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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 523 records · Page 29

Model data for infrastructure-aware simulation of compound flooding at Alligator Bayou Watershed, southeast Texas

This dataset supports infrastructure-aware hydrologic modeling and flood scenario analysis for the Alligator Bayou Watershed, a highly managed urban watershed in Southeast Texas. It includes Jupyter notebooks for figure reproduction, model configuration files, simulation outputs, and derived products used to quantify the influence of engineered stormwater infrastructure on flood behavior across multiple spatial scales. The dataset was generated using the Watershed Workflow Python package and the Advanced Terrestrial Simulator (ATS), enabling integrated surface–subsurface hydrologic simulations on a channel-aligned mesh with explicit representations of pump stations, gate structures, detention basins, and impervious surfaces. Outputs include time series of gate and pump flows, stage observations, and water balance components, as well as spatially explicit fields of peak ponded depth and flood duration across multiple infrastructure scenarios spanning a single-location detention basin expansion, distributed drainage limitations, and compound coastal flooding. These data facilitate full reproducibility of the manuscript figures and support further research on urban flood dynamics and the role of stormwater infrastructure in shaping watershed-scale flood response.

EARTH SCIENCE > OCEANS > COASTAL PROCESSES↗

Modeling antiphase boundary energies of Ni 3 Al-based alloys using automated density functional theory and machine learning

Antiphase boundaries (APBs) are planar defects that play a critical role in strengthening Ni-based superalloys, and their sensitivity to alloy composition offers a flexible tuning parameter for alloy design. Here, we report a computational workflow to enable the development of sufficient data to train machine-learning (ML) models to automate the study of the effect of composition on the (111) APB energy in Ni 3 Al-based alloys. We employ ML to leverage this wealth of data and identify several physical properties that are used to build predictive models for the APB energy that achieve a cross-validation error of 0.033 J m –2 . We demonstrate the transferability of these models by predicting APB energies in commercial superalloys. Moreover, our use of physically motivated features such as the ordering energy and stoichiometry-based features opens the way to using existing materials properties databases to guide superalloy design strategies to maximize the APB energy.

36 MATERIALS SCIENCE↗

Towards a study protocol: A data-driven workflow to identify error sources in direct ink write mechatronics

Abstract Using Direct Ink Write (DIW) technology in a rapid and large-scale production requires reliable quality control for printed parts. Data streams generated during printing, such as print mechatronics, are massive and diverse which impedes extracting insights. In our study protocol approach, we developed a data-driven workflow to understand the behavior of sensor-measured X- and Y- axes positional errors with process parameters, such as print velocity and velocity control. We uncovered patterns showing that instantaneous changes in the velocity, when the build platform accelerates and decelerates, largely influence the positional errors, especially in the X- axis due to the hardware architecture. Since DIW systems share similar mechatronic inputs and outputs, our study protocol approach is broadly applicable and scalable across multiple systems. Graphical abstract

36 MATERIALS SCIENCE↗

The need for standardization and improved open (meta)data practices in metaproteomics

Metaproteomics enables functional insight into microbial communities by identifying and quantifying proteins in complex samples. Yet, heterogeneous analytical workflows and the lack of standardization across experimental and bioinformatics stages hinder reproducibility and comparability, limiting integration with other omics data. We here present a community-developed reporting checklist tailored to the specific needs of metaproteomics. We also outline current efforts to enable structured and interoperable metadata capture, drawing on standards from proteomics and microbiome research wherever possible. By promoting transparent reporting and advancing metadata practices, our recommendations aim to align metaproteomics more closely with FAIR principles and support reproducible and interoperable research practices.

