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DOE OSTI2020

DISCOVR: Development of Integrated Screening, Cultivar Optimization, and Verification Research

The DISCOVR consortium has developed and is applying an integrated platform and workflow for standardized, deep characterization of highly productive and resilient microalgae strains. New strains are screened using three consecutive tiers in a conceptual down-selection funnel to arrive at the most promising strains. At tier I, strains are screened on gradient incubators to determine their temperature and salinity tolerance range, and to evaluate their resistance to infectious agents (e.g., chytrids). At tier II, the strains’ winter and summer season biomass productivities are quantified in Laboratory Environmental Algae Pond Simulator (LEAPS) photobioreactors, and biomass composition is determined under N-replete and N-deplete conditions. At tier III, the best winter and summer season strains are evaluated in indoor crash ponds to determine their resilience to induced infections, and strains are tested in outdoor raceway ponds to confirm high biomass productivity and culture stability. The top strains are then evaluated in seasonal SOT outdoor pond culture trials at AzCATI, the dedicated Department of Energy SOT (State of Technology) testbed. Additional research is carried out on evaluating growth promoting molecules, reducing the impact of oxygen inhibition, optimizing pond operational conditions, measuring compositional shift dynamics, developing integrated pest management strategies, analysing culture health using 96 well-plate tools, implementing spectroradiometric monitoring and using machine learning to predict culture crashes.

Huesemann, Michael H↗

DOE OSTI2021

Genome-Scale Metabolic Modeling Enables In-Depth Understanding of Big Data

Genome-scale metabolic models (GEMs) enable the mathematical simulation of the metabolism of archaea, bacteria, and eukaryotic organisms. GEMs quantitatively define a relationship between genotype and phenotype by contextualizing different types of Big Data (e.g., genomics, metabolomics, and transcriptomics). In this review, we analyze the available Big Data useful for metabolic modeling and compile the available GEM reconstruction tools that integrate Big Data. We also discuss recent applications in industry and research that include predicting phenotypes, elucidating metabolic pathways, producing industry-relevant chemicals, identifying drug targets, and generating knowledge to better understand host-associated diseases. In addition to the up-to-date review of GEMs currently available, we assessed a plethora of tools for developing new GEMs that include macromolecular expression and dynamic resolution. Finally, we provide a perspective in emerging areas, such as annotation, data managing, and machine learning, in which GEMs will play a key role in the further utilization of Big Data.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Uncertainty-driven dynamics for active learning of interatomic potentials

Machine learning (ML) models, if trained to data sets of high-fidelity quantum simulations, produce accurate and efficient interatomic potentials. Active learning (AL) is a powerful tool to iteratively generate diverse data sets. In this approach, the ML model provides an uncertainty estimate along with its prediction for each new atomic configuration. If the uncertainty estimate passes a certain threshold, then the configuration is included in the data set. Here we develop a strategy to more rapidly discover configurations that meaningfully augment the training data set. The approach, uncertainty-driven dynamics for active learning (UDD-AL), modifies the potential energy surface used in molecular dynamics simulations to favor regions of configuration space for which there is large model uncertainty. The performance of UDD-AL is demonstrated for two AL tasks: sampling the conformational space of glycine and sampling the promotion of proton transfer in acetylacetone. The method is shown to efficiently explore the chemically relevant configuration space, which may be inaccessible using regular dynamical sampling at target temperature conditions.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Exploiting Machine Learning to Efficiently Predict Multidimensional Optical Spectra in Complex Environments

The excited-state dynamics of chromophores in complex environments determine a range of vital biological and energy capture processes. Time-resolved, multidimensional optical spectroscopies provide a key tool to investigate these processes. Although theory has the potential to decode these spectra in terms of the electronic and atomistic dynamics, the need for large numbers of excited-state electronic structure calculations severely limits first-principles predictions of multidimensional optical spectra for chromophores in the condensed phase. In this work, we leverage the locality of chromophore excitations to develop machine learning models to predict the excited-state energy gap of chromophores in complex environments for efficiently constructing linear and multidimensional optical spectra. By analyzing the performance of these models, which span a hierarchy of physical approximations, across a range of chromophore–environment interaction strengths, we provide strategies for the construction of machine learning models that greatly accelerate the calculation of multidimensional optical spectra from first principles.

