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At least 127 records · Page 7

A global soil plasmidome resource unveils functional and ecological roles of plasmids in soil microbiomes

Plasmids play significant roles in microbial adaptation to ecosystems, yet their dynamics remain poorly understood due to identification challenges. We present the Global Soil Plasmidome Resource (GSPR), a comprehensive dataset of 98,728 plasmid sequences amassed from 6860 terrestrial microbial communities and isolates. We explore this resource through various computational approaches, including phylogenetic diversity analysis, host prediction, and extensive functional annotation, to understand the contribution of plasmids to the genetic and functional diversity in soil, correlating these findings with sample type, as well as the soil habitat they were retrieved from. Our analysis reveals insights into plasmid-encoded functions such as effector modules, quorum sensing, and stress resistance, which may contribute to their persistence and microbial adaptation in soil. Furthermore, CRISPR analysis suggests a prevalent role of these elements related to intra-plasmid competition. By contrasting plasmids from cultivated and uncultivated organisms, we identify important functions that expand existing knowledge of plasmid roles in these habitats. This study represents a notable step forward in elucidating plasmid diversity and function within soil microbiomes and establishes a foundational framework for exploring their roles in natural environments.

Fiamenghi, Mateus B↗

Using the ATLAS experiment software on heterogeneous resources

With the large dataset expected from 2030 onwards by the HL-LHC at CERN, the ATLAS experiment is reaching the limits of the current data processing model in terms of traditional CPU resources based on x86_64 architectures and an extensive program for software upgrades towards the HL-LHC has been set up. The ARM CPU architecture is becoming a competitive and energy efficient alternative. Accelerators like GPUs are available in any recent HPC. In the past years ATLAS has successfully ported its full data processing and simulation software framework Athena to ARM and has invested significant effort in porting parts of the reconstruction and simulation algorithms to GPUs. We report on the successful usage of the ATLAS experiment offline and online software framework Athena on ARM and GPUs through the PanDA workflow management system at various WLCG sites. Furthermore we report on performance optimizations of the builds for ARM CPUs and the GPU integration efforts. We will discuss performance comparisons of different ARM and x86_64 architectures on WLCG resources and Cloud compute providers like GCP and AWS using ATLAS productions workflows as used in the Hep-Score23 benchmark suite.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Small-Scale Irrigation: Improving Food Security under Changing Climate and Water Resource Conditions in Ethiopia

We develop a new systems modeling tool that integrates knowledge from hydrology, agriculture, and economics to understand the effect of small-scale irrigation on food security and groundwater sustainability in Ethiopia. Irrigation is an effective tool to mitigate climate impacts and improve agricultural yields. Small-scale irrigation, such as decentralized groundwater irrigation, is well suited for developing countries where smallholder farming communities are widely dispersed and can only afford small infrastructure investment. We study the underlying interdependencies between food and water systems in Ethiopia, where small-holder agriculture is the foundation of the nation’s economy and climate variability has led to great challenges to its food security. Our coupled market and crop model with groundwater module captures the interdependencies of climate, water availability (including irrigation), crop yield, farmland allocation, crop production, transport and consumption based on a system approach across multiple spatial scales. We study the implication of small-scale irrigation to Ethiopia’s food security and water resource conditions as a “what-if” question by comparing an irrigation scenario to the calibrated baseline in 2015, a year of significant drought and crop failure over a large portion of Ethiopia. Our model offers fresh insights into geographic disparities in outcomes that are driven by baseline climate variability, soil fertility, and market conditions. In general, we find that small-scale irrigation can potentially improve food security through increases in food consumption, but it requires policy support to direct the increases of production to domestic consumption while maintaining a sustainable groundwater condition. By using Ethiopia as an example, we show the strength of our model to study how water infrastructure resources support critical functions and service in water and food systems.

