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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 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Metagenome-assembled genome extraction and analysis from microbiomes using KBase

Uncultivated Bacteria and Archaea account for the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only become possible recently. In order to realize the hope of capturing Earth’s microbial genetic complement and to facilitate the investigation of the functional roles of specific lineages in a given ecosystem, technologies that accelerate the recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high-quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform (http://www.kbase.us/). Overall, these steps take about a day to obtain extracted genomes when starting from smaller environmental shotgun read libraries, or up to about a week from larger libraries. In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAGs, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq and others. While portions of such capabilities are available individually from other resources, the combination of the intuitive usability, data interoperability and integration of tools in a freely available computational resource makes KBase a powerful platform for obtaining MAGs from microbiomes. While this workflow offers tools for each of the key steps in the genome extraction process, it also provides a scaffold that can be easily extended with additional MAG recovery and analysis tools, via the KBase software development kit (SDK).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Mobility and threshold voltage extraction in transistors with gate-voltage-dependent contact resistance

The mobility of emerging (e.g., two-dimensional, oxide, organic) semiconductors is commonly estimated from transistor current-voltage measurements. However, such devices often experience contact gating, i.e., electric fields from the gate modulate the contact resistance during measurements, which can lead conventional extraction techniques to estimate mobility incorrectly even by a factor >2. Although this error can be minimized by measuring transistors at high gate-source bias |V gs |, this regime is often inaccessible in emerging devices that suffer from high contact resistance or early gate dielectric breakdown. Here, we propose a method of extracting mobility in transistors with gate-dependent contact resistance that does not require operation at high |V gs |, enabling accurate mobility extraction even in emerging transistors with strong contact gating. Our approach relies on updating the transfer length method (TLM) and can achieve <10% error even in regimes where conventional techniques overestimate mobility by >2×

36 MATERIALS SCIENCE↗
DOE OSTI2025

18-membered macrocycle appended on resin for selective rare earth element extraction and separation

The rare earth elements are critically important for a wide range of modern technologies. However, obtaining them selectively and efficiently from natural sources and recycled materials is challenging and often requires harsh or wasteful conditions. Here we show that a macrocyclic chelator appended to a solid resin can overcome this challenge by acting as a robust platform for both the extraction and separation of these elements. This resin preferably captures the large rare earth elements in mixtures of these ions, giving rise to higher extraction efficiencies for them over the smaller ions. We further demonstrate that this resin can be used to separate rare earth elements. As a proof-of-principle validation, this resin was demonstrated to selectively extract rare earth elements in the presence of many different types of competing metal ions in a bioleachate solution obtained from autoslag waste, leading to their enrichment.

Coordination chemistry↗
DOE OSTI2020

Hydrophobic amine-based binary mixtures of active pharmaceutical and food grade ingredients: characterization and application in indium extraction from aqueous hydrochloric acid media

The wide spread use of hazardous and expensive solvents for the liquid-liquid extraction (LLE) of critical metals has been a growing source of waste in the metal refinement industry. We have developed and characterized room temperature liquid hydrophobic binary mixtures based on common pharmaceutical and food grade compounds as sustainable, cost effective alternatives to both ionic liquids and conventional solvents. Additionally, we introduce liquid mixtures with Proton Sponge® (1,8-bis(dimethylamino)naphthalene), one of the strongest known organic bases. These mixtures have been applied to the LLE of indium(III) ions from hydrochloric acid solutions, displaying an extraction efficiency greater than 99% in some systems. Here, a systematic approach to identifying the underlying mechanism of extraction, in particular relating to the charge, solubility, and complexation of the indium species in the organic phase has been developed.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2024

Early-stage oxidation and subsequent damage of the used nuclear fuel extractant TODGA; electron pulse radiolysis and theoretical insights

