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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 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
DOE OSTI2011

Expansion of the Genomic Encyclopedia of Bacteria and Archaea

To date the vast majority of bacterial and archaeal genomes sequenced are of rather limited phylogenetic diversity as they were chosen based on their physiology and/ or medical importance. The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project (Wu et al. 2009) is aimed to systematically filling the gaps of the tree of life with phylogenetically diverse reference genomes. However more than 99percent of microorganisms elude current culturing attempts, severely limiting the ability to recover complete or even partial genomes of these largely mysterious species. These limitations gave rise to the GEBA uncultured project. Here we propose to use single cell genomics to massively expand the Genomic Encyclopedia of Bacteria and Archaea by targeting 80 single cell representatives of uncultured candidate phyla which have no or very few cultured representatives. Generating these reference genomes of uncultured microbes will dramatically increase the discovery rate of novel protein families and biological functions, shed light on the numerous underrepresented phyla that likely play important roles in the environment, and will assist in improving the reconstruction of the evolutionary history of Bacteria and Archaea. Moreover, these data will improve our ability to interpret metagenomics sequence data from diverse environments, which will be of tremendous value for microbial ecology and evolutionary studies to come.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Expansion of the Genomic Encyclopedia of Bacteria and Archaea

To date the vast majority of bacterial and archaeal genomes sequenced are of rather limited phylogenetic diversity as they were chosen based on their physiology and/ or medical importance. The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project (Wu et al. 2009) is aimed at systematically filling the gaps of the tree of life with phylogenetically diverse reference genomes. However more than 99 percent of microorganisms elude current culturing attempts, severely limiting the ability to recover complete or even partial genomes of these largely mysterious species. These limitations gave rise to the GEBA uncultured project. Here we propose to use single cell genomics to massively expand the Genomic Encyclopedia of Bacteria and Archaea by targeting 80 single cell representatives of uncultured candidate phyla which have no or very few cultured representatives. Generating these reference genomes of uncultured microbes will dramatically increase the discovery rate of novel protein families and biological functions, shed light on the numerous underrepresented phyla that likely play important roles in the environment, and will assist in improving the reconstruction of the evolutionary history of Bacteria and Archaea. Moreover, these data will improve our ability to interpret metagenomics sequence data from diverse environments, which will be of tremendous value for microbial ecology and evolutionary studies to come.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

In this study, genome-scale metabolic models are mathematically structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repositories of high-quality models must be established, models must adhere to established standards and model components must be linked to relevant databases. Tools for model visualization further enhance their utility. To meet these needs, we present BiGG Models (http://bigg.ucsd.edu), a completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG Models contains more than 75 high-quality, manually-curated genome-scale metabolic models. On the website, users can browse, search and visualize models. BiGG Models connects genome-scale models to genome annotations and external databases. Reaction and metabolite identifiers have been standardized across models to conform to community standards and enable rapid comparison across models. Furthermore, BiGG Models provides a comprehensive application programming interface for accessing BiGG Models with modeling and analysis tools. As a resource for highly curated, standardized and accessible models of metabolism, BiGG Models will facilitate diverse systems biology studies and support knowledge-based analysis of diverse experimental data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Attention-based functional-group coarse-graining: a deep learning framework for molecular prediction and design

Machine learning (ML) offers considerable promise for the design of new molecules and materials. In real-world applications, the design problem is often domain-specific, and suffers from insufficient data, particularly labeled data, for ML training. In this study, we report a data-efficient, deep-learning framework for molecular discovery that integrates a coarse-grained functional-group representation with a self-attention mechanism to capture intricate chemical interactions. Our approach exploits group-contribution concepts to create a graph-based intermediate representation of molecules, serving as a low-dimensional embedding that substantially reduces the data demands typically required for training. Using a self-attention mechanism to learn the subtle but highly relevant chemical context of functional groups, the method proposed here consistently outperforms existing approaches for predictions of multiple thermophysical properties. In a case study focused on adhesive polymer monomers, we train on a limited dataset comprising only 6,000 unlabeled and 600 labeled monomers. The resulting chemistry prediction model achieves over 92% accuracy in forecasting properties directly from SMILES strings, exceeding the performance of current state-of-the-art techniques. Furthermore, the latent molecular embedding is invertible, enabling the design pipeline to automatically generate new monomers from the learned chemical subspace. We illustrate this functionality by targeting several properties, including high and low glass transition temperatures (Tg), and demonstrate that our model can identify new candidates with values that surpass those in the training set. The ease with which the proposed framework navigates both chemical diversity and data scarcity offers a promising route to accelerate and broaden the search for functional materials.

