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DOE OSTI2024

Automated 3D cytoplasm segmentation in soft X-ray tomography

Cells’ structure is key to understanding cellular function, diagnostics, and therapy development. Soft X-ray tomography (SXT) is a unique tool to image cellular structure without fixation or labeling at high spatial resolution and throughput. Fast acquisition times increase demand for accelerated image analysis, like segmentation. Currently, segmenting cellular structures is done manually and is a major bottleneck in the SXT data analysis. This paper introduces ACSeg, an automated 3D cytoplasm segmentation model. ACSeg is generated using semi-automated labels and 3D U-Net and is trained on 43 SXT tomograms of immune T cells, rapidly converging to high-accuracy segmentation, therefore reducing time and labor. Furthermore, adding only 6 SXT tomograms of other cell types diversifies the model, showing potential for optimal experimental design. ACSeg successfully segmented unseen tomograms and is published on Biomedisa, enabling high-throughput analysis of cell volume and structure of cytoplasm in diverse cell types.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Shock-induced bubble jets: a dual perspective of bubble collapse and interfacial instability theory

Interactions between shock waves and gas bubbles in a liquid can lead to bubble collapse and high-speed liquid jet formation, relevant to biomedical applications such as shock wave lithotripsy and targeted drug delivery. This study reveals a complex interplay between acceleration-induced instabilities that drive jet formation and radial accelerations causing overall bubble collapse under shock wave pressure. Using high-speed synchrotron X-ray phase contrast imaging, the dynamics of micrometre-sized air bubbles interacting with laser-induced underwater shock waves are visualised. These images offer full optical access to phase discontinuities along the X-ray path, including jet formation, its propagation inside the bubble, and penetration through the distal side. Jet formation from laser-induced shock waves is suggested to be an acceleration-driven process. A model predicting jet speed based on the perturbation growth rate of a single-mode Richtmyer–Meshkov instability shows good agreement with experimental data, despite uncertainties in the jet-driving mechanisms. The jet initially follows a linear growth phase, transitioning into a nonlinear regime as it evolves. To capture this transition, a heuristic model bridging the linear and nonlinear growth phases is introduced, also approximating jet shape as a single-mode instability, again matching experimental observations. Upon piercing the distal bubble surface, jets can entrain gas and form a toroidal secondary bubble. Linear scaling laws are identified for the pinch-off time and volume of the ejected bubble relative to the jet’s Weber number, characterising the balance of inertia and surface tension. At low speeds, jets destabilise due to capillary effects, resulting in ligament pinch-off.

Drops and Bubbles: Bubble dynamics↗

DOE OSTI2026

A New 1D Model for Thermal Mixing and Stratification in Advanced Reactor Transients

Thermal mixing and stratification in large pools and enclosures play a critical role in the safety and performance of pool-type nuclear reactors, particularly during transient scenarios involving significant temperature differences between incoming and bulk coolant. Accurate modeling of these phenomena is essential for predicting system behavior and supporting passive safety features such as natural circulation. Here, this paper presents a new 1D model for thermal mixing and stratification, developed and implemented in the SAM code. The model represents a large pool as 1D coolant jet channels and zero-dimensional bulk pool volumes, enabling the simulation of a wide range of flow configurations, including hot and cold jet interactions, stratified layers, and the influence of complex geometries such as ceilings, free surfaces, and internal obstacles. Heat exchange between jet and pool regions is governed by closure relations calibrated against 3D computational fluid dynamics (CFD) simulations. The model improves upon earlier approaches by incorporating time-dependent jet characteristics and capturing the associated delay effects more accurately. Code-to-code comparisons and validation against experimental data from the Thermal Stratification Test Facility demonstrate the model’s accuracy and flexibility. This work offers two key contributions: (1) an efficient and robust method for simulating thermal mixing and stratification at the system level, eliminating the need for external coupling between system analysis codes and CFD, and (2) a significant enhancement of SAM’s capabilities to analyze thermal stratification phenomena in advanced reactor systems.