36 MATERIALS SCIENCE↗

DOE OSTI2025

The design space of E(3)-equivariant atom-centred interatomic potentials

Abstract Molecular dynamics simulation is an important tool in computational materials science and chemistry, and in the past decade it has been revolutionized by machine learning. This rapid progress in machine learning interatomic potentials has produced a number of new architectures in just the past few years. Particularly notable among these are the atomic cluster expansion, which unified many of the earlier ideas around atom-density-based descriptors, and Neural Equivariant Interatomic Potentials (NequIP), a message-passing neural network with equivariant features that exhibited state-of-the-art accuracy at the time. Here we construct a mathematical framework that unifies these models: atomic cluster expansion is extended and recast as one layer of a multi-layer architecture, while the linearized version of NequIP is understood as a particular sparsification of a much larger polynomial model. Our framework also provides a practical tool for systematically probing different choices in this unified design space. An ablation study of NequIP, via a set of experiments looking at in- and out-of-domain accuracy and smooth extrapolation very far from the training data, sheds some light on which design choices are critical to achieving high accuracy. A much-simplified version of NequIP, which we call BOTnet (for body-ordered tensor network), has an interpretable architecture and maintains its accuracy on benchmark datasets.

Computer Science↗

DOE OSTI2020

Using Machine Learning Tools to Predict Compressor Stall

Clean energy has become an increasingly important consideration in today’s power systems. As the push for clean energy continues, many coal-fired power plants are being decommissioned in favor of renewable power sources such as wind and solar. However, the intermittent nature of renewables means that dynamic load following traditional power systems is crucial to grid stability. With high flexibility and fast response at a wide range of operating conditions, gas turbine systems are poised to become the main load following component in the power grid. Yet, rapid changes in load can lead to fluid flow instabilities in gas turbine power systems. These instabilities often lead to compressor surge and stall, which are some of the most critical problems facing the safe and efficient operation of compressors in turbomachinery today. Although the topic of compressor surge and stall has been extensively researched, no methods for early prediction have been proven effective. This study explores the utilization of machine learning tools to predict compressor stall. The long short-term memory (LSTM) model, a form of recurrent neural network (RNN), was trained using real compressor stall datasets from a 100 kW recuperated gas turbine power system designed for hybrid configuration. Two variations of the LSTM model, classification and regression, were tested to determine optimal performance. The regression scheme was determined to be the most accurate approach, and a tool for predicting compressor stall was developed using this configuration. Overall, results show that the tool is capable of predicting stalls 5–20 ms before they occur. With a high-speed controller capable of 5 ms time-steps, mitigating action could be taken to prevent compressor stall before it occurs.

42 ENGINEERING↗

DOE OSTI2024

E-PVT: enhanced position-velocity-time scheduler for computer-controlled optical finishing with comprehensive considerations of dynamics constraints, continuity and efficiency

Deterministic computer-controlled optical finishing is an essential approach for achieving high-quality optical surfaces. Its determinism and convergence rely heavily on precise and smooth motion control to guide the machine tool over an optical surface to correct residual errors. One widely supported and smooth motion control model is position-velocity-time (PVT), which employs piecewise cubic polynomials to describe positions. Our prior research introduced a PVT-based velocity scheduling method, demonstrating sub-nanometer level convergence in ion beam figuring (IBF) processes. However, three challenges remained. Firstly, this method relies on quadratic programming, resulting in computational intensiveness for dense tool paths. Secondly, the dynamics constraints and velocity and acceleration continuities are not comprehensively considered, limiting the full potential of PVT-based control. Thirdly, no compensation mechanism existed when dynamics constraints are exceeded. In this study, in response to these challenges, we proposed the Enhanced PVT (E-PVT) method, reducing the time complexity from O ( n 3 ) to O ( n ) while fully addressing dynamics constraints and continuities. A novel compensation method utilizing particle swarm optimization was proposed to address situations where dynamics constraints might be exceeded while maintaining the overall processing efficiency. Validation through simulation and experimentation confirmed the improved performance of E-PVT.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Physics-informed machine-learning model of temperature evolution under solid phase processes

