this Department of Energy Water Power Technologies Office Cyber Comprehensive Reference list is to be used at a hydroelectric plant to quickly go to appropriate sources during the response and recovery of a cyber incident. In addition to this product, there are three other products meant to be distributed to a hydroelectric plant to assist in their cyber incident response and recovery. The first, a report on the processes of building a R&R flip book based on a large set of existing guidance. The second, a handy flip book meant to be distributed to hydroelectric plants to assist them during a cybersecurity incident occurring on a hydroelectic plant. And the third is a correlated alignment of the steps an hydroelectric plant operator would take for both a cyber incident as well as an emergency response process if the event rises to a cyber incident affecting the safe and reliable operations of a hydroelectric plant.

13 HYDRO ENERGY↗

SplitML

SplitML (Signal Processing Library for Interference rejecTion by Machine Learning) is a code repository for a set of tools for interference rejection in complex time-domain signals. The goal of the tools is to provide machine learning modeling capabilities for rejecting interference. Recent related machine learning algorithms for signal processing have focused mostly on speech enhancement or multi-speaker speech separation; the tools in SplitML will extend these innovations to generic time-domain signals of interest. SplitML includes tools for generating synthetic noisy signals, code for customized machine learning models applicable to interference rejection, and tools for evaluating such algorithms against standard signal processing techniques. These components are written in Python, a high-level programming language that takes advantage of the Python ecosystem of high-quality open-source packages for machine learning and signal processing.

Klein, Natalie↗

An atomic orbital-based formulation of the complete active space self-consistent field method on graphical processing units

Despite its importance, state-of-the-art algorithms for performing complete active space self-consistent field (CASSCF) computations have lagged far behind those for single reference methods. We develop an algorithm for the CASSCF orbital optimization that uses sparsity in the atomic orbital (AO) basis set to increase the applicability of CASSCF. Our implementation of this algorithm uses graphical processing units (GPUs) and has allowed us to perform CASSCF computations on molecular systems containing more than one thousand atoms. Additionally, we have implemented analytic gradients of the CASSCF energy; the gradients also benefit from GPU acceleration as well as sparsity in the AO basis.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Framework for the Evolution of Heuristics in Advanced Manufacturing

Here, in this study, we work toward addressing a knowledge gap in understanding how heuristics are developed, retrieved, employed, and modified by designers. Having a better awareness of one’s own set of heuristics can be beneficial for relaying to other team members, improving a team’s training processes, and aiding others on their path to design expertise. The ability to understand and justify the use of a heuristic should lead to more effective decision-making in systems design. To do this, the heuristics and their characteristics must be extracted using a repeatable scientific research methodology. This study describes a unique extraction and characterization process compared to prior literature. It includes some of the first work towards documenting heuristics for both designers and operators in a hybrid manufacturing setting. Eight participants performed a series of two design journals, two interviews, and one survey. Heuristics were extracted and refined between each method and then verified by participants in the survey. The surveys produced novel statistically significant findings in regard to heuristic characterizations, impacting how participants view how often a heuristic is used, the reliability of the heuristic, and the evolution of the heuristic. Lastly, an alternate perspective of heuristics as an error management bias is highlighted and discussed.

42 ENGINEERING↗

Development and Use of an Ultra-High Resolution Electron Scattering Apparatus

In this LDRD project, we developed a versatile capability for high-resolution measurements of electron scattering processes in gas-phase molecules, such as ionization, dissociation, and electron attachment/detachment. This apparatus is designed to advance fundamental understanding of these processes and to inform predictions of plasmas associated with applications such as plasma-assisted combustion, neutron generation, re-entry vehicles, and arcing that are critical to national security. We use innovative coupling of electron-generation and electron-imaging techniques that leverages Sandia’s expertise in ion/electron imaging methods. Velocity map imaging provides a measure of the kinetic energies of electrons or ion products from electron scattering in an atomic or molecular beam. We designed, constructed, and tested the apparatus. Tests include dissociative electron attachment to O2 and SO2, as well as a new method for studying laser-initiated plasmas. This capability sets the stage for new studies in dynamics of electron scattering processes, including scattering from excited-state atoms and molecules.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Developing evidence-based prescriptive ventilation rate standards for commercial buildings in California: a proposed framework

