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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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97 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

SU-D-206-02: Evaluation of Partial Storage of the System Matrix for Cone Beam Computed Tomography Using a GPU Platform

Purpose: Iterative reconstruction algorithms in computed tomography (CT) require a fast method for computing the intersections between the photons’ trajectories and the object, also called ray-tracing or system matrix computation. This work evaluates different ways to store the system matrix, aiming to reconstruct dense image grids in reasonable time. Methods: We propose an optimized implementation of the Siddon’s algorithm using graphics processing units (GPUs) with a novel data storage scheme. The algorithm computes a part of the system matrix on demand, typically, for one projection angle. The proposed method was enhanced with accelerating options: storage of larger subsets of the system matrix, systematic reuse of data via geometric symmetries, an arithmetic-rich parallel code and code configuration via machine learning. It was tested on geometries mimicking a cone beam CT acquisition of a human head. To realistically assess the execution time, the ray-tracing routines were integrated into a regularized Poisson-based reconstruction algorithm. The proposed scheme was also compared to a different approach, where the system matrix is fully pre-computed and loaded at reconstruction time. Results: Fast ray-tracing of realistic acquisition geometries, which often lack spatial symmetry properties, was enabled via the proposed method. Ray-tracing interleaved with projection and backprojection operations required significant additional time. In most cases, ray-tracing was shown to use about 66 % of the total reconstruction time. In absolute terms, tracing times varied from 3.6 s to 7.5 min, depending on the problem size. The presence of geometrical symmetries allowed for non-negligible ray-tracing and reconstruction time reduction. Arithmetic-rich parallel code and machine learning permitted a modest reconstruction time reduction, in the order of 1 %. Conclusion: Partial system matrix storage permitted the reconstruction of higher 3D image grid sizes and larger projection datasets at the cost of additional time, when compared to the fully pre-computed approach. This work was supported in part by the Fonds de recherche du Quebec - Nature et technologies (FRQ-NT). The authors acknowledge partial support by the CREATE Medical Physics Research Training Network grant of the Natural Sciences and Engineering Research Council of Canada (Grant No. 432290).

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Solvent-mediated secondary building units (SBUs) diversification in a series of Mn{sup II}-based metal-organic frameworks (MOFs)

The role of auxiliary solvents in the formation of MOFs has been investigated for a series of Mn{sup II}-based framework systems. Reactions of 4,4′,4″-nitrilotribenzoic acid (H{sub 3}L) with Mn{sup II} through varying auxiliary solvents of the medium resulted in the formation of diversified multinuclear Mn{sup II} subunits in four new coordination polymers: [Mn{sub 3}(L)(HCOO){sub 3}(DEF){sub 3}] (1), [Mn{sub 3}(L){sub 2}(EtOH){sub 2}]·DMF (2), [Mn{sub 5}(L){sub 4}(H{sub 2}O){sub 2}]·2(H{sub 2}NMe{sub 2}){sup +}·4DMF·2H{sub 2}O (3), and [Mn{sub 3}(L){sub 2}(py){sub 4}(H{sub 2}O)]·H{sub 2}O (4) (H{sub 3}L=4,4′,4′-nitrilotribenzoic acid, DMF=dimethylformamide, DEF=N,N-diethylformamide, py=pyridine). These four compounds were fully characterized by single-crystal X-ray diffraction, showing interesting SBUs variations. For compound 1, it displays a (3,6)-connected kgd net with wheel [Mn{sub 6}] cluster serving as SBU, whereas in 2, the sequence of Mn{sub 3}(COO){sub 9}(EtOH){sub 2} is repeated by inversion centers located between Mn1 and Mn3 to form an infinite Mn-carboxylate chain, which are further interlinked by L{sup 3−} ligands to form a 3D architecture. In 3, the pentanuclear Mn{sub 5}(CO{sub 2}){sub 12} clusters are interlinked to form a layer, which are further pillared by L{sup 3−} to generate a 3D network. Compound 4 has a (3,6)-connected network in which the SBU is a linear trimeric Mn{sub 3}(COO){sub 6}(py){sub 4}(H{sub 2}O) cluster. In addition, the thermal stabilities, X-ray powder diffraction of all the compounds were studied, photoluminescence behaviors of compounds 1, 3 and 4 are discussed. - Graphical abstract: Supramolecular assembly of C{sub 3}-symmetric ligand 4,4′,4″-nitrilotribenzoic acid (H{sub 3}L) with Mn{sup II} through varying auxiliary solvents of the medium resulted in the formation of diversified multinuclear Mn{sup II} subunits in four new coordination polymers. The results exhibit the structures of Mn-SBUs in these MOFs largely depend on the ancillary solvents involved in the reactions. Display Omitted.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