SAM↗

DOE OSTI2026

Brochure for the DOE Office of Science Workshop on Envisioning Frontiers in AI and Computing for Biological Research

In February of 2025 a joint ASCR/BER workshop was held to identify key transformational research directions for understanding biology using artificial intelligence (AI), digital twins and high-performance (HPC) computational methods to facilitate scientific discovery and innovation in support of the Department of Energy mission. AI technologies offer exciting new groundbreaking methods to analyze large volumes of complex biological data, thereby greatly accelerating the ability to understand, predict, and design biological processes for beneficial purposes. In the laboratory, the bridging of AI-enabled automated experimental technologies, HPC and digital twins will provide potent tools for researchers to explore the fundamental nature of biology and harness its inherent metabolic potential for a variety of beneficial purposes. The focus of this workshop was on how high-performance computational methods can impact this objective by exploring digital twins, foundational models, and data-driven approaches with applications to advance automated laboratory experiments, modeling of complex living systems and engineering new functions into plants and microbial systems relevant to DOE mission. Workshop attendees with expertise in plant science, microbiology, mathematics, computer science, and AI assessed the current state of the science, trends, and AI challenges at the interface of plant and microbial systems biology and computational science to identify opportunities for high-impact research. This collaborative effort capitalized on ASCR's advancements in applied mathematics, computer science, and Exascale systems, and BER's expertise in basic genomics-enabled research on DOE relevant plant and microbial systems. The workshop culminated in four key priority research directions to guide future research and development within DOE Office of Science programs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Allometric and Mobile Terrestrial LiDAR Modeling of Aboveground Woody Biomass of Populus in Coppice Production

Poplars ( Populus spp.) and their hybrids are increasingly being grown in coppice production to generate bioenergy feedstocks at frequent intervals. Allometric equations are re-quired to predict aboveground biomass (AGB) of coppiced individuals with minimal field measurements. Likewise, remote sensing tools like LiDAR (light detection and ranging) can be used if models are available to predict AGB from point cloud data. Therefore, this study sought to develop equations to predict dry woody AGB from field measurements and LiDAR data from coppiced poplar field trials containing eastern cottonwood ( P. del-toides ) and hybrid poplar taxa. We found that taxa-specific allometric models containing the summed basal area of the three largest stems in the coppice provided the best predictive model, with stem height and stem count failing to provide additional explanatory power. The best predictive LiDAR-based model was independent of taxa but had slightly lower adjusted R 2 and higher RMSE than the allometric model. It contained four parameters including crown volume, leaf area index, variance of height returns, and the top point density (i.e., density metric 9 or the proportion of points in the highest point interval when the point cloud is evenly divided into ten vertical intervals). In total, these models can be used to quickly and efficiently estimate dry woody AGB of Populus coppice systems for bioenergy feedstock production.

AGB↗

DOE OSTI2022

Inferring the Thermal History of the Intergalactic Medium from the Properties of the Hydrogen and Helium Lyα Forest

The filamentary network of intergalactic medium (IGM) gas that gives origin to the Lyα forest in the spectra of distant quasars encodes information on the physics of structure formation and the early thermodynamics of diffuse baryonic material. Here we use a massive suite of more than 400 high-resolution cosmological hydrodynamical simulations run with the Graphics Processing Unit–accelerated code Cholla to study the IGM at high spatial resolution maintained over the entire computational volume. The simulations capture a wide range of possible IGM thermal histories by varying the photoheating and photoionizing background produced by star-forming galaxies and active galactic nuclei. A statistical comparison of synthetic spectra with the observed 1D flux power spectra of hydrogen at redshifts 2.2 ≤ z ≤ 5.0 and with the helium Lyα opacity at redshifts 2.4 < z < 2.9 tightly constrains the photoionization and photoheating history of the IGM. By leveraging the constraining power of the available Lyα forest data to break model degeneracies, we find that the IGM experienced two main reheating events over 1.2 Gyr of cosmic time. For our best-fit model, hydrogen reionization completes by z R ≈ 6.0 with a first IGM temperature peak of T 0 ≃ 1.3 × 10 4 K and is followed by the reionization of He ii that completes by z R ≈ 3.0 and yields a second temperature peak of T 0 ≃ 1.4 × 10 4 K. We discuss how our results can be used to obtain information on the timing and the sources of hydrogen and helium reionization.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Flow-dependent tagging of $^{214}$Pb decays in the LZ dark matter detector

The LUX-ZEPLIN (LZ) experiment is searching for dark matter interactions in a liquid xenon time projection chamber (LXe-TPC). This article demonstrates how control of the flow state in the LXe-TPC enables the identification of pairs of sequential alpha-decays, which are used to map fluid flow and ion drift in the liquid target. The resulting transport model is used to tag $^{214}$Pb beta-decays, a leading background to dark matter signals in LZ. Temporally evolving volume selections, at a cost of 9.0% of exposure, target the decay of each $^{214}$Pb atom up to 81 minutes after production, resulting in (63 $\pm$ 6$_{\mathrm{stat}}$ $\pm$ 7$_{\mathrm{sys}}$)% identification of $^{214}$Pb decays to ground state. We also demonstrate how flow-based tagging techniques enable a novel calibration side band that is concurrent with science data.

