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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 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Fourier-MIONet: Fourier-enhanced multiple-input neural operators for multiphase modeling of geological carbon sequestration

Geologic carbon sequestration (GCS) is a safety-critical technology that aims to reduce the amount of carbon dioxide in the atmosphere, which also places high demands on reliability. Multiphase flow in porous media is essential to understand CO 2 migration and pressure fields in the subsurface associated with GCS. However, numerical simulation for such problems in 4D is computationally challenging and expensive, due to the multiphysics and multiscale nature of the highly nonlinear governing partial differential equations (PDEs). It prevents us from considering multiple subsurface scenarios and conducting real-time optimization. Here, we develop a Fourier-enhanced multiple-input neural operator (Fourier-MIONet) to learn the solution operator of the problem of multiphase flow in porous media. Fourier-MIONet utilizes the recently developed framework of the multiple-input deep neural operators (MIONet) and incorporates the Fourier neural operator (FNO) in the network architecture. Once Fourier-MIONet is trained, it can predict the evolution of saturation and pressure of the multiphase flow under various reservoir conditions, such as permeability and porosity heterogeneity, anisotropy, injection configurations, and multiphase flow properties. Compared to the enhanced FNO (U-FNO), the proposed Fourier-MIONet has 90% fewer unknown parameters, and it can be trained in significantly less time (about 3.5 times faster) with much lower CPU memory (<15%) and GPU memory (<35%) requirements, to achieve similar prediction accuracy. In addition to the lower computational cost, Fourier-MIONet can be trained with only 6 snapshots of time to predict the PDE solutions for 30 years. Furthermore, we observed that Fourier-MIONet can maintain good accuracy when predicting out-of-distribution (OOD) data. The excellent generalizability of Fourier-MIONet is enabled by its adherence to the physical principle that the solution to a PDE is continuous over time. Furthermore, the developed Fourier-MIONet makes it possible to solve the long-time evolution of geological carbon sequestration in a large-scale three-dimensional space accurately and efficiently.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

A new framework to map fine resolution cropping intensity across the globe: Algorithm, validation, and implication

We report accurate estimation of cropping intensity (CI), an indicator of food production, is well aligned with the ongoing efforts to achieve sustainable development goals (SDGs) under diminishing natural resources. The advancement in satellite remote sensing provides unprecedented opportunities for capturing CI information in a spatially continuous manner. However, challenges remain due to the lack of generalizable algorithms for accurately and efficiently mapping global CI with a fine spatial resolution. In this study, we developed a 30-m planetary-scale CI mapping framework with the reconstructed time series of Normalized Difference Vegetation Index (NDVI) from multiple satellite images. Using a binary crop phenophase profile indicating growing and non-growing periods, we estimated pixel-by-pixel CI by enumerating the total number of valid cropping cycles during the study years. Based on the Google Earth Engine cloud computing platform, we implemented the framework to estimate CI during 2016–2018 in eight geographic regions across continents that are representative of global cropping system diversity. Comparison with PhenoCam network data in four cropland sites suggests that the proposed framework is capable of capturing the seasonal dynamics of cropping practices. Spatially, overall accuracies based on validation samples range from 80.0% to 98.9% across different regions worldwide. Regarding the CI classes, single cropping systems are associated with more robust and less biased estimations than multiple cropping systems. Finally, our CI estimates reveal high agreement with two widely used land surface phenology products, including Vegetation Index and Phenology V004 (VIP4) and Moderate Resolution Imaging Spectroradiometer Land Cover Dynamics (MCD12Q2), meanwhile providing much more spatial details. Due to its robustness, the developed CI framework can be potentially generalized to produce global fine resolution CI products for food security and other applications.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

An adaptive synchronous extraction (ASE) method for estimating intensity and footprint of surface urban heat islands: A case study of 254 North American cities