GROWdb US River Systems - Samples

GROW Overview We developed the Genome Resolved Open Watersheds database (GROWdb), which aims to increase genomic sampling and understanding of global river microbiomes. An emphasis of GROWdb is to create a publicly available and ever-expanding microbial genome database that is focused on rivers while being interoperable with databases from other ecosystems. GROWdb is based on a network-of-networks approach to move beyond a small collection of well-studied rivers, towards a spatially distributed, global network of systematic observations. GROWdb represents the first microbial, river-focused resource parsed at various scales from genes to MAGs to community level including expression and potential based measurements that will be of interest to microbiologists, ecologists, geochemists, hydrologists, and modelers. Dataset Acknowledgement GROWdb contains data from various research campaigns, please acknowledge the following data generators, as appropriate: WHONDRS derived genomes or samples - include this statement in your acknowledgements: “This study used data from the Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) under the River Corridor Science Focus Area (SFA) at the Pacific Northwest National Laboratory (PNNL) that was generated at the U.S. Department of Energy (DOE) Joint Genome Institute User Facility. PNNL is operated by Battelle Memorial Institute for the U.S. DOE under Contract No. DE-AC05-76RL01830. The SFA is supported by the U.S. DOE, Office of Biological and Environmental Research (BER), Environmental System Science (ESS) Program.” Total Samples loaded onto this Narrative: 178 Note: Not all GROW samples may be loaded into KBase Data Availability The data underlying GROWdb are accessible across various platforms to ensure all levels of data structure are widely available. First, all reads and MAGs are publicly hosted on National Center for Biotechnology (NCBI) under Bioproject PRJNA946291. Second, all data related data presented here including MAG annotations, extended data tables, phylogenetic tree files, antibiotic resistance gene database files, and MAG abundance tables are available in Zenodo (link). Beyond the flat database files listed above, our aim for GROWdb was to maximize data use by making the data available in searchable and interactive platforms including the National Microbiome Data Collaborative (NMDC) data portal, the Department of Energy’s Systems Biology Knowledgebase (KBase), and a GROW specific user interface released here, GROWdb Explorer. Each platform provides different ways to interact with GROWdb: NMDC GROWdb formed a pilot project for the NMDC. Specifically, individual GROWdb datasets (metagenomes, metatranscriptomes, etc) are easily accessible and searchable through the NMDC data portal, where they are systematically connected to each other and to a rich suite of sample information and standard analysis results, following Findable, Accessible, Interoperable, and Reusable (FAIR) data practices. KBase GROWdb is publicly available within KBase, including samples (this Narrative), MAGs, and corresponding genome scale metabolic models. Access within KBase allows for immediate access and reuse of data, including comparison to private data using KBase’s 500+ analysis tools. Other linked narratives in KBase: GROW Metagenome Assembled Genomes (MAGs) GROW Metabolic Models GROWdb Explorer GROWdb data is also explorable through a graphical user interface built through the Colorado State University Geospatial Centroid (https://geocentroid.shinyapps.io/GROWdatabase/), allowing users to search and graph microbial and spatial data simultaneously. In summary, this microbial genome resource represents the first publicly available genome collection from rivers and offers data that can be leveraged across microbiome studies. GROWdb is an expanding repository to incorporate and unify global river multi-omic data for the future.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Effect of alkali cations on two-dimensional networks of two new quaternary thioarsenates (III) prepared by a facile surfactant-thermal method

