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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 379 records · Page 21
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Quantifying shifts in natural selection on codon usage between protein regions: a population genetics approach

Codon usage bias (CUB), the non-uniform usage of synonymous codons, occurs across all domains of life. Adaptive CUB is hypothesized to result from various selective pressures, including selection for efficient ribosome elongation, accurate translation, mRNA secondary structure, and/or protein folding. Given the critical link between protein folding and protein function, numerous studies have analyzed the relationship between codon usage and protein structure. The results from these studies have often been contradictory, likely reflecting the differing methods used for measuring codon usage and the failure to appropriately control for confounding factors, such as differences in amino acid usage between protein structures and changes in the frequency of different structures with gene expression. Here we take an explicit population genetics approach to quantify codon-specific shifts in natural selection related to protein structure in S. cerevisiae and E. coli. Unlike other metrics of codon usage, our approach explicitly separates the effects of natural selection, scaled by gene expression, and mutation bias while naturally accounting for a region’s amino acid usage. Bayesian model comparisons suggest selection on codon usage varies only slightly between helix, sheet, and coil secondary structures and, similarly, between structured and intrinsically-disordered regions. Similarly, in contrast to previous findings, we find selection on codon usage only varies slightly at the termini of helices in E. coli. Using simulated data, we show this previous work indicating “non-optimal” codons are enriched at the beginning of helices in S. cerevisiae was due to failure to control for various confounding factors (e.g. amino acid biases, gene expression, etc.), and rather than selection to modulate cotranslational folding. Our results reveal a weak relationship between codon usage and protein structure, indicating that differences in selection on codon usage between structures are slight. In addition to the magnitude of differences in selection between protein structures being slight, the observed shifts appear to be idiosyncratic and largely codon-specific rather than systematic reversals in the nature of selection. Overall, our work demonstrates the statistical power and benefits of studying selective shifts on codon usage or other genomic features from an explicitly evolutionary approach. Limitations of this approach and future potential research avenues are discussed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Distributed Energy Resources Cybersecurity Framework & Risk Manager

Distributed Energy Resource Cybersecurity Framework (DER-CF) provides a holistic assessment for evaluating the cybersecurity posture of DER systems - filling an important gap that expands upon existing cybersecurity frameworks for more modern energy systems. The DER-CF is available as a written framework and an interactive Web tool. Distributed Energy Resource Risk Manager (DER-RM) process adheres closely to NIST's seven risk management steps: prepare, categorize, select, implement, assess, monitor, and authorize. This added feature is independent of the DER-CF's existing self-assessment and allows managers to focus on the RMF process.

cybersecurity↗
DOE OSTI2021

Persistent Acoustic Sensing for Monitoring A Reactor Facility - Oral Presentation

Measurements over the past few years, taking place within the Multi-Informatics for Nuclear Operations Scenarios (MINOS) project, show that infrasound and low-frequency acoustic monitoring can detect, and often quantify, activities that occur on-site at a large research reactor. Observable activities include: crane translation, lifting, and lowering; differentiation between loaded and unloaded crane operations; access door opening and closing; vehicle operations; and cooling tower fan operation. Advanced data analytic and spectral feature extraction methods can be used to interpret selected signatures to reach a deeper understanding of different reactor activities. These measurements are being conducted using a network of smartphones that continuously operate in conjunction with cloud-based architectures. A recent addition to the system is the development and deployment of a real-time, cloud-based analytic framework that supports near-real-time alarming which can facilitate tip-and-cue protocols. This paper will present recent research advances in this area including studies to explore the transferability of learned parameters from one smartphone to another, the detectability of events from multiple sensors at different locations simultaneously, and the feasibility of porting analytical tools directly to the smartphones to allow edge computing with optimized configurations.

42 ENGINEERING↗
DOE OSTI2021

Persistent Acoustic Sensing for Monitoring A Reactor Facility

Measurements over the past few years, taking place within the Multi-Informatics for Nuclear Operations Scenarios project, show that infrasound and low-frequency acoustic monitoring can detect, and often quantify, activities that occur on-site at the High Flux Isotope Reactor. Observable activities include: crane translation, lifting, and lowering; differentiation between loaded and unloaded crane operations; access door opening and closing; vehicle operations; and cooling tower fan operations. Advanced data analytic and spectral feature extraction methods can be used to interpret selected signatures to reach a deeper understanding of different reactor activities. These measurements are being conducted using a network of smartphones that continuously operate in conjunction with cloud-based architectures. A recent addition to the system is the development and deployment of a real-time, cloud-based analytic framework that supports near-real-time alarming which can facilitate tip-and-cue protocols. This paper presents recent research in this area including the use of low-frequency acoustics to tip-off transfer operations and cue a more comprehensive analysis by other sensor networks.

