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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 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Scalable algorithms for physics-informed neural and graph networks

Physics-informed machine learning (PIML) has emerged as a promising new approach for simulating complex physical and biological systems that are governed by complex multiscale processes for which some data are also available. In some instances, the objective is to discover part of the hidden physics from the available data, and PIML has been shown to be particularly effective for such problems for which conventional methods may fail. Unlike commercial machine learning where training of deep neural networks requires big data, in PIML big data are not available. Instead, we can train such networks from additional information obtained by employing the physical laws and evaluating them at random points in the space–time domain. Such PIML integrates multimodality and multifidelity data with mathematical models, and implements them using neural networks or graph networks. Here, we review some of the prevailing trends in embedding physics into machine learning, using physics-informed neural networks (PINNs) based primarily on feed-forward neural networks and automatic differentiation. For more complex systems or systems of systems and unstructured data, graph neural networks (GNNs) present some distinct advantages, and here we review how physics-informed learning can be accomplished with GNNs based on graph exterior calculus to construct differential operators; we refer to these architectures as physics-informed graph networks (PIGNs). We present representative examples for both forward and inverse problems and discuss what advances are needed to scale up PINNs, PIGNs and more broadly GNNs for large-scale engineering problems.

42 ENGINEERING↗
DOE OSTI2025

What more can be done with XPS? Highly informative but underused approaches to XPS data collection and analysis

Because of the importance of surfaces and interfaces in many scientific and technological areas, the use of x-ray photoelectron spectroscopy (XPS) has been growing exponentially. Although XPS is being used to obtain useful information about the surface composition of samples, much more information about materials and their properties can be extracted from XPS data than commonly obtained. This paper describes some of the areas where alternative analysis methods or experimental design can obtain information about the near-surface region of a sample, often information not available in other ways. Experienced XPS analysts are familiar with many of these methods, but they may not be known to new or casual XPS users, and sometimes, they have not been used because of an inappropriately assumed complexity. The information available includes optical, electronic, and electrical properties; nanostructure; expanded chemical information; and enhanced analysis of biological materials and solid/liquid interfaces. Many of these analyses can be conducted on standard laboratory XPS systems, with either no or relatively minor system alterations. Topics discussed include (1) considerations beyond the “traditional” uniform surface layer composition calculation, (2) using the Auger parameter to determine a sample property, (3) use of the D parameter to identify sp 2 and sp 3 carbon information, (4) information from the XPS valence band, (5) using cryocooling to expand range of samples that can be analyzed and minimize damage, and (6) using electrical potential effects on XPS signals to extract chemically resolved electrical measurements including band alignment and electrical property information.

Baer, Donald R. [Pacific Northwest National Labora↗
DOE OSTI2021

A gene-editing/complementation strategy for tissue-specific lignin reduction while preserving biomass yield

Lignification of secondary cell walls is a major factor conferring recalcitrance of lignocellulosic biomass to deconstruction for fuels and chemicals. Genetic modification can reduce lignin content and enhance saccharification efficiency, but usually at the cost of moderate-to-severe growth penalties. We have developed a method, using a single DNA construct that uses CRISPR–Cas9 gene editing to knock-out expression of an endogenous gene of lignin monomer biosynthesis while at the same time expressing a modified version of the gene’s open reading frame that escapes cutting by the Cas9 system and complements the introduced mutation in a tissue-specific manner. Expressing the complementing open reading frame in vessels allows for the regeneration of Arabidopsis plants with reduced lignin, wild-type biomass yield, and up to fourfold enhancement of cell wall sugar yield per plant. The above phenotypes are seen in both homozygous and bi-allelic heterozygous T1 lines, and are stable over at least four generations. The method provides a rapid approach for generating reduced lignin trees or crops with one single transformation event, and, paired with a range of tissue-specific promoters, provides a general strategy for optimizing loss-of-function traits that are associated with growth penalties. This method should be applicable to any plant species in which transformation and gene editing are feasible and validated vessel-specific promoters are available.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Extrapolation Domains for Aggregating Environmental Outcomes from Local to Regional Levels

Billions of dollars are invested every year to run field experiments to quantify the response of crops to new technologies and associated environmental outcomes. Given the diversity of environments where crop production occurs, conducting these research studies without a robust framework for research site selection and upscaling results to larger spatial scales is inefficient. In this project, researchers from the University of Nebraska-Lincoln used their unique Technology Extrapolation Domains framework (TED) as a tool to guide the selection of experimental sites and as basis for aggregating and validating environmental outcomes from local to regional levels. In the present project, we first used the TED framework to evaluate the current distribution and area coverage of the current SMARTFARM sites. The purpose was to showcase how it is possible to use the TED framework to guide site selection and extrapolate results over space. Additionally, the original TED framework was expanded to account for other factors influencing environmental outcomes by inclusion of three additional variables: soil organic matter, soil texture, and topographic wetness index. The resulting expanded framework (TED-E) was validated using nitrogen (N) losses from corn in the United States as a case study. To do so, we used N balance as a proxy to N losses and we evaluated the capacity of the framework to explain variation in N balance across fields and across countries. We found that the TED-E has substantially higher predictive power than the original TED framework to explain spatial variation in N balance. However, improvements in predictive power with the TED-E tool come at the expense of a higher number of TEDs needed to achieve a given crop area coverage compared with the original TED framework. We conclude that the new TED-E framework can help aggregate and extrapolate environmental outcomes from research sites to regional levels and improve the visualization of their spatial patterns across the United States. An online version of the framework is available at: https://www.toolted.org/

