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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 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Carbonate Composite Sorbents: A Novel Technology for Biogas Upgrading

With no signs of slowing, global warming and resource consumption continue to rise. Biogas has been shown to be a reliable renewable energy source in tandem to natural gas. Biogas is naturally sourced as a byproduct from dairy and food waste plants and can be upgraded to biomethane as an alternative to natural gas. Lawrence Livermore National Laboratory (LLNL) has developed carbonate composite sorbents which yield pipeline quality biomethane and cost less than traditional biogas upgrading technologies (e.g., water/chemical scrubbing, pressure swing adsorption). Laboratory-scale experiments using biogas and the composite sorbents resulted in absorption of 0.62 mol of CO 2 per kilogram of material, methane purity of >99% and an energy demand of <0.1 MJ/Nm 3 . The team is currently working on scaling up the production of the composite sorbent to kilogram quantities and to operate a small-scale pilot at a partnered test facility. To ensure market competitiveness, the team is currently working on improving the CO 2 loading capacity of the composite sorbent by optimizing the powder to polymer ratio and developing a confined coaxial powder extrusion method.

36 MATERIALS SCIENCE↗
DOE OSTI2023

CRISPR-COPIES: Web Tool

CRISPR/Cas system has emerged as a powerful genome-editing tool for metabolic engineering and human gene therapy. However, the conundrum of where to integrate heterologous genes on the chromosome using the CRISPR/Cas system remains an open question. Selecting a site for gene integration requires incorporation of complex criteria such as factors involved in CRISPR/Cas-mediated integration, genetic stability, and gene expression and therefore, usually requires strenuous characterization of sites on particular or different chromosomal locations. To address these issues, we developed CRISPR-COPIES, a COmputational Pipeline for the Identification of CRISPR/Cas-facilitated intEgration Sites. The tool applies ScaNN, a state-of-the-art model on the embedding-based nearest neighbor search for fast and accurate off-target search and can identify genome-wide intergenic sites for most bacterial and fungal genomes within minutes. This submission contains the code we developed to create a user-friendly web interface for CRISPR-COPIES (https://biofoundry.web.illinois.edu/copies/). We anticipate CRISPR-COPIES will serve as a useful tool for targeted DNA integration and aid in the characterization of synthetic biology toolkits, rapid strain construction to produce valuable biochemicals, and human gene and cell therapy.

Bioinformatics↗
DOE OSTI2026

Enhancing transfer learning in angle-resolved photoemission spectroscopy (ARPES) with spatially-aware representations via graph convolution

A recent application of machine learning has been to spatially-resolved angle-resolved photoemission spectroscopy (ARPES). Here we advance the state-of-the-art by applying representational learning to transform ARPES data into an embedding space of a pre-trained self-supervised learning model, thus enhancing the pipeline that improves the bandstructure classification and domain assignment/segmentation performance compared to a k-means clustering method. In the current iteration, the real-space information is entered into the domain assignment through the graph convolution method, which improves the transfer learning performance of the original self-supervised model. Lastly, an unsupervised automated tool is developed that incorporates these techniques to enable automatic domain assignment.

ARPES↗
DOE OSTI2022

A consensus protocol for the recovery of mercury methylation genes from metagenomes

Abstract Mercury (Hg) methylation genes ( hgcAB ) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal‐ash amended sediments, chlor‐alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg‐cycling microorganisms in aquatic and terrestrial ecosystems (Hg‐MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce “marky‐coco”, a ready‐to‐use bioinformatic pipeline based on de novo single‐metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky‐coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Plant Metabolic Network 15: A resource of genome-wide metabolism databases for 126 plants and algae

To understand and engineer plant metabolism, we need a comprehensive and accurate annotation of all metabolic information across plant species. As a step towards this goal, we, in this study, generated genome-scale metabolic pathway databases of 126 algal and plant genomes, ranging from model organisms to crops to medicinal plants (https://plantcyc.org). Of these, 104 have not been reported before. We systematically evaluated the quality of the databases, which revealed that our semi-automated validation pipeline dramatically improves the quality. We then compared the metabolic content across the 126 organisms using multiple correspondence analysis and found that Brassicaceae, Poaceae, and Chlorophyta appeared as metabolically distinct groups. To demonstrate the utility of this resource, we used recently published sorghum transcriptomics data to discover previously unreported trends of metabolism underlying drought tolerance. We also used single-cell transcriptomics data from the Arabidopsis root to infer cell type-specific metabolic pathways. This work shows the quality and quantity of our resource and demonstrates its wide-ranging utility in integrating metabolism with other areas of plant biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