Aalbers, J. [SLAC; Stanford U., Phys. Dept.; KIPAC↗

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 OSTI2024

Predicting phase transitions in PbTi⁢O 3 using zentropy through quasiharmonic phonon calculations

According to x-ray diffraction (XRD) measurements, PbTi⁢O 3 undergoes a phase transition from a tetragonal ferroelectric (FE) phase to a cubic paraelectric phase at 763 K. However, x-ray absorption fine-structure (XAFS) measurements indicate that PbTi⁢O 3 is locally tetragonal even after the phase transition. The difference in these results is because XAFS measurements can probe local features of a structure, while XRD averages over such local features. For both measurements to be consistent, PbTi⁢O 3 is macroscopically cubic but locally tetragonal after the phase transition. Despite this, most models, such as the Landau-Ginsburg-Devonshire theory and effective Hamiltonians, are still unable to explain this phenomenon. Moreover, these methods involve model parameters fitted to experimental or theoretical data and do not consider other tetragonal configurations, such as domain walls, to predict the phase transition. In our previous study, we used our zentropy approach to predict the phase transition by considering the tetragonal FE ground-state configuration and the tetragonal 90° and 180° domain wall configurations with their total energies at 0 K. Here, in this paper, the Helmholtz energies of the three configurations are obtained from density functional theory calculations through energy-volume curves and phonon calculations. The predicted phase transition temperature using the meta-GGA 𝑟 2⁢ SCAN and revised multiplicities of configurations is 716 K, showing good agreement with the experimental value of 763 K.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Local wave-number model for inhomogeneous two-fluid mixing

We analyze the local wave-number (LWN) model, a two-point spectral closure model for turbulence, as applied to the Rayleigh-Taylor (RT) instability, the flow induced by the relaxation of a statically-unstable density stratification. Model outcomes are validated against data from 3D simulations of the RT instability. In the first part of the study we consider the minimal model terms required to capture inhomogeneous mixing and show that this version, with suitable model coefficients, is sufficient to capture the evolution of important mean global quantities including mix-width, turbulent mass flux velocity, and Reynolds stress, if the start time is chosen such that the earliest transitions are avoided. However, this simple model does not permit the expected finite asymptote of the density-specific-volume covariance b. In the second part of the study, we investigate two forms for a source term for the evolution of the spectrum of density-specific-volume covariance for the LWN model. The first includes an empirically motivated calibration of the source to achieve the final asymptotic state of constant b. Here, the second form does not require calibration but, in conjunction with enhanced diffusion and drag captures the full evolution of all the dynamical quantities, namely, the mix-layer growth, turbulent mass-flux velocity, Reynolds stress, as well as the desired behavior of b.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

Metal-Supported Ceria Electrolyte-based SOFC Stack for Scalable, Low-Cost, High-Efficiency and Robust Stationary Power Systems (Final Report)

This is the end of project report for the DOE Project DE-FE-0027844 “Metal-Supported Ceria Electrolyte-based SOFC Stack for Scalable, Low-Cost, High-Efficiency and Robust Stationary Power Systems”. The objectives of the project were to develop several technologies required for the mass adoption of Solid Oxide Fuel Cell systems for medium to large power generation applications. The key achievements of this project were: 1) Development of fuel cells with complete internal fuel reforming capability. 2) Fuel cell power scale up with production of cells with larger active areas. 3) Assembly of an integrated 5 kW modular stack platform capable of installation into medium to large power systems. 4) Demonstration of a 10 kW Fuel Cell Power System utilizing the integrated 5 kW modular stack platform. 5) Cost modelling to show system cost of $1,500/kW are achievable at production volumes. 6) Development of cathode air poison getters for reduced degradation and extended fuel cell life. 7) Assessment of fuel poison on anode degradation, particularly poisons frequently produced from the process of gasification of coal. The Cummins led Voice of Customer (VOC) work identified several significant markets for natural gas powered fuel cell systems, where the end customer is interested in reducing energy consumption and emissions, or increasing reliability of electrical supply. Data centers and truck Auxiliary Power Units (APU) were highlighted as 2 key future markets for fuel cell systems.

30 DIRECT ENERGY CONVERSION↗

DOE OSTI2021

Can machine learning predict fuel properties accurately?

