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At least 163 records · Page 9

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DOE OSTI2025

Environmental matrix and moisture influence soil microbial phenotypes in a simplified porous media incubation

Soil moisture and porosity regulate microbial metabolism by influencing factors, such as system chemistry, substrate availability, and soil connectivity. However, accurately representing the soil environment and establishing a tractable microbial community that limits confounding variables is difficult. Here, we use a reduced-complexity microbial consortium grown in a glass bead porous media amended with chitin to test the effects of moisture and a structural matrix on microbial phenotypes. Leveraging metagenomes, metatranscriptomes, metaproteomes, and metabolomes, we saw that our porous media system significantly altered microbial phenotypes compared with the liquid incubations, denoting the importance of incorporating pores and surfaces for understanding microbial phenotypes in soils. These phenotypic shifts were mainly driven by differences in expression of Streptomyces and Ensifer, which included a significant decrease in overall chitin degradation between porous media and liquid. Our findings suggest that the success of Ensifer in porous media is likely related to its ability to repurpose carbon via the glyoxylate shunt amidst a lack of chitin degradation byproducts while potentially using polyhydroxyalkanoate granules as a C source. We also identified traits expressed by Ensifer and others, including motility, stress resistance, and carbon conservation, that likely influence the metabolic profiles observed across treatments. Together, these results demonstrate that porous media incubations promote structure-induced microbial phenotypes and are likely a better proxy for soil conditions than liquid culture systems. Furthermore, they emphasize that microbial phenotypes encompass not only the multi-enzyme pathways involved in metabolism but also include the complex interactions with the environment and other community members.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Jets and Jet Substructure at Future Colliders

Even though jet substructure was not an original design consideration for the Large Hadron Collider (LHC) experiments, it has emerged as an essential tool for the current physics program. We examine the role of jet substructure on the motivation for and design of future energy Frontier colliders. In particular, we discuss the need for a vibrant theory and experimental research and development program to extend jet substructure physics into the new regimes probed by future colliders. Jet substructure has organically evolved with a close connection between theorists and experimentalists and has catalyzed exciting innovations in both communities. We expect such developments will play an important role in the future energy Frontier physics program.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Produced Water DNA Database (PW-DNA): Utilizing KBase to generate an environmental specific curated molecular database

The deep subsurface is estimated to host the majority of Earth’s microbial biomass yet remains one of the most challenging environments to access and study. One common approach to investigate these microbial communities is through the analysis of produced water from subsurface reservoirs, where researchers can assess water and gas chemistry along with molecular (DNA/RNA) sequence data. Advances in high-throughput sequencing have greatly expanded our understanding of these environments and their biotechnological potential. However, further progress requires large-scale, integrative meta-analyses across diverse datasets. To address this need, we developed the Produced Water-DNA (PW-DNA) Database, a curated, publicly available resource that consolidates microbial DNA/RNA sequences, geochemical data, and relevant metadata from in situ hydrocarbon environments such as coal beds, oil reservoirs, and natural gas systems. The PW-DNA database delivers three core benefits to the research community: (1) it improves data sharing by linking environmental microbial datasets with corresponding geochemical parameters, enabling more robust filtering and analysis; (2) it connects with complementary research databases to promote broader dissemination and interoperability; and (3) it supports technological innovation by serving as a resource for identifying microbial trends and exploring genetic potential. While individual studies have highlighted basin-specific microbial communities and functional redundancy in biogeochemical cycling, a comprehensive, system-wide perspective is needed to better understand connectivity and novelty across subsurface ecosystems. By designing the PW-DNA in the KBase platform, we provide a reproducible, visual framework for integrating large-scale genomic and geochemical data, enabling researchers to perform more informed analyses and experimental design. Ultimately, this resource enhances the ability to identify, characterize, and interpret microbial functions across diverse subsurface environments, thereby accelerating discovery in subsurface microbiology and biotechnology.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

IoT-based retrofit information diffusion in future smart communities

Community-scale building retrofits are not merely scaled-up versions of single-building retrofits. They involve complex challenges, such as reconciling individual interests with collective goals and managing the dynamic interplay between buildings through mechanisms like power grids and social connections. Internet of Things (IoT) connectivity holds the potential to leverage these interplays to balance individual and collective interests effectively in smart communities. One critical aspect of this interplay is information diffusion, which shapes how retrofit decisions spread among neighbors, influencing individual choices and ultimately impacting community-level retrofit outcomes. In other words, IoT-based smart devices automatically push tailored retrofit notifications to homeowners, which completely changes the format of information diffusion in the future. To investigate this influence by such information diffusion, the study used CityBES to simulate energy performance for different retrofits and applied an information diffusion model to analyze how decisions spread in a networked community of 192 buildings. The diffusion process was modeled on a weighted, directed network, capturing the dynamics of information flow and decision-making across 16 scenarios. Individual retrofit benefits were evaluated through payback years, while community-level retrofit outcomes were assessed using greenhouse gas (GHG) emission reductions. The results demonstrate that easier information diffusion among neighbors encourages households to prioritize retrofit measures that align with the majority’s optimal choices, even at the expense of individual financial benefits. In this case, such collective prioritization enhanced community-level retrofit performance, increasing GHG emission reductions by up to 29.4 %. However, this improvement came with trade-offs, as the average payback period for households extended by approximately 1.74 years. These findings highlight the potential of IoT-based information diffusion in future smart communities to coordinate individual interests with collective goals, ultimately accelerating community-level building retrofits.

