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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 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

DESI complete calibration of the colour–redshift relation (DC3R2): results from early DESI data

We present initial results from the Dark Energy Spectroscopic Instrument (DESI) complete calibration of the colour–redshift relation (DC3R2) secondary target survey. Our analysis uses 230 k galaxies that overlap with KiDS-VIKING ugriZYJHK s photometry to calibrate the colour–redshift relation and to inform photometric redshift (photo-z) inference methods of future weak lensing surveys. Together with emission line galaxies (ELGs), luminous red galaxies (LRGs), and the Bright Galaxy Survey (BGS) that provide samples of complementary colour, the DC3R2 targets help DESI to span 56 percent of the colour space visible to Euclid and LSST with high confidence spectroscopic redshifts. The effects of spectroscopic completeness and quality are explored, as well as systematic uncertainties introduced with the use of common Self-Organizing Maps trained on different photometry than the analysis sample. We further examine the dependence of redshift on magnitude at fixed colour, important for the use of bright galaxy spectra to calibrate redshifts in a fainter photometric galaxy sample. We find that noise in the KiDS-VIKING photometry introduces a dominant, apparent magnitude dependence of redshift at fixed colour, which indicates a need for carefully chosen deep drilling fields, and survey simulation to model this effect for future weak lensing surveys.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Complete replacement of Arabidopsis oil-producing enzymes with heterologous diacylglycerol acyltransferases

Acyl-CoA:diacylglycerol acyltransferase 1 (DGAT1) and phospholipid:diacylglycerol acyltransferase 1 (PDAT1) share responsibility for triacylglycerol (TAG) biosynthesis, and their selectivities control TAG fatty acid (FA) compositions. For rational metabolic engineering of seed oils, replacing endogenous TAG biosynthesis with exogenous enzymes containing different substrate FA selectivities is desirable; however, the dgat1-1/pdat1-2 double mutant is pollen lethal. Here, we evaluated the ability of 3 DGAT1s, from phylogenetically diverse plants with distinct TAG assembly processes, to completely replace endogenous TAG biosynthesis in Arabidopsis ( Arabidopsis thaliana ). We transformed dgat1-1 mutant plants with expression constructs for DGAT1 s from Camelina sativa , Physaria fendleri , and castor ( Ricinus communis ). Transgene expression was properly “contextualized” by using a previously determined minimum necessary expression unit containing the promoter/5′ UTR and first intron of native AtDGAT1 ; both of these DNA elements are essential for pollen expression. Next, we crossed homozygous lines with a DGAT1/DGAT1/PDAT1/pdat1-2 parent. C. sativa and P. fendleri DGAT1s restored the FA compositions and transcriptional differences of dgat1-1 to near wild-type and rescued the dgat1-1/pdat1-2 pollen lethality. R. communis DGAT1 was active in dgat1-1 seeds but produced unique oil profiles and alterations in the expression of lipid metabolic genes; it also failed to rescue dgat1-1/pdat1-2 lethality. This study confirms that the promoter and first intron of AtDGAT1 can modulate the expression of foreign DGAT1 genes to fit the correct spatiotemporal profile necessary for completely replacing endogenous TAG biosynthesis. Furthermore, it demonstrates an additional layer of unexpected enzyme incompatibility between oilseed lineages, which may complicate bioengineering approaches that seek to replace essential genes with orthologs.

McGuire, Sean T. [Washington State Univ., Pullman,↗
DOE OSTI2020

A method for achieving complete microbial genomes and improving bins from metagenomics data

Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete microbial genomes ( i.e ., circular with no misassemblies) from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Less than 100 circularized bacterial and archaeal genomes have been assembled from metagenomics data despite the thousands of datasets that are available. Circularized genomes are important for (1) building a reference collection as scaffolds for future assemblies, (2) providing complete gene content of a genome, (3) confirming little or no contamination of a genome, (4) studying the genomic context and synteny of genes, and (5) linking protein coding genes to ribosomal RNA genes to aid metabolic inference in 16S rRNA gene sequencing studies. We developed a method to achieve circularized genomes using iterative assembly, binning, and read mapping. In addition, this method exposes potential misassemblies from k-mer based assemblies. We chose species of the Candidate Phyla Radiation (CPR) to focus our initial efforts because they have small genomes and are only known to have one ribosomal RNA operon. We present 34 circular CPR genomes, one circular Margulisbacteria genome, and two circular megaphage genomes from 19 public and published datasets. We demonstrate findings that would likely be difficult without circularizing genomes, including that ribosomal genes are likely not operonic in the majority of CPR, and that some CPR harbor diverged forms of RNase P RNA. Code and a tutorial for this method is available at https://github.com/lmlui/Jorg .