Background - The goal of this project, with a focus on commercial buildings in California, was to develop a new framework for evidence-based minimum ventilation rate (MVR) standards that protect occupants in buildings while also considering energy use and cost. This was motivated by research findings suggesting that current prescriptive MVRs in commercial buildings do not provide occupants with fully safe and satisfactory indoor environments. Methods - The project began with a broad review in several areas ? the diverse strategies now used for standards or guidelines for MVRs or for environmental contaminant exposures, current knowledge about adverse human effects associated with VRs, and current knowledge about contaminants in commercial buildings, including their their presence, their adverse human effects, and their relationships with VRs. Based on a synthesis of the reviewed information, new principles and approaches are proposed for setting evidence-based VRs standards for commercial buildings, considering a range of human effects including health, performance, and acceptability of air. Results ? A review and evaluation is first presented of current approaches to setting prescriptive building ventilation standards and setting acceptable limits for human contaminant exposures in outdoor air and occupational settings. Recent research on approaches to setting acceptable levels of environmental exposures in evidence-based MVR standards is also described. From a synthesis and critique of these materials, a set of principles for setting MVRs is presented, along with an example approach based on these principles. The approach combines two sequential strategies. In a first step, an acceptable threshold is set for each adverse outcome that has a demonstrated relationship to VRs, as an increase from a (low) outcome level at a high reference ventilation rate (RVR, the VR needed to attain the best achievable levels of the adverse outcome); MVRs required to meet each specific outcome threshold are estimated; and the highest of these MVRs, which would then meet all outcome thresholds, is selected as the target MVR. In a second step, implemented only if the target MVR from step 1 is judged impractically high, costs and benefits are estimated and this information is used in a risk management process. Four human outcomes with substantial quantitative evidence of relationships to VRs are identified for initial consideration in setting MVR standards. These are: building-related symptoms (sometimes called sick building syndrome symptoms), poor perceived indoor air quality, and diminished work performance, all with data relating them directly to VRs; and cancer and non-cancer chronic outcomes, related indirectly to VRs through specific VR-influenced indoor contaminants. In an application of step 1 for offices using a set of example outcome thresholds, a target MVR of 9 L/s (19 cfm) per person was needed. Because this target MVR was close to MVRs in current standards, use of a cost/benefit process seemed unnecessary. Selection of more stringent thresholds for one or more human outcomes, however, could raise the target MVR to 14 L/s (30 cfm) per person or higher, triggering the step 2 risk management process. Consideration of outdoor air pollutant effects would add further complexity to the framework. For balancing the objective and subjective factors involved in setting MVRs in a cost-benefit process, it is suggested that a diverse group of stakeholders make the determination after assembling as much quantitative data as possible.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Situating Green Infrastructure in Context: A Framework for Adaptive Socio‐Hydrology in Cities

Abstract Management of urban hydrologic processes using green infrastructure (GI) has largely focused on storm water management. Thus, design and implementation of GI usually rely on physical site characteristics and local rainfall patterns, and do not typically account for human or social dimensions. This traditional approach leads to highly centralized storm water management in a disconnected urban landscape and can deemphasize additional benefits that GI offers, such as increased property value, greenspace aesthetics, heat island amelioration, carbon sequestration, and habitat for biodiversity. We propose the Framework for Adaptive Socio‐Hydrology (FrASH) in which GI planning and implementation moves from a purely hydrology‐driven perspective to an integrated sociohydrological approach. This allows for an iterative, multifaceted decision‐making process that would enable a network of stakeholders to collaboratively set a dynamic, context‐guided project plan for the installation of GI, rather than a “one‐size‐fits‐all” installation. We explain how different sectors (e.g., governance, nongovernmental organizations, communities, academia, and industry) can create a connected network of organizations that work toward a common goal. Through a graphical Chambered Nautilus model, FrASH is experimentally applied to contrasting GI case studies and shows that this multistakeholder, connected, decentralized network with a coevolving decision‐making project plan results in enhanced multifunctionality, potentially allowing for the management of resilience in urban systems at multiple scales.