The urban heat island (UHI) effect has attracted great attention due to its potential impacts on rapidly growing urban areas. Using remotely sensed estimates of land surface temperature (LST), a large number of studies have focused on the surface UHI (SUHI) effect, which can be characterized by its two fundamental properties: intensity and footprint. The SUHI intensity reflects the LST difference between the urban area and the background reference area (BRA), and the SUHI footprint indicates the spatial extent influenced by the heat island. Currently, numerous methods have been developed to estimate the SUHI intensity and footprint, but are still greatly challenged by three main issues. Namely, the discrepancy in BRA selection criterion brings great uncertainty to the estimated SUHI intensity, the estimation of SUHI footprint is largely constrained by the predefined models, and the quantification of SUHI effect is potentially influenced by several confounding factors. Here, we proposed an adaptive synchronous extraction (ASE) method, which is capable of adaptively selecting the most optimal BRA while removing the influence of confounding factors, and achieving synchronous estimation of SUHI intensity and footprint. We applied the ASE method to 254 North American cities and conducted an in-depth comparative analysis to discuss its applicability and benefits. The main results include: (1) The ASE method avoids the limitations of existing methods in BRA selection and model presetting, and shows resilience to parameter variations. This makes the ASE method highly applicable to quantify the SUHI intensity and footprint in cities with various thermal characteristics. (2) The ASE method can better highlight the spatial, seasonal and day-night contrasts in the estimated SUHI intensity. This superiority is particularly evident when comparing it to methods based on the equal-area buffer or the simplified urban-extent algorithm. (3) Confounding factors pose non-negligible impacts on the quantification of the SUHI effect. Typically, ignoring the influence of topographic relief or missing LST data can lead to an overall overestimation of the SUHI intensity, while not removing surrounding urban areas will cause some underestimation of the SUHI intensity. In conclusion, overall, the proposed ASE method provides a new generalizable tool for quantifying the SUHI effect, which has great potentials for future studies and urban climate assessments.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Ecological theory applied to environmental metabolomes reveals compositional divergence despite conserved molecular properties

Stream and river systems transport and process substantial amounts of dissolved organic matter (DOM) from terrestrial and aquatic sources to the ocean, with global biogeochemical implications. However, the underlying mechanisms affecting the spatiotemporal organization of DOM composition are under-investigated. To understand the principles governing DOM composition, we leverage the recently proposed synthesis of metacommunity ecology and metabolomics, termed ‘meta-metabolome ecology.’ Applying this novel approach to a freshwater ecosystem, we demonstrated that despite similar molecular properties across metabolomes, metabolite identity significantly diverged due to environmental filtering and variations in putative biochemical transformations. We refer to this phenomenon as ‘thermodynamic redundancy,’ which is analogous to the ecological concept of functional redundancy. We suggest that under thermodynamic redundancy, divergent metabolomes can support equivalent biogeochemical function just as divergent ecological communities can support equivalent ecosystem function. As these analyses are performed in additional ecosystems, potentially generalizable principles, like thermodynamic redundancy, can be revealed and provide insight into DOM dynamics.

Danczak, Robert E.↗
DOE OSTI2025

Autonomous alloy composition optimization using molecular dynamics guided by a large language model

Here, we present an autonomous materials discovery framework that couples a large language model (LLM) with molecular dynamics (MD) simulations to optimize Fe–Cr–Mn alloy compositions for tensile strength. Starting from six distinct compositions, the LLM operated as an intelligent agent, iteratively proposing changes based on prior simulation results and constraints. Over 50 iterations per case, the LLM adaptively explored the composition space, identifying high-strength regions, not easily accessible by conventional methods. The highest strength, 18.7 GPa, was achieved with Fe 71 Cr 25 Mn 4 composition, identified from a Fe 75 Cr 20 Mn 5 starting point. The LLM autonomously adjusted its strategy in real time, demonstrating closed-loop decision-making using commodity hardware. This approach showcases the potential of LLMs as scientific co-pilots, capable of accelerating materials discovery and generalizable to other domains like biology and drug design.

Autonomy↗
DOE OSTI2021

Revisiting diffusion-based moisture functions: why do they fail?

Microbial activities in soil are controlled by the balance between physical and biological mechanisms that are currently implied by soil moisture-respiration relationships, but not explicitly represented. Diffusion based moisture functions focus on physical controls, while substrate kinetics based models primarily address biological drivers. How to harmonize these two types of models for robust predictions of soil respiration and other processes has not been addressed. Here we derived a generalizable analytical solution of diffusion-limited nonlinear microbial uptake kinetics, in which microbial metabolic rates were governed by both physical and biological drivers via substrate diffusion and microbial affinity. We proposed a soil trait concept to integrate both physical and biological perspectives into one unified function, and tested it using both laboratory and field based observations from a variety of soils. This approach provides a tractable and scalable approach that incorporates soil heterogeneity and functional complexity in macroscopic model descriptions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

SynMADE: synthetic microbiota across diverse ecosystems

The last two decades have witnessed rapid advances in engineering individual microbial strains to produce biochemicals and biomaterials. Furthermore, engineering microbial consortia has been relatively slow. Using systems and synthetic biology approaches, researchers have been developing tools for engineering complex microbiota. In this article, I discuss future directions and visions regarding developing microbiota as a biomanufacturing host. Specifically, I propose that we can develop the soil microbial community itself as a huge bioreactor. Ultimately, researchers will provide a generalizable system that enables us to understand microbial consortium’s interaction and metabolism at diverse temporal and spatial scales to address global problems, including the climate crisis, food inequality, waste issue, and sustainable bioproduction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Producing multiple chemicals through biological upcycling of waste poly(ethylene terephthalate)

