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All sources NASA NTRS DOE OSTI

DOE OSTI2026

Automated Bacterial Identification and Morphological Feature Analysis in Low‐Dose Cryo‐EM Using YOLOv11

Bacteria rapidly adapt to environmental cues through morphological and ultrastructural changes that correlate with physiology and behavior. Cryogenic transmission electron microscopy (cryo‐TEM) can capture these phenotypic changes in near‐native, vitrified states, but manual analysis of low‐dose micrographs is labor intensive and limits throughput. Here, we present an end‐to‐end workflow that combines low‐dose cryo‐TEM imaging with a YOLOv11‐based instance‐segmentation model to automatically identify bacteria and quantify key structural features directly from the micrographs. This workflow enables (i) robust bacterial localization and counting from low‐magnification atlas/montage images, (ii) automated measurements of cell‐envelope (outer–inner membrane) thickness and anisotropy from higher‐magnification views, and (iii) detection and quantification of bacteria–flagella interactions, including overlap length and curvature metrics for interacting versus noninteracting flagella. Using Pantoea sp. YR343 grown under distinct media conditions, we show that the automated measurements agree with manual annotations while substantially reducing analysis time. Together, these tools provide a practical framework for scalable bacterial identification and quantitative phenotyping in low‐dose cryo‐TEM datasets and establish a foundation for extending cryo‐TEM image analysis toward higher‐throughput studies of microbial heterogeneity and biointerfaces.

YOLOv11↗

DOE OSTI2023

Machine learning based approach to predict ductile damage model parameters for polycrystalline metals

Damage models for ductile materials typically need to be parameterized, often with the appropriate parameters changing for a given material depending on the loading conditions. This can make parameterizing these models computationally expensive, since an inverse problem must be solved for each loading condition. Using standard inverse modeling techniques typically requires hundreds or thousands of high-fidelity computer simulations to estimate the optimal parameters. Additionally, the time of a human expert is required to set up the inverse model. Machine learning has recently emerged as an alternative approach to inverse modeling in these settings, where the machine learning model is trained in an offline manner and new parameters can be quickly generated on the fly, after training is complete. Here, this work utilizes such a workflow to enable the rapid parameterization of a ductile damage model called TEPLA with a machine learning inverse model. The machine learning model can efficiently estimate the model parameters much faster, as compared to previously employed methods, such as Bayesian calibration. The results demonstrate good accuracy on a synthetic test dataset and is validated against experimental data.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Reinforcement learning based hybrid bond-order coarse-grained interatomic potentials for exploring mesoscale aggregation in liquid–liquid mixtures

Exploring mesoscopic physical phenomena has always been a challenge for brute-force all-atom molecular dynamics simulations. Although recent advances in computing hardware have improved the accessible length scales, reaching mesoscopic timescales is still a significant bottleneck. Coarse-graining of all-atom models allows robust investigation of mesoscale physics with a reduced spatial and temporal resolution but preserves desired structural features of molecules, unlike continuum-based methods. Here, we present a hybrid bond-order coarse-grained forcefield (HyCG) for modeling mesoscale aggregation phenomena in liquid–liquid mixtures. The intuitive hybrid functional form of the potential offers interpretability to our model, unlike many machine learning based interatomic potentials. We parameterize the potential with the continuous action Monte Carlo Tree Search (cMCTS) algorithm, a reinforcement learning (RL) based global optimizing scheme, using training data from all-atom simulations. The resulting RL-HyCG correctly describes mesoscale critical fluctuations in binary liquid–liquid extraction systems. cMCTS, the RL algorithm, accurately captures the mean behavior of various geometrical properties of the molecule of interest, which were excluded from the training set. The developed potential model along with the RL-based training workflow could be applied to explore a variety of other mesoscale physical phenomena that are typically inaccessible to all-atom molecular dynamics simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Disentangling Electronic Transport and Hysteresis at Individual Grain Boundaries in Hybrid Perovskites via Automated Scanning Probe Microscopy

