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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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DOE OSTI2013

THE PRECISION AND ACCURACY OF EARLY EPOCH OF REIONIZATION FOREGROUND MODELS: COMPARING MWA AND PAPER 32-ANTENNA SOURCE CATALOGS

As observations of the Epoch of Reionization (EoR) in redshifted 21 cm emission begin, we assess the accuracy of the early catalog results from the Precision Array for Probing the Epoch of Reionization (PAPER) and the Murchison Wide-field Array (MWA). The MWA EoR approach derives much of its sensitivity from subtracting foregrounds to <1% precision, while the PAPER approach relies on the stability and symmetry of the primary beam. Both require an accurate flux calibration to set the amplitude of the measured power spectrum. The two instruments are very similar in resolution, sensitivity, sky coverage, and spectral range and have produced catalogs from nearly contemporaneous data. We use a Bayesian Markov Chain Monte Carlo fitting method to estimate that the two instruments are on the same flux scale to within 20% and find that the images are mostly in good agreement. We then investigate the source of the errors by comparing two overlapping MWA facets where we find that the differences are primarily related to an inaccurate model of the primary beam but also correlated errors in bright sources due to CLEAN. We conclude with suggestions for mitigating and better characterizing these effects.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2013

COMPARING THE LIGHT CURVES OF SIMULATED TYPE Ia SUPERNOVAE WITH OBSERVATIONS USING DATA-DRIVEN MODELS

We propose a robust, quantitative method to compare the synthetic light curves of a Type Ia supernova (SN Ia) explosion model with a large set of observed SNe Ia, and derive a figure of merit for the explosion model's agreement with observations. The synthetic light curves are fit with the data-driven model SALT2 which returns values for stretch, color, and magnitude at peak brightness, as well as a goodness-of-fit parameter. Each fit is performed multiple times with different choices of filter bands and epoch range in order to quantify the systematic uncertainty on the fitted parameters. We use a parametric population model for the distribution of observed SN Ia parameters from large surveys, and extend it to represent red, dim, and bright outliers found in a low-redshift SN Ia data set. We discuss the potential uncertainties of this population model and find it to be reliable given the current uncertainties on cosmological parameters. Using our population model, we assign each set of fitted parameters a likelihood of being observed in nature, and a figure of merit based on this likelihood. We define a second figure of merit based on the quality of the light curve fit, and combine the two measures into an overall figure of merit for each explosion model. We compute figures of merit for a variety of one-, two-, and three-dimensional explosion models and show that our evaluation method allows meaningful inferences across a wide range of light curve quality and fitted parameters.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2011

THE INTEGRATED DIFFUSE X-RAY EMISSION OF THE CARINA NEBULA COMPARED TO OTHER MASSIVE STAR-FORMING REGIONS

The Chandra Carina Complex Project (CCCP) has shown that the Carina Nebula displays bright, spatially-complex soft diffuse X-ray emission. Here, we 'sum up' the CCCP diffuse emission work by comparing the global morphology and spectrum of Carina's diffuse X-ray emission to other famous sites of massive star formation with pronounced diffuse X-ray emission: M17, NGC 3576, NGC 3603, and 30 Doradus. All spectral models require at least two diffuse thermal plasma components to achieve adequate spectral fits, a softer component with kT = 0.2-0.6 keV and a harder component with kT = 0.5-0.9 keV. In several cases these hot plasmas appear to be in a state of non-equilibrium ionization that may indicate recent and current strong shocks. A cavity north of the embedded giant H II region NGC 3576 is the only region studied here that exhibits hard diffuse X-ray emission; this emission appears to be nonthermal and is likely due to a recent cavity supernova, as evidenced by a previously-known pulsar and a newly-discovered pulsar wind nebula also seen in this cavity. All of these targets exhibit X-ray emission lines that are not well modeled by variable-abundance thermal plasmas and that might be attributed to charge exchange at the shock between the hot, tenuous, X-ray-emitting plasma and cold, dense molecular material; this is likely evidence for dust destruction at the many hot/cold interfaces that characterize massive star-forming regions.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Comparative analysis of the sensitivity of nanometallic thin film thermometers