Two new quaternary thioarsenates(III) NaAg{sub 2}AsS{sub 3}·H{sub 2}O (1) and KAg{sub 2}AsS{sub 3} (2) with high yields have been successfully prepared through a facile surfactant-thermal method. It is interesting that 2 can only be obtained with the aid of ethanediamine (en), which indicates that weak basicity of solvent is beneficial to the growth of 2 compared with 1. Both 1 and 2 feature the similar two-dimensional (2D) layer structures. However, the distortion of the primary honeycomb-like nets in 2 is more severe than that of 1, which demonstrates that Na{sup +} and K{sup +} cations have different structure directing effects on these two thioarsenates(III). Both experimental and theoretical studies confirm 1 and 2 are semiconductors with band gaps in the visible region. Our success in preparing these two quaternary thioarsenates(III) proves that surfactant-thermal technique is a powerful yet facile synthetic method to explore new complex chalcogenides. - Graphical abstract: Two new quaternary thioarsenates(III) NaAg{sub 2}AsS{sub 3}·H{sub 2}O (1) and KAg{sub 2}AsS{sub 3} (2) with high yields have been successfully prepared through a facile surfactant-thermal method. X-ray single crystal diffraction analyses demonstrate that Na{sup +} and K{sup +} cations have different structure directing effects on these two thioarsenates(III). Both experimental and theoretical studies confirm 1 and 2 are semiconductors with band gaps in the visible region. Display Omitted - Highlights: • NaAg{sub 2}AsS{sub 3}⋅H{sub 2}O (1) and KAg{sub 2}AsS{sub 3} (2) were prepared through surfactant-thermal method. • Crystal structures show Na{sup ±} and K{sup ±} have different structure directing effects. • The weak basicity of solvent is benefit to the growth of 2 compared with 1. • Experimental and theoretical studies confirm 1 and 2 are semiconductors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Modification and analysis of context-specific genome-scale metabolic models: methane-utilizing microbial chassis as a case study

ABSTRACT Context-specific genome-scale model (CS-GSM) reconstruction is becoming an efficient strategy for integrating and cross-comparing experimental multi-scale data to explore the relationship between cellular genotypes, facilitating fundamental or applied research discoveries. However, the application of CS modeling for non-conventional microbes is still challenging. Here, we present a graphical user interface that integrates COBRApy, EscherPy, and RIPTiDe, Python-based tools within the BioUML platform, and streamlines the reconstruction and interrogation of the CS genome-scale metabolic frameworks via Jupyter Notebook. The approach was tested using -omics data collected for Methylotuvimicrobium alcaliphilum 20Z R , a prominent microbial chassis for methane capturing and valorization. We optimized the previously reconstructed whole genome-scale metabolic network by adjusting the flux distribution using gene expression data. The outputs of the automatically reconstructed CS metabolic network were comparable to manually optimized i IA409 models for Ca-growth conditions. However, the CS model questions the reversibility of the phosphoketolase pathway and suggests higher flux via primary oxidation pathways. The model also highlighted unresolved carbon partitioning between assimilatory and catabolic pathways at the formaldehyde-formate node. Only a very few genes and only one enzyme with a predicted function in C1 metabolism, a homolog of the formaldehyde oxidation enzyme ( fae1-2 ), showed a significant change in expression in La-growth conditions. The CS-GSM predictions agreed with the experimental measurements under the assumption that the Fae1-2 is a part of the tetrahydrofolate-linked pathway. The cellular roles of the tungsten (W)-dependent formate dehydrogenase ( fdhAB ) and fae homologs ( fae1-2 and fae3 ) were investigated via mutagenesis. The phenotype of the f dhAB mutant followed the model prediction. Furthermore, a more significant reduction of the biomass yield was observed during growth in La-supplemented media, confirming a higher flux through formate. M. alcaliphilum 20Z R mutants lacking fae1-2 did not display any significant defects in methane or methanol-dependent growth. However, contrary to fae1, the fae1-2 homolog failed to restore the formaldehyde-activating enzyme function in complementation tests. Overall, the presented data suggest that the developed computational workflow supports the reconstruction and validation of CS-GSM networks of non-model microbes. IMPORTANCE The interrogation of various types of data is a routine strategy to explore the relationship between genotype and phenotype. An efficient approach for integrating and cross-comparing experimental multi-scale data in the context of whole-genome-based metabolic network reconstruction becomes a powerful tool that facilitates fundamental and applied research discoveries. The present study describes the reconstruction of a context-specific (CS) model for the methane-utilizing bacterium, Methylotuvimicrobium alcaliphilum 20Z R . M. alcaliphilum 20Z R is becoming an attractive microbial platform for the production of biofuels, chemicals, pharmaceuticals, and bio-sorbents for capturing atmospheric methane. We demonstrate that this pipeline can help reconstruct metabolic models that are similar to manually curated networks. Furthermore, the model is able to highlight previously overlooked pathways, thus advancing fundamental knowledge of non-model microbial systems or promoting their development toward biotechnological or environmental implementations.

