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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 685 records · Page 38
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

AMORE-Isoprene v1.0: a new reduced mechanism for gas-phase isoprene oxidation

Abstract. Gas-phase oxidation of isoprene by ozone (O3) and the hydroxyl (OH) and nitrate (NO3) radicals significantly impacts tropospheric oxidant levels and secondary organic aerosol formation. The most comprehensive and up-to-date chemical mechanism for isoprene oxidation consists of several hundred species and over 800 reactions. Therefore, the computational expense of including the entire mechanism in large-scale atmospheric chemical transport models is usually prohibitive, and most models employ reduced isoprene mechanisms ranging in size from ∼ 10 to ∼ 200 species. We have developed a new reduced isoprene oxidation mechanism using a directed-graph path-based automated model reduction approach, with minimal manual adjustment of the output mechanism. The approach takes as inputs a full isoprene oxidation mechanism, the environmental parameter space, and a list of priority species which are protected from elimination during the reduction process. Our reduced mechanism, AMORE-Isoprene (where AMORE stands for Automated Model Reduction), consists of 12 species which are unique to the isoprene mechanism as well as 22 reactions. We demonstrate its performance in a box model in comparison with experimental data from the literature and other current isoprene oxidation mechanisms. AMORE-Isoprene's performance with respect to predicting the time evolution of isoprene oxidation products, including isoprene epoxydiols (IEPOX) and formaldehyde, is favorable compared with other similarly sized mechanisms. When AMORE-Isoprene is included in the Community Regional Atmospheric Chemistry Multiphase Mechanism 1.0 (CRACMM1AMORE) in the Community Multiscale Air Quality Model (CMAQ, v5.3.3), O3 and formaldehyde agreement with Environmental Protection Agency (EPA) Air Quality System observations is improved. O3 bias is reduced by 3.4 ppb under daytime conditions for O3 concentrations over 50 ppb. Formaldehyde bias is reduced by 0.26 ppb on average for all formaldehyde measurements compared with the base CRACMM1. There was no significant change in computation time between CRACMM1AMORE and the base CRACMM. AMORE-Isoprene shows a 35 % improvement in agreement between simulated IEPOX concentrations and chamber data over the base CRACMM1 mechanism when compared in the Framework for 0-D Atmospheric Modeling (F0AM) box model framework. This work demonstrates a new highly reduced isoprene mechanism and shows the potential value of automated model reduction for complex reaction systems.

58 GEOSCIENCES↗
DOE OSTI2020

Computational Methods in Heterogeneous Catalysis

The unprecedented ability of computations to probe atomic-level details of catalytic systems holds immense promise for the fundamentals-based bottom-up design of novel heterogeneous catalysts, which are at the heart of the chemical and energy sectors of industry. Here, we critically analyze recent advances in computational heterogeneous catalysis. First, we will survey the progress in electronic structure methods and atomistic catalyst models employed, which have enabled the catalysis community to build increasingly intricate, realistic, and accurate models of the active sites of supported transition-metal catalysts. We then review developments in microkinetic modeling, specifically mean-field microkinetic models and kinetic Monte Carlo simulations, which bridge the gap between nanoscale computational insights and macroscale experimental kinetics data with increasing fidelity. Here, we finally review the advancements in theoretical methods for accelerating catalyst design and discovery. Throughout the review, we provide ample examples of applications, discuss remaining challenges, and provide our outlook for the near future.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Uncovering heterogeneous intercommunity disease transmission from neutral allele frequency time series

The COVID-19 pandemic has underscored the need for accurate epidemic forecasting to predict pathogen spread, evolution, and evaluate intervention strategies. Forecast reliability hinges on detailed knowledge of disease transmission across population segments, which may be inferred from contact surveys or mobility data. However, these indirect approaches make it difficult to estimate rare transmissions between socially or geographically distant communities. We show that the steep ramp-up of genome sequencing surveillance during the pandemic can be leveraged to directly identify transmission patterns between geographically defined communities. Our approach uses a hidden Markov model to infer the fraction of infections a community imports from others based on how rapidly allele frequencies in the focal community converge to those in the donor communities. Applying this method to SARS-CoV-2 sequencing data from England and the United States, we uncover networks of intercommunity transmission that reflect geographical relationships while exposing significant long-range interactions. The scaling of importation rate with distance is consistent across both countries, yet weaker than expected based on mobility data, highlighting limitations of indirect inference. We show that transmission patterns can change between waves of variants of concern and analyze how the inferred heterogeneity in intercommunity transmission impacts evolutionary forecasts. While applied here to geographically defined communities, our approach could be applied to those defined by other traits (e.g., age, socioeconomic status), provided time-series data can be stratified accordingly. Overall, our study highlights population genomic time series data as a crucial record of epidemiological interactions, which can be deciphered using tree-free inference methods.

