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DOE OSTI2023

Status of genome function annotation in model organisms and crops

Abstract Since the entry into genome‐enabled biology several decades ago, much progress has been made in determining, describing, and disseminating the functions of genes and their products. Yet, this information is still difficult to access for many scientists and for most genomes. To provide easy access and a graphical summary of the status of genome function annotation for model organisms and bioenergy and food crop species, we created a web application ( https://genomeannotation.rheelab.org ) to visualize, search, and download genome annotation data for 28 species. The summary graphics and data tables will be updated semi‐annually, and snapshots will be archived to provide a historical record of the progress of genome function annotation efforts. Clear and simple visualization of up‐to‐date genome function annotation status, including the extent of what is unknown, will help address the grand challenge of elucidating the functions of all genes in organisms.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

A new efficient grain growth model using a random Gaussian-sampled mode filter

This paper presents the use of a Gaussian neighborhood mode filter for predicting grain growth in a manner similar to the solutions obtained by a Monte Carlo Potts model. This flexible grain growth model can quickly utilize modern, computationally optimized data science strategies on graphics processing units to simulate grain growth up to 100 times faster than the state-of-the-art, publicly available Monte Carlo Potts model. We show that, given the correct neighborhood, the mode filter can replicate normal grain growth in two or three dimensions. In addition, the paper briefly demonstrates the ability to model limited anisotropic in grain boundary energy and mobility. Anisotropic grain boundary energy is modeled by defining a weighted mode filter operation. Anisotropic grain boundary mobility is modeled by scaling and orienting the Gaussian neighborhood in a particular direction.

Anisotropy↗

DOE OSTI2025

JAX-CanVeg: A Differentiable Land Surface Model

Land surface models consider the exchange of water, energy, and carbon along the soil-canopy-atmosphere continuum, which is challenging to model due to their complex interdependency and associated challenges in representing and parameterizing them. Differentiable modeling provides a new opportunity to capture these complex interactions by seamlessly hybridizing process-based models with deep neural networks (DNNs), benefiting both worlds, that is, the physical interpretation of process-based models and the learning power of DNNs. Here, we developed a differentiable land model, JAX-CanVeg. The new model builds on the legacy CanVeg by incorporating advanced functionalities through JAX in the graphic processing unit support, automatic differentiation, and integration with DNNs. We demonstrated JAX-CanVeg's hybrid modeling capability by applying the model at four flux tower sites with varying aridity. To this end, we developed a hybrid version of the Ball-Berry equation that emulates the water stress impact on stomatal closure to explore the capability of the hybrid model in (a) improving the simulations of latent heat fluxes (LE) and net ecosystem exchange (NEE), (b) improving the optimization trade-off when learning observations of both LE and NEE, and (c) benefiting a multi-layer canopy model setup. Our results show that the proposed hybrid model improved the simulations of LE and NEE at all sites, with an improved optimization trade-off over the process-based model. Additionally, the multi-layer canopy set benefited hybrid modeling at some sites. Anchored in differentiable modeling, our study provides a new avenue for modeling land-atmosphere interactions by leveraging the benefits of both data-driven learning and process-based modeling.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Evaluating Process Costs and Performance Metrics of Granular Activated Carbon for the Removal of PFAS Under Model Uncertainty

The data is contained within an oral presentation with graphical results of PFAS process simulation pertaining to an ongoing WaterTAP analysis.

Barber, Hunter↗

DOE OSTI2021

FY21 Progress Report: SRNL Analysis of ICCWR LCM and WAMS data for Corrosion and Cracking