Armengaud, Jean [Universite Paris-Saclay, France]↗

Analysis of Organic Electron Materials using Neutron Scattering (Final Report)

Neutron scattering is a powerful suite of measurement techniques that enable unique analysis of structure and dynamics of a wide variety of materials. Specifically, neutrons interact strongly with protons, which enables excellent contrast in light element organic materials that cannot be obtained with any other measurements. This series of three proposals focused on using inelastic neutron scattering (INS) to study the vibrations (dynamics) of the organic molecules involved in organic electronic devices. Our main goals were to demonstrate that INS is capable of elucidating new, useful, and unique knowledge about organic electronic samples that could be used to improve the function of devices or to solve outstanding problems that could not be solved using other measurement techniques. Since all of the goal involved using INS or other neutron techniques to do something “new” a large part of the effort was focused on complex data interpretation and development of modeling workflows that could be used by other members of the organic electronics community to study their materials. To facilitate the goal of making INS measurements more accessible to a broader community and for a wider range of materials, we optimized and engineered the computational workflows to be well documented, publicly available, and user friendly. The individual titles of the three sequential DOE-BES awards are: (1) Engineering doping profiles in organic semiconducting materials, (2) Measurement and modeling of molecular dopant structure and dynamics, and (3) Quantification of Dynamic Disorder in Electronic and Excitonic Organic Materials. For readability, this report is organized to highlight the progress of the research thematically. Many of the ideas started in one grant period and then spilled over into later awards and collaborative research.

36 MATERIALS SCIENCE↗

A KBase Case Study on Genome-wide Transcriptomics and Plant Primary Metabolism in Sorghum

A better understanding of the genetic and metabolic mechanisms that confer stress resistance and tolerance in plants is key to engineering new crops through advanced breeding technologies. This requires a systems biology approach that builds on a genome-wide understanding of the regulation of gene expression, plant metabolism, physiology and growth. In this study, we examine the response to drought stress in Sorghum, as we leverage the tools for transcriptomics and plant metabolic modeling we have implemented at the U.S. Department of Energy Systems Biology Knowledgebase (KBase). KBase enables researchers worldwide to collaborate and advance research by allowing them to upload private or public data into the KBase Narrative Interface, empowering them to analyze this data using a rich, extensible array of computational and data-analytics tools, and allows them to securely share scientific workflows and conclusions. We demonstrate how to use the current RNA-seq tools in KBase, applicable to both plants and microbes, to assemble and quantify long transcripts and identify differentially expressed genes effectively. More specifically, we demonstrate the utility of the platform by identifying key genes that are differentially expressed during drought-stress in Sorghum bicolor, which is an important sustainable production crop plant. We then show how to use KBase tools to predict the membership of genes in metabolic pathways and examine expression data in the context of metabolic subsystems. We demonstrate the power of the platform by making the data analysis and interpretation available to the biologists in the reproducible, re-usable, point-and-click format of a KBase Narrative thus promoting FAIR (Findable, Accessible, Interoperable and Reusable) guiding principles for scientific data management and stewardship.

59 BASIC BIOLOGICAL SCIENCES↗

The Porous Microstructure Analysis (PuMA) software

The open-source Porous Microstructure Analysis (PuMA) software was created to offer an efficient framework for determining material properties from 3D microstructures. Its development was inspired by progress in X-ray microtomography, an imaging technology that captures the internal structure of materials in 3D, and even in a 4D temporal context. Over recent years, this method has transformed the domain of materials science due to its capability to non-destructively examine material microstructures while presenting digital data about their geometrical details. It has provided insights into materials relevant to several NASA missions, including heatshields, parachute fabrics, meteorites, and other advanced composites. PuMA, in its current version 3, delivers an array of features, spanning from basic geometric insights of a microstructure to intricate anisotropic thermo-elastic and chemical behavior. Specifically, the software evaluates morphological attributes (specific surface area, volume fractions, mean intercept lengths, orientation) and physical characteristics (conductivity, elasticity, permeability, and tortuosity). Additionally, it can model material degradation processes, such as oxidation and surface chemistry interactions. The software can generate synthetic microstructures, from straightforward geometrical designs to intricate woven and non-woven geometries. Coupling material generation and characterization enables parametric studies and sensitivity analysis to optimize the microstructural performance and inform design decisions and reliability assessment based on uncertainty quantification. A recent addition to PuMA includes the TomoSAM plugin, devised to incorporate the cutting-edge Segment Anything Model (SAM) into our image segmentation workflow. SAM is a promptable deep learning model that can identify objects and create image masks in a zero-shot manner, based only on a few user clicks. The synergy between these tools aids in the segmentation of complex 3D datasets from tomography and other imaging techniques, which would otherwise require a laborious manual segmentation process.