Okada, Takashi [Department of Physics; University ↗
DOE OSTI2024

Performance evaluation of the USGS velocity model for the San Francisco Bay Area

In this study, we evaluated the performance of the United States Geological Survey velocity model developed for the San Francisco Bay Area (SFBA), version 21.1. The evaluation was performed through high-resolution three-dimensional physics-based ground motion simulations of seven small-magnitude earthquakes (ranging from magnitude 3.8 to 4.4) that occurred on the eastern side of the San Francisco Bay. The simulations were performed in the frequency range from 0 to 5 Hz with a minimum shear-wave velocity of 250 m/s, which allowed the capture of wave propagation effects of the near-surface soft materials that characterize local basins. Based on the direct comparison of Fourier amplitude spectra between recorded and simulated ground motions for more than 250 stations, we found that the velocity model generally performs well in the frequency range of 0.2–5 Hz. The median value of the Fourier amplitude residuals was found to be near zero for all seven earthquakes. The slight over-prediction of 0.2 log-natural units at frequencies above 3 Hz in our simulations was attributed to the potentially inaccurate representation of the source radiation pattern by a double-couple point source model, and simple representation of shallow small-scale underground structural complexity in the velocity model. Maps of spectral amplitude differences between the simulated and recorded data were used to identify areas responsible for systematic ground motion over-predictions or under-predictions. For example, while some sub-domains over soft sediments show over-prediction patterns, the block east of the Hayward fault is prone to exhibit patterns of under-prediction. These maps can be used to guide future refinements of the SFBA velocity model. Since our simulation methodology allows for the decoupling of the source and wave propagation effects, the ground motion data generated by our simulations can also be used to quantify the epistemic uncertainty due to the velocity model, in empirically based ground motion estimates for the SFBA.

58 GEOSCIENCES↗
DOE OSTI2025

The Aerosol Model Benchmarking Repository: A toolkit for model intercomparison

The Aerosol Model Benchmarking Repository and Standards (AMBRS) project was initiated to provide tools and to establish community standards for benchmarking aerosol models. This report describes a set of open-source tools for building, running, and analyzing aerosol box model simulations in a standardized framework. The framework consists of three core components: AMBuilder, a CMake-based build system that compiles supported models consistently; AMBRS, a Python module that defines unified numerical experiments and executes them with aligned inputs; and PyParticle, an aerosol analysis package that standardizes output, computes diagnostics, and visualizes simulation results. Together, these tools enable reproducible intercomparison of aerosol schemes and support process-level evaluation of how model simplifications affect predictions of size distributions, cloud condensation nuclei activity, and other relevant properties relevant for the Earth-Energy system. Beyond its role in benchmarking, AMBRS provides a platform for studying aerosol processes across scales and can be used to generate training data for AI/ML applications in support of a broader hierarchical aerosol modeling strategy.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Harmonization of global land use change and management for the period 850–2100 (LUH2) for CMIP6

Abstract. Human land use activities have resulted in large changes to the biogeochemical and biophysical properties of the Earth's surface, with consequences for climate and other ecosystem services. In the future, land use activities are likely to expand and/or intensify further to meet growing demands for food, fiber, and energy. As part of the World Climate Research Program Coupled Model Intercomparison Project (CMIP6), the international community has developed the next generation of advanced Earth system models (ESMs) to estimate the combined effects of human activities (e.g., land use and fossil fuel emissions) on the carbon–climate system. A new set of historical data based on the History of the Global Environment database (HYDE), and multiple alternative scenarios of the future (2015–2100) from Integrated Assessment Model (IAM) teams, is required as input for these models. With most ESM simulations for CMIP6 now completed, it is important to document the land use patterns used by those simulations. Here we present results from the Land-Use Harmonization 2 (LUH2) project, which smoothly connects updated historical reconstructions of land use with eight new future projections in the format required for ESMs. The harmonization strategy estimates the fractional land use patterns, underlying land use transitions, key agricultural management information, and resulting secondary lands annually, while minimizing the differences between the end of the historical reconstruction and IAM initial conditions and preserving changes depicted by the IAMs in the future. The new approach builds on a similar effort from CMIP5 and is now provided at higher resolution (0.25∘×0.25∘) over a longer time domain (850–2100, with extensions to 2300) with more detail (including multiple crop and pasture types and associated management practices) using more input datasets (including Landsat remote sensing data) and updated algorithms (wood harvest and shifting cultivation); it is assessed via a new diagnostic package. The new LUH2 products contain > 50 times the information content of the datasets used in CMIP5 and are designed to enable new and improved estimates of the combined effects of land use on the global carbon–climate system.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Evaluating the Hybrid Modelling Competition: A Step Towards Developing Good Modelling Practice