High-potential molecules derived from biomass sources may suitably replace or supplement traditional nonrenewable hydrocarbon fuels to reduce pollution and fuel processing cost. Experimental property testing of these bioproducts is usually conducted years after initial bench-scale experiments, due to high experimental costs and/or high volume requirements. However, neglecting to conduct property testing early in the pathway development cycle can lead to investments spent on scaling-up production of bioproducts and biofuels that do not perform as expected. Instead, machine-learning techniques can be used to develop quantitative structure–property relationships for molecules using a relatively large training set of molecular descriptor data. For this study, we compiled measured properties, IR spectra, and molecular descriptors of bio-based molecules from databases and published studies for training models of bioproduct properties. We trained regression models with molecular descriptors and will compare results of different estimators. This study describes the first steps towards a performance prediction tool for bio-based alternative fuels. Keywords: Machine learning, biofuels, jet fuels, fuel properties

Mayer, Morgan A.↗

DOE OSTI2020

Revised Kimberlina Groundwater Simulations

Kimberlina Groundwater Qaulity Simulations (Version 3: 2015 October) by Lawrence Livermore National Labratory. Submitted to the EDX team at the National Energy Technology Laboratory for research use. This dataset contains 562 updated groundwater quality simulations based on the Kimberlina site. It is a six-layer model including the aquifers and aquitards inbetween the ground surface and the reservoir. The input files and associated leakage information for these simulations are included in the zip file "nrap_kim_well31_fluxes and inputs.tar.gz". These 562 simulations are the successful results out of 1000 monte carlo simulations, with time length greater than 5 years. Each simulation consists 6 output files, therefore, there are 3372 files (6*562) in total. One single example simulation of full time length (200 year) is also provided in the zip file "single_simulation_200yr_sim0012.tar.gz". These 6 groundwater quality parameters are: - pH (use absolute value) - TDS (mg/kg) - Pressure (Pa) - CO2 Liquid Saturation (fraction range 0.0-1.0) - CO2 Gas Concentration (mol/L) - CO2 Liquid Concentration (mol/kg) Their correponding file names, take the first simulation for example, are: ph0001.ntab (for pH) , tds0001.ntab (for TDS), usnt0001.p.ntab (for pressure), usnt0001.s_liquid.ntab (for liquid saturation), usnt0001.c_co2_gas.ntab (for CO2 gas concentration) and usnt0001.c_co2_liquid.ntab (for CO2 liquid concentration). Each output file contains at least 19 columns (variables). The total number of columns depends on the simulation time length. The column data include the information of numerical records, geologic location and sizes and the simulated parameter values over time. The first 13 variables are about numerical records and relative geologic information for a simulation grid: 1. index: simulation index 2. i: the ith grid of x-axis 3. j: the jth grid of y-axis 4. k: the kth grid of z-axis 5. element_ref: element type reference 6. nuft_ind: nuft index 7. x: grid location in the x axis direction 8. y: grid location in the y axis direction 9. z: grid location in the z axis direction 10. dx: grid length in the x axis direction 11. dy: grid length in the y axis direction 12. dz: grid length in the z axis direction 13. volume: volume of the simulation grid The rest (14, 15, 16...) variables are the simulated parameter values over time, take pH as an example, are: 14. ph000y: initial pH value. 15. ph001y: simulated pH value at the end of the 1st year. 16. ph002y: simulated pH value at the end of the 2nd year. ... (and so on)... The zip input files have the input fluxes of brine and CO2 (in kg/s) allocated to model layers 1,2,3 and 5 (layers 4 and 6 are assumed to be no-flow aquitards) through the following nodes: (src1 WELL 7 7 25 25 10 32) #Etchegoin (src2 WELL 7 7 25 25 33 72) #Macoma Chanac (src3 WELL 7 7 25 25 73 83) #Santa Margarita Mclure (src4 WELL 7 7 25 25 84 89) #Fruitvale Round Mountain (aquitard) (src5 WELL 7 7 25 25 90 96) #Olcese Sand (thief zone) (src6 WELL 7 7 25 25 97 99) #tremblor Freeman (aquitard) ex: brn1 is assigned to src 1 from i=(7,7), j=(25,25), k=(10,32) Edited by Ya-Mei Yang at National Energy Technology Laboratory

brine leakage↗

DOE OSTI2022

Identifying Disinformation Using Rhetorical Devices in Natural Language Models

Foreign disinformation campaigns are strategically organized, extended efforts using disinformation – false or misleading information deliberately placed by an adversary – to achieve some goal. Disinformation campaigns pose severe threats to our nation’s security by misinforming decision makers and negatively influencing their actions when they are operating on limited amounts of evidence. Current efforts rely on subject matter experts to manually identify disinformation, or on computers and traditional natural language processing algorithms to identify patterns in data to calculate the probability that something is disinformation or not. While both have their merits and successes, subject matter experts are unable to keep up with the high volumes of global information and traditional natural language algorithms do not do well in identifying “why” something is disinformation or not. Our hypothesis is that we can identify disinformation by looking at the way someone speaks, in the rhetorical devices they use. We have curated and annotated a dataset designed for multiple natural language processing tasks, but specifically useful for disinformation detection algorithms.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