Zhang, Ying↗

Using multiple high-resolution datasets to benchmark the energy exascale earth system model (E3SM) for renewable resource assessment

The United States is accelerating its shift toward a renewable energy system. However, renewable resources, which harness energy from the Earth system, are susceptible to both present-day climate variability and future climate change. For example, variations in regional climate can alter renewable energy production patterns and site viability. The use of high-resolution climate model projections can therefore facilitate and may be critical to long-term planning of renewable energy investments. However, climate models must first be validated for renewable resource assessment. This research employs multiple high-spatiotemporal-resolution datasets to assess the capability of the Department of Energy’s (DOE) Energy Exascale Earth System Model version 2 North American Regionally Refined Model (E3SMv2-NARRM) for predicting multi-year climatological values of solar and wind energy capacity factors in the continental U.S., with a focus on regional and seasonal variability. Present-day E3SMv2-NARRM simulations are compared with reported utility-scale production data obtained from the Energy Information Administration (EIA). In addition, E3SMv2-NARRM data are evaluated against non-climate benchmark models from the National Renewable Energy Laboratory, including the Wind Integration National Dataset Toolkit and the National Solar Radiation Database (NSRDB), as well as three wind energy datasets from PLUSWIND. Our analysis indicates that solar capacity factors from E3SM closely match those from the NSRDB dataset. However, both datasets tend to overestimate values by 10% in comparison to EIA data. Furthermore, biases in wind capacity factors within E3SM are notably pronounced in the West Coast regions, where the seasonal cycle diverges from EIA data.

Energy forecasting, Capacity factor, Renewable ene↗

Population structure limits the use of genomic data for predicting phenotypes and managing genetic resources in forest trees

There is overwhelming evidence that forest trees are locally adapted to climate. Thus, genecological models based on population phenotypes have been used to measure local adaptation, infer genetic maladaptation to climate, and guide assisted migration. However, instead of phenotypes, there is increasing interest in using genomic data for gene resource management. We used whole-genome resequencing and common-garden experiments to understand the genetic architecture of adaptive traits in black cottonwood. We studied the potential of using genome-wide association studies (GWAS) and genomic prediction to detect causal loci, identify climate-adapted phenotypes, and inform gene resource management. We analyzed population structure by partitioning phenotypic and genomic (single-nucleotide polymorphism) variation among 840 genotypes collected from 91 stands along 16 rivers. Most phenotypic variation (60 to 81%) occurred among populations and was strongly associated with climate. Population phenotypes were predicted well using genomic data (e.g., predictive abilityr> 0.9) but almost as well using climate or geography (r> 0.8). In contrast, genomic prediction within populations was poor (r< 0.2). We identified many GWAS associations among populations, but most appeared to be spurious based on pooled within-population analyses. Hierarchical partitioning of linkage disequilibrium and haplotype sharing suggested that within-population genomic prediction and GWAS were poor because allele frequencies of causal loci and linked markers differed among populations. Given the urgent need to conserve natural populations and ecosystems, our results suggest that climate variables alone can be used to predict population phenotypes, delineate seed zones and deployment zones, and guide assisted migration.

Science & Technology - Other Topics↗

Financial-technical co-design for capital-intensive, resource-responsive energy systems

Because of their capital-intensive operation, wind energy systems that are competitive in terms of the cost of the energy that they produce lead to risk-reward trade-offs that make their business cases less favorable than those of conventional energy generation technologies. However, wind energy systems tend to be designed to maximize energy production or minimize cost of energy rather than to maximize their business cases. In this work, we attempt to exploit designs specifically tailored to business cases. We develop a novel framework for analyzing energy systems that ties their design variables to monthly operating incomes using simple models and historical hourly market and resource data. Using this approach, we demonstrate that for a wind site with abundant wind resource in the California Independent System Operator market, we can control the trade-off between mean and 5th percentile monthly returns by choosing the specific power of the turbine at a fixed modeled initial capital cost. Our framework gives a measure of the risk-reward spectrum of energy generation assets that could be built at a given site with respect to the sub-annual resource/market variation.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Investigating resource-efficient neutron/gamma classification ML models targeting eFPGAs