Hybrid modelling, a combination of mechanistic and data-driven modelling, is a promis¬ing approach to advance current mathematical models towards improved deci¬sion support tools for today's water-related challenges. Researchers have been develop¬ing guidelines or references for good modelling practices in the water field for mecha¬nistic (Rieger et al., 2012) and data-driven (Zhu et al., 2023) modelling, respectively. However, good modelling practices for hybrid modelling are currently missing (Schneider et al., 2022). Therefore, the International Water Association’s (IWA) hybrid modelling working group initiated the first competition on a data science competition platform (i.e. Kaggle) for water resource recovery modelling at the Watermatex con¬ference in September 2023 in Quebec. The main objective of this competition was to gain insights and experience to create good modelling practices. Further goals were to motivate students, researchers, and practitioners model, foster a vibrant and engaged community, and evaluate the efficacy of com¬petitions in solving modelling challenges within the water domain. Our next goal is that facilities will measure and gather relevant data for future competitions to solve their challenges from a modeller’s perspective.

Schneider, Mariane↗
DOE OSTI2026

Conditional distribution estimation of building characteristics with diffusion models for urban energy modeling

Understanding current energy consumption behavior in communities is critical for informing future energy use decisions and enabling efficient energy management. Urban energy models, which are used to simulate these energy use patterns, require large datasets with detailed building characteristics for accurate outcomes. However, such detailed characteristics at the individual building level are often unknown and costly to acquire, or unavailable. Through this work, we propose using a generative modeling approach to generate realistic building attributes to fill in the data gaps and finally provide complete characteristics as inputs to energy models. Our model learns complex, building-level patterns from training on a large-scale residential building stock model containing 2.2 million buildings. We employ a tabular diffusion-based framework that is designed to handle heterogeneous (discrete and continuous) features in tabular building data, such as occupancy, floor area, heating, cooling, and other equipment details. We develop a capability for conditional diffusion, enabling the imputation of missing building characteristics conditioned on known attributes. We conduct a comprehensive validation of our conditional diffusion model, firstly by comparing the generated conditional distributions against the underlying data distribution, and secondly, by performing a case study for a Baltimore residential region, showing the practical utility of our approach. Our work is one of the first to demonstrate the potential of generative modeling to accelerate building energy modeling workflows.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2026

Roadmap for the future of extreme wildfire events

Background Extreme wildfire events (EWEs) represent a growing threat globally, posing substantial risks to ecosystems, human communities, and infrastructure. Despite increased recognition of their ecological, social, and economic significance, current definitions of EWEs vary widely, reflecting disciplinary biases and regional contexts. This article emerges from an interdisciplinary workshop convened to reassess and refine the definition of EWEs, examine their impacts across ecological and social dimensions, and identify critical knowledge gaps impeding our understanding of these infrequent but important events. Results Our synthesis highlights significant limitations with existing definitions, particularly their reliance on subjective thresholds and their emphasis on extreme fire behavior alone. EWEs encompass a spectrum of complex, multi-dimensional phenomena that extend beyond immediate biophysical characteristics to include cumulative social, economic, and ecological impacts. These impacts often manifest over extended timeframes and include hazardous environmental contamination, severe geomorphic disturbances, ecosystem transformations, and unintended consequences of post-fire management actions. Current wildfire modeling frameworks inadequately capture these compounding factors, particularly the interactions among social systems, ecological conditions, and extreme fire behavior. To overcome these issues, we advocate for an interdisciplinary and context-sensitive approach to defining and studying EWEs. This revised definition emphasizes wildfires exhibiting anomalies in fire behavior, ecological outcomes, or social impacts relative to historically observed baselines, accommodating variability across different geographic regions and ecological settings. Conclusions Adopting an interdisciplinary framework that integrates biophysical and social sciences will enhance the predictive capability of wildfire models and improve resilience planning and response strategies. Filling identified knowledge gaps—such as limited high-quality empirical fire behavior data and insufficient integration of social dynamics into modeling—will better prepare communities and ecosystems to cope with and adapt to EWEs. This inclusive approach underscores the necessity for collaboration across disciplines and sectors, essential to managing extreme wildfires in an era of increasing climatic and ecological uncertainty.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Stabilized Hyperfoam Modeling of the General Plastics EF4003 (3 PCF) Flexible Foam