Lui, Lauren↗
DOE OSTI2013

Directed Shotgun Proteomics Guided by Saturated RNA-seq Identifies a Complete Expressed Prokaryotic Proteome

Prokaryotes, due to their moderate complexity, are particularly amenable to the comprehensive identification of the protein repertoire expressed under different conditions. We applied a generic strategy to identify a complete expressed prokaryotic proteome, which is based on the analysis of RNA and proteins extracted from matched samples. Saturated transcriptome profiling by RNA-seq provided an endpoint estimate of the protein-coding genes expressed under two conditions which mimic the interaction of Bartonella henselae with its mammalian host. Directed shotgun proteomics experiments were carried out on four subcellular fractions. By specifically targeting proteins which are short, basic, low abundant, and membrane localized, we could eliminate their initial underrepresentation compared to the estimated endpoint. A total of 1250 proteins were identified with an estimated false discovery rate below 1%. This represents 85% of all distinct annotated proteins and ~90% of the expressed protein-coding genes. Genes that were detected at the transcript but not protein level, were found to be highly enriched in several genomic islands. Furthermore, genes that lacked an ortholog and a functional annotation were not detected at the protein level; these may represent examples of overprediction in genome annotations. A dramatic membrane proteome reorganization was observed, including differential regulation of autotransporters, adhesins, and hemin binding proteins. Particularly noteworthy was the complete membrane proteome coverage, which included expression of all members of the VirB/D4 type IV secretion system, a key virulence factor.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2024

Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements

Asgard archaea are of great interest as the progenitors of Eukaryotes, but little is known about the mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs that replicate in Atabeyarchaeia, a wetland Asgard archaea lineage represented by two complete genomes. We used soil depth–resolved population metagenomic data sets to track 18 MGEs for which genome structures were defined and precise chromosome integration sites could be identified for confident host linkage. Additionally, we identified a complete 20.67 kbp circular plasmid and two family-level groups of viruses linked to Atabeyarchaeia, via CRISPR spacer targeting. Closely related 40 kbp viruses possess a hypervariable genomic region encoding combinations of specific genes for small cysteine-rich proteins structurally similar to restriction-homing endonucleases. One 10.9 kbp integrative conjugative element (ICE) integrates genomically into theAtabeyarchaeum deiterrae-1chromosome and has a 2.5 kbp circularizable element integrated within it. The 10.9 kbp ICE encodes an expressed Type IIG restriction-modification system with a sequence specificity matching an active methylation motif identified by Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing. Restriction-modification of Atabeyarchaeia differs from that of another coexisting Asgard archaea, Freyarchaeia, which has few identified MGEs but possesses diverse defense mechanisms, including DISARM and Hachiman, not found in Atabeyarchaeia. Overall, defense systems and methylation mechanisms of Asgard archaea likely modulate their interactions with MGEs, and integration/excision and copy number variation of MGEs in turn enable host genetic versatility.

Biochemistry & Molecular Biology↗
DOE OSTI2025

Complete definition of 𝑁 →Δ transition generalized parton distributions

We revisit the definition of the leading-twist chiral-even generalized parton distributions (GPDs) for 𝑁 →Δ baryon transitions. We identify and address deficiencies in previous definitions of the transition GPDs inspired by the transition form factors of the vector and axial vector currents. Through systematic analysis of all possible covariant structures, respecting discrete symmetries and the baryon spinor equations of motion, we derive complete sets of independent structures for the transition matrix elements of the vector and axial vector partonic operators. They contain additional structures proportional to the light-cone vector, corresponding to transition GPDs of vanishing first moment, which were not included in previous parametrizations. Their presence is confirmed independently by the light-front multipole expansion and the cross-channel SO(3) partial-wave analysis of the transition matrix elements. Our analysis provides a complete definition of the 𝑁 →Δ transition GPDs for use in theoretical and phenomenological studies.

baryons↗
DOE OSTI2024

Simulating a numerical UV completion of quartic Galileons

The Galileon theory is a prototypical effective field theory that incorporates the Vainshtein screening mechanism—a feature that arises in some extensions of general relativity, such as massive gravity. The Vainshtein effect requires that the theory contain higher order derivative interactions, which results in Galileons, and theories like them, failing to be technically well posed. While this is not a fundamental issue when the theory is correctly treated as an effective field theory, it nevertheless poses significant practical problems when numerically simulating this model. These problems can be tamed using a number of different approaches: introducing an active low-pass filter and/or constructing a UV completion at the level of the equations of motion, which controls the high momentum modes. These methods have been tested on cubic Galileon interactions, and have been shown to reproduce the correct low-energy behavior. Here we show how the numerical UV-completion method can be applied to quartic Galileon interactions, and present the first simulations of the quartic Galileon model using this technique. We demonstrate that our approach can probe physics in the regime of the effective field theory in which the quartic term dominates, while successfully reproducing the known results for cubic interactions. Published by the American Physical Society 2024