Han, Ming [Univ. of Chicago, IL (United States)]↗
DOE OSTI2014

Flexible and Scalable Data Fusion using Proactive Schemaless Information Services

Exascale data environments are fast approaching, driven by diverse structured and unstructured data such as system and application telemetry streams, open-source information capture, and on-demand simulation output. Storage costs having plummeted, the question is now one of converting vast stores of data to actionable information. Complicating this problem are the low degrees of awareness across domain boundaries about what potentially useful data may exist, and write-once- read-never issues (data generation/collection rates outpacing data analysis and integration rates). Increasingly, technologists and researchers need to correlate previously unrelated data sources and artifacts to produce fused data views for domain-specific purposes. New tools and approaches for creating such views from vast amounts of data are vitally important to maintaining research and operational momentum. We propose to research and develop tools and services to assist in the creation, refinement, discovery and reuse of fused data views over large, diverse collections of heterogeneously structured data. We innovate in the following ways. First, we enable and encourage end-users to introduce customized index methods selected for local benefit rather than for global interaction (flexible multi-indexing). We envision rich combinations of such views on application data: views that span backing stores with different semantics, that introduce analytic methods of indexing, and that define multiple views on individual data items. We specifically decline to build a big fused database of everything providing a centralized index over all data, or to export a rigid schema to all comers as in federated query approaches. Second, we proactively advertise these application-specific views so that they may be programmatically reused and extended (data proactivity). Through this mechanism, both changes in state (new data in existing view collected) and changes in structure (new or derived view exists) are made known. Lastly, we embrace found data heterogeneity by coupling multi-indexing to backing stores with appropriate semantics (as opposed to a single store or schema).

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2014

Flexible and Scalable Data Fusion using Proactive, Schemaless Information Services

Exascale data environments are fast approaching, driven by diverse structured and unstructured data such as system and application telemetry streams, open-source information capture, and on-demand simulation output. Storage costs having plummeted, the question is now one of converting vast stores of data to actionable information. Complicating this problem are the low degrees of awareness across domain boundaries about what potentially useful data may exist, and write-once-read- never issues (data generation/collection rates outpacing data analysis and integration rates). Increasingly, technologists and researchers need to correlate previously unrelated data sources and artifacts to produce fused data views for domain-specific purposes. New tools and approaches for creating such views from vast amounts of data are vitally important to maintaining research and operational momentum. We propose to research and develop tools and services to assist in the creation, refinement, discovery and reuse of fused data views over large, diverse collections of heterogeneously structured data. We innovate in the following ways. First, we enable and encourage end-users to introduce customized index methods selected for local benefit rather than for global interaction (flexible multi-indexing). We envision rich combinations of such views on application data: views that span backing stores with different semantics, that introduce analytic methods of indexing, and that define multiple views on individual data items. We specifically decline to build a big fused database of everything providing a centralized index over all data, or to export a rigid schema to all comers as in federated query approaches. Second, we proactively advertise these application-specific views so that they may be programmatically reused and extended (data proactivity). Through this mechanism, both changes in state (new data in existing view collected) and changes in structure (new or derived view exists) are made known. Lastly, we embrace found data heterogeneity by coupling multi-indexing to backing stores with appropriate semantics (as opposed to a single store or schema).

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2024

Identifying microbial drivers in biological phenotypes with a Bayesian network regression model

Abstract In Bayesian Network Regression models, networks are considered the predictors of continuous responses. These models have been successfully used in brain research to identify regions in the brain that are associated with specific human traits, yet their potential to elucidate microbial drivers in biological phenotypes for microbiome research remains unknown. In particular, microbial networks are challenging due to their high dimension and high sparsity compared to brain networks. Furthermore, unlike in brain connectome research, in microbiome research, it is usually expected that the presence of microbes has an effect on the response (main effects), not just the interactions. Here, we develop the first thorough investigation of whether Bayesian Network Regression models are suitable for microbial datasets on a variety of synthetic and real data under diverse biological scenarios. We test whether the Bayesian Network Regression model that accounts only for interaction effects (edges in the network) is able to identify key drivers (microbes) in phenotypic variability. We show that this model is indeed able to identify influential nodes and edges in the microbial networks that drive changes in the phenotype for most biological settings, but we also identify scenarios where this method performs poorly which allows us to provide practical advice for domain scientists aiming to apply these tools to their datasets. BNR models provide a framework for microbiome researchers to identify connections between microbes and measured phenotypes. We allow the use of this statistical model by providing an easy‐to‐use implementation which is publicly available Julia package at https://github.com/solislemuslab/BayesianNetworkRegression.jl .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

