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At least 91 records · Page 5

Harnessing the Power of Machine Learning and Omics to Identify Environmental Regulation on Microbial Functional Composition for Soil C, N, and P Cycling

Microbial enzyme-mediated soil organic matter (SOM) decomposition regulates many key ecosystem functions, such as elemental cycling, soil carbon sequestration, and soil fertility. However, representing microbial processes in Earth system models (ESMs) remains challenging due to a limited understanding of the spatial patterns of diverse microbial functions responsible for soil carbon (C), nitrogen (N), and phosphorus (P) cycling as well as the underlying mechanisms regulating their relative abundances across various environments. We collected published metagenomics data across the continental US (CONUS) to identify hundreds of microbial genes involved in soil C, N, and P cycling and grouped them into eight enzyme functional classes (EFCs). Each EFC represented a group of gene-encoded potential enzymes that decompose similar soil compounds. By integrating the abundances of omics-informed EFCs with the corresponding environmental information, we trained a machine learning (ML) model to identify key edaphic, climate, and vegetation factors regulating the abundances of each EFC. Quantitative analysis of effects of these factors revealed that the spatial distribution of eight EFCs for soil C, N, and P cycling across CONUS reflected potential resource optimization strategies of microbial communities under nutrient limitation, preferential organic-mineral associations, and climatological stresses. This insight, together with the interpreted ML tool and the CONUS-level benchmark for EFCs abundances, paves the way for parameterizing environmental-regulated microbial functional dynamics in biogeochemical models.

machine learning

Simulating Atmospheric Processes in Earth System Models and Quantifying Uncertainties With Deep Learning Multi‐Member and Stochastic Parameterizations

Abstract Deep learning is a powerful tool to represent subgrid processes in climate models, but many application cases have so far used idealized settings and deterministic approaches. Here, we develop stochastic parameterizations with calibrated uncertainty quantification to learn subgrid convective and turbulent processes and surface radiative fluxes of a superparameterization embedded in an Earth System Model (ESM). We explore three methods to construct stochastic parameterizations: (a) a single Deep Neural Network (DNN) with Monte Carlo Dropout; (b) a multi‐member parameterization; and (c) a Variational Encoder Decoder with latent space perturbation. We show that the multi‐member parameterization improves the representation of convective processes, especially in the planetary boundary layer, compared to individual DNNs. The respective uncertainty quantification illustrates that methods (b) and (c) are advantageous compared to a dropout‐based DNN parameterization regarding the spread of convective processes. Hybrid simulations with our best‐performing multi‐member parameterizations remained challenging and crash within the first days. Therefore, we develop a pragmatic partial coupling strategy relying on the superparameterization for condensate emulation. Partial coupling reduces the computational efficiency of hybrid Earth‐like simulations but enables model stability over 5 months with our multi‐member parameterizations. However, our hybrid simulations exhibit biases in thermodynamic fields and differences in precipitation patterns. Despite this, the multi‐member parameterizations enable improvements in reproducing tropical extreme precipitation compared to a traditional convection parameterization. Despite these challenges, our results indicate the potential of a new generation of multi‐member machine learning parameterizations leveraging uncertainty quantification to improve the representation of stochasticity of subgrid effects.

Behrens, Gunnar [Deutsches Zentrum für Luft‐ und R

Interconnection of Aerosol‐Cloud Interactions and Cloud Feedback Through Warm Rain Process

Recent research has revealed a correlation within the Coupled Model Intercomparison Project Phase 6 (CMIP6) simulations: models exhibiting more pronounced warming due to positive cloud feedback simultaneously show enhanced cooling from aerosol‐cloud interactions (ACI). However, the interplay between ACI and cloud feedback is not well understood in these models. Our study addresses this gap by modifying the autoconversion rate in two Earth system models (ESMs), elucidating how ACI could connect with cloud feedback through the warm rain process. We find that higher autoconversion rates, which are associated with stronger ACI, suppress the increase in cloud liquid water path (LWP) and cloud optical depth with warming by enhancing the precipitation efficiency over the extratropical regions, leading to a larger positive cloud feedback. This study offers new insights into the compensatory mechanism between ACI and cloud feedback through the warm rain process and highlights the importance of constraining the autoconversion parameterization in models.