42 ENGINEERING↗
DOE OSTI2020

Why Boron Nitride is such a Selective Catalyst for the Oxidative Dehydrogenation of Propane

Abstract Boron‐containing materials, and in particular boron nitride, have recently been identified as highly selective catalysts for the oxidative dehydrogenation of alkanes such as propane. To date, no mechanism exists that can explain both the unprecedented selectivity, the observed surface oxyfunctionalization, and the peculiar kinetic features of this reaction. We combine catalytic activity measurements with quantum chemical calculations to put forward a bold new hypothesis. We argue that the remarkable product distribution can be rationalized by a combination of surface‐mediated formation of radicals over metastable sites, and their sequential propagation in the gas phase. Based on known radical propagation steps, we quantitatively describe the oxygen pressure‐dependent relative formation of the main product propylene and by‐product ethylene. Free radical intermediates most likely differentiate this catalytic system from less selective vanadium‐based catalysts.

Venegas, Juan M.↗
DOE OSTI2020

Why Boron Nitride is such a Selective Catalyst for the Oxidative Dehydrogenation of Propane

Boron–containing materials, and in particular boron nitride, have recently been identified as highly selective catalysts for the oxidative dehydrogenation of alkanes such as propane. To date, no mechanism exists that can explain both the unprecedented selectivity, the observed surface oxyfunctionalization, and the peculiar kinetic features of this reaction. Here, we combine catalytic activity measurements with quantum chemical calculations to put forward a bold new hypothesis. We argue that the remarkable product distribution can be rationalized by a combination of surface–mediated formation of radicals over metastable sites, and their sequential propagation in the gas phase. Based on known radical propagation steps, we quantitatively describe the oxygen pressure–dependent relative formation of the main product propylene and by–product ethylene. Free radical intermediates most likely differentiate this catalytic system from less selective vanadium–based catalysts.

03 NATURAL GAS↗
DOE OSTI2024

Autonomous hybrid optimization of a SiO 2 plasma etching mechanism

Computational modeling of plasma etching processes at the feature scale relevant to the fabrication of nanometer semiconductor devices is critically dependent on the reaction mechanism representing the physical processes occurring between plasma produced reactant fluxes and the surface, reaction probabilities, yields, rate coefficients, and threshold energies that characterize these processes. The increasing complexity of the structures being fabricated, new materials, and novel gas mixtures increase the complexity of the reaction mechanism used in feature scale models and increase the difficulty in developing the fundamental data required for the mechanism. This challenge is further exacerbated by the fact that acquiring these fundamental data through more complex computational models or experiments is often limited by cost, technical complexity, or inadequate models. In this paper, we discuss a method to automate the selection of fundamental data in a reduced reaction mechanism for feature scale plasma etching of SiO 2 using a fluorocarbon gas mixture by matching predictions of etch profiles to experimental data using a gradient descent (GD)/Nelder–Mead (NM) method hybrid optimization scheme. These methods produce a reaction mechanism that replicates the experimental training data as well as experimental data using related but different etch processes.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Status of the Characterization of DEs from the Full Circumference Examination of the Inner Container Closure Weld Region (FY2020)

One of the main focus areas of the 3013 Surveillance Program is a thorough evaluation of the inner container closure weld region (ICCWR) opened for destructive examination (DE). As part of the protocol to investigate the corrosion in the ICCWR a laser confocal microscope (LCM) is used to perform close visual examination of the surface and measurements of corrosion features on the surface. DE containers from FY13 through FY16 were screened with three candidates selected for full circumference evaluation (FCE) according to the ICCWR examination protocol, During the FCE, FY16 DE05 and FY15 DE07 showed suspect major corrosion events, FY16 DE05 Section C2 shows two crack-like features, identified as Denebola and Draco. Both features are located at the boundary of Zone 2 and Zone 3. Consequently, Section C2 of FY16 DE05 was selected for examination by serial metallography at Savannah River National Laboratory (SRNL). For FY15 DE07 the suspect corrosion events were observed on Sections Cl and C2. Section Cl shows one crack-like feature, identified as Acrux. Section C2 shows three crack-like features, identified as Bellatrix, Cursa Minor and Cursa Major. Unlike Acrux and Bellatrix, which are located at the boundary of Zone 2 and Zone 3, Cursa Minor and Cursa Major are located in Zone 2. Sections Cl and C2 of FY15 DE07 were sent to Los Alamos National Laboratory (LANE) for characterization by X-Ray Tomography (XRT).