Tomography↗

Active and Transfer Learning of High-Dimensional Neural Network Potentials for Transition Metals

Classical molecular dynamics (MD) simulations represent a very popular and powerful tool for materials modeling and design. The predictive power of MD hinges on the ability of the interatomic potential to capture the underlying physics and chemistry. There have been decades of seminal work on developing interatomic potentials, albeit with a focus predominantly on capturing the properties of bulk materials. Such physics-based models, while extensively deployed for predicting the dynamics and properties of nanoscale systems over the past two decades, tend to perform poorly in predicting nanoscale potential energy surfaces (PESs) when compared to high-fidelity first-principles calculations. These limitations stem from the lack of flexibility in such models, which rely on a predefined functional form. Machine learning (ML) models and approaches have emerged as a viable alternative to capture the diverse size-dependent cluster geometries, nanoscale dynamics, and the complex nanoscale PESs, without sacrificing the bulk properties. Here, in this study, we introduce an ML workflow that combines transfer and active learning strategies to develop high-dimensional neural networks (NNs) for capturing the cluster and bulk properties for several different transition metals with applications in catalysis, microelectronics, and energy storage, to name a few. Our NN first learns the bulk PES from the high-quality physics-based models in literature and subsequently augments this learning via retraining with a higher-fidelity first-principles training data set to concurrently capture both the nanoscale and bulk PES. Our workflow departs from status-quo in its ability to learn from a sparsely sampled data set that nonetheless covers a diverse range of cluster configurations from near-equilibrium to highly nonequilibrium as well as learning strategies that iteratively improve the fingerprinting depending on model fidelity. All the developed models are rigorously tested against an extensive first-principles data set of energies and forces of cluster configurations as well as several properties of bulk configurations for 10 different transition metals. Our approach is material agnostic and provides a methodology to transfer and build upon the learnings from decades of seminal work in molecular simulations on to a new generation of ML-trained potentials to accelerate materials discovery and design.

36 MATERIALS SCIENCE↗

Non-destructive structural characterization of graphite components using mechanical resonance and deep learning

As compared to conventional nuclear reactors, microreactors have the potential to significantly reduce construction timelines and capital costs, decreasing the barriers for advanced nuclear reactor technologies. However, the lower power output of these microreactors (typically < 20 MWe) creates challenging economics if operation and maintenance costs cannot be sufficiently reduced. The compact size of these designs presents an opportunity for comprehensive in-situ structural health monitoring to provide real-time feedback in order to reduce operational costs associated with maintenance and downtime. Many microreactor concepts use graphite for both in-core neutron moderation and as a structural material, which has typically required some form of periodic and laborious inspection. This report provides a description and assessment of recent work with graphite to couple acoustic-based experimental measurements and characterization with machine learning models to mature structural health monitoring capabilities and generate benefits for the nuclear microreactor industry. With resilient embedded sensors in development in other programs funded by the US Department of Energy’s Office of Nuclear Energy and elsewhere, the work described herein builds upon previously funded efforts to mature non-destructive testing technology that relates measured vibrational signatures to structural changes, using a combination of new experimental measurements and machine learning processing. Building on past successful demonstrations of predictive workflows to identify structural changes in a hexagonal stainless steel test article with excellent acoustic propagation, we first performed baseline characterization on graphite samples with canonical geometries to ensure compatibility and confidence in the applied techniques for a material with distinctly different mechanical properties. In contrast to efforts in previous years, we worked exclusively with unidirectional vibration data that is more comparable to those expected from the existing embedded sensor technologies which are suitable for deployment in a reactor setting. Established acoustic and modern machine-learning-based characterization approaches were applied to the resulting datasets from these simple geometries. Both approaches were found to be highly capable of detecting even small geometric irregularities amongst nominally identical samples. As such, we then moved to testing these approaches for detection of artificial local stress perturbations introduced into a more complex geometry: a hexagonal block with drilled holes. A main outcome of this work is that a generalizable ML workflow can be used to detect and predict the characteristics of small artificial anomalies in a graphite component with a relevant geometry. While this work was performed using surficial vibration data, we expect the approach to be flexible and viable for other monitoring scenarios, such as those with different arrangements or types of sensor arrays. As compared to previously funded efforts, an existing ML workflow based on neural networks was enhanced through the addition of recently developed Fourier neural operators. As applied to previously collected and new vibration datasets, prediction accuracies of anomaly characterizations were greatly improved with minimal added computational cost. As trained on small durations of vibration data (tens of seconds) collected over a realistic number of locations, the model was able to reliably determine the presence of a subtle stress anomaly and begin to provide location estimates. Such an approach is likely to be viable for more relevant reactor damage scenarios for graphite components, such as progressive crack growth or creep.