54 ENVIRONMENTAL SCIENCES

ELM‐MOSART‐DOC: A Large‐Scale Riverine Dissolved Organic Carbon Model and Its Application Over the United States

Riverine dissolved organic carbon (DOC), primarily sourced from soil organic carbon (SOC), plays a crucial role in regional and global carbon cycles. However, the complexities of the underlying mechanisms and limited observations present significant challenges for predictive understanding of DOC at regional or larger scales. Recently, we developed a machine learning‐based (ML) map of DOC transformation rates, bridging the gap between SOC and DOC leaching flux and simplifying terrestrial DOC representation. Building on this advancement, we introduce ELM‐MOSART‐DOC, a DOC module integrated into the riverine component of the Energy Exascale Earth System Model (E3SM)—the Model for Scale Adaptive River Transport (MOSART). ELM‐MOSART‐DOC simulates DOC transport and transformation across both headwater streams and river networks, including those managed. Model validation demonstrates the ability of ELM‐MOSART‐DOC to accurately capture long‐term average DOC concentrations, with Kling‐Gupta Efficiency (KGE) scores of 0.58 and 0.76 at large and local stations, respectively. We further assess the impact of reservoirs through different simulation schemes, revealing that reservoirs significantly alter DOC fluxes by regulating streamflow patterns and promoting DOC mineralization. Model simulations indicate that reservoirs reduce total DOC flux from the Mississippi River into the ocean by 7.5%, with the long‐term average annual export decreasing from 3.34 to 3.14 teragrams (Tg) per year. ELM‐MOSART‐DOC integrates process‐based modeling with ML parameterization to enhance the predictive understanding of riverine biogeochemical processes. This approach reduces uncertainties in modeling regional and global carbon cycle ESMs and provides new insights into carbon cycling and its implications for global environmental change.

Li, Lingbo [Univ. of Houston, TX (United States);

Observed declines in upper ocean phosphate-to-nitrate availability

Climate warming is increasing ocean stratification, which in turn should decrease the nutrient flux to the upper ocean. This may slow marine primary productivity, causing cascading effects throughout food webs. However, observing changes in upper ocean nutrients is challenging because surface concentrations are often below detection limits. We show that the nutricline depth, where nutrient concentrations reach well-detected levels, is tied to productivity and upper ocean nutrient availability. Next, we quantify nutricline depths from a global database of observed vertical nitrate and phosphate profiles to assess contemporary trends in global nutrient availability (1972–2022). We find strong evidence that the P-nutricline (phosphacline) is mostly deepening, especially throughout the southern hemisphere, but the N-nutricline (nitracline) remains mostly stable. Earth System Model (ESM) simulations support the hypothesis that reduced iron stress and increased nitrogen fixation buffer the nitracline, but not phosphacline, against increasing stratification. These contemporary trends are expected to continue in the coming decades, leading to increasing phosphorus but not nitrogen stress for marine phytoplankton, with important ramifications for ocean biogeochemistry and food web dynamics.

54 ENVIRONMENTAL SCIENCES

Developments for Novel Module Architecture for Lower CapEx and Improved Recyclability for c-Si PV Modules

Photovoltaic (PV) energy production is currently increasing at a significant rate. A novel module architecture has been demonstrated that has potential for reducing manufacturing cost while improving module reliability and recycling for c-Si PV which utilizes an edge-seal. Referred to as Edge Sealed Module (ESM), this architecture eliminates the vacuum lamination process and cross-linked encapsulants on the interior of the module. Functioning prototypes of c-Si have been fabricated for stress testing in collaboration with National Renewable Energy Laboratories (NREL). These modules are being tested and compared to traditionally manufactured modules. Based on preliminary results, this module architecture is a potentially viable solution for improving the manufacturing cost and recyclability of PV modules while enhancing module performance.

costs

PCMDI Metrics Package

The Program for Climate Model Diagnosis & Intercomparison (PCMDI) Metrics Package (PMP) is used to provide "quick-look" objective comparisons of Earth System Models (ESMs) with one another and available observations. The PMP provides a diverse suite of analysis utilities each of which produce summary statistics that gauge the consistency between climate model simulations and available observations. The primary application of the PMP is to evaluate simulations from the Coupled Model Intercomparison Project (CMIP). It can also be used to provide objective performance summaries during the model development process as well as selected research purposes.