Radiation induced damage of extractant molecules is a well-known phenomenon responsible for reducing efficiency and increasing the waste and cost of reprocessing used nuclear fuel (UNF). As such, understanding early-stage (pico- to nanoseconds) radiation-induced reaction mechanisms is essential for informing the design of next generation extractants with enhanced radiation robustness. Here, in this work, we utilized picosecond and nanosecond electron pulse radiolysis experiments to probe the early-stage radioactive environment experienced by the organic phase extractant N,N,N',N'-tetraoctyldiglycolamide (TODGA), proposed for separating highly radioactive trivalent minor actinides (specifically americium and curium) from the trivalent lanthanides. Using comparisons to the similar ionization potential (IP) solute p-xylene, this work determined the mechanism of reaction with the ionized diluent (i.e., n-dodecane radical cation, DD˙ + ) is hole transfer to produce TODGA˙ + . At high TODGA concentrations (>100 mM), the majority of this transfer occurs faster than 10 ps via the capture of DD˙ + holes prior to their solvation with a C 37 = 300 mM. The surviving solvated holes were captured with k = (2.38 ± 0.15) × 10 10 M -1 s -1 . Attempts at subsequent hole transfer to lower IP solutes found that only 10% of holes were transferred, indicating bond rupture of TODGA˙ + occurs within 2.6 ns at 200 mM TODGA. Possible reaction pathways for the rapid decomposition of TODGA˙ + were explored using a combination of experiments and density functional theory (DFT) calculations.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2024

Enhanced charge carrier extraction and transport with interface modification for efficient tin-based perovskite solar cells

Interface modification improves charge carrier extraction in tin-based perovskite solar cells. Tin-based perovskites have become the most promising non-lead perovskites due to their ideal band gap and low toxicity. Although the open circuit voltage of tin-based perovskite solar cells (TPSCs) continues to approach the theoretical value, the short-circuit current is still far from the theoretical value. Here, we describe an interface modification method by regulating the property of hole transport layer, PEDOT:PSS, which improves the surface molecular morphology and the energy level alignment of PEDOT:PSS/perovskite interface. Advanced GIWAXS and IR s-SNOM characterization are conducted to achieve multi-dimensional characterization of nanoscale surface morphology and chemical distribution of PEDOT:PSS. With the multi-attribute optimization, charge carrier extraction and non-radiative recombination are also improved. The resultant TPSCs exhibit a higher power conversion efficiency of 13.32% in compared with the control device of 10.50%, accompanied with an increase in the short-circuit current from 18.10 to 20.50 mA cm −2 and FF from 68.23% to 76.43%. This work demonstrates a reliable strategy for improving charge carrier extraction and device performance for lead-free TPSCs.

Zhao, Zhenzhu↗
DOE OSTI2023

Utility of Shockley–Read–Hall analysis to extract defect properties from semiconductor minority carrier lifetime data

The semiconductor minority carrier lifetime contains information about several important material properties, including Shockley–Read–Hall defect levels/concentrations and radiative/Auger recombination rates, and the complex relationships between these parameters produce a non-trivial temperature-dependence of the measured lifetime. It is tempting to fit temperature-dependent lifetime data to extract the properties of the Shockley–Read–Hall recombination centers; however, without a priori knowledge of the distribution of the Shockley–Read–Hall states across the bandgap, this fit problem is under-constrained in most circumstances. Shockley–Read–Hall lifetime data are not well-suited for the extraction of Shockley–Read–Hall defect levels but can be used effectively to extract minority carrier recombination lifetimes. The minority carrier recombination lifetime is observed at temperatures below 100 K in a Si-doped n-type InGaAs/InAsSb superlattice, and deviation from its expected temperature-dependence indicates that the capture cross section of the defect associated with Si-doping has an activation energy of 1.5 meV or a characteristic temperature of 17 K. This lower temperature regime is also preferrable for the analysis of the physics of defect introduction with displacement-damage-generating particle irradiation.

Physics↗
DOE OSTI2025

An Application of Molecular Recognition for the Efficient Removal of Cesium from Hanford Nuclear Waste by Modular Solvent Extraction