Astronomy & Astrophysics↗
DOE OSTI2025

Hadronic vacuum polarization for the muon 𝑔 − 2 from lattice QCD: Complete short and intermediate windows

We present complete results for the hadronic vacuum polarization (HVP) contribution to the muon anomalous magnetic moment 𝑎 𝜇 in the short- and intermediate-distance window regions, which account for roughly 10% and 35% of the total HVP contribution to 𝑎 𝜇 , respectively. In particular, we perform lattice-QCD calculations for the isospin-symmetric connected and disconnected contributions, as well as corrections due to strong-isospin breaking. For the short-distance window observables, we investigate the so-called log-enhancement effects as well as the significant oscillations associated with staggered quarks in this region. For the dominant, isospin-symmetric light-quark-connected contribution, we obtain 𝑎$^{𝑙⁢𝑙,SD}_{𝜇⁡}$(conn) = 48.139⁢(11) stat ⁢(91) syst ⁢[92] total × 10 −10 and 𝑎$^{𝑙⁢𝑙,W}_{𝜇}$⁡(conn) = 206.90⁢(14) stat ⁢(61) syst ⁢[63] total × 10 −10 . We use Bayesian model averaging to fully estimate the covariance matrix between the individual contributions. Our determinations of the complete window contributions are 𝑎$^{SD}_{𝜇}$ = 69.05⁢(1) stat⁢ (21) syst ⁢[21] total × 10 −10 and 𝑎$^{W}_{𝜇}$ = 236.45⁢(17) stat⁢ (83) syst ⁢[85] total × 10 −10 . This work is part of our ongoing effort to compute all contributions to HVP with an overall uncertainty at the few-permille level.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Complete quasilinear model for the acceleration-driven lower hybrid drift instability and a computational assessment of its validity

A complete quasilinear model is derived for the electrostatic acceleration-driven lower hybrid drift instability in a uniform two-species low-beta plasma in which current is perpendicular to the background magnetic field. The model consists of coupled nonlinear velocity space diffusion equations for the volume-averaged ion and electron distribution functions. Each species' diffusion coefficient depends on a time-evolving spectral density of the electric-field energy per unit volume and a time-evolving dispersion relation. The dispersion relation is expressed analytically in integral form without the use of asymptotic limits and applies to arbitrary distribution functions, so long as they can be expressed as a function of one velocity coordinate, e.g., f⁡(vy) or f⁡(v⊥). The quasilinear model conserves energy and is complete in that it fully describes the evolution of the distribution functions, including resonant and nonresonant particle-wave interactions, while accounting for distribution-function-dependent mixed-complex frequencies. Further, the quasilinear diffusion model is solved numerically and self-consistently using a Crank-Nicolson temporal discretization and a second-order finite-volume velocity-space discretization. Numerical solutions are compared to nonlinear fourth-order accurate continuum kinetic Vlasov-Poisson simulations. Evolution of electric-field energy, growth rates, distribution functions, and diffusion coefficients are shown to be in agreement with Vlasov simulations. The quasilinear model is shown to predict anomalous transport terms, like resistivity and heating, to within a factor of order unity. Discrepancies between the quasilinear model and Vlasov simulations are assessed and attributed primarily to lack of damping in the quasilinear description and to the use of unperturbed-orbit susceptibilities in the linear theory dispersion relation. The results illuminate the predictive accuracy of the quasilinear model, place approximate bounds on its validity, and provide much needed vetting of quasilinear theory's ability to predict the nonlinear state of a microturbulent plasma.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Joint Matrix Completion and Compressed Sensing for State Estimation in Low-observable Distribution System

Limited measurement availability at the distribution grid presents challenges for state estimation and situational awareness. This paper combines the advantages of two sparsity-based state estimation approaches (matrix completion and compressive sensing) that have been proposed recently to address the challenge of unobservability. The proposed approach exploits both the low rank structure and a suitable transform domain representation to leverage the correlation structure of the spatio-temporal data matrix while incorporating the powerflow constraints of the distribution grid. Simulations are carried out on three phase unbalanced IEEE 37 test system to verify the effectiveness of the proposed approach. The performance results reveal - (1) the superiority over traditional matrix completion and (2) very low state estimation errors for high compression ratios representing very low observability.