Constitutive model parameterizations for the General Plastics EF4003 low density 3 pound per cubic foot are needed for design and qualification purposes in normal and abnormal mechanical simulations. The material is expected to be deformed in two ways: first during preloading, and second under impact conditions of the system (transient dynamic). All analyses are to be performed at room temperature. The goal is to provide the analysis community a robust constitutive model parameterization to represent the compression behavior of the EF4003 foam from small deformations up to massive compressive deformations when the foam is densifying. It is worth noting the EF4003 exhibits anisotropy in its stress-strain behavior between the rise and transverse directions (See figure 2.8c-d) as well as plateau behavior that is very likely to cause material stability issues, due to the buckling transition, (and has historically done so) when using Sandia’s current workhorse models for flexible foams, Hyperfoam and Flex Foam. A Stability-informed Hyperfoam parameterization procedure is developed and executed to calibrate a hyperfoam model for the EF4003 room temperature, transversely loaded data. A rise orientation parameterization was not attempted due to localization in the experiments.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Documenting numerical experiments in support of the Coupled Model Intercomparison Project Phase 6 (CMIP6)

Abstract. Numerical simulation, and in particular simulation of the earth system, relies on contributions from diverse communities, from those who develop models to those involved in devising, executing, and analysing numerical experiments. Often these people work in different institutions and may be working with significant separation in time (particularly analysts, who may be working on data produced years earlier), and they typically communicate via published information (whether journal papers, technical notes, or websites). The complexity of the models, experiments, and methodologies, along with the diversity (and sometimes inexact nature) of information sources, can easily lead to misinterpretation of what was actually intended or done. In this paper we introduce a taxonomy of terms for more clearly defining numerical experiments, put it in the context of previous work on experimental ontologies, and describe how we have used it to document the experiments of the sixth phase for the Coupled Model Intercomparison Project (CMIP6). We describe how, through iteration with a range of CMIP6 stakeholders, we rationalized multiple sources of information and improved the clarity of experimental definitions. We demonstrate how this process has added value to CMIP6 itself by (a) helping those devising experiments to be clear about their goals and their implementation, (b) making it easier for those executing experiments to know what is intended, (c) exposing interrelationships between experiments, and (d) making it clearer for third parties (data users) to understand the CMIP6 experiments. We conclude with some lessons learnt and how these may be applied to future CMIP phases as well as other modelling campaigns.

Pascoe, Charlotte (ORCID:0000000223616778)↗
DOE OSTI2025

Organic molecules are deterministically assembled in variably inundated river sediments, but drivers remain unclear

Dissolved organic matter (DOM) is central to ecosystem function. A fundamental challenge is understanding the processes leading to variation in the chemistry of organic molecules that comprise DOM. Here we study these processes in variably inundated riverbed sediments, as an understudied, yet ubiquitous component of rivers. Using null-model approaches adopted from community ecology, we found that within-site variation in environmental conditions caused non-random (i.e., deterministic) shifts in DOM chemistry. Deterministic shifts were observed across diverse biomes, though the strength of determinism varied substantially. We found that the strength of determinism decreased with increasing sediment moisture, but in the form of a constraint space. Many systems fell below the upper constraint boundary, however. We propose a conceptual model based on our results and other publications in which DOM assemblages are hypothesized to be increasingly deterministic across the continuum from the river water column to saturated sediment pore spaces to unsaturated and dry soils/sediments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Predicting secondary organic aerosol phase state and viscosity and its effect on multiphase chemistry in a regional-scale air quality model