Shu, Lei↗

DOE OSTI2021

Assessing dynamic vegetation model parameter uncertainty across Alaskan arctic tundra plant communities

Abstract As the Arctic region moves into uncharted territory under a warming climate, it is important to refine the terrestrial biosphere models (TBMs) that help us understand and predict change. One fundamental uncertainty in TBMs relates to model parameters, configuration variables internal to the model whose value can be estimated from data. We incorporate a version of the Terrestrial Ecosystem Model (TEM) developed for arctic ecosystems into the Predictive Ecosystem Analyzer (PEcAn) framework. PEcAn treats model parameters as probability distributions, estimates parameters based on a synthesis of available field data, and then quantifies both model sensitivity and uncertainty to a given parameter or suite of parameters. We examined how variation in 21 parameters in the equation for gross primary production influenced model sensitivity and uncertainty in terms of two carbon fluxes (net primary productivity and heterotrophic respiration) and two carbon (C) pools (vegetation C and soil C). We set up different parameterizations of TEM across a range of tundra types (tussock tundra, heath tundra, wet sedge tundra, and shrub tundra) in northern Alaska, along a latitudinal transect extending from the coastal plain near Utqiaġvik to the southern foothills of the Brooks Range, to the Seward Peninsula. TEM was most sensitive to parameters related to the temperature regulation of photosynthesis. Model uncertainty was mostly due to parameters related to leaf area, temperature regulation of photosynthesis, and the stomatal responses to ambient light conditions. Our analysis also showed that sensitivity and uncertainty to a given parameter varied spatially. At some sites, model sensitivity and uncertainty tended to be connected to a wider range of parameters, underlining the importance of assessing tundra community processes across environmental gradients or geographic locations. Generally, across sites, the flux of net primary productivity (NPP) and pool of vegetation C had about equal uncertainty, while heterotrophic respiration had higher uncertainty than the pool of soil C. Our study illustrates the complexity inherent in evaluating parameter uncertainty across highly heterogeneous arctic tundra plant communities. It also provides a framework for iteratively testing how newly collected field data related to key parameters may result in more effective forecasting of Arctic change.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

A Peer-to-Peer Market-Based Control Strategy for a Smart Residential Community with Behind-the-Meter Distributed Energy Resources

This paper presents a distributed peer-to-peer market control strategy to manage and to enable resource sharing of behind-the-meter distributed energy resources in a residential community. In the proposed strategy, each consumer or prosumer determines the flexibility of their point of connection to the power network such that the obtained flexibility is network-feasible. Based on the feasible flexibility, the consumers and the prosumers trade power among each other at each time instance to fulfill their preferred load requirements while maximizing their payoffs and helping to regulate node voltages inside the community. Because the problem to be solved is non-convex, a distributed particle swarm optimization algorithm is used to coordinate the consumers/prosumers in a fully autonomous manner without any centralized or hierarchical coordination. Numerical simulations performed on a community of 48 homes demonstrate the efficacy of the proposed approach.

behind-the-meter↗

DOE OSTI2022

A Peer-to-Peer Market-Based Control Strategy for a Smart Residential Community with Behind-the-Meter Distributed Energy Resources: Preprint

behind-the-meter↗

DOE OSTI2023

A Peer-to-Peer Market-Based Control Strategy for a Smart Residential Community with Behind-the-Meter Distributed Energy Resources

This paper presents a distributed peer-to-peer market control strategy to manage and to enable resource sharing of behind-the-meter distributed energy resources in a residential community. In the proposed strategy, each consumer or prosumer determines the flexibility of their point of connection to the power network such that the obtained flexibility is network-feasible. Based on the feasible flexibility, the consumers and the prosumers trade power among each other at each time instance to fulfil their preferred load requirements while maximizing their payoffs and helping to regulate node voltages inside the community. Because the problem to be solved is non-convex, a distributed particle swarm optimization algorithm is used to coordinate the consumers/prosumers in a fully autonomous manner without any centralized or hierarchical coordination. Numerical simulations performed on a community of 48 homes demonstrate the efficacy of the proposed approach.