Dahale, Shweta↗
DOE OSTI2014

SU-E-T-330: To Analyze the Calculation Error of Live Dose-Volume Indices Applying 4D-CT in Radiotherapy for PTVs Within the Liver Completely

Purpose: To study the variation rule of normal liver dose-volume indices calculation for the liver malignancy patients whose plan target volumes were in the liver completely in all breath phases. Methods: Ten patients who accepted radiotherapy for malignant tumor were selected in our study. All patients underwent 4D-CT simulation and 3D-CT simulation in free breathing(FB). 4D-CT was sorted into 10 series CT images according to breath phase, named CT0, CT10 to CT90, respectively. And GTVs were contoured on different CT series, and the individual target volume(ITV) was obtained by merging 10 GTVs from 4D-CT. The PTVs were obtained from ITV applying margins. The PTVs were not beyond the boundary of liver in all breath phase observed by dynamic 4D-CT. The radiotherapy plans were designed and irradiation dose was calculated on 3D-CT images, and the livers were contoured on different series CT images and mapped to 3D-CT images applying rigid registration. To compare the dose-volume difference of livers based on distinct CT images. Results: (1)The liver volumes were similar on 4D-CT and 3D-CT images(CTFB 1485±500cm{sup 3}, CT0 1413±377cm{sup 3}, CT10 1409±396cm{sup 3}, CT20 1419±418cm{sup 3},CT30 1485±500cm{sup 3}, CT40 1438±392cm{sup 3}, CT50 1437±404cm{sup 3}, CT60 1439±409cm{sup 3}, CT70 1408±393cm{sup 3}, CT80 1384±397cm{sup 3}, CT90 1398±397cm{sup 3}; F=0.064,p=1.00) (2) The PTVs volume were 30.17±14.62cm{sup 3};(3) The mean dose and V5 to V10 of liver were similar among 4D-CT different series CT images(p>0.05), and the indices varied less than ±4% refer to liver on CT50. Conclusion: The calculation affection of liver dose-volume indices induced by breath motion were not significant for the PTV within liver completely as estimation before. And more objective prediction indices for radiation induced l.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

SU-E-T-435: Development and Commissioning of a Complete System for In-Vivo Dosimetry and Range Verification in Proton Therapy

Purpose: In-vivo dose and beam range verification in proton therapy could play significant roles in proton treatment validation and improvements. Invivo beam range verification, in particular, could enable new treatment techniques one of which, for example, could be the use of anterior fields for prostate treatment instead of opposed lateral fields as in current practice. We have developed and commissioned an integrated system with hardware, software and workflow protocols, to provide a complete solution, simultaneously for both in-vivo dosimetry and range verification for proton therapy. Methods: The system uses a matrix of diodes, up to 12 in total, but separable into three groups for flexibility in application. A special amplifier was developed to capture extremely small signals from very low proton beam current. The software was developed within iMagX, a general platform for image processing in radiation therapy applications. The range determination exploits the inherent relationship between the internal range modulation clock of the proton therapy system and the radiological depth at the point of measurement. The commissioning of the system, for in-vivo dosimetry and for range verification was separately conducted using anthropomorphic phantom. EBT films and TLDs were used for dose comparisons and range scan of the beam distal fall-off was used as ground truth for range verification. Results: For in-vivo dose measurement, the results were in agreement with TLD and EBT films and were within 3% from treatment planning calculations. For range verification, a precision of 0.5mm is achieved in homogeneous phantoms, and a precision of 2mm for anthropomorphic pelvic phantom, except at points with significant range mixing. Conclusion: We completed the commissioning of our system for in-vivo dosimetry and range verification in proton therapy. The results suggest that the system is ready for clinical trials on patient.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2016

The rotate-plus-shift C-arm trajectory. Part I. Complete data with less than 180° rotation