Underlying the rapidly increasing photovoltaic efficiency and stability of metal halide perovskites (MHPs) is the advancement in the understanding of the microstructure of polycrystalline MHP thin film. Over the past decade, intense efforts have been aimed at understanding the effect of microstructures on MHP properties, including chemical heterogeneity, strain disorder, phase impurity, etc. It has been found that grain and grain boundary (GB) are tightly related to lots of microscale and nanoscale behavior in MHP thin films. Atomic force microscopy (AFM) is widely used to observe grain and boundary structures in topography and subsequently to study the correlative surface potential and conductivity of these structures. For now, most AFM measurements have been performed in imaging mode to study the static behavior; in contrast, AFM spectroscopy mode allows us to investigate the dynamic behavior of materials, e.g., conductivity under sweeping voltage. However, a major limitation of AFM spectroscopy measurements is that they require manual operation by human operators, and as such only limited data can be obtained, hindering systematic investigations of these microstructures. Here, we designed a workflow combining the conductive AFM measurement with a machine learning (ML) algorithm to systematically investigate grain boundaries in MHPs. The trained ML model can extract GBs locations from the topography image, and the workflow drives the AFM probe to each GB location to perform a current–voltage (IV) curve automatically. Then, we are able to have IV curves at all GB locations, allowing us to systematically understand the property of GBs. Using this method, we discovered that the GB junction points are less conductive, potentially more photoactive, and can play critical roles in MHP stability, while most previous works only focused on the difference between GB and grains.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Overview of FY20 Q2 milestone completion: Actuator Disk Improvements and Hardening PowerPoint]

Milestone Description: Enhance Nalu-Wind's actuator disc model through hardening, documenting, stress-testing, verifying, and validating. Existing workflows will be improved by reducing the data output stream, and by making the analysis capabilities more modular and generally better. These model capabilities are needed by other A2e areas, namely Wake Dynamics, AWAKEN, and VV&UQ.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Xanthos-Lake Model Source Code

This repository contains the source code for Xanthos-Lake, a lake-modeling extension of the Xanthos framework that introduces a coupled lake component comprising the Xanthos-Lake Snow and Ice Model (xLSIM) and the Xanthos-Lake Water Balance Model (xLWBM). xLSIM is a basin-aware machine-learning model for lake snow, ice, and thermal conditions. It predicts monthly lake ice thickness, snow depth, snow-cover fraction, mixing-layer temperature, and lake ice fraction from meteorological forcing and lake surface-area information. It uses sequence-based deep-learning architectures, including Transformer and hybrid Long Short-Term Memory–Transformer (LSTM–Transformer) models, together with seasonal encoding, multi-lake learning, physical masking, and basin-level cryospheric and non-cryospheric classification. The training workflow uses Ray for scalable execution and includes optional Ray Tune hyperparameter optimization. Model predictions, observations, diagnostics, and feature-importance outputs are written in NetCDF. xLWBM is the water-balance component of the new lake framework. It simulates monthly lake storage, surface area, evaporation, inflow, outflow, and lake–groundwater exchange. It combines physical water-balance equations with calibrated bathymetric relationships, weir-based outlet flow, modified Penman open-water evaporation, groundwater head relaxation, Penman–Monteith snow and ice sublimation, and snow, ice, and thermal conditions supplied by xLSIM. The model calibrates lake parameters against satellite-derived surface-area data, using evaporation-based calibration where surface-area data are unavailable, and supports small, medium, and large lake classes. For large lakes, xLWBM is integrated with the managed-routing workflow so that lake storage and outflow interact directly with downstream river routing and reservoir operations. Together, xLSIM and xLWBM provide Xanthos with a coupled lake-modeling capability. xLSIM supplies the snow, ice, and thermal conditions that affect lake evaporation and snow- and ice-related water exchanges, while xLWBM translates those conditions into dynamic lake storage, surface area, evaporation, and discharge. In return, xLWBM supplies evolving lake surface area to xLSIM. This coupling enables Xanthos to represent lakes as active hydrologic components within basin-scale water-availability and routing simulations.