In this work, experimental results leading to flowsheet design are presented showing how a calixarene-crown ether based solvent-extraction process can meet the challenge of cesium removal from nuclear tank wastes stored at the US Department of Energy Hanford site. Cleanup of legacy Cold War nuclear waste stored in underground tanks represents one of the greatest environmental challenges facing the US Department of Energy in terms of risk, cost, and effectiveness of applicable science and technology. Planning for the cleanup at the Hanford Site calls for the removal of the radioactive fission product 137Cs from its alkaline salt waste, including the use of modular processes that can be deployed near the tank farms. To meet the resulting need for extremely high selectivity, the Next-Generation Caustic-Side Solvent Extraction (NG-CSSX) process employing a calix[4]arene-crown ether in modified kerosene has been adapted to remove sub-millimolar cesium in competition with molar sodium and potassium in a high-nitrate alkaline matrix. Potassium loading in the solvent was determined in extraction, scrubbing, and stripping, leading to an empirical model closely approximating cesium distribution ratios for a variety of Hanford waste types. Process chemistry has been developed based on this molecular-recognition approach, focusing on the competitive effect of potassium loading and the mitigating process modifications needed, including extending the scrub section. The result is a modular flowsheet design that can achieve cesium decontamination factors well in excess of 15,000 even for the worst-case Hanford waste.

Williams, Neil [ORNL] (ORCID:000000023159226X)↗
DOE OSTI2024

Extraction of ion beam from laser ion source for direct plasma injection scheme

Laser ion sources are expected to be used in various applications of heavy ion beam technology. The plasma direct injection scheme (DPIS) is a method in which ion beams extracted from a laser ion source are directly injected into a radio frequency quadrupole (RFQ) linear accelerator. In this study, a new shape of the plasma electrode with a concave surface for the DPIS was proposed to inject a converging beam to a cavity of RFQ accelerator. This approach allows the use of a large-diameter extraction electrode, which is not limited by the aperture of the RFQ electrode rods. The DPIS, using the concave surface electrode, was employed to accelerate C 6+ ion beams. The results indicated that both the beam current and the number of ions increased nearly twice with the proposed electrode shape compared to values obtained with the conventional electrode. This enhancement corresponded to the increased extraction area of the beam.

43 PARTICLE ACCELERATORS↗
DOE OSTI2024

Automated annotation of scientific texts for ML-based keyphrase extraction and validation

Advanced omics technologies and facilities generate a wealth of valuable data daily; however, the data often lack the essential metadata required for researchers to find, curate, and search them effectively. The lack of metadata poses a significant challenge in the utilization of these data sets. Machine learning (ML)–based metadata extraction techniques have emerged as a potentially viable approach to automatically annotating scientific data sets with the metadata necessary for enabling effective search. Text labeling, usually performed manually, plays a crucial role in validating machine-extracted metadata. However, manual labeling is time-consuming and not always feasible; thus, there is a need to develop automated text labeling techniques in order to accelerate the process of scientific innovation. This need is particularly urgent in fields such as environmental genomics and microbiome science, which have historically received less attention in terms of metadata curation and creation of gold-standard text mining data sets. In this paper, we present two novel automated text labeling approaches for the validation of ML-generated metadata for unlabeled texts, with specific applications in environmental genomics. Our techniques show the potential of two new ways to leverage existing information that is only available for select documents within a corpus to validate ML models, which can then be used to describe the remaining documents in the corpus. The first technique exploits relationships between different types of data sources related to the same research study, such as publications and proposals. The second technique takes advantage of domain-specific controlled vocabularies or ontologies. In this paper, we detail applying these approaches in the context of environmental genomics research for ML-generated metadata validation. Our results show that the proposed label assignment approaches can generate both generic and highly specific text labels for the unlabeled texts, with up to 44% of the labels matching with those suggested by a ML keyword extraction algorithm.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2024

Extraction of the neutron F 2 structure function from inclusive proton and deuteron deep-inelastic scattering data

The available world deep-inelastic scattering (DIS) data on proton and deuteron structure functions F 2 p , F 2 d , and their ratios are leveraged to extract the free neutron F 2 n structure function, the F 2 n / F 2 p ratio, and associated uncertainties using the latest nuclear effect calculations in the deuteron. Special attention is devoted to the normalization of the proton and deuteron experimental datasets and to the treatment of correlated systematic errors, as well as the quantification of procedural and theoretical uncertainties. The extracted F 2 n dataset is utilized to evaluate the Q 2 dependence of the Gottfried sum rule and the nonsinglet F 2 p − F 2 n moments. To facilitate replication of our study, as well as for general applications, we provide a comprehensive DIS database including all recent Jefferson Lab 6 GeV measurements, the extracted F n 2 , a modified CTEQ-JLab global parton distribution function fit named CJ15nlo_mod, and grids with calculated proton, neutron, and deuteron DIS structure functions. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