SECARB 2020 Semi-Annual Field Review Reports - Anthropogenic Test

The Southern States Energy Board (SSEB) managed the overall Southeast Regional Carbon Sequestration Partnership (SECARB) Phase III project and the Electric Power Research Institute (EPRI) managed all activities associated with the Anthropogenic Test site. Advanced Resources International, Inc. (ARI) assisted EPRI with the management of site activities. EPRI and ARI followed reporting procedures that included monthly and quarterly technical progress reports, as well as periodic reporting on key field activities. Subsequent sections of this report catalog the field activities and are organized in a semi-annual chronology. The SECARB Anthropogenic Test was the largest demonstration of a fully integrated, pulverized coal-fueled carbon capture and storage (CCS) project in the United States as of 2012 and supports a commercial prototype of CO 2 capture; transportation; subsurface storage; and monitoring, verification, and accounting (MVA); and assessment. The demonstration-scale, post-combustion CO 2 capture facility at Alabama Power Company’s Plant Barry diverted flue gas (25MW equivalent) from its Unit #5 coal burning facility and captured the CO 2 using Mitsubishi Heavy Industries (MHI) KM-CDRTM advanced amine technology. The captured CO2 was compressed at Plant Barry and transported by pipeline to the injection location southeast of Citronelle, Alabama. The Citronelle Project’s geologic storage and MVA sites were located on the flanks of the Citronelle Dome, approximately three miles southeast of the city of Citronelle. The injection zone, the Paluxy Formation, a saline formation that occurs at approximately 9,400 feet and overlies the oil production horizon of the Citronelle oilfield, presents a favorable injection reservoir in terms of areal extent and petrophysical characteristics. The confining zone, the basal shale of the overlying Washita-Fredericksburg Formation, is persistent throughout the Citronelle area and possesses the appropriate criteria to act as an effective CO 2 seal.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2023

BatAnalysis - A Comprehensive Python Pipeline for Swift BAT Survey Analysis

The Swift Burst Alert Telescope (BAT) is a coded-aperture gamma-ray instrument with a large field of view that primarily operates in survey mode when it is not triggering on transient events. The survey data consist of 80- channel detector plane histograms that accumulate photon counts over periods of at least 5 minutes. These histograms are processed on the ground and are used to produce the survey data set between 14 and 195 keV. Survey data comprise >90% of all BAT data by volume and allow for the tracking of long-term light curves and spectral properties of cataloged and uncataloged hard X-ray sources. Until now, the survey data set has not been used to its full potential due to the complexity associated with its analysis and the lack of easily usable pipelines. Here, we introduce the BatAnalysis Python package, a wrapper for HEASoftpy, which provides a modern, opensource pipeline to process and analyze BAT survey data. BatAnalysis allows members of the community to use BAT survey data in more advanced analyses of astrophysical sources, including pulsars, pulsar wind nebula, active galactic nuclei, and other known/unknown transient events that may be detected in the hard X-ray band. We outline the steps taken by the Python code and exemplify its usefulness and accuracy by analyzing survey data of the Crab Nebula, NGC 2992, and a previously uncataloged MAXI transient. The BatAnalysis package allows for ~18 yr of BAT survey data to be used in a systematic way to study a large variety of astrophysical sources.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

Gas Hydrate Film Growth in Microfluidic Channels for Carbon Dioxide Capture and Sequestration Applications

Gas or clathrate hydrates are a solid, crystalline compound composed of water and guest molecules that typically form at high pressure and low temperature conditions. Carbon dioxide (CO2) hydrates may be involved in several carbon dioxide capture and sequestration (CCS) applications, including CO2 pipeline transportation and CO2 offshore sequestration. Within these applications, the formation mechanism and kinetics must be well understood to manage the CCS processes, either by preventing or promoting hydrate formation. In this work, a high-pressure glass microfluidic reactor is used in tandem with visual microscopy and in-situ Raman spectroscopy to study both the morphological and kinetic behavior of gas hydrate crystals. Subcooling, pressure, and CO2 flow rate are investigated for their impact on the thickening behavior of pure CO2 hydrates, with flow rate being the only parameter to have a significant effect. Visual and Raman spectroscopy evidence show that both a dense hydrate layer and a porous hydrate layer form, and the latter may provide a path for mass transfer to continue hydrate crystallization. A first principles mass transfer model is developed to describe CO2 hydrate crystal thickening at the interface between gas and water. The impacts of gas impurities and channel wettability are also studied. This method is further applied to investigate the conversion of methane hydrate to CO2 hydrate for combined energy recovery and methane hydrate formation. The authors acknowledge the US Department of Energy Basic Energy Science award # DE-SC0022162.