Thin film platinum resistive thermometers are conventionally applied for resistance thermometry techniques due to their stability and proven measurement accuracy. Depending upon the required thermometer thickness and temperature measurement, however, performance benefits can be realized through the application of alternative nanometallic thin films. Herein, a comparative experimental analysis is provided on the performance of nanometallic thin film thermometers most relevant to microelectronics and thermal sensing applications: Al, Au, Cu, and Pt. Sensitivity is assessed through the temperature coefficient of resistance, measured over a range of 10–300 K for thicknesses nominally spanning 25–200 nm. In this work, the interplay of electron scattering sources, which give rise to the temperature-dependent TCR properties for each metal, are analyzed in the framework of a Mayadas–Shatzkes based model. Despite the prevalence of evaporated Pt thin film thermometers, Au and Cu films fabricated in a similar manner may provide enhanced sensitivity depending upon thickness. These results may serve as a guide as the movement toward smaller measurement platforms necessitates the use of smaller, thinner metallic resistance thermometers.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Exploring the fusion power plant design space: comparative analysis of positive and negative triangularity tokamaks through optimization

The optimal configuration choice between positive triangularity (PT) and negative triangularity (NT) tokamaks for fusion power plants hinges on navigating different operational constraints rather than achieving specific plasma performance metrics. This study presents a systematic comparison using constrained multi-objective optimization with the integrated FUsion Synthesis Engine (FUSE) framework. Over 200 000 integrated design evaluations were performed exploring the trade-offs between capital cost minimization and operational reliability (maximizing q 95 ) while satisfying engineering constraints including 250 ± 50 MW net electric power, tritium breeding ratio > 1.1, power exhaust limits and an hour flattop time. Both configurations achieve similar cost-performance Pareto fronts through contrasting design philosophies. PT, while demonstrating resilience to pedestal degradation (compensating for up to 40% reduction), are constrained to larger machines (R 0 > 6.5 m) by the narrow operational window between L–H threshold requirements and the research-established power exhaust limit (P sol /R < 15 MW m –1 ). This forces optimization through comparatively reduced magnetic field (∼8 T). NT configurations exploit their freedom from these constraints to access compact, high-field designs (R 0 ~ 5.5 m, B 0 >12 T), creating natural synergy with advancing HTS technology. Sensitivity analyses reveal that PT’s economic viability depends critically on uncertainties in L–H threshold scaling and power handling limits. Notably, a 50% variation in either could eliminate viable designs or enable access to the compact design space. These results suggest configuration selection should be risk-informed: PT offers the lowest-cost path when operational constraints can be confidently predicted, while NT is robust to large variations in constraints and physics uncertainties.

FUSE framework↗

DOE OSTI2020

Deeply uncertain: comparing methods of uncertainty quantification in deep learning algorithms

We present a comparison of methods for uncertainty quantification (UQ) in deep learning algorithms in the context of a simple physical system. Three of the most common uncertainty quantification methods - Bayesian Neural Networks (BNN), Concrete Dropout (CD), and Deep Ensembles (DE) - are compared to the standard analytic error propagation. We discuss this comparison in terms endemic to both machine learning ("epistemic" and "aleatoric") and the physical sciences ("statistical" and "systematic"). The comparisons are presented in terms of simulated experimental measurements of a single pendulum - a prototypical physical system for studying measurement and analysis techniques. Our results highlight some pitfalls that may occur when using these UQ methods. For example, when the variation of noise in the training set is small, all methods predicted the same relative uncertainty independently of the inputs. This issue is particularly hard to avoid in BNN. On the other hand, when the test set contains samples far from the training distribution, we found that no methods sufficiently increased the uncertainties associated to their predictions. This problem was particularly clear for CD. In light of these results, we make some recommendations for usage and interpretation of UQ methods.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Validating and Comparing Energy Estimation Methods at Water Resource Recovery Facilities