There has been considerable interest and resulting progress in implementing machine learning (ML) models in hardware over the last several years from the particle and nuclear physics communities. A big driver has been the release of the Python package, hls4ml, which has enabled porting models specified and trained using Python ML libraries to register transfer level (RTL) code. So far, the primary end targets have been commercial field-programmable gate arrays (FPGAs) or synthesized custom blocks on application specific integrated circuits (ASICs). However, recent developments in open-source embedded FPGA (eFPGA) frameworks now provide an alternate, more flexible pathway for implementing ML models in hardware. These customized eFPGA fabrics can be integrated as part of an overall chip design. In general, the decision between a fully custom, eFPGA, or commercial FPGA ML implementation will depend on the details of the end-use application. In this work, we explored the parameter space for eFPGA implementations of fully-connected neural network (fcNN) and boosted decision tree (BDT) models using the task of neutron/gamma classification with a specific focus on resource efficiency. We used data collected using an AmBe sealed source incident on Stilbene, which was optically coupled to an OnSemi J-series silicon photomultiplier (SiPM) to generate training and test data for this study. We investigated relevant input features and the effects of bit-resolution and sampling rate as well as trade-offs in hyperparameters for both ML architectures while tracking total resource usage. The performance metric used to track model performance was the calculated neutron efficiency at a gamma leakage of 10 -3 . The results of the study will be used to aid the specification of an eFPGA fabric, which will be integrated as part of a test chip.

47 OTHER INSTRUMENTATION↗

The impact of regional resources and technology availability on carbon dioxide removal potential in the United States

To achieve net zero carbon emissions by mid-century, the United States may need to rely on carbon dioxide removal (CDR) to offset emissions from difficult-to-decarbonize sectors and/or shortfalls in near-term mitigation efforts. CDR can be delivered using many approaches with different requirements for land, water, geologic carbon storage capacity, energy, and other resources. The availability of these resources varies by region in the U.S. suggesting that CDR deployment will be uneven across the country. Using the global change analysis model for the United States (GCAM-USA), we modeled six classes of CDR and explored their potential using four scenarios: a scenario where all the CDR pathways are available (Full Portfolio), a scenario with restricted carbon capture and storage (Low CCS), a scenario where the availability of bio-based CDR options is limited (Low Bio), and a scenario with constraints on enhanced rock weathering (ERW) capabilities (Low ERW). We find that by employing a diverse set of CDR approaches, the U.S. could remove between 1 and 1.9 GtCO 2 /yr by midcentury. In the Full Portfolio scenario, direct air carbon capture and storage (DACCS) predominates, delivering approximately 50% of CO 2 removal, with bioenergy with carbon capture and storage contributing 25%, and ERW delivering 11.5%. Texas and the agricultural Midwest lead in CDR deployment due to their abundant agricultural land and geological storage availability. In the Low CCS scenario, reliance on DACCS decreases, easing pressure on energy systems but increasing pressure on the land. In all cases CDR deployment was found to drive important impacts on energy, land, or materials supply chains (to supply ERW, for example) and these effects were generally more pronounced when fewer CDR technologies were available.

54 ENVIRONMENTAL SCIENCES↗

Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes

Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is still extremely limited. Viral diversity from genomic and metagenomic datasets has led to an explosion of uncultivated virus genomes (UViGs) and the development of specialized databases to catalog this viral diversity, though many lack comprehensive integration. Here, we introduce meta-virus resource (MetaVR), the successor of the IMG/VR database, designed to overcome previous limitations such as large-scale querying and programmatic access. Drawing on the increase of publicly available genomes and metagenomes, MetaVR significantly expands viral diversity, now comprising 24,435,662 UViGs, a 57.6% increase from its predecessor, organized into over 12 million viral operational taxonomic units. Key enhancements include the integration of curated eukaryotic host information, the integration of protein clusters and predicted structures for comparative studies, and an API for programmatic data access. Furthermore, MetaVR features an updated taxonomic framework based on ICTV release 39, assignment to Baltimore classes, and enhanced host assignment through novel computational tools like iPHoP. These advancements position MetaVR as a unique resource for exploring viral diversity, evolution, and host interactions across diverse environments. MetaVR can be freely accessed at https://www.meta-virome.org/.