Machine Learning↗

DOE OSTI2020

URBANopt: An Open-Source Software Development Kit for Community and Urban District Energy Modeling: Preprint

Urban building modeling tools are developing rapidly; these tools use emerging simulation workflows for specific urban environmental design tasks, such as assessing the impacts of energy efficiency technologies at a district scale. However, with the emergence of new environmental design tasks, addressing all possible use cases and tasks is challenging and cannot be covered by a single tool. Urban-scale analysis at this level of complexity often requires linking multiple emerging tools, rather than using a single tool, to adequately evaluate a variety of possible fields in urban environmental design. To achieve this, flexible platforms are needed to support multiple input formats (e.g., geometric and non-geometric building properties), enabling the mapping of such inputs to underlying simulation engines. This paper provides an overview of the open-source URBANopt Software Development Kit (SDK) for modeling high-performance buildings and energy systems at a district scale. URBANopt's flexible SDK is composed of several modules that can be customized to integrate with other tools and generate new workflows to perform urban environmental design tasks, such as capturing interactions between individual buildings, district energy systems, distributed energy resources, and the electric distribution grid. We describe the functionality of the core SDK modules in URBANopt (called Core Gem, GeoJSON Gem, and Scenario Gem) and discuss the flexibility of these modules as a means of integration with a variety of tools. We also document and demonstrate technical details of writing and combining new modules to create customized workflows. Finally, we present a case study that uses the URBANopt SDK to model a hypothetical mixed-use urban project and simulate various scenarios to meet district energy performance goals.

buildings↗

DOE OSTI2023

Efficient Optimization of Energy Recovery From Geothermal Reservoirs With Recurrent Neural Network Predictive Models

Improving the long-term energy production performance of geothermal reservoirs can be accomplished by optimizing field development and management plans. Reliable prediction models, however, are needed to evaluate and optimize the performance of the underlying reservoirs under various operation and development strategies. In traditional frameworks, physics-based simulation models are used to predict the energy production performance of geothermal reservoirs. However, detailed simulation models are not trivial to construct, require a reliable description of the reservoir conditions and properties, and entail high computational complexity. Data-driven predictive models can offer an efficient alternative for use in optimization workflows. This paper presents an optimization framework for net power generation in geothermal reservoirs using a variant of the recurrent neural network (RNN) as a data-driven predictive model. The RNN architecture is developed and trained to replace the simulation model for computationally efficient prediction of the objective function and its gradients with respect to the well control variables. The net power generation performance of the field is optimized by automatically adjusting the mass flow rate of production and injection wells over 12 years, using a gradient-based local search algorithm. Two field-scale examples are presented to investigate the performance of the developed data-driven prediction and optimization framework. Furthermore, the prediction and optimization results from the RNN model are evaluated through comparison with the results obtained by using a numerical simulation model of a real geothermal reservoir.

15 GEOTHERMAL ENERGY↗

DOE OSTI2024

New metric improving Bayesian calibration of a multistage approach studying hadron and inclusive jet suppression

We study parton energy-momentum exchange with the quark gluon plasma (QGP) within a multistage approach composed of in-medium Dokshitzer-Gribov-Lipatov-Altarelli-Parisi evolution at high virtuality, and (linearized) Boltzmann transport formalism at lower virtuality. This multistage simulation is then calibrated in comparison with high- p T charged hadrons, D mesons, and the inclusive jet nuclear modification factors, using Bayesian model-to-data comparison, to extract the virtuality-dependent transverse momentum broadening transport coefficient q ̂ . To facilitate this undertaking, we develop a quantitative metric for validating the Bayesian workflow, which is used to analyze the sensitivity of various model parameters to individual observables. The usefulness of this new metric in improving Bayesian model emulation is shown to be highly beneficial for future such analyses. Published by the American Physical Society 2024

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

Assessing the impact of substrate-level enzyme regulations limiting ethanol titer in Clostridium thermocellum using a core kinetic model