A GPU-based 2D shallow water quality model

In this paper, a 2D shallow water flow solver integrated with a water quality model is presented. The interaction between the main water quality constituents included is based on the Water Quality Analysis Simulation Program. Efficiency is achieved by computing with a combination of a Central Processing Unit (CPU) and a Graphics Processing Unit (GPU) device. This technique is intended to provide robust and accurate simulations with high computation speedups with respect to a single-core CPU in real events. The proposed numerical model is evaluated in cases that include the transport and reaction of water quality components over irregular bed topography and dry–wet fronts, verifying that the numerical solution in these situations conserves the required properties (C-property and positivity). The model can operate in any steady or unsteady form allowing an efficient assessment of the environmental impact of water flows. The field data from an unsteady river reach test case are used to show that the model is capable of predicting the measured temporal distribution of dissolved oxygen and water temperature, proving the robustness and computational efficiency of the model, even in the presence of noisy signals such as wind speed.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Improving evapotranspiration computation with electrical resistivity tomography in a maize field

Abstract Hydrogeophysical methods have been increasingly used to study subsurface soil–water dynamics, yet their application beyond the soil compartment or the quantitative link to soil hydraulic properties remains limited. To examine how these methods can inform model‐based evapotranspiration (ET) calculation under varying soil water conditions, we conducted a pilot‐scale field study at an experimental maize plot with manipulated irrigation treatments. Our goal was to develop a workflow for (1) acquiring and inverting field electrical resistivity tomography (ERT) data, (2) correlating ERT to soil hydraulic properties, (3) spatially characterizing soil water stress that feeds into ET modeling (the FAO‐56 model), and (4) evaluating the performance of ERT‐based ET computation. Our results showed that ERT was able to capture decimeter‐scale soil water content (SWC) dynamics from root water uptake and irrigation manipulation and the contrast of soil water stress between deficiently and fully irrigated maize. We also demonstrated the flexibility of using ERT to spatially integrate soil water stress in the soil volume of interest, which could be adjusted based on different crops and plot layouts. The integration of the ERT datasets into ET modeling provided insights into the spatial heterogeneity of the subsurface that has been challenging for point‐based sensing, which can further our understanding of the hydraulic dynamics in the soil‐plant‐atmosphere continuum.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

A nonparametric approach to modeling dependence among production parameters for energy cost estimation

Dependence existing among production parameters can significantly affect energy costs. For material removal processes, processing times and material amounts to be cut have positive dependence, and the dependence can affect energy costs by varying a peak electricity load. Existing methods to model the dependence of production parameters are based on parametric approaches that cannot accurately represent the dependence due to the rigid nature of parametric models. To address this issue, this study proposes a method to quantify dependence among manufacturing parameters through the application of the empirical copula to the dependence between the milling processing time and the amount of volume to be cut. The proposed method is illustrated by a case study of a manufacturing facility consisting of milling machines; a total of 27 scenarios are simulated for energy cost estimations. The case study clearly shows that the proposed method can capture the dependence between the milling parameters more accurately than a conventional dependence measure from parametric correlation models. Furthermore, the findings from this study would be useful to estimate energy costs in that the proposed method provides a better fit to real production data than conventional parametric approaches can.

42 ENGINEERING↗

DOE OSTI2025

Detecting thermodynamic phase transition via explainable machine learning of photoemission spectroscopy

Identifying thermodynamic signatures of electronic phases, such as superconductivity, is challenging in low-dimensional materials due to strong fluctuations and low probing volume. Spectroscopic methods are often used to identify new bulk phases, but their main measurable quantity—electronic energy gaps—is no longer an effective order parameter in low-dimensional and fluctuating systems. Combining angle-resolved photoemission with a domain-adversarial neural network, we report a data-driven method to identify thermodynamic phase transitions solely based on single-particle spectra. We demonstrate 97.6% accuracy in cuprate superconductor Bi 2 Sr 2 CaCu 2 O 8+δ with strong superconducting fluctuations. This model notably compensates for the scarcity of experimental data by leveraging virtually inexhaustible simulated data. Further, its explainability reveals the crucial role of in-gap spectral weight in detecting phase fluctuations and thermodynamic transitions. Our work pinpoints the spectroscopic signatures of fluctuating orders and enables using spectroscopy for machine-learning-assisted material discovery for low-dimensional and strong coupling systems.

2D materials↗