We model temperature dynamics during Shear Assisted Proccess Extrusion (ShAPE), a solid phase process that plasticizes feedstock with a rotating tool and subsequently extrudes it into a consolidated tube, rod, or wire. Control of temperature is critical during ShAPE processing to avoid liquefaction, ensure smooth extrusion, and develop desired material properties in the extruded products. Accurate modeling of the complicated thermo-mechanical feedbacks between process inputs, material temperature, and heat generation presents a significant barrier to predictive modeling and process design. In particular, connecting micro-structural scale mechanisms of heat generation to macro-scale predictions of temperature can become computationally intractable. In this work we use a neural network (NN) model of heat generation to bridge this gap, by combining it with a simplified model of the temperature dynamics due to conduction and convection to capture the macro scale evolution of temperature. We inform the construction of the NN heat generation model using crystal plasticity simulations at the micro-structural scale to model the effects of process inputs on generation of heat. We achieved close fits of the temperature dynamics model to a diverse experimental data-set. Further, the relationships learned by the NN model between process inputs and heat generation showed qualitative agreement with those predicted by crystal plasticity simulations.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Improved detection of low-frequency within-host variants from deep sequencing: A case study with human papillomavirus

Abstract High-coverage sequencing allows the study of variants occurring at low frequencies within samples, but is susceptible to false-positives caused by sequencing error. Ion Torrent has a very low single nucleotide variant (SNV) error rate and has been employed for the majority of human papillomavirus (HPV) whole genome sequences. However, benchmarking of intrahost SNVs (iSNVs) has been challenging, partly due to limitations imposed by the HPV life cycle. We address this problem by deep sequencing three replicates for each of 31 samples of HPV type 18 (HPV18). Errors, defined as iSNVs observed in only one of three replicates, are dominated by C→T (G→A) changes, independently of trinucleotide context. True iSNVs, defined as those observed in all three replicates, instead show a more diverse SNV type distribution, with particularly elevated C→T rates in CCG context (CCG→CTG; CGG→CAG) and C→A rates in ACG context (ACG→AAG; CGT→CTT). Characterization of true iSNVs allowed us to develop two methods for detecting true variants: (1) VCFgenie, a dynamic binomial filtering tool which uses each variant’s allele count and coverage instead of fixed frequency cut-offs; and (2) a machine learning binary classifier which trains eXtreme Gradient Boosting models on variant features such as quality and trinucleotide context. Each approach outperforms fixed-cut-off filtering of iSNVs, and performance is enhanced when both are used together. Our results provide improved methods for identifying true iSNVs in within-host applications across sequencing platforms, specifically using HPV18 as a case study.

Virology↗

DOE OSTI2025

Computational epidemiological tools for pandemic analysis, understanding, and response

This suite of software tools is being developed to enhance and analyze computational epidemiological models that incorporate realistic disease dynamics and human behavior, with the goal of supporting epidemic and pandemic response. Specifically, the tools enable data analysis, feature extraction, data synthesis, machine learning model development, and prediction of key public health outcomes, such as cases, hospitalizations, deaths, and behavioral responses, for airborne infectious diseases like COVID-19 and influenza.

Butts, David↗

DOE OSTI2025

Digital twin framework for PIP-II linac: AI-driven multi-scale modeling from ion source to 800 MeV

The PIP-II superconducting linac at Fermilab is designed to deliver multi-megawatt proton beams for neutrino physics and other high-intensity applications. To expedite commissioning and enhance operational reliability, we have developed an EPICS-based data flow framework that seamlessly integrates digital twins (DT) with physical twins (PT). These digital twins comprise high-fidelity beam dynamics models or data-driven surrogate models connected to their physical counterparts through real-time diagnostics and advanced machine-learning algorithms.Central to this framework is Linac_Gen, an accelerated simulation tool that incorporates convolutional neural networks, random forests, and genetic algorithms to provide up to a tenfold speedup in optimizing the accelerator geometry model. An EPICS translator layer ensures interoperability by efficiently mapping lattice parameters across diverse simulation platforms.Our EPICS-based framework supports multiple operational modes—monitoring, passive learning, closed-loop control, and online learning—covering the entire machine lifecycle. By leveraging HPC resources and multi-objective optimization techniques, the digital twin enables adaptive trajectory correction, real-time fault detection, and predictive modeling of beam stability. This comprehensive approach paves the way for robust, high-intensity operation and data-driven accelerator R&D at Fermilab.