The Recent Improvements of the SNS Extraction Kicker Power Supplies

A total of 14 extraction kickers., with one as the hot spare., are in service to extract protons out of the storage ring at the SNS. The jitter issue and the short lifetime of the switches were resolved after the thyratrons were replaced with solid state switches in 2018. This paper discusses the recent improvements. Two thyristor switches suffered overheating damage in separate incidents. One was due to the oil pump failure and the other was the result of a disconnected oil hose. An ultrasonic flow meter and a fiber optic temperature monitoring system have been installed for each extraction kicker power supply. The flow meter continuously monitors the entire tank oil flow. The temperature monitor detects the thyristor switch real-time temperatures in three locations. Fault thresholds are selected so that the thyristor switches are protected from overheating damage. Alarms are configured to alert staff to take actions before faults occur. In addition., the cause of an intermittent misfire issue was identified, and the solution was implemented. Lastly., a future oscilloscope upgrade and an oil level sensor are discussed.

Tan, Yugang↗
DOE OSTI2021

Segmentation of Deposition Periods: An Opportunity to Improve PV Soiling Extraction

Soiling profiles are commonly assumed to have sawtooth shapes, made of alternating cleaning events and soiling deposition periods. The rates at which soiling deposit on the PV modules are considered to be constant for each period. In reality, events such as changes in climatic conditions can lead to a sudden variation in soiling deposition rate. These changes cannot be reproduced if cleanings are the only events modelled to extract soiling profiles directly from PV performance data. For this reason, in this work, the use of change points and segmented regression is proposed to improve the extraction of soiling profiles through the model of up to two deposition rates per period in between cleanings. The results show that the quality of soiling extraction can be enhanced compared to a cleanings-only identification approach if both cleanings and change points are considered.

monitoring↗
DOE OSTI2024

Foundations of automatic feature extraction at LHC–point clouds and graphs

Abstract Deep learning algorithms will play a key role in the upcoming runs of the Large Hadron Collider (LHC), helping bolster various fronts ranging from fast and accurate detector simulations to physics analysis probing possible deviations from the Standard Model. The game-changing feature of these new algorithms is the ability to extract relevant information from high-dimensional input spaces, often regarded as “replacing the expert” in designing physics-intuitive variables. While this may seem true at first glance, it is far from reality. Existing research shows that physics-inspired feature extractors have many advantages beyond improving the qualitative understanding of the extracted features. In this review, we systematically explore automatic feature extraction from a phenomenological viewpoint and the motivation for physics-inspired architectures. We also discuss how prior knowledge from physics results in the naturalness of the point cloud representation and discuss graph-based applications to LHC phenomenology.

Bhardwaj, Akanksha↗
DOE OSTI2024

Modeling the Moisture Content and Dry Matter Loss in Dynamic Woody Biomass Storage Piles with Variable Extraction

The urgent need to mitigate climate change has spurred significant interest in renewable energy sources. This paper explores the storage and processing of woody biomass for biofuel production, considering the dynamic nature of biomass piles in real-world scenarios. A model has been developed to analyze moisture content changes and dry matter loss in woody biomass stored in piles prior to processing, taking into account varying extraction methods and environmental conditions. Case studies that examine the effects of different unpiling methods (FIFO, LIFO, and homogeneous) on moisture content and dry matter loss under various feedstock arrival rates and weather conditions are presented. Results indicate that unpiling methods significantly impact moisture content, with LIFO typically resulting in higher moisture content due to the utilization of fresher feedstock. Dry matter loss increases with pile size and time, emphasizing the importance of accurate modeling for assessing carbon emissions and feedstock quality. Furthermore, the model highlights the importance of process loading order and extraction methods in biomass storage, suggesting potential cost benefits associated with decreased moisture content. The difference between different extraction methods could vary the moisture content in the feedstock reaching the biofuel process by as much as 37.6%, however dry matter loss varies minimally for realistic pile changes. Overall, this research contributes to a better understanding of biomass storage dynamics and informs sustainable biofuel production practices.