Clostridium thermocellum is a promising candidate for consolidated bioprocessing because it can directly ferment cellulose to ethanol. Despite significant efforts, achieved yields and titers fall below industrially relevant targets. This implies that there still exist unknown enzymatic, regulatory, and/or possibly thermodynamic bottlenecks that can throttle back metabolic flow. By (i) elucidating internal metabolic fluxes in wild-type C. thermocellum grown on cellobiose via 13 C-metabolic flux analysis ( 13 C-MFA), (ii) parameterizing a core kinetic model, and (iii) subsequently deploying an ensemble-docking workflow for discovering substrate-level regulations, this paper aims to reveal some of these factors and expand our knowledgebase governing C. thermocellum metabolism. Generated 13 C labeling data were used with 13 C-MFA to generate a wild-type flux distribution for the metabolic network. Notably, flux elucidation through MFA alluded to serine generation via the mercaptopyruvate pathway. Using the elucidated flux distributions in conjunction with batch fermentation process yield data for various mutant strains, we constructed a kinetic model of C. thermocellum core metabolism (i.e. k-ctherm138). Subsequently, we used the parameterized kinetic model to explore the effect of removing substrate-level regulations on ethanol yield and titer. Upon exploring all possible simultaneous (up to four) regulation removals we identified combinations that lead to many-fold model predicted improvement in ethanol titer. In addition, by coupling a systematic method for identifying putative competitive inhibitory mechanisms using K-FIT kinetic parameterization with the ensemble-docking workflow, we flagged 67 putative substrate-level inhibition mechanisms across central carbon metabolism supported by both kinetic formalism and docking analysis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Doppler Backscattering Data Analysis and Integrated Modeling with OMFIT

One Modeling Framework for Integrated Tasks (OMFIT) is a widely used software tool in the magnetic fusion research community. OMFIT provides magnetic fusion energy researchers with a framework for the development of special-purpose physics modules. This paper describes an OMFIT physics module pertaining to the Doppler Backscattering (DBS) fusion plasma diagnostic. DBS measures density fluctuations and flow velocity through plasma scattering of electromagnetic waves. The OMFIT DBS module was developed to analyze experimental DBS data and facilitate modeling of DBS systems installed on multiple tokamak devices. The OMFIT DBS module is designed to support several analysis workflows: detailed analysis of experimental data, experimental planning, and theory-based synthetic diagnostic modeling. The DBS module uses integrated modeling by leveraging other OMFIT physics modules to perform tasks related to DBS, e.g. ray/beam–tracing simulations, edge-localized mode–synchronized data analysis, magnetic equilibrium reconstruction, and fitting kinetic profile data. Furthermore, this paper describes several supported workflows and serves a reference for the OMFIT DBS module.

Doppler backscattering↗

DOE OSTI2020

A lightweight method for evaluating in situ workflow efficiency

Performance evaluation is crucial to understanding the behavior of scientific workflows. In this study, we target an emerging type of workflow, called in situ workflows. These workflows tightly couple components such as simulation and analysis to improve overall workflow performance. To understand the tradeoffs of various configurable parameters for coupling these heterogeneous tasks, namely simulation stride, and component placement, separately monitoring each component is insufficient to gain insights into the entire workflow behavior. Through an analysis of the state-of-the-art research, we propose a lightweight metric, derived from a defined in situ step, for assessing resource usage efficiency of an in situ workflow execution. By applying this metric to a synthetic workflow, which is parameterized to emulate behaviors of a molecular dynamics simulation, we explore two possible scenarios (Idle Simulation and Idle Analyzer) for the characterization of in situ workflow execution. In addition to preliminary results from a recently published study [11], we further exploit the proposed metric to evaluate a practical in situ workflow with a real molecular dynamics application, i.e., GROMACS. Here, experimental results show that the in transit placement (analytics on dedicated nodes) sustains a higher frequency for performing in situ analysis compared to the helper-core configuration (analytics co-allocated with simulation).

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Insights into scale translation of methane transport in nanopores

Accurate prediction of flow behavior in shale matrix is critical for efficient development of shale gas reservoirs. In these systems, the majority of pores are in the nano-size range. As a result, continuum-based approaches may not be appropriate to simulate flow in such systems. Molecular dynamics (MD) simulations are capable of capturing the relevant microscale physics. Their relatively high computational expense, however, restricts MD simulations to rather small systems and domains. This limitation creates a gap between computational need of macroscale systems and capabilities of MD simulations. The lattice Boltzmann method (LBM) is a suitable candidate to bridge this gap. In this work, the multiple-relaxation-time (MRT)-LBM is used to study methane transport in nano-size pores. Adsorption effects near solid boundaries, as well as non-ideal behavior of fluids, are accounted for via incorporating appropriate force terms in LBM. In this work, parameters associated with the force terms in the equation of state are studied in detail, and a workflow is proposed to determine optimal values of these parameters for gas flow in slit pores. Specifically, we establish these parameters such that the range of density values that the model is able to simulate is maximized. We demonstrate this workflow by simulating gas flow where velocity and density profiles from MD simulations are used as reference data. Results from LBM simulations are in good agreement with MD reference data for pores that are 4 nm in width or larger. Moreover, we propose a preconditioning scheme to improve the stability of LBM in dealing with complex geometries. The robustness of this scheme is demonstrated by simulating several roughness geometries. This work motivates the use of LBM in scale translation of the physics of mass transport in more complex permeable media.