Pathak, Abhishek [Fermilab]↗

DOE OSTI2024

CMLM (Co-Optimized Machine-Learned Manifolds) [SWR-23-41]

Co-optimized Machine-Learned Manifolds (CMLM) is a data-driven approach for developing reduced-order manifold models for high-dimensional chemically reacting systems. It involves a specially designed neural network, the training of which simultaneously optimizes linear combinations of species that define the manifold, nonlinear mapping to outputs of interest such as reaction rates, and (optionally) subfilter closure for large eddy simulation. This software package provides an implementation of the CMLM approach in Python using the PyTorch machine learning library. A few example cases are included, showing how the tool can be applied to different types of data from 0D and 1D reacting simulations performed using Cantera. The neural networks can be saved in a format that is readable by the Pele suite of combustion solvers for use in reacting computational fluid dynamics simulations. This software repository contains several python scripts to perform various tasks associated with the Co-optimized Machine Learned Manifolds (CMLM) model, which is described in Perry, Henry de Frahan, and Yellapantula, CNF, 2022 (https://doi.org/10.1016/j.combustflame.2022.112286). This includes not only the code that defines the CMLM model, but also scripts to generate suitable training data, scripts to pre-process the data, scripts to train the CMLM model, and scripts to plot the output, as well as various other helper files. The scripts depend on several commonly used python libraries for data analysis and chemical reaction computations. The trained models that result from this tool are designed to work with the an interface being implemented in the Pele suite of reacting flow solvers (https://github.com/AMReX-Combustion).

Perry, Bruce↗

DOE OSTI2026

Phenomenological opportunities at the EIC

This review presents a comprehensive overview of key phenomenological opportunities at the future Electron–Ion Collider (EIC), synthesizing discussions and collaborative research efforts developed within the Korean EIC community and the EICφ collaboration. We explore a diverse range of physics topics central to the EIC scientific program, including the multidimensional tomography of nucleon and nuclear structure, precision Quantum Chromodynamics studies through jet physics and event-shape observables, heavy quarkonium production as a probe of partonic dynamics, and the spectroscopy of exotic hadrons. Furthermore, we discuss the transformative potential of emerging technologies—specifically Machine Learning and Quantum Computing—as essential tools for addressing the computational challenges and maximizing the scientific discovery potential of the EIC era.

Electron–Ion collider↗

DOE OSTI2025

Computational Modeling to Advance Novel Medical Isotopes for Radiotheranostics: A DOE-NIH Joint Workshop Executive Summary

The DOE-NIH Joint Workshop on Computational Modeling to Advance Novel Medical Isotopes for Radiotheranostics, held on September 27, 2024, brought together experts from government, academia, and industry to address critical challenges in radionuclide production and clinical translation. Here, the workshop emphasized interdisciplinary collaboration, particularly between the Department of Energy (DOE) and the National Institutes of Health (NIH), to strengthen the domestic isotope supply, streamline regulatory pathways, and further integrate computational tools into radiopharmaceutical therapy (RPT). Key discussions explored the role of AI-driven modeling, machine learning, and digital twin technologies in optimizing dosimetry, dynamically personalizing treatments, and reducing time to clinical adoption. Advances in predictive computational modeling were highlighted as essential for improving radionuclide yield, purity, and synthesis efficiency. Regulatory considerations and equitable access were central themes, with participants advocating for harmonized global standards, adaptive trial designs, and expanded infrastructure for clinical implementation. DOE computational and production infrastructure was emphasized. Future priorities identified include increased investment in radionuclide production infrastructure, expanded workforce development in radiopharmaceutical sciences and computational modeling, and the creation of robust public-private partnerships. The workshop concluded that continued strategic collaboration and sustained resources will be vital for advancing next-generation radiotheranostics, ensuring safe and effective therapies accessible to all patients.

digital twins↗

DOE OSTI2020

Inference offers a metric to constrain dynamical models of neutrino flavor transformation