Wadsworth, Lindsey [Colorado School of Mines, Gold↗
DOE OSTI2020

Application of emerging monitoring techniques at the Illinois Basin – Decatur Project

The Illinois Basin – Decatur Project is a large-scale carbon capture and storage demonstration project located in Decatur, Illinois, USA. In this project, one million metric tons of carbon dioxide (CO 2 ) was captured from an ethanol production facility and successfully injected into a deep saline reservoir over a period of three years. The scale of this project presented an opportunity to explore emerging technologies for effective long-term monitoring of the carbon capture and storage site. This research documents the application of three emerging monitoring techniques: (1) a prototype “open-path” sensor, a method of continuously monitoring atmospheric CO 2 by applying tunable diode laser absorption spectroscopy to provide a warning system for personnel safety along pipelines and at wellheads; (2) the Greenhouse Gas Laser Imaging Tomography Experiment (GreenLITE), an automated system for measuring two-dimensional spatial distribution of atmospheric CO 2 concentrations; and (3) periodic aerial imagery, a method of documenting surface-vegetation dynamics to detect vegetative responses to CO 2 leaks. The objective of this work was to assess the advantages and limitations of these monitoring techniques and quantify their reliability over an extended deployment at an active industrial site. These results will aid in determining viability of long-term monitoring on a commercial scale.

42 ENGINEERING↗
DOE OSTI2023

Workflow for High-throughput Screening of Enzyme Mutant Libraries Using Matrix-assisted Laser Desorption/Ionization Mass Spectrometry Analysis of Escherichia coli Colonies

High-throughput molecular screening of microbial colonies and DNA libraries are critical procedures that enable applications such as directed evolution, functional genomics, microbial identification, and creation of engineered microbial strains to produce high-value molecules. A promising chemical screening approach is the measurement of products directly from microbial colonies via optically guided matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Measuring the compounds from microbial colonies bypasses liquid culture with a screen that takes approximately 5 s per sample. We describe a protocol combining a dedicated informatics pipeline and sample preparation method that can prepare up to 3,000 colonies in under 3 h. The screening protocol starts from colonies grown on Petri dishes and then transferred onto MALDI plates via imprinting. The target plate with the colonies is imaged by a flatbed scanner and the colonies are located via custom software. The target plate is coated with MALDI matrix, MALDI-MS analyzes the colony locations, and data analysis enables the determination of colonies with the desired biochemical properties. This workflow screens thousands of colonies per day without requiring additional automation. The wide chemical coverage and the high sensitivity of MALDI-MS enable diverse screening projects such as modifying enzymes and functional genomics surveys of gene activation/inhibition libraries.

Choe, Kisurb↗
DOE OSTI2023

Single-cell spatial metabolomics with cell-type specific protein profiling for tissue systems biology

Metabolic reprogramming in cancer and immune cells occurs to support their increasing energy needs in biological tissues. Here we propose Single Cell Spatially resolved Metabolic (scSpaMet) framework for joint protein-metabolite profiling of single immune and cancer cells in male human tissues by incorporating untargeted spatial metabolomics and targeted multiplexed protein imaging in a single pipeline. We utilized the scSpaMet to profile cell types and spatial metabolomic maps of 19507, 31156, and 8215 single cells in human lung cancer, tonsil, and endometrium tissues, respectively. The scSpaMet analysis revealed cell type-dependent metabolite profiles and local metabolite competition of neighboring single cells in human tissues. Deep learning-based joint embedding revealed unique metabolite states within cell types. Trajectory inference showed metabolic patterns along cell differentiation paths. Here we show scSpaMet’s ability to quantify and visualize the cell-type specific and spatially resolved metabolic-protein mapping as an emerging tool for systems-level understanding of tissue biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Radionuclide Waste Disposal: Development of Multi-scale Experimental and Modeling Capabilities (Final Report)