36 MATERIALS SCIENCE↗

Final report- UFL - RAPIDS2: A SciDAC Institute for Computer Science, Data, and Artificial Intelligence

The research initiatives supported by the U.S. Department of Energy (DOE) Grant DE-SC0022265 are fundamentally aimed at pioneering advanced machine learning (ML) techniques for scientific data compression within high-performance computing (HPC) environments. This comprehensive body of work addresses the critical challenge posed by the exponential growth of data generated by scientific simulations in domains such as fusion energy, climate modeling, and computational fluid dynamics (CFD). A core objective is to develop compression algorithms that achieve substantial data reduction—often by orders of magnitude—while rigorously ensuring the fidelity of both the primary data (PD) and scientifically crucial derived quantities of interest (QoI). The methodologies deployed under this grant integrate sophisticated deep learning architectures, prominently featuring autoencoders, advanced generative models like conditional diffusion, and hybrid learning techniques. Key innovations include the development of Guaranteed Autoencoders (GAE) and the Guaranteed Conditional Diffusion with Tensor Correction (GCDTC) framework, which provide explicit, instance-level error bounds on reconstructed data. Furthermore, specialized strategies such as nonlinear constraint satisfaction are employed to preserve the integrity of QoI, a vital requirement for the trustworthiness of downstream scientific analyses. This research also focuses on the design and implementation of scalable, GPU-accelerated software pipelines that seamlessly integrate into existing HPC workflows, ensuring both computational efficiency and practical applicability. The CAESAR framework, for example, unifies foundation and generative models to create an adaptive and efficient compression solution for spatio-temporal scientific data. Collectively, these efforts represent a significant advancement in mitigating the scientific data deluge, enabling more effective data management, accelerated scientific discovery, and optimized utilization of HPC resources.

97 MATHEMATICS AND COMPUTING↗

An Adaptive Geometry-Free Thermo-Mechanical Model for Directed Energy Deposition Process Modeling

This presentation describes a novel, geometry-free thermo-mechanical model with adaptive subdomain con- struction to accurately predict the thermal conditions, distortions, and residual stresses throughout the directed energy deposition (DED) process. A novel finite element workflow is designed to con- duct the numerical analysis, based on the multi-app and data transfer capabilities in the open-source Multiphysics Object-Oriented Simulation Environment (MOOSE). Unlike with traditional methods, the part geometry in this model is not predefined. Instead, it is a combined effect of the processing parameters and material properties. At each time step, the model utilizes a subdomain construction paradigm to model the material deposition. A specialized mesh adaptivity scheme is incorporated to provide an accurate prediction while reducing the overall computational cost. The results generated by the proposed model show general agreement with the experimental measurements for the single track scan with varying processing parameters and demonstrate reasonable predictions for higher material buildups.

36 MATERIALS SCIENCE↗

Seeking regularity from irregularity: unveiling the synthesis–nanomorphology relationships of heterogeneous nanomaterials using unsupervised machine learning