The development of algorithms for machine learning and data analysis for the 3013 Surveillance Program is a collaborative effort by the Savannah River National Laboratory (SRNL) and the University of South Carolina (USC). For corrosion detection, Laser Confocal Microscope (LCM) or Wide Area 3D Measurement System (WAMS) data is extracted from large binary files, with software written to convert the data to physical attributes (e.g., height, color and grayscale values; all as functions of a location in a plane projection). A user-friendly Matlab Graphical User Interface (GUI) that reads data from either LCM or WAMS files was developed to integrate input data with software developed for processing and evaluation. The GUI can selectively download binary data, interrogate data attributes, label data, flag significant features, execute Machine Learning (ML) algorithms, output parameters for trained ML algorithms, report ML model accuracy with respect to labeled data, and generate graphical representations for various analyses. Features can be called out by user-specified thresholds, manual labeling or machine learning algorithms when they have been completed. The ability to rapidly label data is important because of the volume of data required for training machine learning algorithms. The GUI has the flexibility to allow addition of improved ML algorithms, methods for data visualization, and statistical computations. Statistical analyses via the GUI include areas of pits within a defined range of pit depths, correlations between Red-Green-Blue (RGB) or grayscale intensity and relative surface height, covariances between values associated with features, and feature histograms. The development of supervised machine learning algorithms, however, has been hindered by a lack of training data. The machine learning algorithms for crack identification are being refined but require improvements to the true positive rate for crack detection. This shortcoming is an artifact of the limited training data currently available, perhaps more so than the structure of the neural networks. At present, the best results are had from a consensus over an ensemble of randomly generated Deep Neural Network (DNN) or Convolutional Neural Network (CNN) algorithms. Although the consensus accuracy method has yielded optimum true positive and true negative rates in excess of 80%, additional validation testing is necessary. In addition to the suite of LCM data that was initially used, and which represents the majority of the work presented in this report, WAMS image data was also reviewed at a preliminary level. The review included a comparison between image resolution and dynamic range for each method. WAMS (ZON file) image data was found to have a pixel pitch of 3.69μm compared to 1 μm for the LCM (vk4 file) data, which implies a lower resolution for the WAMS images. Conversely, the ratio of dynamic range of the WAMS data to the LCM data was approximately 41:20 for height data, suggesting that information from WAMS should more accurately determine the depth of pits. At present, the significance of the greater dynamic range of the WAMS data relative to the LCM data has not yet been evaluated.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2022

FY22 Progress Report: SRNL Analysis of ICCWR LCM and WAMS Data for Corrosion and Cracking

Algorithms for machine learning and data analysis for the 3013 Surveillance Program are being developed in an ongoing collaborative effort by the Savannah River National Laboratory (SRNL) and the University of South Carolina (USC). To detect the presence of corrosion and cracking, data is collected from large binary files generated by a Laser Confocal Microscope (LCM) or Wide Area 3D Measurement System (WAMS). Software is being developed to use the physical attributes in the data files (e.g., height, color, and grayscale values; all as functions of a location in a plane projection) to detect the presence of surface corrosion and cracking. A user-friendly Matlab Graphical User Interface (GUI) that reads data from either LCM or WAMS files was developed to integrate input data with software developed for processing and evaluation. The GUI can selectively download binary data, interrogate data attributes, label data for training ML algorithms, flag significant features, execute Machine Learning (ML) algorithms, output parameters from trained ML algorithms, report ML model accuracy with respect to labeled data, and generate graphical representations for various analyses. Surface defects can be called out by setting user-specified thresholds, feature based analysis or machine learning algorithms. Enhancements to data labeling capability have been developed to address this essential precursor to application of ML routines. Efficient labeling is particularly important in view of the very large volume of data required to train ML algorithms.

3013 Corrosion↗

DOE OSTI2023

Uncertainty Quantification of PV Annual Energy Estimates in the System Advisor Model

This work will detail a proposed uncertainty quantification method for PV annual energy estimates. Motivations behind the proposed methodology will be discussed, including the frequent underperformance of installed PV systems to calculated probability of exceedance values being seen in industry. A methodology in which uncertainty factors correlated to different parts of the PV annual energy model chain are applied to annual energy estimates in conjunction with uncertainty from inter-annual solar resource variability will be described. The application of this methodology in the System Advisor Model (SAM) will also be discussed with example cases and graphical outputs of the probability of exceedance data calculated for the PV annual energy estimates.

energy modeling↗

DOE OSTI2021

Measurement of the inclusive and differential Higgs boson production cross sections in the leptonic WW decay mode at $\sqrt{s} =$ 13 TeV