The multimessenger astrophysics of compact objects presents a vast range of environments where neutrino flavor transformation may occur and may be important for nucleosynthesis, dynamics, and a detected neutrino signal. Development of efficient techniques for surveying flavor evolution solution spaces in these diverse environments, which augment and complement existing sophisticated computational tools, could leverage progress in this field. To this end we continue our exploration of statistical data assimilation (SDA) to identify solutions to a small-scale model of neutrino flavor transformation. SDA is a machine learning formula wherein a dynamical model is assumed to generate any measured quantities. Specifically, we use an optimization formulation of SDA wherein a cost function is extremized via the variational method. Regions of state space in which the extremization identifies the global minimum of the cost function will correspond to parameter regimes in which a model solution can exist. Our example study seeks to infer the flavor transformation histories of two monoenergetic neutrino beams coherently interacting with each other and with a matter background. We require that the solution be consistent with measured neutrino flavor fluxes at the point of detection, and with constraints placed upon the flavor content at various locations along their trajectories, such as the point of emission, and the locations of the Mikheyev-Smirnov-Wolfenstein resonances. We show how the procedure efficiently identifies solution regimes and rules out regimes where solutions are infeasible. Overall, results in this work intimate the promise of this “variational annealing” methodology to efficiently probe an array of fundamental questions that traditional numerical simulation codes render difficult to access.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Using Knowledge-Guided Machine Learning To Assess Patterns of Areal Change in Waterbodies across the Contiguous United States

Lake and reservoir surface areas are an important proxy for freshwater availability. Advancements in machine learning (ML) techniques and increased accessibility of remote sensing data products have enabled the analysis of waterbody surface area dynamics on broad spatial scales. However, interpreting the ML results remains a challenge. While ML provides important tools for identifying patterns, the resultant models do not include mechanisms. Thus, the “black-box” nature of ML techniques often lacks ecological meaning. Using ML, we characterized temporal patterns in lake and reservoir surface area change from 1984 to 2016 for 103,930 waterbodies in the contiguous United States. We then employed knowledge-guided machine learning (KGML) to classify all waterbodies into seven ecologically interpretable groups representing distinct patterns of surface area change over time. Many waterbodies were classified as having “no change” (43%), whereas the remaining 57% of waterbodies fell into other groups representing both linear and nonlinear patterns. This analysis demonstrates the potential of KGML not only for identifying ecologically relevant patterns of change across time but also for unraveling complex processes that underpin those changes.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Using Knowledge-Guided Machine Learning To Assess Patterns of Areal Change in Waterbodies across the Contiguous United States

58 GEOSCIENCES↗

DOE OSTI2023

Electrochemical Characterization of Molten Salt Chemistry During Atmospheric Ingressions

This report describes the salt chemistry and sedimentation studies that were completed in FY23 as part of the Pyrochemical Fuel Cycles – ANL project. The primary objective of these activities was to employ electrochemical methods in order to quantify and gain insights into the reaction mechanisms associated with the interaction of O2 and moisture impurities with the molten chloride salts used for the pyrochemical processing of nuclear materials. If not monitored and controlled, the ingression of these atmospheric impurities can lead to changes in the salt redox conditions and initiate the formation of oxide particles, potentially resulting in operational and safeguards challenges. By elucidating the mechanisms underlying the formation of oxide particles, we can effectively monitor the conditions of the salt and design systems to mitigate the influence of atmospheric O2 and H2O. To achieve these goals, we designed a test system that allowed for precisely controlled gas ingressions into the molten salt vessel. This system included on-line monitoring provided by electrochemical probes that enable near real-time measurements of the salt conditions throughout the course of the experiment. Using this system, we systematically varied experimental conditions, including O2/Ar flow rates and O2 concentrations, to comprehensively understand their impact on solid particle formation. We also used a particle size and shape analyzer to characterize the particles that were generated. Tests in FY23 concentrated on the formation of CeO2 particles, but we also prepared a separate apparatus targeting UO2 particles for use in FY24. We additionally conducted extensive modeling activities in support of this work. This included multiphysics simulations of the gas ingressions along with the development of a machine learning workflow to enable accelerated molecular dynamics modeling of the molten salt chemistry of LiCl-KCl-UCl3. The combination of experimental and modeling tools has allowed us to begin to get a more complete understanding of the reactions that occur when atmospheric ingressions occur in pyroprocessing systems.

Guo, Jicheng↗