Ullrich, PaulA [Lawrence Livermore National Labora

PRIME: Protein Representation Inference for Mutation Evaluation

Protein language machine learning models built upon existing ESM-2 model developed by Evolutionary Scale (evolutionaryscale.ai) and an in-house protein language model based on the BERT model developed by Google. The code also includes model training scripts and saved checkpoints from our own training using publicly available SARS-CoV-2 protein sequences.

Gibson, Kaetlyn [Los Alamos National Lab]

PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space

Background Protein language models (PLMs) have revolutionized protein fitness prediction, yet their application to rapidly evolving viral pathogens is often confounded by extreme sequence homology. This homology leads to “data leakage” in standard random validation splits, yielding inflated performance metrics that fail to translate into real-world biosurveillance utility. Results We present Protein Representation Inference for Mutation Evaluation (PRIME), a framework that integrates domain-specific fine-tuning with a rigorous position-stratified validation protocol to evaluate viral threats. Using a dataset of 347,432 SARS-CoV-2 receptor binding domain (RBD) sequences, we demonstrate that while random training data split yields deceptive R 2 values (> 0.90), they fail to generalize to novel mutational sites. By benchmarking models up to 650 M parameters, we show that domain-specific fine-tuning of the ESM-C 600 M model with correctly stratified data provides an initial demonstration of predictive signal for binding affinity and expression at unseen mutational sites of binding affinity and expression on unseen sites (R 2 ~0.23), a significant advancement over base foundation models which exhibit no predictive power (R 2 <0). PRIME’s embedding-based clustering identified 3.03% of bat coronavirus sequences as candidates for further experimental prioritization based on their functional similarity to human-infective strains in embedding space, offering a perspective complementary to traditional phylogenetic methods. Conclusion PRIME establishes a new benchmark for the application of PLMs in pathogen surveillance. Our findings demonstrate that state-of-the-art models and fine-tuning, when paired with stratified validation, provide biologically meaningful insights into pathogen evolution and zoonotic risk.

59 BASIC BIOLOGICAL SCIENCES

Towards provision of regularly updated climate data from the Coupled Model Intercomparison Project

The Coupled Model Intercomparison Project (CMIP) is a flagship of the World Climate Research Programme (WCRP). CMIP has become a recognised ‘brand’ in climate circles evolving over the last thirty years from a targeted research activity by a small number of climate modelling centres intercomparing their Earth System Model (ESM) simulations to a broad international coordinated research effort (Durack et al, 2025). CMIP is organized as a research activity leveraging funded and in-kind contributions from experts within modelling centres and the broader scientific community supported more recently by a fully-funded International Project Office. Within CMIP, Model Intercomparison Projects (MIPs) are community-designed to understand past, present and future climate. CMIP data provides a valuable resource for climate research and is routinely used to assess model representation of climate processes and test scientific hypotheses in the context of model uncertainty and (forced and internal) variability as evident from its prolific use in scientific publications1 . The impact relies on enabling infrastructure (most prominently via the Earth System Grid Federation (ESGF)), which allows sharing of simulation output, provision of the boundary conditions used in each simulation, and definition of the data standards that are essential to facilitating wide use of the data. The impact is supplemented by the wide-ranging scrutiny to which model simulations are subjected. Beyond its use in research, CMIP data is a key resource for communities producing derived climate information from downscaling and impact studies, such as the Coordinated Regional Downscaling Experiment (CORDEX; Gutowski et al., 2016) and the Intersectoral Impacts MIP (ISIMIP; Frieler et al., 2024). Government, academic and commercial entities also increasingly rely on CMIP and its downstream data for climate risk assessments and climate services (for example, Copernicus Climate Change Service and World Bank portal). This means that, although CMIP is a research activity, it increasingly serves a secondary and very relevant role as a provider of climate data – a long-recognised dichotomy (Stevens, 2024). Research and applications have distinct needs, with the former requiring flexibility and generality and the latter consistency. Here we explain how the design of the research activity has been adapted to reduce the burdens imposed by applications and how the research infrastructure might evolve to further enable scientific inquiry. We propose one possible approach to consistently providing model information and projections for applications in the future.