The DOE EPSCoR Implementation project “Radioactive waste management: Development of multi-scale experimental and modeling capabilities” helped to develop a team of scientists and engineers from Clemson University, South Carolina State University, and the University of South Carolina to address the disposition of nuclear wastes and study the transport of radioisotopes from a waste repository in the near and far field. The project involved 20 faculty from the three institutions as well as 13 postdoctoral fellows, 32 graduate students, and 32 undergraduate students and was active from 2014-2019. Additionally, we forged new collaborations with nine researchers from DOE laboratories SRNL, LLNL, and ANL as well as the University of Manchester and the China Academy of Engineering Physics. The overarching goal of the project was to understand the conditions under which important classes of co-reactants, ranging from counter ions in crystal lattices to dissolved oxygen in pores, control the chemistry and transport characteristics of radionuclides in engineered waste forms and natural soils. Our approach was to characterize the time and length scales over which non-equilibrium states are maintained by rate-limiting, or rate-enhancing, reactions between radionuclides and co-reactants due to interactions between physical mass-transfer processes (i.e., advection, diffusion) and (biogeo) chemical reactions. We have focused our project on three specific classes of reactions relevant to radionuclide transport at DOE legacy sites: ion exchange/substitution, ligand complexation, and redox-mediated reactions. Understanding radionuclide migration requires detailed knowledge of how changes to a system – whether engineered or natural – drive the behavior of co-reactants, which in turn provide the geochemical context controlling radionuclide transport. Student engagement and training were a primary focus of the project in order to create a pipeline of researchers who could work in the area of nuclear waste disposition to support the state and the nation. Over the duration of the project we worked with 32 undergraduate, graduated 18 M.S. students and 14 Ph.D. students, and advised 13 postdoctoral fellows. The Ph.D students and postdocs have primarily taken positions at DOE laboratories, academia, and industry. Through our collaborative team, numerous follow on projects have been started with over $5M in sponsored research. Additionally, thus far the team has published 53 peer reviewed papers and given over 75 technical presentations.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2022

A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling

Mechanistic models of how single cells respond to different perturbations can help integrate disparate big data sets or predict response to varied drug combinations. However, the construction and simulation of such models have proved challenging. Here, we developed a python-based model creation and simulation pipeline that converts a few structured text files into an SBML standard and is high-performance- and cloud-computing ready. We applied this pipeline to our large-scale, mechanistic pan-cancer signaling model (named SPARCED) and demonstrate it by adding an IFNγ pathway submodel. We then investigated whether a putative crosstalk mechanism could be consistent with experimental observations from the LINCS MCF10A Data Cube that IFNγ acts as an anti-proliferative factor. The analyses suggested this observation can be explained by IFNγ-induced SOCS1 sequestering activated EGF receptors. This work forms a foundational recipe for increased mechanistic model-based data integration on a single-cell level, an important building block for clinically-predictive mechanistic models.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Automated Model for Improved Mapping of Country-Scale High-Resolution Coastal Bathymetry

Accurate and up-to-date maps of coastal bathymetry are critical for a variety of sectors from vessel navigation to port construction and are increasingly vital to inform coastal infrastructure management amid accelerating sea-level rise and more frequent and severe storm-surge events. The primary challenges to accurate and efficient bathymetric mapping from optical remote sensing are: accurately modeling light attenuation in both the atmosphere and water column; and inefficient data processing pipelines for highresolution satellite imagery. To address the effects of light attenuation within the water-column we have developed a novel physics-based bathymetry model that accounts for variations in water-column inherent optical properties on a pixel-by-pixel basis in optically-shallow aquatic environments, which represents a major advancement. For applications to satellite imagery, we have developed a software package that automatically applies the robust 6S atmospheric correction algorithm, estimates the bottom depth from the physics-based bathymetry model, which corrects for attenuation by suspended particulate matter and colored dissolved organic matter in the water column on a pixel-by-pixel basis, and leverages highperformance computing for rapid application to region-scale (e.g., CONUS) 2-meter resolution imagery datasets. Our approach is tailored to sensors that collect data at two-meter resolution with high return times for frequent updates. We mapped 591 WorldView satellite images for Florida, North Carolina, and Alaska and validated the maps against LiDAR-derived bathymetry data. Results show median RMSE of 1.75, 1.59, and 2.67 meters, respectively. By combining the strengths of Oak Ridge National Laboratory in high-performance computing and remote-sensing science with the water-column modeling expertise of Scripps Institution of Oceanography we advance the state of bathymetric mapping capability.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Multiplexed CRISPR-Cas9 mutagenesis of rice PSBS1 noncoding sequences for transgene-free overexpression

Understanding CRISPR-Cas9’s capacity to produce native overexpression (OX) alleles would accelerate agronomic gains achievable by gene editing. To generate OX alleles with increased RNA and protein abundance, we leveraged multiplexed CRISPR-Cas9 mutagenesis of noncoding sequences upstream of the rice PSBS1 gene. We isolated 120 gene-edited alleles with varying non-photochemical quenching (NPQ) capacity in vivo—from knockout to overexpression—using a high-throughput screening pipeline. Overexpression increased OsPsbS1 protein abundance two- to threefold, matching fold changes obtained by transgenesis. Increased PsbS protein abundance enhanced NPQ capacity and water-use efficiency. Across our resolved genetic variation, we identify the role of 5'UTR indels and inversions in driving knockout/knockdown and overexpression phenotypes, respectively. Complex structural variants, such as the 252-kb duplication/inversion generated here, evidence the potential of CRISPR-Cas9 to facilitate significant genomic changes with negligible off-target transcriptomic perturbations. Our results may inform future gene-editing strategies for hypermorphic alleles and have advanced the pursuit of gene-edited, non-transgenic rice plants with accelerated relaxation of photoprotection.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Structure-guided discovery of ancestral CRISPR-Cas13 ribonucleases