Water resource recovery facilities play a crucial role in the water-energy nexus, consuming a substantial amount of energy in the United States. Growing treatment volumes and more stringent water quality standards are expected to increase the amount of energy needed to treat wastewater, but accurately estimating energy consumption and potential remains challenging due to variability in scale, treatment methods, and effluent treatment standards. In this study, we used publicly available data to evaluate the accuracy of methods for estimating energy consumption and generation, then quantified uncertainty based on key factors like flow rate, treatment level, and geographic location. To validate methods, we estimated energy consumption and generation at the facility-level, then compared estimates to self-reported data from utilities in major U.S. cities. We found that process models of treatment trains under best practice configurations were accurate relative to other methods for estimating electricity use, total energy use, and electricity generation from biogas utilization, and less complex methods based on effluent treatment level and prime movers also performed well for estimating electricity consumption and generation, respectively. Applying the evaluated methods to a national inventory of treatment facilities, we estimate that annual energy consumption ranged from 56.3 x 10^3 to 82.5 x 10^3 TJ in 2012 and 83.6 x 10^3 to 127 x 10^3 TJ in 2042. Our results indicate that not all estimation methods are suited for every use case, so we recommend that researchers and practitioners select an estimation method based on data availability and desired computational intensity.

Hodson, Abigayle↗

DOE OSTI2013

Comparative genomics analysis of Trichoderma reesei strains

Trichoderma reesei is a key fungus for industrial production of lignocellulolytic enzymes. The genome sequences of the Trichoderma reesei hyper-cellulolytic strain RUT-C30 and its parental strain QM6a were compared at the nucleotide level. Approximately 97 % of the 87 genomic sequence scaffolds of T. reesei QM6a (33Mb) were detected to have the correspondent nucleotide in the 182 genome sequence scaffolds of RUT-C30 (32Mb). There are 455 loci within the QM6 sequence not detected in the RUT-C30 sequence. Regions at the termini of QM6a scaffolds as well as 14 small scaffolds do not have corresponding regions in RUT-C30 genomic scaffolds. Seventy-eight protein encoding genes are included within these regions. Mutated nucleotide(s) in 2,371 positions, including short insertion/deletions (indels) were detected in the aligned regions. The predicted protein coding regions of 97 gene models contain mutations, 34 of which were not previously described. Twenty-seven out of 34 newly discovered genes were found to have mutations in the peptide amino acid sequence. This is in addition to 63 genes described in a previous study based on low coverage sequencing of RUT-C30. These newly identified proteins are involved in signal transduction, transcription, RNA processing and modification, post-translational modification according to their annotations. Similar distributions of eukaryotic orthologous group (KOG) categories between the mutated and all other proteins suggest random mutation. The roles of the mutated genes and potential regulatory regions in the observed phenotype of RUT-C30 remain to be explored in a targeted fashion.

Trichoderma, genomics, biofuels, enzymes, cellulas↗

DOE OSTI2016

Species diversity driven by morphological and ecological disparity: a case study of comparative seed morphology and anatomy across a large monocot order

Phenotypic variation can be attributed to genetic heritability as well as biotic and abiotic factors. Across Zingiberales, there is a high variation in the number of species per clade and in phenotypic diversity. Factors contributing to this phenotypic variation have never been studied in a phylogenetic or ecological context. Seeds of 166 species from all eight families in Zingiberales were analyzed for 51 characters using synchrotron based 3D X-ray tomographic microscopy to determine phylogenetically informative characters and to understand the distribution of morphological disparity within the order. All families are distinguishable based on seed characters. Non-metric multidimensional scaling analyses show Zingiberaceae occupy the largest seed morphospace relative to the other families, and environmental analyses demonstrate that Zingiberaceae inhabit both temperate and tropical regions, while other Zingiberales are almost exclusively tropical. Temperate species do not cluster in morphospace nor do they share a common suite of character states. This suggests that the diversity seen is not driven by adaptation to temperate niches; rather, the morphological disparity seen likely reflects an underlying genetic plasticity that allowed Zingiberaceae to repeatedly colonize temperate environments. The notable morphoanatomical variety in Zingiberaceae seeds may account for their extraordinary ecological success and high species diversity as compared to other Zingiberales.