Nanoscale morphology of functional materials determines their chemical and physical properties. However, despite increasing use of transmission electron microscopy (TEM) to directly image nanomorphology, it remains challenging to quantify the information embedded in TEM data sets, and to use nanomorphology to link synthesis and processing conditions to properties. We develop an automated, descriptor-free analysis workflow for TEM data that utilizes convolutional neural networks and unsupervised learning to quantify and classify nanomorphology, and thereby reveal synthesis–nanomorphology relationships in three different systems. While TEM records nanomorphology readily in two-dimensional (2D) images or three-dimensional (3D) tomograms, we advance the analysis of these images by identifying and applying a universal shape fingerprint function to characterize nanomorphology. After dimensionality reduction through principal component analysis, this function then serves as the input for morphology grouping through unsupervised learning. We demonstrate the wide applicability of our workflow to both 2D and 3D TEM data sets, and to both inorganic and organic nanomaterials, including tetrahedral gold nanoparticles mixed with irregularly shaped impurities, hybrid polymer-patched gold nanoprisms, and polyamide membranes with irregular and heterogeneous 3D crumple structures. In each of these systems, unsupervised nanomorphology grouping identifies both the diversity and the similarity of the nanomaterial across different synthesis conditions, revealing how synthetic parameters guide nanomorphology development. Our work opens possibilities for enhancing synthesis of nanomaterials through artificial intelligence and for understanding and controlling complex nanomorphology, both for 2D systems and in the far less explored case of 3D structures, such as those with embedded voids or hidden interfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DISCo-microbe: design of an identifiable synthetic community of microbes

Microbiomes are extremely important for their host organisms, providing many vital functions and extending their hosts’ phenotypes. Natural studies of host-associated microbiomes can be difficult to interpret due to the high complexity of microbial communities, which hinders our ability to track and identify individual members along with the many factors that structure or perturb those communities. For this reason, researchers have turned to synthetic or constructed communities in which the identities of all members are known. However, due to the lack of tracking methods and the difficulty of creating a more diverse and identifiable community that can be distinguished through next-generation sequencing, most such in vivo studies have used only a few strains. To address this issue, we developed DISCo-microbe, a program for the design of an identifiable synthetic community of microbes for use in in vivo experimentation. The program is composed of two modules; (1) create, which allows the user to generate a highly diverse community list from an input DNA sequence alignment using a custom nucleotide distance algorithm, and (2) subsample, which subsamples the community list to either represent a number of grouping variables, including taxonomic proportions, or to reach a user-specified maximum number of community members. As an example, we demonstrate the generation of a synthetic microbial community that can be distinguished through amplicon sequencing. The synthetic microbial community in this example consisted of 2,122 members from a starting DNA sequence alignment of 10,000 16S rRNA sequences from the Ribosomal Database Project. We generated simulated Illumina sequencing data from the constructed community and demonstrate that DISCo-microbe is capable of designing diverse communities with members distinguishable by amplicon sequencing. Using the simulated data we were able to recover sequences from between 97–100% of community members using two different post-processing workflows. Furthermore, 97–99% of sequences were assigned to a community member with zero sequences being misidentified. We then subsampled the community list using taxonomic proportions to mimic a natural plant host–associated microbiome, ultimately yielding a diverse community of 784 members. DISCo-microbe can create a highly diverse community list of microbes that can be distinguished through 16S rRNA gene sequencing, and has the ability to subsample (i.e., design) the community for the desired number of members and taxonomic proportions. Although developed for bacteria, the program allows for any alignment input from any taxonomic group, making it broadly applicable. The software and data are freely available from GitHub and Python Package Index (PYPI).

16S rRNA↗

CASTELO: clustered atom subtypes aided lead optimization—a combined machine learning and molecular modeling method

Background: Drug discovery is a multi-stage process that comprises two costly major steps: pre-clinical research and clinical trials. Among its stages, lead optimization easily consumes more than half of the pre-clinical budget. We propose a combined machine learning and molecular modeling approach that partially automates lead optimization workflow in silico, providing suggestions for modification hot spots. Results: The initial data collection is achieved with physics-based molecular dynamics simulation. Contact matrices are calculated as the preliminary features extracted from the simulations. To take advantage of the temporal information from the simulations, we enhanced contact matrices data with temporal dynamism representation, which are then modeled with unsupervised convolutional variational autoencoder (CVAE). Finally, conventional and CVAE-based clustering methods are compared with metrics to rank the submolecular structures and propose potential candidates for lead optimization. Conclusion: With no need for extensive structure-activity data, our method provides new hints for drug modification hotspots which can be used to improve drug potency and reduce the lead optimization time. It can potentially become a valuable tool for medicinal chemists.