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2021

A meta-learning based distribution system load forecasting model selection framework

This paper presents a meta-learning based, automatic distribution system load forecasting model selection framework. Furthermore, the framework includes the following processes: feature extraction, candidate model preparation and labeling, offline training, and online model recommendation. Using load forecasting needs and data characteristics as input features, multiple metalearners are used to rank the candidate load forecast models based on their forecasting accuracy. Then, a scoring-voting mechanism is proposed to weights recommendations from each meta-leaner and make the final recommendations. Heterogeneous load forecasting tasks with different temporal and technical requirements at different load aggregation levels are set up to train, validate, and test the performance of the proposed framework. Simulation results demonstrate that the performance of the meta-learning based approach is satisfactory in both seen and unseen forecasting tasks.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2024

Characterization of spent nuclear fuel canister surface roughness using surface replicating molds

In this study we present a replication method to determine surface roughness and to identify surface features when a sample cannot be directly analyzed by conventional techniques. As a demonstration, this method was applied to an unused spent nuclear fuel dry storage canister to determine variation across different surface features. In this study, an initial material down-selection was performed to determine the best molding agent and determined that non-modified Polytek PlatSil23-75 provided the most accurate representation of the surface while providing good usability. Other materials that were considered include Polygel Brush-On 35 polyurethane rubber (with and without Pol-ease 2300 release agent), Polytek PlatSil73-25 silicone rubber (with and without PlatThix thickening agent and Pol-ease 2300 release agent), and Express STD vinylpolysiloxane impression putty. The ability of PlatSil73-25 to create an accurate surface replica was evaluated by creating surface molds of several locations on surface roughness standards representing ISO grade surfaces N 3 , N 5 , N 7 , and N 8 . Overall, the molds were able to accurately reproduce the expected roughness average (R a ) values, but systematically over-estimated the peak-valley maximum roughness (R z ) values. Using a 3D printed sample cell, several locations across the stainless steel spent nuclear fuel canister were sampled to determine the surface roughness. These measurements provided information regarding variability in normal surface roughness across the canister as well as a detailed evaluation on specific surface features (e.g., welds, grind marks, etc.). The results of these measurements can support development of dry storage canister ageing management programs, as surface roughness is an important factor for surface dust deposition and accumulation. This method can be applied more broadly to different surfaces beyond stainless steel to provide rapid, accurate surface replications for analytical evaluation by profilometry.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

Genomic factors shaping codon usage across the Saccharomycotina subphylum

Codon usage bias, or the unequal use of synonymous codons, is observed across genes, genomes, and between species. It has been implicated in many cellular functions, such as translation dynamics and transcript stability, but can also be shaped by neutral forces. We characterized codon usage across 1,154 strains from 1,051 species from the fungal subphylum Saccharomycotina to gain insight into the biases, molecular mechanisms, evolution, and genomic features contributing to codon usage patterns. We found a general preference for A/T-ending codons and correlations between codon usage bias, GC content, and tRNA-ome size. Codon usage bias is distinct between the 12 orders to such a degree that yeasts can be classified with an accuracy >90% using a machine learning algorithm. We also characterized the degree to which codon usage bias is impacted by translational selection. We found it was influenced by a combination of features, including the number of coding sequences, BUSCO count, and genome length. Our analysis also revealed an extreme bias in codon usage in the Saccharomycodales associated with a lack of predicted arginine tRNAs that decode CGN codons, leaving only the AGN codons to encode arginine. Analysis of Saccharomycodales gene expression, tRNA sequences, and codon evolution suggests that avoidance of the CGN codons is associated with a decline in arginine tRNA function. Consistent with previous findings, codon usage bias within the Saccharomycotina is shaped by genomic features and GC bias. However, we find cases of extreme codon usage preference and avoidance along yeast lineages, suggesting additional forces may be shaping the evolution of specific codons.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

RESIN: Responsible Innovation for Highly Recyclable Plastics - TASK 4: Risk Assessment Framework