Poly(ethylene terephthalate) (PET) waste is of low degradability in nature, and its mismanagement threatens numerous ecosystems. To combat the accumulation of waste PET in the biosphere, PET bio-upcycling, which integrates chemical pretreatment to produce PET-derived monomers with their microbial conversion into value-added products, has shown promise. The recently discovered Rhodococcus jostii strain PET (RPET) can metabolically degrade terephthalic acid (TPA) and ethylene glycol (EG) as sole carbon sources, and it has been developed into a microbial chassis for PET upcycling. However, the scarcity of synthetic biology tools, specifically designed for the non-model microbe RPET, limits the development of a microbial cell factory for expanding the repertoire of bioproducts from post-consumer PET. Herein, we describe the development of potent genetic tools for RPET, including (1) two inducible and titratable expression systems for tunable gene expression and (2) Serine Integrase-based Recombinational Tools (SIRT) for genome editing. Using these tools, we systematically engineer the RPET strain to ultimately establish microbial supply chains for producing multiple chemicals, including lycopene, lipids, and succinate, from post-consumer PET waste bottles, achieving the highest titer of lycopene ever reported thus far in RPET (i.e., 22.6 mg/L of lycopene, approximately 10,000-fold higher than that of the wild-type strain). Furthermore, this work highlights the great potential of plastic upcycling as a generalizable means of sustainable production of diverse chemicals.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Can protein expression be ‘solved’?

Recombinant protein expression is central to biotechnology’s application in academic exploration as well as human health, climate applications and the bioeconomy in general. However, not all proteins can be expressed in all organisms, and the field lacks a predictive model of soluble protein overexpression that could replace laborious experimental trial-and-error. Here, we discuss the state of the field and identify the lack of large, high-fidelity datasets as the primary bottleneck to progress. We review possible assays that could be used for data collection to identify a path toward an extensible experimental platform for collecting soluble recombinant protein overexpression data across organisms. We suggest that the resulting dataset should be used to train increasingly generalizable predictive models of protein expression to answer the question: “How can predictive protein expression be solved?”.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

UEMtomaton: A Source-Available Platform to Aid in Start-up of Ultrafast Electron Microscopy Labs

The steady rise in the number of ultrafast electron microscopy (UEM) labs, in addition to the opacity and lack of detailed descriptions of current approaches that would enable point-by-point construction, has created an opportunity for sharing common methods and instrumentation for (for example) automating data acquisition to assist in efficient lab start-up and to learn about common and robust protocols. In the spirit of open sharing of methods, we provide here a description of an entry-level method and user interface (UI) for automating UEM experiments, and we provide access to the source code and scripts (source-available) for ease of implementation or as a starting reference point for those entering or seeking to enter the field (https://github.com/CEMSFlannigan/UEMtomaton/releases/tag/v1.0). Core instrumentation and physical connections in the UEM lab at Minnesota are described. Interface communication schemes consisting of duo server-client pairs between critical components – the optical delay stage and the UEM digital camera – are presented, with emphasis placed on describing the logic and communications sequence designed to conduct automated series acquisitions. An application designed and programmed with C++/CLI as Windows Forms in Microsoft Visual Studio – dubbed UEMtomaton – is also presented. Key to the UI layout is centralization of the automation tasks and establishment of communication within the software rather than by interfacing with each individual workstation. It is our hope that this note provides useful insight for current and future UEM researchers, particularly with respect to generalizability and portability of the approach to emerging labs. Here, we note that while this basic, entry-level approach is certainly not the most sophisticated or comprehensive of those currently in use, we feel there is nevertheless value in clearly communicating a proven straightforward method to hopefully lower the barrier to entry into the field.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Predicting Local Material Thickness from Steady-State Ultrasonic Wavefield Measurements Using a Convolutional Neural Network