59 BASIC BIOLOGICAL SCIENCES↗

Toward Urban Water Security: Broadening the Use of Machine Learning Methods for Mitigating Urban Water Hazards

Due to the complex interactions of human activity and the hydrological cycle, achieving urban water security requires comprehensive planning processes that address urban water hazards using a holistic approach. However, the effective implementation of such an approach requires the collection and curation of large amounts of disparate data, and reliable methods for modeling processes that may be co-evolutionary yet traditionally represented in non-integrable ways. In recent decades, many hydrological studies have utilized advanced machine learning and information technologies to approximate and predict physical processes, yet none have synthesized these methods into a comprehensive urban water security plan. In this paper, we review ways in which advanced machine learning techniques have been applied to specific aspects of the hydrological cycle and discuss their potential applications for addressing challenges in mitigating multiple water hazards over urban areas. We also describe a vision that integrates these machine learning applications into a comprehensive watershed-to-community planning workflow for smart-cities management of urban water resources.

54 ENVIRONMENTAL SCIENCES↗

Database and deep-learning scalability of anharmonic phonon properties by automated brute-force first-principles calculations

Understanding the anharmonic phonon properties of crystal compounds—such as phonon lifetimes and thermal conductivities—is essential for investigating and optimizing their thermal transport behaviors. These properties also impact optical, electronic, and magnetic characteristics through interactions between phonons and other quasiparticles and fields. In this study, we develop an automated first-principles workflow to calculate anharmonic phonon properties and build a comprehensive database encompassing more than 6500 inorganic compounds. Utilizing this dataset, we train a graph neural network model to predict thermal conductivity values and spectra from structural parameters, demonstrating a scaling law in which prediction accuracy improves with increasing training data size. High-throughput screening with the model enables the identification of materials exhibiting extreme thermal conductivities—both high and low. The resulting database offers valuable insights into the anharmonic behavior of phonons, thereby accelerating the design and development of advanced functional materials.

Ohnishi, Masato [University of Tokyo (Japan); Inst↗

HydraGNN v5.0

HydraGNN v5.0 expands the code base into a more portable, scalable, and flexible framework for scientific graph learning, with particular strength in atomistic machine-learning interatomic potentials and large-scale distributed training. The release adds Fully Sharded Data Parallel (FSDP) support alongside existing DDP and DeepSpeed paths, including FSDP-aware checkpointing and optimizer integration, and introduces a configurable multi-precision training workflow supporting FP32, BF16, and FP64 across GPUs and Intel XPUs. For atomistic modeling, HydraGNN v5.0 strengthens its MLIP capabilities through dynamic graph construction at every forward pass, energy-conserving force prediction via automatic differentiation, and per-atom energy loss formulations, while extending EGNN models to properly handle periodic boundary conditions. The release also broadens model expressiveness through graph-level attribute conditioning, adds new multi-task and model-parallel extensions such as MACE support and encoder/decoder branch optimization, and expands application coverage with integrated examples for datasets including OC25, Nabla2-DFT, QCML, Open Polymers 2026, and OPF. In parallel, HydraGNN v5.0 improves production readiness through performance optimizations for large-scale runs, stratified sampling and linear-regression preprocessing utilities, and tested installation scripts for DOE supercomputers including Frontier, Aurora, Perlmutter, and Andes. Overall, the release advances HydraGNN as a robust software platform for scalable graph neural networks across materials science, chemistry, and scientific machine learning workflows

Lupo Pasini, Massimiliano [Oak Ridge National Labo↗

Integrative SP3 Workflow for Multi-PTM Proteomics Profiling (TZ-DP0)

The goal of the experiment was to demonstrate that the optimized multiplexed multi-PTM profiling workflow can comprehensively and quantitatively capture dynamic changes in protein abundance, cysteine oxidation, phosphorylation, and acetylation in cytokine-induced inflammatory stress in mouse pancreatic ß-cells. Global proteomic, redox proteomic, phosphoproteomic, and acetylomic were data collected from mouse Beta-TC-6 pancreatic Beta-cells, untreated (mock) and cytokine-treated Beta-cells at 4, 8, and 24 hours with 4 biological replicates. Samples were digested with trypsin and Lys-C, then analyzed by LC-MS/MS. Data were searched with MS-GF+, MASIC, and MaxQuant using PNNL's DMS processing pipeline.

59 BASIC BIOLOGICAL SCIENCES↗