03 NATURAL GAS↗

DOE OSTI2024

MFiX Development Updates

This presentation discusses recent developments of the Multiphase Flow with Interphase eXchanges (MFiX) software. A brief review of all modeling approaches along with their cost versus accuracy is provided to guide users when selecting a model for a given application. The main new features of the past five official releases of MFiX are described. Improvement in chemistry management allow for easier simulation setup, and faster simulation speed. Progress in the implementation of a thin-wall boundary condition is presented. The major new model development over the past year is the release of the Glued Sphere Particle model (GSP), where component spheres are combined together to represent non-spherical particles. The integration of Machine Learning (ML) workflow in the CFD process is discussed with two applications: a surrogate model for stiff chemistry and the development of a PIC stress model using ML.

Dietiker, Jeff↗

DOE OSTI2024

IDAES-PSE 2.4.0 Release

The Institute for the Design of Advanced Energy Systems (IDAES) Integrated Platform is a versatile computational environment offering extensive process systems engineering (PSE) capabilities for optimizing the design and operation of complex, interacting technologies and systems. IDAES enables users to efficiently search vast, complex design spaces to discover the lowest cost, most environmentally sustainable solutions while supporting the full process modeling lifecycle, from conceptual design to dynamic optimization and control. The extensible, open platform empowers users to create models of novel processes and rapidly develop custom analyses, workflows, and end-user applications.. Deprecations • Convergence Analysis tool (idaes/core/util/convergence): deprecated in favor of new Parameter Sweep tools. To be removed in v3.0.0. New Beta Capabilities • Parameter Sweep Tool (idaes.core.util.parameter_sweep) o A new API for defining and performing parameter sweep studies on IDAES models has been developed • Diagnostics Tools (idaes.core.util.model_diagnostics) o New methods for identifying duplicate variables and constraints have been added to the diagnostics toolbox o New tools for detecting ill conditioning in Jacobians have been developed and are available in the model_diagnostics module. These provide alternatives to the existing DegeneracyHunter toolbox, and will eventually be merged with this capability, but initial working versions have been provided as beta capabilities for interested users o IpoptConvergenceAnalysis (replaces deprecated Convergence Analysis tool):  A new tool for performing convergence analysis studies that leverages the new Parameter Sweep tools has been developed. This tool allows users to define the input parameters to their model and sampling methods for these (leveraging Pysmo's sampling tools) and to then solve their model across the sampled domains and return a summary of the solver performance (IPOPT only) Improved Models • Thickener model (idaes.models.unit_models.solid_liquid.thickener) o Improved model to include predictive correlations for unit sizing based on settling velocity measurements (steady-state only) • Modular Property Packages o Added general support for calculating critical properties of mixtures using defined Equation of State modules. New API defined for Equation of State modules in order to define the necessary constraints for calculating critical properties (most EoS modules DO NOT support calculation of critical properties (yet)) o Added new methods to Cubic Equation of State module to support calculation of critical properties