Measurements of the fiducial inclusive and differential production cross sections of the Higgs boson in proton-proton collisions at $ \sqrt{s} $ = 13 TeV are performed using events where the Higgs boson decays into a pair of W bosons that subsequently decay into a final state with an electron, a muon, and a pair of neutrinos. The analysis is based on data collected with the CMS detector at the LHC during 2016–2018, corresponding to an integrated luminosity of 137 fb$^{−1}$. Production cross sections are measured as a function of the transverse momentum of the Higgs boson and the associated jet multiplicity. The Higgs boson signal is extracted and simultaneously unfolded to correct for selection efficiency and resolution effects using maximum-likelihood fits to the observed distributions in data. The integrated fiducial cross section is measured to be 86.5 ± 9.5 fb, consistent with the Standard Model expectation of 82.5 ± 4.2 fb. No significant deviation from the Standard Model expectations is observed in the differential measurements.[graphic not available: see fulltext]

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

First measurement of large area jet transverse momentum spectra in heavy-ion collisions

Jet production in lead-lead (PbPb) and proton-proton (pp) collisions at a nucleon-nucleon center-of-mass energy of 5.02 TeV is studied with the CMS detector at the LHC, using PbPb and pp data samples corresponding to integrated luminosities of 404 μb$^{−1}$ and 27.4 pb$^{−1}$, respectively. Jets with different areas are reconstructed using the anti-k$_{T}$ algorithm by varying the distance parameter R. The measurements are performed using jets with transverse momenta (p$_{T}$) greater than 200 GeV and in a pseudorapidity range of |η| < 2. To reveal the medium modification of the jet spectra in PbPb collisions, the properly normalized ratio of spectra from PbPb and pp data is used to extract jet nuclear modification factors as functions of the PbPb collision centrality, p$_{T}$ and, for the first time, as a function of R up to 1.0. For the most central collisions, a strong suppression is observed for high-p$_{T}$ jets reconstructed with all distance parameters, implying that a significant amount of jet energy is scattered to large angles. The dependence of jet suppression on R is expected to be sensitive to both the jet energy loss mechanism and the medium response, and so the data are compared to several modern event generators and analytic calculations. The models considered do not fully reproduce the data.[graphic not available: see fulltext]

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2026

Ground and excited state gradients with end-to-end differentiable semiempirical quantum chemistry

Accurate and efficient gradients of molecular energy with respect to nuclear degrees of freedom are essential for geometry optimization and molecular dynamics, including simulations that go beyond the Born–Oppenheimer regime. A common approach involves deriving analytical formulas for new electronic structure methods, which is often conceptually difficult and requires tedious coding. Here, we implement analytical, semi-numerical, and automatic differentiation (AD)-based gradient pathways for semiempirical Hamiltonian models in the PYSEQM software package, leveraging both graphics processing unit (GPU) and central processing unit (CPU) architectures. We further extend these capabilities to excited states calculated using the configuration interaction singles and time-dependent Hartree–Fock ansätze. We benchmark wall time, peak memory usage, and accuracy across three molecular families of varying chemical complexity, including systems of up to a thousand atoms. For ground-state simulations, analytical and AD gradients achieve near-identical GPU runtimes, while semi-numerical gradients are slower on GPU but remain competitive on CPU. For excited states, both analytical and custom AD approaches using implicit differentiation show similar performance and low memory requirements, whereas gradients with full AD are memory-limited. AD gradients match analytical ones in accuracy across all tested systems, aided by a quaternion-based diatomic frame rotation for two-center quantities that ensures smooth energy surfaces. Overall, automatic differentiation emerges as a practical alternative to analytical gradients in semiempirical quantum chemistry, offering high accuracy while allowing seamless integration in AI-driven workflows and popular packages, such as PyTorch and JAX. Our results provide actionable guidance for selecting optimal gradient strategies in large-scale ground- and excited-state molecular dynamics simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Spatial Environmental Assessment Tool (SEAT)

SAND2024-08551O The Spatial Environmental Assessment Tool (SEAT) evaluates potential environmental risk associated with marine energy device deployment by coupling modeled impacts with risk severity maps. As a graphical user interface-based software, it interacts with marine energy stressor and receptor data to evaluate the risk of changes to marine environment. SEAT, which relies on spatial and temporal data, is a plug-in for geospatial software QGIS. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Chartrand, Chris↗