This report covers the entirety of Task 4, but its main purpose is to deliver milestones ML4.4 and ML4.5, the last two SOPO milestones under Task 4. ML4.4 reports on the compatibility of polymer properties that affect both environmental performance and functional performance and the tradeoffs involved in turning these properties to the benefit of each. ML4.5 presents a complete set of information on the critical properties of benign target products, where benign products are defined as those with the shortest environmental lifetime which meet performance requirements. To support and provide context to the discussions of ML4.4 and ML4.5 and to provide a complete picture of Task 4, milestones 4.1-4.3 are briefly summarized at the beginning of the report. The discussion of ML4.4 introduces the notion of polymer persistence as a proxy for environmental risk. It then discusses the development and comparison of two machine leaning models explored for estimating polymer degradation rates, a random forest (RF) classifier and an RF regressor. Given the advantage of continuous outputs rather than simple classes, the RF regressor was incorporated in the Excel risk calculator, which to this point could implement the objectives of subtasks 4.1-4.3, estimating polymer release and redistribution. The ML4.4 discussion then addresses the effect of each of the three polymer features used by the RF regressor on polymer functional performance. These features are number molecular weight (Mn), glass transition temperature (T g ) and heat of fusion (H fus ). The discussion of ML4.5 reviews the conceptual framework of the risk model, which served as the foundation for developing the Excel risk calculator and describes the use of, and assumptions within, the calculator. Appendix A is further provided as a user’s guide for the calculator. To demonstrate how the calculator is intended to be used by developers in the design of low-risk polymers, an analysis of 27 hypothetical polymers defined by varying values for the three polymer features used by the RF regressor is presented. The range of parameter values selected produces estimates of polymer degradation rates and lifetimes that may be typical of various consumer products made from polyurethane polymers and shows how changes in polymer features affect lifetimes. The demonstration also predicts the final distribution of released polymer materials in environmental compartments as a function of consumer product mix and assumed leakage rates of end-of-life processes. Lastly, this report summarizes the achievement of Task 4 goals from original conception to final delivery and discusses how and to what degree to which each subtask goal was achieved.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Genetics and Genomics of Pathogen Resistance in Switchgrass (Final Report)

This project was funded by DOE under Grant no. DE-SC0016108. Originally approved for the 2016-2019 period, two no-cost extensions were solicited and approved, which prolonged the lifespan through July 2021. This final report informs on the results obtained so far from the research implemented. The research hinged on integrating genomics (genomic selection, RNAseq, virus-plant interactions) with classical genetics (conventional breeding) to incorporate durable resistance to fungal (rust) and viral (mosaic) diseases in switchgrass (Panicum virgatum) populations being bred for bioenergy. Higher biomass yield, higher quality (low lignin content), and durable disease resistance are key features to make lignocellulosic switchgrass feedstocks economically competitive and sustainable. Genomic selection is being applied on three generations of a switchgrass population derived from crossing two ecotypes (Kanlow as lowland female and Summer as upland male) with differential performance in terms of biomass yield and quality, disease resistance, and winter survivability. Target populations were screened for rust and mosaic in field and/or lab and phenotyped for biomass yield and quality traits. Genetic analyses were applied across generations to capture the joint inheritance of the targeted traits and predict breeding values for parents and progeny with greater accuracy. Parental and a panel of different switchgrass populations were genotyped with the DArTseq technology to develop SNP (0, 1, 2) and in-silico (presence/absence) DArT markers. Rust inoculations techniques were developed and applied successfully on switchgrass. The original populations (Kanlow and Summer) were sequenced with RNAseq to capture the gene expression profiles across sequential time-points and appraise the basis of greater resistance in the Kanlow vs the Summer ecotype. Constructs of PMV and sPMV mosaic virus were assembled and tested first on proso millet to find the best protocol to use later on switchgrass. Results from the preliminary analyses indicate that 1) ample additive genetic variation is available for selection and improving this inter-ecotypic population for yield, quality, and disease traits, 2) significant gains are to be expected with the genetic correlations being favorable between yield and lignin content and between yield and disease ratings, 3) substantial differences exist in the genetic regions controlling rust resistance in the two ecotypes, 4) co-infection with PMV isolates from Nebraska and its satellite from Kansas elicit severe mosaic symptoms, and 5) two different genetic systems are responsible for imparting resistance to rust and virus in switchgrass.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

High-Order Mesh Morphing for Boundary and Interface Fitting to Implicit Geometries