Acoustic steady-state excitation spatial spectroscopy (ASSESS) is a full-field, ultrasonic non-destructive evaluation (NDE) technique used to locate and characterize defects in plate-like structures. ASSESS generates a steady-state, single-tone ultrasonic excitation in a structure and a scanning laser Doppler Vibrometer (LDV) measures the resulting full-field surface velocity response. Traditional processing techniques for ASSESS data rely on wavenumber domain analysis. This paper presents the alternative use of a convolutional neural network (CNN), trained using simulated ASSESS data, to predict the local plate thickness at every pixel in the wavefield measurement directly. The defect detection accuracy of CNN-based thickness predictions are shown to improve for defects of greater size, and for defects with higher thickness reductions. The CNN demonstrates the ability to predict thickness accurately in regions where Lamb wave dispersion relations are complex or unknown, such as near the boundaries of a test specimen, so long as the CNN is trained on data that accounts for these regions. The CNN also shows generalizability to ASSESS experimental data, despite an entirely simulated training dataset.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2026

Knowledge-guided graph machine learning for spatially distributed prediction of daily discharge and nitrogen export dynamics

Spatially distributed prediction of streamflow and nitrogen export dynamics is essential for precision management of agricultural watersheds. While temporal deep learning models such as Long Short-Term Memory (LSTM) have shown strong performance at basin scales, their ability to generalize spatially is limited by insufficient representation of spatial dependencies and flow paths, particularly under data-scarce conditions. To address this gap, we propose HydroGraphNet, a knowledge-guided graph machine learning framework that integrates process-based knowledge and explicit spatial learning into temporal modeling. This framework incorporates directed graph topology to encode watershed connectivity and upstream inflows, with mass balance constraints to improve physical consistency. To enhance generalization in sparsely monitored regions, HydroGraphNet is pretrained on synthetic data generated by the SWAT+ (Soil and Water Assessment Tool Plus) model. We evaluated HydroGraphNet in the Upper Sangamon River Basin (44 HUC-12 subwatersheds, 2001–2020) against two LSTM baselines: a lumped basin-level model and a distributed variant. When benchmarked on SWAT+ simulations in pretraining, HydroGraphNet improved test NSEs by 8.9% (discharge) and 13.7% (NO₃–N load) in temporal extrapolation, and by 27.1% and 34.7% in spatial extrapolation, relative to the Lumped LSTM baseline. After fine-tuning with USGS monitoring data, the model achieved mean test NSE (KGE) scores of 0.768 (0.861) for discharge and 0.626 (0.664) for NO₃–N load, substantially outperforming baselines. Attribution analysis further highlighted the importance of upstream inflow representation and graph-based spatial learning in capturing cross-subwatershed dependencies. The model also reproduced seasonal hydrological and biogeochemical patterns consistent with known processes, demonstrating its robustness and process fidelity for spatially distributed prediction. Altogether, HydroGraphNet advances the integration of physical knowledge and spatially explicit learning in hydrological modeling, offering a generalizable framework for distributed modeling to support spatially targeted water quality management in data-scarce watersheds.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Deep learning integrates histopathology and proteogenomics at a pan-cancer level

We introduce a pioneering approach that integrates pathology imaging with transcriptomics and proteomics to identify predictive histology features associated with critical clinical outcomes in cancer. We utilize 2,755 H&E-stained histopathological slides from 657 patients across 6 cancer types from CPTAC. Our models effectively recapitulate distinctions readily made by human pathologists: tumor vs. normal (AUROC = 0.995) and tissue-of-origin (AUROC = 0.979). We further investigate predictive power on tasks not normally performed from H&E alone, including TP53 prediction and pathologic stage. Importantly, we describe predictive morphologies not previously utilized in a clinical setting. The incorporation of transcriptomics and proteomics identifies pathway-level signatures and cellular processes driving predictive histology features. Model generalizability and interpretability is confirmed using TCGA. We propose a classification system for these tasks, and suggest potential clinical applications for this integrated human and machine learning approach. A publicly available web-based platform implements these models.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Computational design and analysis of modular cells for large libraries of exchangeable product synthesis modules

Microbial metabolism can be harnessed to produce a large library of useful chemicals from renewable resources such as plant biomass. However, it is laborious and expensive to create microbial biocatalysts to produce each new product. To tackle this challenge, we have recently developed modular cell (ModCell) design principles that enable rapid generation of production strains by assembling a modular (chassis) cell with exchangeable production modules to achieve overproduction of target molecules. Previous computational ModCell design methods are limited to analyze small libraries of around 20 products. In this study, we developed a new computational method, named ModCell-HPC, that can design modular cells for large libraries with hundreds of products with a highly-parallel and multi-objective evolutionary algorithm and enable us to elucidate modular design properties. We demonstrated ModCell-HPC to design Escherichia coli modular cells towards a library of 161 endogenous production modules. From these simulations, we identified E. coli modular cells with few genetic manipulations that can produce dozens of molecules in a growth-coupled manner with different types of fermentable sugars. These designs revealed key genetic manipulations at the chassis and module levels to accomplish versatile modular cells, involving not only in the removal of major by-products but also modification of branch points in the central metabolism. We further found that the effect of various sugar degradation on redox metabolism results in lower compatibility between a modular cell and production modules for growth on pentoses than hexoses. To better characterize the degree of compatibility, we developed a method to calculate the minimal set cover, identifying that only three modular cells are all needed to couple with up 85 compatible production modules. By determining the unknown compatibility contribution metric, we further elucidated the design features that allow an existing modular cell to be re-purposed towards production of new molecules. Altogether, ModCell-HPC is a useful tool for understanding modularity of biological systems and guiding more efficient and generalizable design of modular cells that help reduce research and development cost in biocatalysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Controlling selectivity of modular microbial biosynthesis of butyryl-CoA-derived designer esters