Schifman, L. A.↗

Ultrafast Spin-to-Charge Conversion at the Surface of Topological Insulator Thin Films

Strong spin–orbit coupling, resulting in the formation of spin–momentum–locked surface states, endows topological insulators with superior spin–to–charge conversion characteristics, though the dynamics that govern it have remained elusive. Here, an all–optical method is presented, which enables unprecedented tracking of the ultrafast dynamics of spin–to–charge conversion in a prototypical topological insulator Bi 2 Se 3 /ferromagnetic Co heterostructure, down to the sub–picosecond timescale. Compared to pure Bi 2 Se 3 or Co, a giant terahertz emission is observed in the heterostructure that originates from spin–to–charge conversion, in which the topological surface states play a crucial role. A 0.12 ps timescale is identified that sets a technological speed limit of spin–to–charge conversion processes in topological insulators. Additionally, it is shown that the spin–to–charge conversion efficiency is temperature independent in Bi 2 Se 3 as expected from the nature of the surface states, paving the way for designing next–generation high–speed optospintronic devices based on topological insulators at room temperature.

36 MATERIALS SCIENCE↗

Identifying hydrologic signatures associated with streamflow depletion caused by groundwater pumping

Abstract Groundwater pumping can reduce streamflow in nearby waterways (‘streamflow depletion’), a process which must be accounted for in integrated management of surface and groundwater resources. However, causal identification of streamflow depletion from hydrographs alone is challenging because pumping impacts are masked by other drivers of hydrologic variability. To identify potential indicators of streamflow depletion, we used synthetic hydrographs and an analytical streamflow depletion model to assess potential pumping impacts on specific hydrograph characteristics (‘hydrologic signatures’) for 215 streamgages spanning the conterminous United States (CONUS). We found that streamflow depletion commonly impacts signatures associated with seasonal and annual low flows and low flow recessions. The largest impacts occurred during dry years, suggesting streamflow depletion may be evident in dry years even where impacts are unmeasurable in wet years. Random forest models indicated that streamflow depletion could significantly impact Annual, Summer, and Fall signatures in most streams. Our finding that multiple hydrologic signatures are consistently responsive to streamflow depletion across CONUS suggests that the underlying hydrological processes linking pumping to streamflow reductions are consistent across diverse settings, information that will aid in identifying indicators of streamflow depletion from streamflow hydrographs.

Lapides, Dana A.↗

Studies of new Higgs boson interactions through nonresonant $HH$ production in the $ b\overline{b}\gamma \gamma $ final state in $pp$ collisions at $ \sqrt{s} $ = 13 TeV with the ATLAS detector

A search for nonresonant Higgs boson pair production in the $ b\overline{b}\gamma \gamma $ final state is performed using 140 fb –1 of proton-proton collisions at a centre-of-mass energy of 13 TeV recorded by the ATLAS detector at the CERN Large Hadron Collider. This analysis supersedes and expands upon the previous nonresonant ATLAS results in this final state based on the same data sample. The analysis strategy is optimised to probe anomalous values not only of the Higgs (H) boson self-coupling modifier κλ but also of the quartic HHVV (V = W, Z) coupling modifier κ 2V . No significant excess above the expected background from Standard Model processes is observed. An observed upper limit μHH < 4.0 is set at 95% confidence level on the Higgs boson pair production cross-section normalised to its Standard Model prediction. The 95% confidence intervals for the coupling modifiers are –1.4 < κ λ < 6.9 and –0.5 < κ 2V < 2.7, assuming all other Higgs boson couplings except the one under study are fixed to the Standard Model predictions. The results are interpreted in the Standard Model effective field theory and Higgs effective field theory frameworks in terms of constraints on the couplings of anomalous Higgs boson (self-)interactions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A dual mesh method with adaptivity for stress-constrained topology optimization

This paper is concerned with the topological optimization of elastic structures, with the goal of minimizing the compliance and/or mass of the structure, subject to a stress constraint. It is well known that depending upon the geometry and the loading conditions, the stress field can exhibit singularities, if these singularities are not adequately resolved, the topological optimization process will be ineffective. For computational efficiency, adaptive mesh refinement is required to adequately resolve the stress field. This poses a challenge for the traditional Solid Isotropic Material with Penalization (SIMP) method that employs a one-to-one correspondence between the finite element mesh and the optimization design variables because as the mesh is refined, the optimization process must somehow be re-started with a new set of design variables. The proposed solution here is a dual mesh approach, one finite element mesh defines the material distribution, a second finite element mesh is used for the computation of the displacement and stress fields. This allows for stress-based adaptive mesh refinement without modifying the definition of the optimization design variables. A second benefit of this dual mesh approach is that there is no need to apply a filter to the design variables to enforce a length scale, instead the length scale is determined by the design mesh. This reduces the number of design variables and allows the designer to apply spatially varying length scale if desired. The efficacy of this dual mesh approach is established via several stress-constrained topology optimization problems.