From molecules to dynamic biological communities

Microbial ecology is flourishing, and in the process, is making contributions to how the ecology and biology of large organisms is understood. Ongoing advances in sequencing technology and computational methods have enabled the collection and analysis of vast amounts of molecular data from diverse biological communities. While early studies focused on cataloguing microbial biodiversity in environments ranging from simple marine ecosystems to complex soil ecologies, more recent research is concerned with community functions and their dynamics over time. Models and concepts from traditional ecology have been used to generate new insight into microbial communities, and novel system-level models developed to explain and predict microbial interactions. The process of moving from molecular inventories to functional understanding is complex and challenging, and never more so than when many thousands of dynamic interactions are the phenomena of interest. We outline the process of how epistemic transitions are made from producing catalogues of molecules to achieving functional and predictive insight, and show how those insights not only revolutionize what is known about biological systems but also about how to do biology itself. Examples will be drawn primarily from analyses of different human microbiota, which are the microbial consortia found in and on areas of the human body, and their associated microbiomes (the genes of those communities). Molecular knowledge of these microbiomes is transforming microbiological knowledge, as well as broader aspects of human biology, health and disease.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

SAM-I-Am: Semantic boosting for zero-shot atomic-scale electron micrograph segmentation

Image segmentation is a critical enabler for tasks ranging from medical diagnostics to autonomous driving. However, the correct segmentation semantics — where are boundaries located? what segments are logically similar? — change depending on the domain, such that state-of-the-art foundation models can generate meaningless and incorrect results. Moreover, in certain domains, fine-tuning and retraining techniques are infeasible: obtaining labels is costly and time-consuming; domain images (micrographs) can be exponentially diverse; and data sharing (for third-party retraining) is restricted. To enable rapid adaptation of the best segmentation technology, we propose the concept of semantic boosting: given a zero-shot foundation model, guide its segmentation and adjust results to match domain expectations. Here, we apply semantic boosting to the Segment Anything Model (SAM) to obtain microstructure segmentation for transmission electron microscopy. Our booster, SAM-I-Am, serves as a post-processing engine that extracts geometric and textural features of various intermediate masks to perform mask removal and mask merging operations. We demonstrate a zero-shot performance increase of (absolute) +21.35%, +12.6%, +5.27% in mean IoU, and a -9.91%, -18.42%, -4.06% drop in mean false positive masks across images of three difficulty classes over vanilla SAM (ViT-L).

36 MATERIALS SCIENCE↗
DOE OSTI2018

The F-t-Pj-RG method: An adjacent-rolling-windows based steady-state detection technique for application to kinetic Monte Carlo simulations

A window-based steady-state detection algorithm has been developed for application to kinetic Monte Carlo simulation data. The algorithm, termed F-t-Pj-RG sequentially applies an F-test, a t-test, and a projection test on adjacent windows of the data while rolling (or shifting) and growing the windows when any of the tests fail. In aggregate, the algorithm is able to (a) automatically reject the warm-up period as not being at steady-state, as well as (b) determine an appropriate window size for converged statistics when sampling the data, which is necessary for detection of steady-state, and (c) detect steady-state within a particular tolerance. The last step, the projection test, is actually an oscillating-slope projection test, and is performed on j sequential data windows (i.e., more than two adjacent windows). It requires more than simply being within the user defined tolerance: the oscillating-slope projection test includes a condition that the slope must oscillate around zero when 2, which is an additional indication of steady-state. When all three tests are passed, the F-t-Pj test is passed, indicating that the prerequisites of steady-state detection have been met and also that conditions consistent with the definition of steady-state have been realized. This algorithm is applied to a variety of data sets that correspond to the diverse type of data trends that can be produced by kinetic Monte Carlo simulations. The algorithm is shown to be robust in its ability to handle differing functional forms, and is able to detect steady-state with low computational cost. Finally, the low computational cost of this method and its robustness towards varied data trends make it suitable for on-the-fly use in kinetic Monte Carlo simulations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Play fairway analysis of geothermal resources across the state of Hawaii: 2. Resource probability mapping