distributed energy resource↗

DOE OSTI2021

Reduction of the molecular hamiltonian matrix using quantum community detection

Abstract Quantum chemistry is interested in calculating ground and excited states of molecular systems by solving the electronic Schrödinger equation. The exact numerical solution of this equation, frequently represented as an eigenvalue problem, remains unfeasible for most molecules and requires approximate methods. In this paper we introduce the use of Quantum Community Detection performed using the D-Wave quantum annealer to reduce the molecular Hamiltonian matrix in Slater determinant basis without chemical knowledge. Given a molecule represented by a matrix of Slater determinants, the connectivity between Slater determinants (as off-diagonal elements) is viewed as a graph adjacency matrix for determining multiple communities based on modularity maximization. A gauge metric based on perturbation theory is used to determine the lowest energy cluster. This cluster or sub-matrix of Slater determinants is used to calculate approximate ground state and excited state energies within chemical accuracy. The details of this method are described along with demonstrating its performance across multiple molecules of interest and bond dissociation cases. These examples provide proof-of-principle results for approximate solution of the electronic structure problem using quantum computing. This approach is general and shows potential to reduce the computational complexity of post-Hartree–Fock methods as future advances in quantum hardware become available.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Assessing the Viability of Geothermal Microgrid Deployment: A Geospatial Analysis Across the United States

Geothermal microgrids hold a potential of supplying clean and dependable power to communities throughout the United States (US), all while sidestepping the expenses associated with connecting to strained or isolated power grids. Nonetheless, their implementation is still in its early stages in the country. The objective of this analysis is to leverage available data to pinpoint regions across the US that exhibit favorable conditions for the development of geothermal microgrids. Drawing from a variety of sources, including estimates of geothermal resources, the costs associated with geothermal energy generation and electricity transmission, existing microgrid locations, and subsidy programs, we aim to identify promising areas for further exploration. By mapping out the contiguous US, Alaska, and Hawaii, we delineate regions with high relative favorability for geothermal microgrid deployment. Our findings reveal the presence of highly favorable regions across the Western states of the contiguous US, as well as isolated areas in Alaska and Hawaii. Furthermore, we delve into a discussion on state policies and incentive programs, considering their role in fostering favorable conditions or posing barriers to geothermal microgrid development.

Alaska↗

DOE OSTI2021

Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology

Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Editorial: Neuroscience, computing, performance, and benchmarks: Why it matters to neuroscience how fast we can compute

At the turn of the millennium the computational neuroscience community realized that neuroscience was in a software crisis: software development was no longer progressing as expected and reproducibility declined. The International Neuroinformatics Coordinating Facility (INCF) was inaugurated in 2007 as an initiative to improve this situation. The INCF has since pursued its mission to help the development of standards and best practices. In a community paper published this very same year, Brette et al. tried to assess the state of the field and to establish a scientific approach to simulation technology, addressing foundational topics, such as which simulation schemes are best suited for the types of models we see in neuroscience. In 2015, a Frontiers Research Topic “Python in neuroscience” by Muller et al. triggered and documented a revolution in the neuroscience community, namely in the usage of the scripting language Python as a common language for interfacing with simulation codes and connecting between applications. The review by Einevoll et al. documented that simulation tools have since further matured and become reliable research instruments used by many scientific groups for their respective questions. Open source and community standard simulators today allow research groups to focus on their scientific questions and leave the details of the computational work to the community of simulator developers. A parallel development has occurred, which has been barely visible in neuroscientific circles beyond the community of simulator developers: Supercomputers used for large and complex scientific calculations have increased their performance from ~10 TeraFLOPS (10 13 floating point operations per second) in the early 2000s to above 1 ExaFLOPS (10 18 floating point operations per second) in the year 2022. This represents a 100,000-fold increase in our computational capabilities, or almost 17 doublings of computational capability in 22 years. Moore's law (the observation that it is economically viable to double the number of transistors in an integrated circuit every other 18–24 months) explains a part of this; our ability and willingness to build and operate physically larger computers, explains another part. It should be clear, however, that such a technological advancement requires software adaptations and under the hood, simulators had to reinvent themselves and change substantially to embrace this technological opportunity. It actually is quite remarkable that—apart from the change in semantics for the parallelization—this has mostly happened without the users knowing. The current Research Topic was motivated by the wish to assemble an update on the state of neuroscientific software (mostly simulators) in 2022, to assess whether we can see more clearly which scientific questions can (or cannot) be asked due to our increased capability of simulation, and also to anticipate whether and for how long we can expect this increase of computational capabilities to continue.

biophysically detailed models↗

DOE OSTI2022

Knoxville's Community Development Corporation

Develop and field validate integrated retrofit solutions (overclad composite panels, easy-to-install panel connections, and a cost-effective approach to gather measurements of existing facades) that are applicable to residential and mid-size commercial buildings, although components of the retrofit package can be implemented in other buildings.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2022