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

DRAM example narrative

DRAM example narrative DRAM on KBase let's anyone run annotations using DRAM in the cloud. DRAM is an annotation tool that can annotate bacterial, archaeal and viral genomes and distills those annotatios into represetations of the functional genomic potential of those organisms. If you want to read more about DRAM you can check out the GitHub, wiki and journal article. DRAM annotate assemblies In KBase Assembly objects contain nucleotide sequences from genomes or metagenomes. DRAM can predict genes and annotate their function from KBase Assembly objects which may be microbial isolate genomes, metagenome assembled genomes or metagenomes. This is done with the Annotate and Distill Assemblies with DRAM app. This app can also anntoate AssemblySet objects which contain collection of Assembly objects. It also generates a Genome object and a GenomeSet object which can be used for further analysis with other KBase apps. The full annotations and other DRAM files are also available for download in the app.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Application of Systems Engineering Principles and Techniques in Biological Big Data Analytics: A Review

In the past few decades, we have witnessed tremendous advancements in biology, life sciences and healthcare. These advancements are due in no small part to the big data made available by various high-throughput technologies, the ever-advancing computing power, and the algorithmic advancements in machine learning. Specifically, big data analytics such as statistical and machine learning has become an essential tool in these rapidly developing fields. As a result, the subject has drawn increased attention and many review papers have been published in just the past few years on the subject. Different from all existing reviews, this work focuses on the application of systems, engineering principles and techniques in addressing some of the common challenges in big data analytics for biological, biomedical and healthcare applications. Specifically, this review focuses on the following three key areas in biological big data analytics where systems engineering principles and techniques have been playing important roles: the principle of parsimony in addressing overfitting, the dynamic analysis of biological data, and the role of domain knowledge in biological data analytics.

dynamic analysis↗
DOE OSTI2024

Simulated nitrogen deposition and precipitation events alter microbial carbon cycling during early stages of litter decomposition

Plant litter decomposition is a major nutrient input to terrestrial ecosystems that is primarily driven by microorganisms. Litter quality is considered a key drive of decomposition; however, human-induced global disturbance like nitrogen deposition and increasing extreme precipitation events will shift nutrient availability during litter decomposition. Little is known about how shifting nutrient availability will impact dissolved organic matter concentrations and microbially driven carbon cycling that are critical to soil organic matter formation. This study investigated the effect of simulated nitrogen deposition and repeated precipitation events on microbially driven carbon flow during short-term litter decomposition using a ‘common garden’ experiment with microcosms containing sand and blue grama grass litter inoculated with different microbial communities. Overall, nitrogen deposition decoupled respiration and dissolved organic carbon (DOC) by increasing respiration and not affecting DOC concentrations. Moreover, nitrogen deposition had no effect on microbial carbon use efficiency (CUE). Repeated simulated precipitation events significantly increased DOC concentrations, decreased microbial CUE, increased the microbial metabolic quotient (qCO2), and altered microbial composition and diversity. These findings highlight the complex interactions and responses of surface litter decomposers to shifting nutrient availability and contradicts previous findings that nitrogen deposition will increase soil carbon sequestration from a larger supply of DOC and reduced respiration.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Burning questions for a warming and changing world: 15 unknowns in plant abiotic stress

Abstract We present unresolved questions in plant abiotic stress biology as posed by 15 research groups with expertise spanning eco-physiology to cell and molecular biology. Common themes of these questions include the need to better understand how plants detect water availability, temperature, salinity, and rising carbon dioxide (CO2) levels; how environmental signals interface with endogenous signaling and development (e.g. circadian clock and flowering time); and how this integrated signaling controls downstream responses (e.g. stomatal regulation, proline metabolism, and growth versus defense balance). The plasma membrane comes up frequently as a site of key signaling and transport events (e.g. mechanosensing and lipid-derived signaling, aquaporins). Adaptation to water extremes and rising CO2 affects hydraulic architecture and transpiration, as well as root and shoot growth and morphology, in ways not fully understood. Environmental adaptation involves tradeoffs that limit ecological distribution and crop resilience in the face of changing and increasingly unpredictable environments. Exploration of plant diversity within and among species can help us know which of these tradeoffs represent fundamental limits and which ones can be circumvented by bringing new trait combinations together. Better defining what constitutes beneficial stress resistance in different contexts and making connections between genes and phenotypes, and between laboratory and field observations, are overarching challenges.

Biochemistry & Molecular Biology↗
DOE OSTI2020

Biological Valorization of Natural Gas for the Production of Lactic Acid: Techno-Economic Analysis and Life Cycle Assessment

Due to the availability of natural gas, shale gas, and flared gas, there is increased interest in converting methane in these gases into commodity chemicals via cost-effective and sustainable processes. Recently, we have demonstrated an efficient process concept converting methane to lactic acid (LA) by methanotrophic bacteria with high carbon flux, pivoting potentials for commercialization. Herein, we present a first-of-kind conceptual design and a techno-economic analysis (TEA) of a biorefinery process with calculated minimum selling prices. This study includes both sensitivity analysis and scenario analysis for key cost drivers and for projecting path forwards in research and development. The analyses reveal that the conversion efficiency, LA product titer, LA productivity, and gas flow rate have the most significant impacts on cost. The MSP varies from $5.83-$2.17/kg LA depending on these key process attributes. Further, a life cycle assessment of this process concept is evaluated and compared to understand the sustainable aspects. In this TEA study, the bio-upgrading process from natural gas to LA presents a potentially promising approach in terms of the feedstock versatility, economic viability, and environmental impact.

BIOMASS FUELS,NATURAL GAS↗