Short-chain esters have broad utility as flavors, fragrances, solvents, and biofuels. Controlling selectivity of ester microbial biosynthesis has been an outstanding metabolic engineering problem. In this study, we enabled the de novo fermentative microbial biosynthesis of butyryl-CoA-derived designer esters (e.g., butyl acetate, ethyl butyrate, butyl butyrate) in Escherichia coli with controllable selectivity. Using the modular design principles, we generated the butyryl-CoA-derived ester pathways as exchangeable production modules compatible with an engineered chassis cell for anaerobic production of designer esters. We designed these modules derived from an acyl-CoA submodule (e.g., acetyl-CoA, butyryl-CoA), an alcohol submodule (e.g., ethanol, butanol), a cofactor regeneration submodule (e.g., NADH), and an alcohol acetyltransferase (AAT) submodule (e.g., ATF1, SAAT) for rapid module construction and optimization by manipulating replication (e.g., plasmid copy number), transcription (e.g., promoters), translation (e.g., codon optimization), pathway enzymes, and pathway induction conditions. To further enhance production of designer esters with high selectivity, we systematically screened various strategies of protein solubilization using protein fusion tags and chaperones to improve the soluble expression of multiple pathway enzymes. Finally, our engineered ester-producing strains could achieve 19-fold increase in butyl acetate production (0.64 g/L, 96% selectivity), 6-fold increase in ethyl butyrate production (0.41 g/L, 86% selectivity), and 13-fold increase in butyl butyrate production (0.45 g/L, 54% selectivity) as compared to the initial strains. Altogether, this study presented a generalizable framework to engineer modular microbial platforms for anaerobic production of butyryl-CoA-derived designer esters from renewable feedstocks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

An Automated Scanning Transmission Electron Microscope Guided by Sparse Data Analytics

Abstract Artificial intelligence (AI) promises to reshape scientific inquiry and enable breakthrough discoveries in areas such as energy storage, quantum computing, and biomedicine. Scanning transmission electron microscopy (STEM), a cornerstone of the study of chemical and materials systems, stands to benefit greatly from AI-driven automation. However, present barriers to low-level instrument control, as well as generalizable and interpretable feature detection, make truly automated microscopy impractical. Here, we discuss the design of a closed-loop instrument control platform guided by emerging sparse data analytics. We hypothesize that a centralized controller, informed by machine learning combining limited a priori knowledge and task-based discrimination, could drive on-the-fly experimental decision-making. This platform may unlock practical, automated analysis of a variety of material features, enabling new high-throughput and statistical studies.

47 OTHER INSTRUMENTATION↗
DOE OSTI2026

Quantitative 14 N NMR with Monte Carlo Uncertainty Analysis of Nitrate/Nitrite in Alkaline Nuclear Waste

While monitoring of nitrate and nitrite concentrations is important for managing corrosion in nuclear waste systems, existing analytical methods are hindered by turbidity, spectral interference, and delays from sample handling. Here, we demonstrate quantitative 14 N nuclear magnetic resonance (qNMR) spectroscopy as a direct, matrix-tolerant approach for nitrate and nitrite detection at natural abundance. Monte Carlo resampling was integrated into the workflow to quantify random error, establish precision–time tradeoffs, and separate noise-limited uncertainty from systematic bias arising from shimming, transmitter offset, or excitation pulse conditions. Quantification of nitrate and nitrite were validated in controlled alkaline matrix challenges and in 18-component Hanford-type simulants. These results establish 14 N qNMR as a practical, uncertainty-bounded tool for monitoring redox-active nitrogen species in chemically complex environments and provide a generalizable framework for quantitative analysis of quadrupolar nuclei.

Graham, Trent R. [Pacific Northwest National Labor↗