Fiamenghi, Mateus B↗

Quantified Fast Frequency Response of Inverter-Based Resources for Bulk-Power System Study

Quantifying fast frequency response (FFR) of inverter-based resources (IBRs) is crucial for robust frequency regulation, managing resources, and improving system reliability in the power grids with high penetration levels of IBRs. This paper proposes a concept of frequency response scheme that its response is quantifiable and applicable to the generic IBR models. To achieve this, a stepwise-energy function is derived as a control module by considering operational constraints of IBRs. Then the module is implemented along with generic IBR models in electromagnetic transient (EMT) and electromechanical-based software. To quantify the FFR, the implemented module calculates available incremental active power for a specific time duration. This energy profile is being updated depending on IBR’s operating conditions and is provided into a power grid upon detecting a frequency event. Thus, due to this characteristic, this scheme can quantify the FFR and enable applicable IBRs to provide their available headroom within frequency arrest period. Thereby, this scheme can help estimate IBRs’ frequency response and is more effective in improving the initial frequency response than frequency-dependent control schemes: rate-of-change-of-frequency based and droop-based control schemes. The performance of the proposed scheme was tested under different IBR penetration levels using PSLF and PSCAD simulators.

Kim, Jinho↗

A Large Language Model for Determining Partial Tripping of Distributed Energy Resources

Knowing the status of individual distributed energy resources, i.e., being tripped or not, after a contingency can inform the development of an aggregated DER model. Here, this letter presents a large language model application to determine the partial tripping of distributed energy resources depending on the types, locations, and duration of faults in the transmission network. The large language model, or more specifically BERT-based approach can streamline the fault information into tokenized input, which not only reduces the complexity of the machine learning model but also demonstrates a robust performance with only limited data sets.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

arco (Assembled Resource-Constrained Optimization) [SWR-26-030]

Arco (Assembled Resource-Constrained Optimization) is a memory-smart optimization DSL and solver for LP and MIP problems on constrained hardware. The software is an optimization framework built around a KDL-based domain-specific language and a CLI compiler/solver. You write optimization models in .kdl files, and the arco CLI compiles, validates, inspects, and solves them. Language bindings (Python today, more planned) provide programmatic access to the same engine. Built for harder optimization problems on constrained resources, Arco is intentional about every allocation, careful with stack and heap behavior, and relentless about minimizing memory usage so more systems can run real workloads. Arco is built primarily for internal use within our organization. You are welcome to try it, but we make no guarantees about API stability or robustness at this stage

Sanchez Perez, Pedro Andres [National Laboratory o↗

Clear Sky Tampa Bay: Project and Toolkit Overview - Resilience-Based Resources for Assessing Solar + Storage on Critical Facilities

The Clear Sky Tampa Bay Team, convened by the Tampa Bay Regional Planning Council (TBRPC) and composed of county and city partners, private and public sector stakeholders, solar energy experts, and academic partners, collaboratively developed a set of resources to support the expanded use of solar + storage in the context of community resilience in Florida. Key questions guiding the project included: (1) What types of buildings and systems provide the maximum resilience benefits? (2) Where within our communities should we prioritize future solar + storage analysis or investment to mitigate the impacts of disasters? (3) How might other societal variables be incorporated into a site assessment when considering solar + storage for resilience? (4) Can a standardized process be developed that leverages existing resources to assist local governments with solar + storage for resilience research and decision-making?

14 SOLAR ENERGY↗

Community Planning for Solar: Conducting a Solar Resource and Infrastructure Assessment

This guide describes how to conduct a Solar Resource and Infrastructure Assessment. The guide is designed to assist community officials, volunteers, and regional planning agency staff in conducting a preliminary assessment for a municipality, community, or other jurisdiction, based primarily on a desktop analysis of existing documents and data. The guide provides a process that can be used to inventory and describe existing infrastructure, community needs, and resources from the perspective of solar development planning.

14 SOLAR ENERGY↗

Assessing the Impacts of CO 2 Reduction and Utilization Technologies on Regional Freshwater Resources

This work, a product of the Bioenergy Technologies Office (BETO)-supported multi-lab CO 2 Reduction and Upgrading for e-Fuels Consortium (CO 2 RUe), focuses on advanced research and development and cross-cutting evaluation of environmental, economic, and social sustainability for CO 2 reduction and upgrading for fuels and chemicals. The Consortium develops and de-risks advanced technologies that use renewable electricity to convert CO 2 into e-fuels and commodity chemicals. One key aspect of environmental sustainability consideration is water resources. This report summarizes a three-year study that analyzed the impacts of water consumption in select CO 2 reduction and utilization technologies in two future scenarios using a pair of water indices—water availability index and water stress footprint. The analyses also account for projected electricity grid mixes and their water withdrawal and water consumption demand in grid regions. The work identifies drivers, challenges, and critical areas in water sustainability, along with valuable insights into technological and regional factors. The study also explores the potential of using non-traditional water resources to reduce water stress and increase availability. These findings are intended to support industry stakeholders and BETO with the knowledge needed for informed decision-making, contributing to strategies to mitigate risks associated with the implementation of CO 2 utilization technologies.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