We develop a new geostatistical method to combine evidence provided by diverse geological data sets and produce maps of geothermal resource probability. The application is to the State of Hawaii, and the data sets include the locations and ages of mapped volcanic centers, gravity and magnetotelluric measurements, groundwater temperature and geochemistry, ground surface deformation, seismicity, water table elevation, and groundwater recharge. Using the basic principles of Bayesian statistics, these data and expert knowledge about the effects and importance of the data are used to compute the probabilities of the primary resource qualities of elevated subsurface heat, reservoir permeability, and reservoir fluid content. The product of these marginal probabilities estimates the joint probability of all three qualities and hence the probability of a successful geothermal prospect at each map point. An analogous set of algorithms is used to quantify the confidence in the probability at each point. Not surprisingly, we find that successful geothermal prospects are most probable on the active volcanoes of Hawaii Island, including the area of Hawaii’s single geothermal energy plant. Probability decreases primarily with shield volcano age, being relatively moderate in select locations on Maui and Lanai, relatively low on Oahu, and minimal on Kauai. Future exploration efforts should consider these results as well as the practical, societal, and economic conditions that influence development viability. Here, the difficulties of interisland power transmission mean that even areas with moderate to low probabilities are worth investigating on islands with population centers.

15 GEOTHERMAL ENERGY↗
DOE OSTI2024

Foundation Models for the Electric Power Grid

Foundation models (FMs) currently dominate news headlines. They employ advanced deep learning architectures to extract structural information autonomously from vast datasets through self-supervision. The resulting rich representations of complex systems and dynamics can be applied to many downstream applications. Therefore, advances in FMs can find uses in electric power grids, challenged by the energy transition and climate change. This paper calls for the development of FMs for electric grids. We highlight their strengths and weaknesses amidst the challenges of a changing grid. It is argued that FMs learning from diverse grid data and topologies, which we call grid foundation models (GridFMs), could unlock transformative capabilities, pioneering a new approach to leveraging AI to redefine how we manage complexity and uncertainty in the electric grid. Finally, we discuss a practical implementation pathway and road map of a GridFM-v0, a first GridFM for power flow applications based on graph neural networks, and explore how various downstream use cases will benefit from this model and future GridFMs.

AI-based power flow simulation↗
DOE OSTI2015

Molecular dynamics simulations of large macromolecular complexes

Connecting dynamics to structural data from diverse experimental sources, molecular dynamics simulations permit the exploration of biological phenomena in unparalleled detail. Advances in simulations are moving the atomic resolution descriptions of biological systems into the million-to-billion atom regime, in which numerous cell functions reside. In this opinion, we review the progress, driven by large-scale molecular dynamics simulations, in the study of viruses, ribosomes, bioenergetic systems, and other diverse applications. Finally, these examples highlight the utility of molecular dynamics simulations in the critical task of relating atomic detail to the function of supramolecular complexes, a task that cannot be achieved by smaller-scale simulations or existing experimental approaches alone.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Spatiotemporal and Statistical Mapping of Transition Metal Equilibria in Alkaline Media

Transition metal dissolution and redeposition (D/R) kinetics in alkaline media play a critical role in various chemical and electrochemical processes. Competitive reaction kinetics between different transition metals can modulate individual metal behavior in these processes. To date, these phenomena have remained largely unmeasured, and even when captured, they are difficult to statistically characterize due to their dynamic nature, simultaneous occurrence, and spatially heterogeneous nature. Here, in this study, we develop a statistical analysis framework based on in situ and operando X-ray fluorescence microscopy (XFM) to investigate the relative D/R kinetics of multiple transition metals in alkaline media. By employing statistical analysis, we quantify the spatial distribution of D/R species and assess the rate at which the system reaches equilibrium under varying reaction conditions. We show that pH does not simply change the rate of dissolution and redeposition, but reorganizes the cross-element kinetic correlations among Ni, Fe, and Mn and accelerates the spatial equilibration of D/R events, as quantified through correlation analysis, reaction-rate estimation, probability function distributions, and texture-based monitoring statistics. Additionally, we demonstrate how modifying the solvent environment can influence D/R kinetics, providing a pathway for tuning materials synthesis and process optimization. Our study offers valuable insights into the complex interplay between different transition metals and provides a reliable statistical framework for spatial analysis of diverse imaging data sets, enabling deeper extraction of latent information across multiple modalities.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Characterizing Defect Dynamics in Silicon Carbide Using Symmetry-Adapted Collective Variables and Machine Learning Interatomic Potentials