Niska, Janel↗
DOE OSTI2021

Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC

Large amounts of metagenomically-derived data are submitted to PATRIC for analysis. In the future, we expect even more jobs submitted to PATRIC will use metagenomic data. One in-demand use case is the extraction of near-complete draft genomes from assembled contigs of metagenomic origin. The PATRIC metagenome binning service utilizes the PATRIC database to furnish a large, diverse set of reference genomes. We provide a new service for supervised extraction and annotation of high-quality, near-complete genomes from metagenomically-derived contigs. Reference genomes are assigned to putative draft genome bins based on the presence of single-copy universal marker roles in the sample, and contigs are sorted into these bins by their similarity to reference genomes in PATRIC. Each set of binned contigs represents a draft genome that will be annotated by RASTtk in PATRIC. A structured-language binning report is provided containing quality measurements and taxonomic information about the contig bins. The PATRIC metagenome binning service emphasizes extraction of high-quality genomes for downstream analysis using other PATRIC tools and services. Due to its supervised nature, the binning service is not appropriate for mining novel or extremely low-coverage genomes from metagenomic samples.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Soil and Water Chemistry and Trace Metal Extractability and Speciation in Wetland Soils from Illinois and South Carolina and Stream Sediments from Tennessee

Dataset revised on October 15, 2021. This revision adds sulfur and iron X-ray absorption near-edge structure spectra for the wetland soils and stream sediments from the field areas. It also renames the sample locations in a way that is more intuitive to readers of the companion paper that is under review. Finally, the data filenames and organization have been updated in their labeling to parallel the data sources in the associated paper. The abstract text and methods were also revised to reflect the data that was added to the dataset.Trace metals are essential for microbially-mediated biogeochemical processes occurring in anoxic wetland soils and stream bed sediments, such as denitrification, methanogenesis, and mercury methylation. Low availability of these elements may potentially inhibit key components of anaerobic carbon and nitrogen cycling and contaminant transformation. The solid-phase speciation of trace metals likely plays an important role in controlling their bioavailability. Metal speciation is well studied in contaminated soils and sediments as well as those naturally elevated in trace metals. However, less is known regarding the chemical forms of trace metals in systems having concentrations similar to geological background levels, the very settings where metal limitations may be most prevalent. We have investigated trace metal concentrations, extractability, and solid-phase speciation in three freshwater subsurface aquatic systems: marsh wetland soils, riparian wetland soils, and the sediments of a streambed.Data are provided for marsh wetland soils at Argonne National Laboratory, riparian wetland soils in the Tims Branch watershed at Savannah River National Laboratory, and stream bed sediments from East Fork Poplar Creek near Oak Ridge National Laboratory. Soil and sediment elemental abundances, mineralogy, and extractable nutrients as well as dissolved major elements, anions, trace metals, and nutrients in the overlying surface waters are provided. In addition, the results of sequential chemical extraction for the trace metals cobalt, nickel, copper, and zinc from the soils and sediment are reported as well as X-ray absorption near-edge structure (XANES) spectra in these materials are reported. To aid interpretation of these data, XANES spectra of sulfur in the soils and sediments as well as both XANES and extended X-ray absorption fine structure (EXAFS) spectra of iron in these materials are reported. The data package also includes the XANES spectra of reference standards and a potential interferent in the measurements. All data are provided in text-based CSV format with header sections indicating the data contained in each file and the corresponding units. Note that "u" is used in place of Greek lower case mu to indicate the micro prefix on units.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Extracting Material Property Measurement Data from Scientific Articles

Machine learning-based prediction of material properties is often hampered by the lack of sufficiently large training datasets. The majority of such measurement data is embedded in scientific literature and the ability to automatically extract these data is essential to support the development of reliable property prediction methods. In this work, we describe a methodology for an automatic property extraction framework using material solubility as the target property. We create an annotated dataset containing tags for solubility-related entities using a combination of regular expressions and manual tagging. We then compare five entity recognition models leveraging both token-level and span-level architectures on the task of classifying solute names, solubility values, and solubility units. Additionally, we explore a novel pretraining approach that leverages automated chemical name and quantity extraction tools to generate large datasets that do not rely on intensive manual effort. Finally, we perform an analysis to identify the causes of classification errors.

Panapitiya, Gihan U.↗