DOE OSTI2021

Multiphysics coupling in the Exascale computing project

Multiphysics coupling presents a significant challenge in terms of both computational accuracy and performance. Achieving high performance on coupled simulations can be particularly challenging in a high-performance computing context. The US Department of Energy Exascale Computing Project has the mission to prepare mission-relevant applications for the delivery of the exascale computers starting in 2023. Many of these applications require multiphysics coupling, and the implementations must be performant on exascale hardware. In this special issue we feature six articles performing advanced multiphysics coupling that span the computational science domains in the Exascale Computing Project.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

BatteryPro: A Python Toolkit for Battery Data Analysis and Machine Learning Predictions

Analyzing battery test data for research & development can be time-consuming since battery tests often run on the order of months to years, generating large volumes of data. BatteryPro is a comprehensive Python package and software designed to facilitate advanced analysis and performance predictions for battery test data. Developed for battery researchers, it supports data types from widely used battery testing instruments, including MACCOR and Biologic cycling systems. The software provides a variety of tools for extracting and plotting key battery parameters such as time, voltage, capacity, current, and pressure. In addition to its extensive data analysis capabilities, BatteryPro features a dedicated machine learning module that employs a Bayesian Gaussian Mixture Model (GMM) to predict battery performance and degradation. Users can generate synthetic capacity fade data, calculate fade metrics, and leverage predictive models to forecast long-term battery behavior. The software's graphical user interface (GUI) enhances usability, allowing researchers to upload, merge, and analyze multiple data files with full customizability. The GUI also supports machine learning predictions, enabling users to fit models and make predictions based on selected data and parameters. BatteryPro is built using QtDesigner, scikit-learn, matplotlib, and pandas, ensuring a high level of customization, flexibility, and accuracy in battery data analysis. This tool aims to empower researchers with the ability to perform detailed battery analysis and make informed predictions, ultimately advancing the field of battery research.

25 - ENERGY STORAGE↗

DOE OSTI2023

Dimensionally reduced machine learning model for predicting single component octanol–water partition coefficients

Abstract MF-LOGP, a new method for determining a single component octanol–water partition coefficients ( $$LogP$$ LogP ) is presented which uses molecular formula as the only input. Octanol–water partition coefficients are useful in many applications, ranging from environmental fate and drug delivery. Currently, partition coefficients are either experimentally measured or predicted as a function of structural fragments, topological descriptors, or thermodynamic properties known or calculated from precise molecular structures. The MF-LOGP method presented here differs from classical methods as it does not require any structural information and uses molecular formula as the sole model input. MF-LOGP is therefore useful for situations in which the structure is unknown or where the use of a low dimensional, easily automatable, and computationally inexpensive calculations is required. MF-LOGP is a random forest algorithm that is trained and tested on 15,377 data points, using 10 features derived from the molecular formula to make $$LogP$$ LogP predictions. Using an independent validation set of 2713 data points, MF-LOGP was found to have an average $$RMSE$$ RMSE = 0.77 ± 0.007, $$MAE$$ MAE = 0.52 ± 0.003, and $${R}^{2}$$ R 2 = 0.83 ± 0.003. This performance fell within the spectrum of performances reported in the published literature for conventional higher dimensional models ( $$RMSE$$ RMSE = 0.42–1.54, $$MAE$$ MAE = 0.09–1.07, and $${R}^{2}$$ R 2 = 0.32–0.95). Compared with existing models, MF-LOGP requires a maximum of ten features and no structural information, thereby providing a practical and yet predictive tool. The development of MF-LOGP provides the groundwork for development of more physical prediction models leveraging big data analytical methods or complex multicomponent mixtures. Graphical Abstract

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Collaborative Research: Improved Efficiency and Coupling of the Radiation Code in the ACME Earth System Model. Final Report