EDX ClaiMM: Digital Resources for the Critical Minerals and Materials Community

Securing critical mineral supply chains is essential for transitioning to a clean energy economy and for maintaining national security. Big-data analytics can serve as a cost-effective means of identifying new domestic critical mineral resources but only if data can be easily located and digested. Using ArcGIS Enterprise Sites, EDX ClaiMM was developed to increase the accessibility of critical minerals data, reducing time spent on data collection and integration. Hosted tools provide rapid visualization and exploration of key datasets, unlocking insights to support resource assessments.

Yesenchak, Rachel↗

Assessing the Impacts of CO 2 Reduction and Utilization Technologies on Regional Freshwater Resources

This work, a product of the Bioenergy Technologies Office (BETO)-supported multi-lab CO 2 Reduction and Upgrading for e-Fuels Consortium (CO 2 RUe), focuses on advanced research and development and cross-cutting evaluation of environmental, economic, and social sustainability for CO 2 reduction and upgrading for fuels and chemicals. The Consortium develops and de-risks advanced technologies that use renewable electricity to convert CO 2 into e-fuels and commodity chemicals. One key aspect of environmental sustainability consideration is water resources. This report summarizes a three-year study that analyzed the impacts of water consumption in select CO 2 reduction and utilization technologies in two future scenarios using a pair of water indices—water availability index and water stress footprint. The analyses also account for projected electricity grid mixes and their water withdrawal and water consumption demand in grid regions. The work identifies drivers, challenges, and critical areas in water sustainability, along with valuable insights into technological and regional factors. The study also explores the potential of using non-traditional water resources to reduce water stress and increase availability. These findings are intended to support industry stakeholders and BETO with the knowledge needed for informed decision-making, contributing to strategies to mitigate risks associated with the implementation of CO 2 utilization technologies.

09 BIOMASS FUELS↗

Enabling Capabilities and Resources: 2024 Principal Investigator Meeting Proceedings

As a major supporter of basic genome-enabled research, BER’s Biological Systems Science Division (BSSD) fosters scientific discovery by funding - fundamental biological research across disciplines in conjunction with enabling investigational tools and computational capabilities that include world-class user facilities. The overarching goal of BSSD is to provide the necessary fundamental science to understand, predict, manipulate, and design biological systems that underpin innovations for bioenergy and bioproduct production and enhance understanding of natural, DOE-relevant environmental processes (Biological Systems Science Division Strategic Plan, 2021). To accelerate the U.S. bioeconomy, BSSD pursues innovative science underpinning advances in sustainable biofuels and bioproducts and the development of next-generation technologies and computational resources for systems biology research. The 2024 BSSD Enabling Capabilities and Resources (ECR) Principal Investigator (PI) meeting brought together PIs across the BSSD ECR portfolio to confer on shared interests and opportunities. The meeting was held concurrently with the Genomic Science program (GSP) PI meeting to optimize collaboration on research to advance bioenergy and the bioeconomy. Rick Stevens of Argonne National Laboratory gave a keynote on How Generative Artificial Intelligence Can Impact Biological Research (see Keynote: How Generative Artificial Intelligence Can Impact Biological Research, this page). Plenary presentations included several joint sessions that illuminated the integration and understanding of the larger BSSD mission. GSP’s objective is to provide systems-level understanding of plants, microbes, and their communities through its Bioenergy Research, Biosystems Design, and Environmental Microbiome Research portfolios. The objective of the ECR portfolio is to support development of computational and instrumental platforms to advance fundamental GSP research—and BER more broadly— toward the overall goal of understanding the functional principles of living systems and their response to environmental challenges.

59 BASIC BIOLOGICAL SCIENCES↗