Atmospheric aerosols are a significant public health hazard and have substantial impacts on the climate. Secondary organic aerosols (SOAs) have been shown to phase separate into a highly viscous organic outer layer surrounding an aqueous core. This phase separation can decrease the partitioning of semi-volatile and low-volatile species to the organic phase and alter the extent of acid-catalyzed reactions in the aqueous core. A new algorithm that can determine SOA phase separation based on their glass transition temperature (T g ), oxygen to carbon (O:C) ratio and organic mass to sulfate ratio, and meteorological conditions was implemented into the Community Multiscale Air Quality Modeling (CMAQ) system version 5.2.1 and was used to simulate the conditions in the continental United States for the summer of 2013. SOA formed at the ground/surface level was predicted to be phase separated with core–shell morphology, i.e., aqueous inorganic core surrounded by organic coating 65.4 % of the time during the 2013 Southern Oxidant and Aerosol Study (SOAS) on average in the isoprene-rich southeastern United States. Our estimate is in proximity to the previously reported ~70 % in literature. The phase states of organic coatings switched between semi-solid and liquid states, depending on the environmental conditions. The semi-solid shell occurring with lower aerosol liquid water content (western United States and at higher altitudes) has a viscosity that was predicted to be 10 2 –10 12 Pa s, which resulted in organic mass being decreased due to diffusion limitation. Organic aerosol was primarily liquid where aerosol liquid water was dominant (eastern United States and at the surface), with a viscosity <10 2 Pa s. Phase separation while in a liquid phase state, i.e., liquid–liquid phase separation (LLPS), also reduces reactive uptake rates relative to homogeneous internally mixed liquid morphology but was lower than aerosols with a thick viscous organic shell. The sensitivity cases performed with different phase-separation parameterization and dissolution rate of isoprene epoxydiol (IEPOX) into the particle phase in CMAQ can have varying impact on fine particulate matter (PM 2.5 ) organic mass, in terms of bias and error compared to field data collected during the 2013 SOAS. This highlights the need to better constrain the parameters that govern phase state and morphology of SOA, as well as expand mechanistic representation of multiphase chemistry for non-IEPOX SOA formation in models aided by novel experimental insights.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

cabbi-bio/BECT-ABM

The emergence of the cellulosic bioeconomy requires not only adequate technological, economic, and policy advances, but also effective communication and coordination among the multiple stakeholders in the bioeconomy community. Aiming to facilitate stakeholder communication and collaboration for cellulosic bioeconomy growth, an agent-based model is developed as a community communication tool in this study. The tool simulates the behaviors and interactions of key stakeholders, as well as the responses and interactions between the stakeholders and biophysical, socioeconomic, and environmental conditions. The agent behavior rules are developed and validated based on behavior and economic theories and information attained from a stakeholder focus group study and a land use survey.

Yang, Pan↗
DOE OSTI2022

New Lightning-Derived Vertical Total Electron Content Data Provide Unique Global Ionospheric Measurements

A newly released, novel ionospheric data set of global gridded vertical total electron content (VTEC) is introduced in this paper. This VTEC data set, provided by Los Alamos National Laboratory (LANL), is derived from very high frequency (VHF; defined as 30–300 MHz) broadband radio-frequency (RF) measurements of lightning made by U.S. Department of Defense sensing systems on board Global Positioning System (GPS) satellites. This paper presents the new data set (LANL VTEC), discusses the errors inherent in VHF TEC estimation due to ionospheric dispersion, and compares the LANL VTEC to two community standard VTEC gridded products: Jet Propulsion Laboratory's Global Ionospheric Model (JPL GIM) and the CEDAR community's Open Madrigal VTEC gridded measurements of L-band GNSS (global navigation satellite systems) TEC. We find that the LANL VTEC data have an offset of 3 TECU from CEDAR Madrigal GNSS VTEC and a full-width-half-maximum (FWHM) of 6 TECU. In comparison, the offset between LANL VTEC and the JPL GIM model is –3 TECU, but with a FWHM of 5 TECU. We also compare to Jason-3 VTEC measurements over the ocean, finding an offset of less than 0.5 TECU and an FWHM of <5 TECU. Because this technique uses a completely different methodology to determine TEC, the sources of errors are distinct from the typical ground-based GNSS L-band (GHz) TEC measurements. Also, because it is derived from RF lightning signals, this data set provides measurements in regions that are not well covered by ground-based GPS measurements, such as over oceans and over central Africa.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Enhancing power grid resilience to winter storms via generator winterization with equity considerations