Environmental sciences

Improving North American Wildfire Prediction by Integrating a Machine-Learning Fire Model in a Land Surface Model

Wildfires have shown increasing trends in both frequency and severity across the Contiguous United States (CONUS). However, process-based fire models have difficulties in accurately simulating the burned area over the CONUS due to a simplification of the physical process and cannot capture the interplay among fire, ignition, climate, and human activities. The deficiency of burned area simulation deteriorates the description of fire impact on energy balance, water budget, and carbon fluxes in the Earth System Models (ESMs). Alternatively, machine learning (ML) based fire models, which capture statistical relationships between the burned area and environmental factors, have shown promising burned area predictions and corresponding fire impact simulation. We develop a hybrid framework (ML4Fire-XGB) that integrates a pretrained eXtreme Gradient Boosting (XGBoost) wildfire model with the Energy Exascale Earth System Model (E3SM) land model (ELM) version 2.1. A Fortran-C-Python deep learning bridge is adapted to support online communication between ELM and the ML fire model. Specifically, the burned area predicted by the ML-based wildfire model is directly passed to ELM to adjust the carbon pool and vegetation dynamics after disturbance, which are then used as predictors in the ML-based fire model in the next time step. Evaluated against the historical burned area from Global Fire Emissions Database 5 from 2001-2020, the ML4Fire-XGB model outperforms process-based fire models in terms of spatial distribution and seasonal variations. Sensitivity analysis confirms that the ML4Fire-XGB well captures the responses of the burned area to rising temperatures. The ML4Fire-XGB model has proved to be a new tool for studying vegetation-fire interactions, and more importantly, enables seamless exploration of climate-fire feedback, working as an active component in E3SM.

54 ENVIRONMENTAL SCIENCES

A Multi-Model, Multi-Scale Research Program in Stressors, Responses, and Coupled Systems Dynamics at the Energy-Water-Land Nexus and for Concentrated, Interdependent Infrastructures: Toward Next Generation Capabilities in Integrated Impacts, Adaptation, and Vulnerability (I-IAV) Modeling and a Community of Practice

The goal of this research program was to build a next generation integrated suite of science-driven modeling and analytic capabilities, and a more expanded and connected community of practice, for analyses of the stressors, impacts, adaptations and vulnerabilities of global and regional change. The emphasis was on understanding energy-water-land interactions and feedbacks and interdependent infrastructures at appropriate regional and temporal scales. Although the scope spans many complex facets of data, modeling, and analysis, as well as scales appropriate for integrated impacts and adaptation research, the focus of this effort was the development of multi-model, multi-scale capabilities spanning the domains of Multi-Sector Dynamics (MSD) models; Impact, Adaptation, and Vulnerability (IAV) models; and Earth System Models (ESMs).

54 ENVIRONMENTAL SCIENCES

Advancing Understanding of Deep Convective Anvil Clouds

In this project we use ground-based DOE ARM observations, satellite observations, and Weather Research and Forecasting (WRF) model simulations to arrive at a more complete understanding (or, new theory) of how atmospheric heating profiles in thunderstorm cores drives how quickly air rises in the storms. The rate at which air motion increases or decreases with altitude directly relates to how much cloud mass is ejected laterally into the adjacent atmosphere, which then influences the development and maintenance of “stratiform raining cloud anvils”. Our work has led to new equations connecting the heating in these thunderstorms to these stratiform clouds, with the connection modulated by the stability structure of the atmosphere (i.e., if more stable, then a more rapid change in thunderstorm heating with altitude results in more stratiform cloud, independent of whether over land or ocean, or how organized the thunderstorms are). Improving knowledge of stratiform clouds is important, since they contribute to substantial accumulated rainfall (important to agriculture and local hydrology) as well as radiation, given their large areal extents and lifetime. The radiation impacts likely impact simulated cloud feedback in all Earth System models (ESMs).