Cannaceae↗

DOE OSTI2017

Comparative genomics of the genus Desulfitobacterium

The Desulfitobacterium genus comprises anaerobic Gram-positive bacteria, of which the majority are facultative organohalide respirers. We here present the genomes of eight strains of Desulfitobacterium spp., including five strains of Desulfitobacterium hafniense, one strain each from D. dichloroeliminans and D. metallireducens, and one strain that had not been assigned to any species prior to this study. The newly sequenced genomes were compared with four previously published desulfitobacterial genomes. The average genome sizes are 5.5, 4.3 and 3.4 Mbp for D. hafniense, D. dehalogenans and D. dichloroeliminans/metallireducens, respectively. The genomes encode up to seven reductive dehalogenases, the genomes of both D. hafniense DP7 and D. metallireducens 853–15A T did not encode any reductive dehalogenase. The latter result was a surprise as D. metallireducens 853–15A T has been reported to carry out organohalide respiration. Unlike reported for the pce ABCT gene cluster, the other reductive dehalogenase gene clusters do not show any signs of being genetically mobile. All analyzed desulfitobacterial genomes encode a complete cobalamin synthesis pathway. A menaquinone synthesis pathway was found in all strains except D. dichloroeliminans DCA1T. The detailed analysis of the genome sequence of 12 desulfitobacteria from four different species confirmed that this genus has an extremely large metabolic repertoire.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Identification of candidate host-specificity genes in Exserohilum turcicum using comparative genomics and transcriptomics

Abstract Exserohilum turcicum causes northern corn leaf blight and sorghum leaf blight. While the same species cause disease in both crops, the strains are host-specific. Here, we report the sequence and de novo annotated assemblies of one sorghum- and one maize-specific E. turcicum strain. The strains were sequenced using the PacBio Sequel II system. The total genome length for both assemblies was between 44 and 45 Mb with N50 of ∼2.5 Mb. Ninety-eight percent of the Benchmarking Universal Single-Copy Orthologs (BUSCO) for both assemblies had complete status. The estimated number of genes was 11,762 and 12,029 in the sorghum- and maize-specific isolates, respectively. Funannotate, EffectorP, SignalP, and transcriptome data were used to create functional annotation of each genome. The whole-genome comparison identified ten large-scale inversions and three translocations between the maize- and sorghum-specific strains, along with homologous genes and gene duplications. RNA was sequenced from the maize- and sorghum-specific isolate 10 days post-inoculation in maize and sorghum and from axenic cultures. Gene expression data from planta and axenic growth experiments were compared for each strain. Candidate host-specificity genes were identified by combining results from whole-genome comparison, synteny analysis, gene annotations, and transcriptome data. Overall, this study identified several candidate host-specificity genes that provide insights into E. turcicum interaction with its hosts.

Krone, Mara J. (ORCID:0000000159006624)↗

DOE OSTI2012

An Independent Genome Duplication Inferred from Hox Paralogs in the American Paddlefish—A Representative Basal Ray-Finned Fish and Important Comparative Reference