Silicon carbide (SiC) divacancies are attractive candidates for spin-defect qubits possessing long coherence times and optical addressability. The high activation barriers associated with SiC defect formation and motion pose challenges for their study by first-principles molecular dynamics. In this work, we develop and deploy machine learning interatomic potentials (MLIPs) to accelerate defect dynamics simulations while retaining ab initio accuracy. We employ an active learning strategy comprising symmetry-adapted collective variable discovery and enhanced sampling to compile configurationally diverse training data, calculation of energies and forces using density functional theory (DFT), and training of an E(3)-equivariant MLIP based on the Allegro model. Here, the trained MLIP reproduces DFT-level accuracy in defect transition activation free energy barriers, enables the efficient and stable simulation of multidefect 216-atom supercells, and permits an analysis of the temperature dependence of defect thermodynamic stability and formation/annihilation kinetics to propose an optimal annealing temperature to maximally stabilize VV divacancies.

Computer simulations↗
DOE OSTI2021

Uncertainties in Atmospheric River Lifecycles by Detection Algorithms: Climatology and Variability

Atmospheric rivers (ARs) are long and narrow filaments of vapor transport that are responsible for most poleward moisture transport outside of the tropics. Many AR detection algorithms have been developed to automatically identify ARs in climate data. The diversity of these algorithms has introduced appreciable uncertainties in quantitative measures of AR properties and thereby impedes the construction of a unified and internally consistent climatology of ARs. This paper compares nine global AR detection algorithms from the perspective of AR lifecycles following the propagation of ARs from origin to termination in the MERRA2 reanalysis over the period 1980–2017. Uncertainties in AR lifecycle characteristics, including event number, lifetime, intensity, and frequency distribution are discussed. Notably, the number of AR events per year in the Northern Hemisphere can vary by a factor of 5 with different algorithms. Although all algorithms show that the maximum AR origin (termination) frequency is located over the western (eastern) portion of ocean basins, significant disagreements appear in regional distribution. Spreads are large in AR lifetime and intensity. Here, the number of landfalling AR events produced by the algorithms can vary from 16 to 80 events per year, although the agreement improves for stronger ARs. By examining the ARs' connections with the Madden-Julian Oscillation and El Niño Southern Oscillation, we find that the overall responses of ARs (such as changes in AR frequency, origin, and landfall activity) to climate variability are consistent among algorithms.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Big data analytics in smart grids: state-of-the-art, challenges, opportunities, and future directions

Big data has a potential to unlock novel groundbreaking opportunities in the power grid sector that enhances a multitude of technical, social, and economic gains. The currently untapped potential of applying the science of big data for better planning and operation of the power grid is a very challenging task and needs significant efforts all-around. As power grid technologies evolve in conjunction with measurement and communication technologies, this results in unprecedented amount of heterogeneous big data sets from diverse sources. In particular, computational complexity, data security, and operational integration of big data into utility decision frameworks are the key challenges to transform the heterogeneous large dataset into actionable outcomes. Moreover, due to the complex nature of power grids along with the need to balance power in real time, seamless integration of big data into utility operations is very critical. In this context, big data analytics combined with grid visualization can lead to better situational awareness and predictive decisions. This paper presents a comprehensive state-of-the-art review of big data analytics and its applications in power grids, and also identifies challenges and opportunities from utility, industry, and research perspectives. The paper analyzes research gaps and presents insights on future research directions to integrate big data analytics into electric utility decision framework. Detailed information for utilities looking to apply big data analytics and details insights on how utilities can enhance revenue streams and bring disruptive innovation in the industry are discussed. More importantly, general guidelines for utilities to make the right investment in the adoption of big data analytics by unveiling interdependencies among critical infrastructures and operations are also provided.

13 HYDRO ENERGY↗