The RNA-guided ribonuclease CRISPR-Cas13 enables adaptive immunity in bacteria and programmable RNA manipulation in heterologous systems. Cas13s share limited sequence similarity, hindering discovery of related or ancestral systems. Here, to address this, we developed an automated structural-search pipeline to identify an ancestral clade of Cas13 (Cas13an) and further trace Cas13 origins to defense-associated ribonucleases. Despite being one-third the size of other Cas13s, Cas13an mediates robust programmable RNA depletion and defense against diverse bacteriophages. However, unlike its larger counterparts, Cas13an uses a single active site for both CRISPR RNA processing and RNA-guided cleavage, revealing that the ancestral nuclease domain has two modes of activity. Discovery of Cas13an deepens our understanding of CRISPR-Cas evolution and expands opportunities for precision RNA editing, showcasing the promise of structure-guided genome mining.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Progressive Dynamics for Cloth and Shell Animation

We propose Progressive Dynamics, a coarse-to-fine, level-of-detail simulation method for the physics-based animation of complex frictionally contacting thin shell and cloth dynamics. Progressive Dynamics provides tight-matching consistency and progressive improvement across levels, with comparable quality and realism to high-fidelity, IPC-based shell simulations [Li et al. 2021] at finest resolutions. Together these features enable an efficient animation-design pipeline with predictive coarse-resolution previews providing rapid design iterations for a final, to-be-generated, high-resolution animation. In contrast, previously, to design such scenes with comparable dynamics would require prohibitively slow design iterations via repeated direct simulations on high-resolution meshes. We evaluate and demonstrate Progressive Dynamics's features over a wide range of challenging stress-tests, benchmarks, and animation design tasks. Here Progressive Dynamics efficiently computes consistent previews at costs comparable to coarsest-level direct simulations. Its matching progressive refinements across levels then generate rich, high-resolution animations with high-speed dynamics, impacts, and the complex detailing of the dynamic wrinkling, folding, and sliding of frictionally contacting thin shells and fabrics.

Computer Science↗
DOE OSTI2025

EvoNet: A phylogenomic and systems biology approach to identify genes underlying plant survival in marginal, low‐N soils

The DOE‐BER “EvoNet” project investigates the genetic and molecular basis of plant resilience in extreme environments. We do this by identifying key genes that enable “extreme survivor” species to thrive in the nitrogen-poor soils of Chile’s hyper-arid Atacama Desert. Our collections focus on 32 Atacama extremophile species, including seven grass species with potential biofuel applications. To identify genes-of-importance to survival we compared genomic and transcriptomic profiles of extremophile species that thrive in the Atacama to those of closely related “sister” species from nitrogen-rich arid and mesic regions of California. Deep RNA sequencing and de novo transcriptome assembly across these triplet species sets supported a phylogenomic framework for identifying positively selected genes associated with adaptive divergence. Our integrative analysis combined ecological and environmental data, metagenomics, evolutionary and systems biology, and metabolomics. This enabled us to create an unprecedented framework for systematically understanding how non-model plants have adapted to survive in extreme conditions. Our resulting database of positively selected ortholog groups in the extremophile plants offers promising targets for engineering crop and biofuel species with enhanced resilience to drought and extreme weather. Additionally, our newest dataset explores and exploits a complementary metabolomic approach. This new aspect provides innovative strategies to manipulate plant cell metabolism, further supporting efforts to improve agricultural productivity in the face of extreme climates. Importantly, our combined evolutionary- and metabolomic-based strategies focused on convergent patterns of adaptation, providing a genetic and metabolomic toolkit for improving crop and biofuel resilience across diverse plant species. Finally, our novel exploration of ecological and evolutionary dynamics delivered to the community a phylogenomic computational pipeline called “PhyloGeneious.” Our continued adaptations of this pipeline are publicly available to expedite evolutionary genomic research for future scientific discoveries. In total, our DOE-BER has provided genomic, metabolomic, and computational strategies to understand how extremophile plants provide evolutionary and physiological targets for improving agricultural and biofuel production.

59 BASIC BIOLOGICAL SCIENCES↗