Vertebrates have experienced two rounds of whole-genome duplication (WGD) in the stem lineages of deep nodes within the group and a subsequent duplication event in the stem lineage of the teleosts—a highly diverse group of ray-finned fishes. Here, we present the first full Hox gene sequences for any member of the Acipenseriformes, the American paddlefish, and confirm that an independent WGD occurred in the paddlefish lineage, approximately 42 Ma based on sequences spanning the entire HoxA cluster and eight genes on the HoxD gene cluster. These clusters comprise different HOX loci and maintain conserved synteny relative to bichir, zebrafish, stickleback, and pufferfish, as well as human, mouse, and chick. We also provide a gene genealogy for the duplicated fzd8 gene in paddlefish and present evidence for the first Hox14 gene in any ray-finned fish. Taken together, these data demonstrate that the American paddlefish has an independently duplicated genome. Substitution patterns of the “alpha” paralogs on both the HoxA and HoxD gene clusters suggest transcriptional inactivation consistent with functional diploidization. Further, there are similarities in the pattern of sequence divergence among duplicated Hox genes in paddlefish and teleost lineages, even though they occurred independently approximately 200 Myr apart. We highlight implications on comparative analyses in the study of the “fin-limb transition” as well as gene and genome duplication in bony fishes, which includes all ray-finned fishes as well as the lobe-finned fishes and tetrapod vertebrates.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Comparing galaxy formation in the L-GALAXIES semi-analytical model and the IllustrisTNG simulations

ABSTRACT We perform a comparison, object by object and statistically, between the Munich semi-analytical model, L-GALAXIES, and the IllustrisTNG hydrodynamical simulations. By running L-GALAXIES on the IllustrisTNG dark matter-only merger trees, we identify the same galaxies in the two models. This allows us to compare the stellar mass, star formation rate, and gas content of galaxies, as well as the baryonic content of subhaloes and haloes in the two models. We find that both the stellar mass functions and the stellar masses of individual galaxies agree to better than ${\sim} 0.2\,$dex. On the other hand, specific star formation rates and gas contents can differ more substantially. At z = 0, the transition between low-mass star-forming galaxies and high-mass quenched galaxies occurs at a stellar mass scale ${\sim} 0.5\,$dex lower in IllustrisTNG than that in L-GALAXIES. IllustrisTNG also produces substantially more quenched galaxies at higher redshifts. Both models predict a halo baryon fraction close to the cosmic value for clusters, but IllustrisTNG predicts lower baryon fractions in group environments. These differences are primarily due to differences in modelling feedback from stars and supermassive black holes. The gas content and star formation rates of galaxies in and around clusters and groups differ substantially, with IllustrisTNG satellites less star forming and less gas rich. We show that environmental processes such as ram-pressure stripping are stronger and operate to larger distances and for a broader host mass range in IllustrisTNG. We suggest that the treatment of galaxy evolution in the semi-analytic model needs to be improved by prescriptions that capture local environmental effects more accurately.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

A comparative analysis of the chemical compositions of Gaia-Enceladus/Sausage and Milky Way satellites using APOGEE

ABSTRACT We use data from the 17th data release of the Apache Point Observatory Galactic Evolution Experiment (APOGEE 2) to contrast the chemical composition of the recently discovered Gaia Enceladus/Sausage system (GE/S) to those of 10 Milky Way (MW) dwarf satellite galaxies: LMC, SMC, Boötes I, Carina, Draco, Fornax, Sagittarius, Sculptor, Sextans, and Ursa Minor. Our main focus is on the distributions of the stellar populations of those systems in the [Mg/Fe]–[Fe/H] and [Mg/Mn]–[Al/Fe] planes, which are commonly employed in the literature for chemical diagnosis and where dwarf galaxies can be distinguished from in situ populations. We show that, unlike MW satellites, a GE/S sample defined purely on the basis of orbital parameters falls almost entirely within the locus of ‘accreted’ stellar populations in chemical space, which is likely caused by an early quenching of star formation in GE/S. Due to a more protracted history of star formation, stars in the metal-rich end of the MW satellite populations are characterized by lower [Mg/Mn] than those of their GE/S counterparts. The chemical compositions of GE/S stars are consistent with a higher early star formation rate (SFR) than MW satellites of comparable and even higher mass, suggesting that star formation in the early universe was strongly influenced by other parameters in addition to mass. We find that the direction of the metallicity gradient in the [Mg/Mn]–[Al/Fe] plane of dwarf galaxies is an indicator of the early SFR of the system.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2019

Comparing IMF-sensitive indices of intermediate-mass quiescent galaxies in various environments