Purpose: In the last decade, C-arm-based cone-beam CT became a widely used modality for intraoperative imaging. Typically a C-arm CT scan is performed using a circular or elliptical trajectory around a region of interest. Therefore, an angular range of at least 180° plus fan angle must be covered to ensure a completely sampled data set. However, mobile C-arms designed with a focus on classical 2D applications like fluoroscopy may be limited to a mechanical rotation range of less than 180° to improve handling and usability. The method proposed in this paper allows for the acquisition of a fully sampled data set with a system limited to a mechanical rotation range of at least 180° minus fan angle using a new trajectory design. This enables CT like 3D imaging with a wide range of C-arm devices which are mainly designed for 2D imaging. Methods: The proposed trajectory extends the mechanical rotation range of the C-arm system with two additional linear shifts. Due to the divergent character of the fan-beam geometry, these two shifts lead to an additional angular range of half of the fan angle. Combining one shift at the beginning of the scan followed by a rotation and a second shift, the resulting rotate-plus-shift trajectory enables the acquisition of a completely sampled data set using only 180° minus fan angle of rotation. The shifts can be performed using, e.g., the two orthogonal positioning axes of a fully motorized C-arm system. The trajectory was evaluated in phantom and cadaver examinations using two prototype C-arm systems. Results: The proposed trajectory leads to reconstructions without limited angle artifacts. Compared to the limited angle reconstructions of 180° minus fan angle, image quality increased dramatically. Details in the rotate-plus-shift reconstructions were clearly depicted, whereas they are dominated by artifacts in the limited angle scan. Conclusions: The method proposed here employs 3D imaging using C-arms with less than 180° rotation range adding full 3D functionality to a C-arm device retaining both handling comfort and the usability of 2D imaging. This method has a clear potential for clinical use especially to meet the increasing demand for an intraoperative 3D imaging.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Complete Genome Sequences of the Soil Oxalotrophic Bacterium Cupriavidus oxalaticus Strain Ox1 and Its Derived mCherry-Tagged Strain

Here, we report the complete genome sequences of the soil oxalotrophic bacterium Cupriavidus oxalaticus Ox1 and a derived mCherry-tagged strain. The genome size is approximately 6.69 Mb, with a GC content of 66.9%. The genome sequence of C. oxalaticus Ox1 contains a complete operon for the degradation and assimilation of oxalate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Complete Genome Sequences of Five Isolated Pseudomonas Strains that Catabolize Pentose Sugars and Aromatic Compounds Obtained from Lignocellulosic Biomass

We report on complete genome sequences of five Pseudomonas soil isolates that are capable of metabolizing pentose sugars and aromatic monomers. These complete genome sequence data provide insight into possible alternative hosts for the production of biofuels and bio-based chemicals from lignocellulosic feedstock.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Neuromorphic Computing is Turing-Complete

Neuromorphic computing is a non-von Neumann computing paradigm that performs computation by emulating the human brain. Neuromorphic systems are extremely energy-efficient and known to consume thousands of times less power than CPUs and GPUs. They have the potential to drive critical use cases such as autonomous vehicles, edge computing and internet of things in the future. For this reason, they are sought to be an indispensable part of the future computing landscape. Neuromorphic systems are mainly used for spike-based machine learning applications, although there are some non-machine learning applications in graph theory, differential equations, and spike-based simulations. These applications suggest that neuromorphic computing might be capable of general-purpose computing. However, general-purpose computability of neuromorphic computing has not been established yet. In this work, we prove that neuromorphic computing is Turing-complete and therefore capable of general-purpose computing. Specifically, we present a model of neuromorphic computing, with just two neuron parameters (threshold and leak), and two synaptic parameters (weight and delay). We devise neuromorphic circuits for computing all the μ-recursive functions (i.e., constant, successor and projection functions) and all the μ-recursive operators (i.e., composition, primitive recursion and minimization operators). Given that the μ-recursive functions and operators are precisely the ones that can be computed using a Turing machine, this work establishes the Turing-completeness of neuromorphic computing.

Date, Prasanna↗
DOE OSTI2018

Classification of Complete Proteomes of Different Organisms and Protein Sets Based on Their Protein Distributions in Terms of Some Key Attributes of Proteins

The existence of complete genome sequences makes it important to develop different approaches for classification of large-scale data sets and to make extraction of biological insights easier. Here, we propose an approach for classification of complete proteomes/protein sets based on protein distributions on some basic attributes. We demonstrate the usefulness of this approach by determining protein distributions in terms of two attributes: protein lengths and protein intrinsic disorder contents (ID). The protein distributions based on L and ID are surveyed for representative proteome organisms and protein sets from the three domains of life. The two-dimensional maps (designated as fingerprints here) from the protein distribution densities in the LD space defined by ln( L ) and ID are then constructed. The fingerprints for different organisms and protein sets are found to be distinct with each other, and they can therefore be used for comparative studies. As a test case, phylogenetic trees have been constructed based on the protein distribution densities in the fingerprints of proteomes of organisms without performing any protein sequence comparison and alignments. The phylogenetic trees generated are biologically meaningful, demonstrating that the protein distributions in the LD space may serve as unique phylogenetic signals of the organisms at the proteome level.

59 BASIC BIOLOGICAL SCIENCES↗