DiagnosticsToolbox↗

DOE OSTI2024

IDAES-PSE 2.7.0 Release

The Institute for the Design of Advanced Energy Systems (IDAES) Integrated Platform is a versatile computational environment offering extensive process systems engineering (PSE) capabilities for optimizing the design and operation of complex, interacting technologies and systems. IDAES enables users to efficiently search vast, complex design spaces to discover the lowest cost solutions while supporting the full process modeling lifecycle, from conceptual design to dynamic optimization and control. The extensible, open platform empowers users to create models of novel processes and rapidly develop custom analyses, workflows, and end-user applications. IDAES-PSE 2.7.0 Release Highlights New features: AutoScaler and CustomScalerBase classes: Such tools are the core of the new scaling framework being implemented in IDAES. Wider adoption of scaling tools among users will result in quicker and more robust model solutions. Scaler for equilibrium reactor and saponification properties: These scaler models are examples to follow for how to use the new scaling tools. ONNX Surrogate support from Optimization & Machine Learning Toolkit (OMLT): ONNX is an open standard format to save and load ML/AI models that is widely supported by all major frameworks. This capability makes it easier for IDAES users to create surrogate models and use them without having to support each framework individually. 1D Membrane Model for CO2 Capture and Utilization: Supports ongoing efforts for modeling and optimizing polymer membrane processes for CO2 capture and conversion into formic acid. StreamScaler unit model: Unrelated to the CustomScalerBase, this unit model allows a stream’s extensive variables to be scaled by a fixed factor. This allows streams being processed by multiple units in parallel to be scaled down to unit scale and scaled back up to process scale. Bug fixes or improvements: Scaling, EoS, Diagnostics tool, Modular Properties, tests & documentation Deprecations: Old Cubic EoS

AS↗

DOE OSTI2026

Revealing EDL-driven reduction mechanisms in binary, ternary, and quaternary fluorinated electrolytes via an integrated MD–DFT–ML framework

Accurately predicting solid electrolyte interphase (SEI) formation requires explicitly resolving the electric double layer (EDL) structure, which deviates significantly from that of the bulk electrolyte. Although an established molecular dynamics (MD) and Density Functional Theory (DFT) framework can model SEI formation by evaluating reduction reactions of local clusters in the EDL, it suffers from a combinatorial computational bottleneck. To overcome this limitation, we introduce a machine-learning-accelerated simulation workflow (MD–DFT–ML), integrating a gradient-boosted regression model trained on EDL composition data to efficiently predict reduction potentials. We apply this framework to seven fluorinated electrolytes comprising fluorinated anions, a fluorinated ester solvent, two types of diluent (ion-solvating ester vs. non-solvating ether), and an FEC additive. The analysis shows that the EDL selectively accumulates cation-binding species; consequently, the non–cation-binding ether diluent rarely enters the EDL and makes minimal contributions to SEI formation. DFT calculations on statistically representative EDL clusters provide reduction potentials and fluorine-release pathways, while the ML model, which substantially reduces the DFT workload, predicts cluster reduction energies with a mean absolute error of 0.1 eV. The combined MD–DFT–ML approach also quantifies contributions from different sources to LiF formation in the SEI. This methodology establishes a generalizable route for multiscale modeling electrolyte and interphase design for next-generation electrochemical energy-storage systems.

DFT-MD-ML workflow↗

DOE OSTI2021

Adoption of image-driven machine learning for microstructure characterization and materials design: A Perspective

Microstructure characterization enables the development of structure-processing-property relationships critical to several research areas within the broad field of materials science, from alloy design to the assessment of corrosion resistance, and failure analysis. Conventional approaches to material characterization have relied on either qualitative inference by the human ex-pert or software applications that can extract high-level features from images, such as boundary segmentation, average grain diameter, etc. Such approaches rely heavily on subject matter expert user intervention and knowledge of what phases or more generally, what microstructural features, are of interest. The recent surge in the adoption of machine learning techniques to address problems in materials engineering has brought with it an increased interest and application of Image Driven Machine Learning (IDML) approaches. In this work, we review the applications of IDML to the field of materials characterization. A canonical hierarchy of stages is defined, which when put sequentially together completes an IDML study: problem definition, dataset building, model selection and training, model evaluation, and integration with existing instrumentation or simulation workflow. The studies reviewed in this work are analyzed from the perspective of each of these stages. Such a review permits agranular assessment of the field, for example the impact of IDML on materials characterization at the nanoscale, the size of a typical dataset required to train a semantic segmentation model on electron microscopy images, ubiquitousness of transfer learning in the domain, etc. Finally, we discuss the importance of interpretability and explainability in the field of IDML for materials characterization, and provide an overview of two emerging techniques in the field: semantic segmentation and generative adversarial networks.

Baskaran, Arun↗