Here, we propose a method that morphs high-order meshes such that their boundaries and interfaces coincide/align with implicitly defined geometries. Our focus is particularly on the case when the target surface is prescribed as the zero isocontour of a smooth discrete function. Common examples of this scenario include using level set functions to represent material interfaces in multimaterial configurations, and evolving geometries in shape and topology optimization. The proposed method formulates the mesh optimization problem as a variational minimization of the sum of a chosen mesh-quality metric using the Target-Matrix Optimization Paradigm (TMOP) and a penalty term that weakly forces the selected faces of the mesh to align with the target surface. The distinct features of the method are use of a source mesh to represent the level set function with sufficient accuracy, and adaptive strategies for setting the penalization weight and selecting the faces of the mesh to be fit to the target isocontour of the level set field. We demonstrate that the proposed method is robust for generating boundary- and interface-fitted meshes for curvilinear domains using different element types in 2D and 3D.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Scalable Fabrication of a Fibrous Amine-functionalized Matrix (FAM) Sorbent for Critical Mineral Recovery

We report a novel flat sheet Fibrous Amine-functionalized Matrix (FAM) sorbent platform designed for efficient and selective capture of CM from dilute solutions. The FAM sorbent features crosslinked amine microfilms coated onto/within a glass fiber matrix, providing fast mass transfer and excellent mechanical stability. Systematic batch and flow-through tests with FAM revealed rapid metal uptake kinetics and high capacity for representative species, achieving ~90 mg/g of Gallium, ~100 mg/g of Cobalt, and ~90 mg/g for Neodymium. Moreover, multiple eluents, including mineral acids and complexing agents, enabled highly effective desorption of adsorbed metals, demonstrating the feasibility of regenerating FAM sorbents. Importantly, tests with authentic coal ash leachate demonstrated strong selectivity toward U.S. Department of Energy (DOE)-listed CM and rare earth elements over abundant base cations, confirming the robustness of FAM in realistic complex solutions. The flat sheet geometry was amenable to scaling into durable spiral wound modules, highlighting the potential for future regeneration and reuse. This work establishes FAM sorbents as a promising platform for the recovery of CM from wastewaters, advancing both resource sustainability and environmental stewardship.

critical mineral recovery↗
DOE OSTI2020

Chapter 10: Crystallography of Metabolic Enzymes

The metabolic enzymes like any enzymes generally display globular architecture where secondary structure elements and interactions between them preserve the spatial organization of the protein. A typical enzyme features a well-defined active site, designed for selective binding of the reaction substrate and facilitating a chemical reaction converting the substrate into a product. While many chemical reactions could be facilitated using only the functional groups that are found in proteins, the large percentage or intracellular reactions require use of cofactors, varying from single metal ions to relatively large molecules like numerous coenzymes, nucleotides and their derivatives, dinucleotides or hemes. Quite often these large cofactors become important not only for the catalytic function of the enzyme but also for the structural stability of it, as those are buried deep in the enzyme.

BASIC BIOLOGICAL SCIENCES,BIOMASS FUELS↗
DOE OSTI2021

Brain-implantable multifunctional probe for simultaneous detection of glutamate and GABA neurotransmitters

We report Glutamate (GLU) and gamma-aminobutyric acid (GABA) are neurotransmitters (NTs) with an essential role in signal transmission in the brain. Brain disorders, such as epilepsy, Alzheimer's and Parkinson's diseases, and traumatic brain injury can be linked to imbalances in the GLU-GABA homeostasis that occurs in sub-second to seconds time frames. Current measurement techniques can detect these two NT concentrations simultaneously only in vitro. The present work reports on the fabrication of a silicon multifunctional biosensor microarray probe for sub-second simultaneous GLU-GABA detection in real-time, with excellent analyte sensitivity and selectivity and in vivo capabilities. The novel Si probes feature four surface-functionalized platinum ultramicroelectrodes (UMEs) for simultaneous amperometric detection of GLU and GABA with a sentinel, and a built-in microfluidic channel for the introduction of neurochemicals in the proximity of the UMEs. The microchannel also allows functioning of an On-Demand In-situ Calibrator that runs in-situ biosensor calibration. The probe exhibited excellent robustness at insertion in agarose-gel brain-tissue-mimicking test, and remarkably high hydrogen peroxide sensitivity (a by-product of GLU-GABA enzyme biosensor) with values on the order of 5000 nA μM -1 cm -2 and maximum sensitivities of 204 ± 15 nA μM -1 cm -2 and 37 ± 7 nA μM -1 cm -2 for GLU and GABA, respectively. Furthermore, the limit of detection of the biosensors reached as low as 7 nM, 165 nM and 750 nM for H 2 O 2 , GLU and GABA, respectively and a temporal resolution of hundreds of milliseconds during in vivo studies using freely moving rats.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