Kulyashov, M. A.↗
DOE OSTI2022

Heavy-Duty Vehicle Activity Updates for MOVES Using NREL Fleet DNA and CE-CERT Data

The U.S. Environmental Protection Agency's (EPA's) Motor Vehicle Emission Simulator (MOVES) is a publicly available tool used by researchers and policymakers to help understand motor vehicle emission sources at a national, county, and project level. Estimates of heavy-duty activity in the most recent version of the model at the time this work was conducted, MOVES2014, was identified as an area in need of improvement. The start activity in MOVES2014 is based on a limited and dated data set. In addition, MOVES2014 relies on drive cycles that represent on-network activity but do not account for idling activity that occurs on off-network roads, such as at a distribution center, while the truck is queuing or during loading and unloading. As a result, MOVES2014 may currently underestimate the number of starts and idle and soak time for heavy-duty trucks in real-world operation. The National Renewable Energy Laboratory (NREL) has previously leveraged its expansive Fleet DNA database of heavy-duty vehicles to idle and start activity for six of the nine heavy-duty vehicle source types of classes in the MOVES model. The data available in Fleet DNA from 416 conventional, diesel-powered vehicles provided activity estimates from more than 120,000 hours of operation throughout 14,682 vehicle days between October 2006 and January 2016. NREL calculated start fraction, starts per day, soak fraction, and idle fraction by hour of the day for each vehicle type, state, and vocation, and provided results in .CSV files that can be translated to MOVES table inputs. The idle and start activity from this initial analysis of Fleet DNA data was used to develop default idle and start data for heavy-duty vehicles in MOVES3. Satisfied with the results from the Fleet DNA data used for MOVES3, the EPA asked NREL to extend this start/soak/idle analysis using additional data from a larger number of vehicles for a potential future update to the MOVES model. Such a data set was achieved from a project led by the University of California at Riverside, College of Engineering, Center for Environmental Research & Technology (CE-CERT) and funded by California Air Resources Board. Specifically, this data set consists of 90 heavy-duty vehicles operated mainly in California, which can be separated into five of the nine heavy-duty vehicle classes in the MOVES model. In addition, the heavy-duty activity database collected by CE-CERT provided activity estimates from more than 44,000 hours of operation throughout 4,724 vehicle days between November 2014 and September 2016. This report details the analysis of the heavy-duty activity database collected from the University of California at Riverside by providing graphical analysis and context for the start, soak, and idle distributions. The comparison of the related results from both the Fleet DNA and CE-CERT data sets are documented as well.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2021

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective.

59 BASIC BIOLOGICAL SCIENCES↗