This final report details all work performed on the project by both project partners. This project provided support to properly couple RTE+RRTMGP, a high-performance broadband radiation code, within DOE’s Energy Exascale Earth System Model (E3SM). RTE+RRTMGP is a successor to the RRTMG radiation code, which has been widely accepted for its speed and accuracy by the global modeling community, and has been in use in the NCAR CESM for many years and was implemented in the initial version of E3SM. However, the computational cost of RRTMG remains high relative to other components in part due to its complexity and to its inefficient use of modern optimization strategies, issues that were rectified by the development of RTE+RRTMGP. Many of the accomplishment in this project necessitated significant collaboration with the E3SM development team. One focus of the project was to enhance the code’s optimization on the limited number of emerging computing systems on which the model is expected be used, including Many Integrated Core (MIC) architectures and Graphics Processing Unit (GPU) hardware. We also developed additional capabilities for RTE+RRTMGP that E3SM scientists identified as important for the planned applications of the model. The result of our project was optimization of a key physical component (radiative transfer calculations) of E3SM, directly supporting E3SM’s overarching global modeling objectives. More broadly, this project provided overall advancements in the use of radiative transfer calculations in atmospheric modeling and simulation, particularly for climate.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Development of a Performance Portable Non-Equilibrium Plasma Fluid Solver on Adaptive Grids

This presentation will describe the numerical techniques, programming paradigms, verification, and performance of a non-equilibrium plasma fluid solver that can effectively utilize current and upcoming central processing and graphics processing unit (CPU+GPU) architectures. Our plasma fluid model solves the conservation equations for self-consistent electrostatic Poisson, electron and heavy species transport, and electron temperature on adaptive Cartesian grids. Our solver is written using performance portable adaptive mesh management library, AMReX (Zhang et al., JOSS, 4 (37) 1370, 2019), and can be built and run on widely available vendor specific GPU architectures (NVIDIA/AMD/Intel). We utilize a non-subcycled second order semi-implicit time-stepping method where all adaptive mesh refinement (AMR) levels are advanced with the same time step. The composite multi-level multigrid solver from within AMReX is used for each of the governing equations that are cast into a Helmholtz equation form. We have also developed a python based chemical mechanism parser framework that uses a similar format as CANTERA (Goodwin et al., Zenodo, 2018) yaml files as input. Our custom parser reads the yaml file and provides C++ files with transport and production rate functions that can be executed on both host (CPU) and device (GPU). We present verification of our solver using method of manufactured solutions that indicate formal second order accuracy with central diffusion and fifth order weighted-essentially-non-oscillatory (WENO) advection scheme. We also verify our solver with published literature on low-pressure capacitive and high-pressure streamer discharges. Our initial performance studies indicate 10X speed-up using 20 NVIDIA GPUs versus 200 CPUs for an atmospheric streamer discharge problem solved on a 512 x 1024 x 512 grid.

graphics processing units↗

DOE OSTI2020

SRNL Analysis of ICCWR LCM and WAMS data for Corrosion and Cracking (FY2020 Progress Report)

3013 corrosion↗

DOE OSTI2022

VizBrick: A GUI-based Interactive Tool for Authoring Semantic Metadata for Building Datasets

Brick ontology is a unified semantic metadata schema to address the stand-ardization problem of buildings' physical, logical, and virtual assets and the relationships between them. Creating a Brick model for a building dataset means that the dataset's contents are semantically described using the standard terms defined in the Brick ontology. It will enable the benefits of data standardization, without having to recollect or reorganize the data and opens the possibility of automation leveraging the machine readability of the semantic metadata. The problem is that authoring Brick models for building datasets often requires knowledge of semantic technology (e.g., on-tology declarations and RDF syntax) and leads to repeated manual trial and error processes, which can be time-consuming and challenging to do with-out an interactive visual representation of the data. We developed VizBrick, a tool with a graphical user interface that can assist users in creating Brick models visually and interactively without having to understand the Re-source Description Framework (RDF) syntax. VizBrick provides handy ca-pabilities such as keyword search for easy find of relevant brick concepts and relations to their data columns and automatic suggestions of concept mapping. In this demonstration, we present a use-case of VizBrick to show-case how a Brick model can be created for a real-world building dataset.

Lee, Sangkeun (Matt)↗