Ants disperse seeds farther in habitat patches with corridors

Habitat fragmentation impacts ecosystems worldwide through habitat loss, reduced connectivity, and edge effects. Yet, these landscape factors are often confounded, leaving much to be investigated about their relative effects, especially on species interactions. In a landscape experiment, we investigated the consequences of connectivity and edge effects for seed dispersal by ants. We found that ants dispersed seeds farther in habitat patches connected by corridors, but only in patch centers. We did not see an effect on the total number of seeds moved or the rate ants detected seeds. Furthermore, we did not see any differences in ant community composition across patch types, suggesting that shifts in ant behavior or other factors increased ant seed dispersal in patches connected by corridors. Long-distance seed dispersal by ants that requires an accumulation of short-distance dispersal events over generations may be an underappreciated mechanism through which corridors increase plant diversity.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Deep learning techniques to disentangle water use efficiency, climate change, and carbon sequestration across ecosystem scales

Focal Areas: We plan to use machine learning (ML) to disentangle the impact of climate change on plant water use efficiency (WUE) across the leaf level, structured canopy, and community ecosystem scales. Due to the complex behavior of modeling plant WUE’s connection to carbon storage (and hidden co-varying interactions) we suggest that physics-based deep learning must be utilized. The second topic we propose is, based on a better understanding of WUE response to climate change, there is a need to predict how WUE will limit or enhance the recycling of water from transpiration by vegetation back to the land surface worldwide, and thus impact water storage capacity (i.e., natural and reservoirs), using machine learning optimization techniques such as genetic algorithms.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Microbial metabolic dependency and its impacts on the soil carbon cycle (Final Technical Report, DE-SC0016364)

The terrestrial biosphere contains a large fraction of global carbon (C) and nearly 70% of the organic C in terrestrial systems is found in soils. Global changes in atmospheric CO 2 , temperature, precipitation, and ecosystem N inputs, will impact primary production and carbon inputs to soils, but it remains difficult to predict soil responses to these environmental conditions. Our ability to predict C-cycle responses to global change remains limited by unexplained variability within the terrestrial C-cycle. Our difficulty in predicting responses of the soil C-cycle to environmental change suggests a need for a greater understanding of the biotic mechanisms that govern soil C-transformations. Changes in microbial community structure and function have been proposed to impact soil processes, but mechanistic connections between microbial activity and C-cycle transformations remain poorly described. We assembled an interdisciplinary team to conduct cross-scale examination of microbial contributions to C-cycle dynamics and C-fate in soils. We investigated microbial contributions to soil C-transformations using a suite of complementary isotopic techniques including DNA-Stable Isotope Probing (DNA-SIP), metagenomic-SIP, metabolomic-SIP, proteomic-SIP, and microspatial analysis of soil organic C. These techniques were deployed in experiments that tested fundamental assumptions that underlie terrestrial C-cycle models. We characterized the functional characteristics of soil microorganisms responsible for major C-transformations in soil, evaluated the metabolic and ecological interactions that underlie soil C-cycle dynamics, and evaluated the degree to which these interactions impact rates of C mineralization and stabilization in soils.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

The Core-collapse Supernova Sensitivity Machine (Final Technical Report)

Core-collapse supernovae are vital phenomena for understanding the extreme physics of stellar evolution, nuclear interactions, and the origins of elements in the universe. This project developed high-resolution 3D simulations and innovative 1D turbulence models to study the explosion mechanisms, yielding critical insights into the role of turbulence, magnetohydrodynamics, and neutrino physics. The outcomes include enhanced sensitivity analyses connecting nuclear physics inputs to observable supernovae characteristics, tools for the broader research community, and substantial contributions to the training of future scientists.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Community-Driven Methods for Open and Reproducible Software Tools for Analyzing Datasets from Atom Probe Microscopy

Atom probe tomography, and related methods, probe the three-dimensional architecture of a material. The software tools that microscopists use, and how these tools are connected into workflows, makes a substantial contribution to the accuracy and precision of such a material characterization experiment. Typically, we adapt methods from other communities like mathematics, data science, computational geometry, artificial intelligence, or scientific computing. We also realize that improving on research data management is a challenge when it comes to align with the FAIR data stewardship principles. Faced with this global challenge, we are convinced that collaborating is useful. Here, we report the results and challenges with an inter-laboratory call for developing test cases for several types of atom probe software tools. The results support why defining detailed recipes of software workflows and sharing these recipes is necessary and rewarding: Open source tools and (meta)data exchange can help to make our day-to-day data processing tasks become more efficient, the training of new users and knowledge transfer become easier, and assist us with automated quantification of uncertainties to gain access to substantiated results.

36 MATERIALS SCIENCE↗