ABSTRACT Using samples drawn from the Sloan Digital Sky Survey, we study for the first time the relation between large-scale environments (clusters, groups, and voids) and the stellar initial mass function (IMF). We perform an observational approach based on the comparison of IMF-sensitive indices of quiescent galaxies with similar mass in varying environments. These galaxies are selected within a narrow redshift interval (0.020 < z < 0.055) and spanning a range in velocity dispersion from 100 to 200 km s−1. The results of this paper are based upon analysis of composite spectra created by stacking the spectra of galaxies, binned by their velocity dispersion and redshift. The trends of spectral indices as measured from the stacked spectra, with respect to velocity dispersion, are compared in different environments. We find a lack of dependence of the IMF on the environment for intermediate-mass galaxy regime. We verify this finding by providing a more quantitative measurement of the IMF variations among galactic environments using MILES stellar population models with a precision of ΔΓb ∼ 0.2.

Eftekhari, Elham↗

DOE OSTI2019

Chemical abundances of Seyfert 2 AGNs – I. Comparing oxygen abundances from distinct methods using SDSS

ABSTRACT We compare the oxygen abundance (O/H) of the narrow-line regions (NLRs) of Seyfert 2 AGNs obtained through strong-line methods and from direct measurements of the electron temperature (Te-method). The aim of this study is to explore the effects of the use of distinct methods on the range of metallicity and on the mass–metallicity relation of active galactic nuclei (AGNs) at low redshifts (z ≲ 0.4). We used the Sloan Digital Sky Survey (SDSS) and NASA/IPAC Extragalactic Database (NED) to selected optical (3000 < λ(Å) < 7000) emission line intensities of 463 confirmed Seyfert 2 AGNs. The oxygen abundances of the NLRs were estimated using the theoretical Storchi-Bergmann et al. calibrations, the semi-empirical N2O2 calibration, the Bayesian H ii-Chi-mistry code and the Te-method. We found that the oxygen abundance estimations via the strong-line methods differ from each other up to ∼0.8 dex, with the largest discrepancies in the low-metallicity regime ($\rm 12+\log (O/H) \: \lesssim \: 8.5$). We confirmed that the Te-method underestimates the oxygen abundance in NLRs, producing unreal subsolar values. We did not find any correlation between the stellar mass of the host galaxies and the metallicity of their AGNs. This result is independent of the method used to estimate Z.

Dors, O. L.↗

DOE OSTI2013

IMG/M 4 version of the integrated metagenome comparative analysis system

IMG/M (http://img.jgi.doe.gov/m) provides support for comparative analysis of microbial community aggregate genomes (metagenomes) in the context of a comprehensive set of reference genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG/M’s data content and analytical tools have expanded continuously since its first version was released in 2007. Since the last report published in the 2012 NAR Database Issue, IMG/M’s database architecture, annotation and data integration pipelines and analysis tools have been extended to cope with the rapid growth in the number and size of metagenome data sets handled by the system. IMG/M data marts provide support for the analysis of publicly available genomes, expert review of metagenome annotations (IMG/M ER: http://img.jgi.doe.gov/mer) and Human Microbiome Project (HMP)-specific metagenome samples (IMG/M HMP: http://img.jgi.doe.gov/ imgm_hmp).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2013

IMG 4 version of the integrated microbial genomes comparative analysis system

The Integrated Microbial Genomes (IMG) data warehouse integrates genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG provides tools for analyzing and reviewing the structural and functional annotations of genomes in a comparative context. IMG’s data content and analytical capabilities have increased continuously since its first version released in 2005. Since the last report published in the 2012 NAR Database Issue, IMG’s annotation and data integration pipelines have evolved while new tools have been added for recording and analyzing single cell genomes, RNA Seq and biosynthetic cluster data. Finally, different IMG datamarts provide support for the analysis of publicly available genomes (IMG/W: http://img.jgi.doe.gov/w), expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er) and teaching and training in the area of microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu).

59 BASIC BIOLOGICAL SCIENCES↗