Here we develop two-stage stochastic programming models for generator winterization that enhance power grid resilience while incorporating social equity. The first stage in our models captures the investment decisions for generator winterization, and the second stage captures the operation of a degraded power grid, with the objective of minimizing load shed and social inequity. To incorporate equity into our models, we propose a concept called adverse effect probability that captures the disproportionate effects of power outages on communities with varying vulnerability levels. Grid operations are modeled using DC power flow, and equity is captured through mean or maximum adverse effects experienced by communities. We apply our models to a synthetic Texas power grid, using winter storm scenarios created from the generator outage data from the 2021 Texas winter storm. Our extensive numerical experiments show that more equitable outcomes, in the sense of reducing adverse effects experienced by vulnerable communities during power outages, are achievable with no impact on total load shed through investing in winterization of generators in different locations and capacities.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2024

Models, data, and scripts associated with “Prediction of Distributed River Sediment Respiration Rates using Community-Generated Data and Machine Learning”

This data package is associated with the publication “Prediction of Distributed River Sediment Respiration Rates using Community-Generated Data and Machine Learning’’ submitted to the Journal of Geophysical Research: Machine Learning and Computation (Scheibe et al. 2024). River sediment respiration observations are expensive and labor intensive to obtain and there is no physical model for predicting this quantity. The Worldwide Hydrobiogeochemisty Observation Network for Dynamic River Systems (WHONDRS) observational data set (Goldman et al.; 2020) is used to train machine learning (ML) models to predict respiration rates at unsampled sites. This repository archives training data, ML models, predictions, and model evaluation results for the purposes of reproducibility of the results in the associated manuscript and community reuse of the ML models trained in this project. One of the key challenges in this work was to find an optimum configuration for machine learning models to work with this feature-rich (i.e. 100+ possible input variables) data set. Here, we used a two-tiered approach to managing the analysis of this complex data set: 1) a stacked ensemble of ML models that can automatically optimize hyperparameters to accelerate the process of model selection and tuning and 2) feature permutation importance to iteratively select the most important features (i.e. inputs) to the ML models. The major elements of this ML workflow are modular, portable, open, and cloud-based, thus making this implementation a potential template for other applications. This data package is associated with the GitHub repository found at Please see the file level metadata (flmd; “sl-archive-whondrs_flmd.csv”) for a list of all files contained in this data package and descriptions for each. Please see the data dictionary (dd; “sl-archive-whondrs_dd.csv”) for a list of all column headers contained within comma separated value (csv) files in this data package and descriptions for each. The GitHub repository is organized into five top-level directories: (1) “input_data” holds the training data for the ML models; (2) “ml_models” holds machine learning models trained on the data in “input_data”; (3) “scripts” contains data preprocessing and postprocessing scripts and intermediate results specific to this data set that bookend the ML workflow; (4) “examples” contains the visualization of the results in this repository including plotting scripts for the manuscript (e.g., model evaluation, FPI results) and scripts for running predictions with the ML models (i.e., reusing the trained ML models); (5) “output_data” holds the overall results of the ML model on that branch. Each trained ML model resides on its own branch in the repository; this means that inputs and outputs can be different branch-to-branch. Furthermore, depending on the number of features used to train the ML models, the preprocessing and postprocessing scripts, and their intermediate results, can also be different branch-to-branch. The “main-*” branches are meant to be starting points (i.e. trunks) for each model branch (i.e. sprouts). Please see the Branch Navigation section in the top-level README.md in the GitHub repository for more details. There is also one hidden directory “.github/workflows”. This hidden directory contains information for how to run the ML workflow as an end-to-end automated GitHub Action but it is not needed for reusing the ML models archived here. Please the top-level README.md in the GitHub repository for more details on the automation.

13C↗
DOE OSTI2021

Multisubstrate DNA stable isotope probing reveals guild structure of bacteria that mediate soil carbon cycling

Significance Soil organic matter contains a large fraction of global C whose fate is largely governed by soil microbial communities. Global C-cycle models can be improved using information about microbial processes in soil, but the inner workings of soil communities remain largely hidden from view. We used stable isotopes to characterize the guild structure of soil bacteria based on how they assimilated C from different sources. Guild structure corresponded with growth dynamics and rrn copy number. We also show that this guild structure explains microbial biogeographical patterns at continental and global scales. These results suggest that microbial contributions to soil C cycling are largely governed by an anabolic process that governs energy allocation to growth, competition, and survival.

59 BASIC BIOLOGICAL SCIENCES↗