54 ENVIRONMENTAL SCIENCES

Advancing the Understanding of Cloud Microphysical Processes and Aerosol Indirect Effects in High-Latitude Mixed-Phase Clouds by Linking ARM Measurements with Climate Model Simulations (Final Report)

The key objectives of this project were to advance our understanding of cloud microphysical characteristics and aerosol indirect effects on mixed-phase clouds in high latitudes. To improve the representation of ice and mixed-phase clouds in Earth System Models (ESMs), we propose an integrated observation and modeling study of cloud macro- and microphysical properties, including spatial heterogeneities, mass partitioning between ice crystals and supercooled liquid water, effects of ice nucleating particles (INPs), and efficiency of secondary ice production (SIP), etc. Specifically, we took four main approaches in this project: (1) examining macro- and microphysical properties of ice and mixed-phase clouds based on in-situ and ground-based observations from multiple field campaigns funded by the U.S. Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) program, including the Mixed-Phase Arctic Cloud Experiment (M-PACE), Indirect and Semi-Direct Aerosol Campaign (ISDAC), Ice Nucleating Particle Sources at Oliktok Point (INPOP), ARM West Antarctic Radiation Experiment (AWARE), Measurements of Aerosols, Radiation, and Clouds over the Southern Ocean (MARCUS), and Macquarie Island Cloud and Radiation Experiment (MICRE); (2) evaluating the DOE Energy Exascale Earth System Model (E3SM) simulations based on observations, particularly for ice and mixed-phase cloud microphysical properties; (3) examining the impacts of INPs on ice and mixed-phase clouds. Specifically, a series of comparisons were conducted using observations over the Arctic, Southern Ocean, and Antarctica, including comparisons between the lower and higher southern latitudes as well as comparisons between the northern and southern hemispheres. In addition, aerosol indirect effects from distinct sources of dust particles were examined; and (4) investigating the impacts of SIP. Ultimately, these results helped to improve cloud microphysics and aerosol-cloud interaction parameterizations in the E3SM model. Overall, the project provided improved understanding regarding various factors, including thermodynamic, dynamic, and aerosol conditions, on the micro- and macrophysical properties of ice and mixed-phase clouds in the high latitudes. Resulting analysis helped to provide an improved physical basis for refining the current cloud microphysics parameterizations related to ice and mixed-phase clouds in E3SM.

54 ENVIRONMENTAL SCIENCES

ARM Cloud and Precipitation Measurements and Science Group (CPMSG) 2024 Workshop Report

The mission of the U.S. Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) user facility is to improve the understanding and representation of cloud and aerosol processes and their interaction with the Earth's surface in Earth system models (ESMs) by providing comprehensive field observations and supporting advanced data analytics. The ARM Cloud and Precipitation Measurements and Science Group (CPMSG) was chartered in March 2019 to help improve the performance and scientific impact of ARM measurements of clouds and precipitation. The group aims to identify and address gaps in measurement capabilities, maximize the scientific impact of ARM data, and effectively serve the scientific community. To achieve these goals, the group includes experts in cloud and precipitation science, as well as representatives from ARM infrastructure, including instrument mentors, engineers, data quality officers, and data product translators. Prior to CPMSG, early discussions on cloud and precipitation measurements primarily focused on improving radar systems, but have since evolved to include a broader scope involving radiometers and other instruments. Since its formation, the CPMSG has gathered feedback using science traceability matrices. CPMSG aims to keep these as living documents to show the measurement needs, scientific drivers, roadblocks, maturity of measurements and retrievals, and pathways to model improvements. The group meets quarterly to discuss and prioritize measurement and operational improvements.

54 ENVIRONMENTAL SCIENCES

ARM Cloud and Precipitation Measurements and Science Group (CPMSG) 2024 Workshop Report

The mission of the U.S. Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) user facility is to improve the understanding and representation of cloud and aerosol processes and their interaction with the Earth's surface in Earth system models (ESMs) by providing comprehensive field observations and supporting advanced data analytics. The ARM Cloud and Precipitation Measurements and Science Group (CPMSG) was chartered in March 2019 to help improve the performance and scientific impact of ARM measurements of clouds and precipitation. The group aims to identify and address gaps in measurement capabilities, maximize the scientific impact of ARM data, and effectively serve the scientific community. To achieve these goals, the group includes experts in cloud and precipitation science, as well as representatives from ARM infrastructure, including instrument mentors, engineers, data quality officers, and data product translators. Prior to CPMSG, early discussions on cloud and precipitation measurements primarily focused on improving radar systems, but have since evolved to include a broader scope involving radiometers and other instruments. Since its formation, the CPMSG has gathered feedback using science traceability matrices. CPMSG aims to keep these as living documents to show the measurement needs, scientific drivers, roadblocks, maturity of measurements and retrievals, and pathways to model improvements. The group meets quarterly to discuss and prioritize measurement and operational improvements.

54 ENVIRONMENTAL SCIENCES