36 MATERIALS SCIENCE↗

A deep learning model for automatic analysis of cavities in irradiated materials

Transmission electron microscopy (TEM) is a commonly used technique in materials science for defect investigation. Quantitative analysis of defects is important for understanding the properties of a material, but manual analysis of TEM micrographs can be time-consuming and prone to error, especially when the defects have irregular shapes rather than spherical shapes. Many existing methods or deep learning models do not handle a wide range of sizes for the same object type within a single image. In this work, we present a framework that enables users to train an instance segmentation model called Mask R- CNN on any microstructure dataset, perform multi-detection on the same image at different scales, and obtain properties (e.g., size, area) of the objects based on the desired shape (e.g., circle, ellipse, rectangle). Additionally, we have developed a parallel detection module that uses multiple GPUs to increase the efficiency of the object detection process. We demonstrate the capabilities of our framework using a set of TEM images of cavities with different shapes, size distributions, and background contrasts. Finally, we show that the performance of our model in terms of density, size, and swelling of the cavities is comparable to the human average and that our model achieves the highest recall value compared to existing methods due to the use of image multi-rescaling.

36 MATERIALS SCIENCE↗

Model-based compositional predictions for a differential scanning calorimetry/thermogravimetric analysis-mass spectrometry system used for heat of vaporization measurements

A Differential Scanning Calorimetry/Thermogravimetric Analysis (DSC/TGA) procedure for determination of Heat of Vaporization (HOV) of fuel and surrogate fuel mixtures has been previously utilized for evaluation of oxygenate impacts on spark ignition fuels. This analysis has been further leveraged with mass spectrometry (MS) to elucidate vapor phase compositional changes during evaporation. In this study we focus on a simple system of three compounds (ethanol, n-hexane, and n-octane) to provide a model-based understanding of the evaporation process under these experimental conditions. An Aspen Plus model was set up to provide liquid and vapor phase concentration predictions during mixture evaporation using the initial mixture composition, and measured temperature and mass loss profiles from DSC/TGA experiments. Agreements between the trends of the MS ion count profiles and model composition predictions provide a degree of validation of this modeling approach that can allow the interpretation and extrapolation of DSC/TGA measurements for more complex fuel mixtures.

33 ADVANCED PROPULSION SYSTEMS↗

Additive manufacturing of AISI M2 tool steel by binder jetting (BJ): Investigation of microstructural and mechanical properties

The presented research demonstrates for the first time the successful processing of AISI M2 tool steel by binder jetting, a promising additive manufacturing technique capable of producing complex shapes with minimal residual stresses and isotropic properties. The optimal printing parameters were explored by varying processing parameters such as the binder saturation (45 %–105 %), binder set time (0 to 10 s), targeted bed temperature (50–60 °C), oscillator (2600–2750 rpm), recoater (20–28 mm/s), and roller speeds (200–300 rpm). Microstructural characterization and evaluation of mechanical properties of binder jetted parts were performed using x-ray diffraction (XRD), scanning electron microscopy (SEM), and energy dispersive spectroscopy (EDS) to study their chemical composition, powder morphology, microstructure, carbide morphologies, relative density, hardness, compressive strength, and ductility. Two powder sizes (5 and 10 μm) were used, and sintering was performed at varying temperatures (1270, 1280, and 1300 °C) and durations (60 and 120 min), followed by a furnace, air, and water cooling. An optimum hardness of ~970 HV was obtained when parts were sintered at 1270 °C for 60 min, followed by water quenching. Impressive compressive strength of ~ 3580 MPa was observed in the sample sintered at 1280 °C for 60 min duration, followed by air cooling. Furnace-cooled parts showed the highest density of ~95 %, whereas the relative density of air- and water-cooled parts varied between ~91 to 93.50 %, respectively. The microstructure of sintered samples revealed the formation of M 6 C stable carbide, M 2 C metastable carbide, MC as a secondary carbide, and a-Fe matrix, which contributed to the observed increase in mechanical properties.

36 MATERIALS SCIENCE↗