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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 667 records · Page 37
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Comparing the DES-SN5YR and Pantheon+ SN cosmology analyses: investigation based on ‘evolving dark energy or supernovae systematics’?

Recent cosmological analyses measuring distances of type Ia supernovae (SNe Ia) and baryon acoustic oscillations (BAO) have all given similar hints at time-evolving dark energy. To examine whether underestimated SN Ia systematics might be driving these results, Efstathiou (2025) compared overlapping SN events between Pantheon+ and DES-SN5YR (20 per cent SNe are in common), and reported evidence for an $\sim$0.04 mag offset between the low- and high-redshift distance measurements of this subsample of events. If this offset is arbitrarily subtracted from the entire DES-SN5YR sample, the preference for evolving dark energy is reduced. In this paper, we show that this offset is mostly due to different corrections for Malmquist bias between the two samples; therefore, an object-to-object comparison can be misleading. Malmquist bias corrections differ between the two analyses for several reasons. First, DES-SN5YR used an improved model of SN Ia luminosity scatter compared to Pantheon+ but the associated scatter-model uncertainties are included in the error budget. Secondly, improvements in host mass estimates in DES-SN5YR also affected SN standardized magnitudes and their bias corrections. Thirdly, and most importantly, the selection functions of the two compilations are significantly different, hence the inferred Malmquist bias corrections. Even if the original scatter model and host properties from Pantheon+ are used instead, the evidence for evolving dark energy from CMB, DESI BAO Year 1 and DES-SN5YR is only reduced from 3.9$\sigma$ to 3.3$\sigma$, consistent with the error budget. Finally, in this investigation, we identify an underestimated systematic uncertainty related to host galaxy property uncertainties, which could increase the final DES-SN5YR error budget by 3 per cent. In conclusion, we confirm the validity of the published DES-SN5YR results.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Comparative mitogenomics of kingdom Fungi – evolutionary insights and metagenomic applications

Mitochondria are essential components of eukaryotic cells, responsible for ATP production through oxidative phosphorylation. Despite their biological importance, unique challenges have hindered the adoption of automated mitochondrial genome (mitogenome) annotation methods, obstructing mitochondrial comparative genomics in a broad evolutionary context. Using Fungi as a study system and a Joint Genome Institute (JGI) annotated high-quality reference set, we observed broad patterns of mitochondrial evolution across the kingdom. We found that the median fungal mitogenome size is 58 kb and identified exceptionally large examples over 1 Mb in Pezizomycetes. All 14 expected oxidative phosphorylation protein-coding genes, plus rps3, were generally conserved. We found evidence of major evolutionary transitions within the Ascomycota, including the transfer of mitochondrially encoded atp8 and atp9 to the nuclear genomes across the Pezizomycotina and shifts in mitogenome tRNA patterns across the kingdom. We found substantial concordance between mitochondrial and nuclear evolution, enabling us to document 3131 total fungal mitogenomes from JGI-derived metagenomic datasets. We also identified 6467 total undeclared mitogenomes embedded in Genbank fungal nuclear assemblies. We provide interactive tools for mitogenome analysis through the JGI MycoCosm platform. Collectively, this work generated nearly 10 000 new fungal mitogenome annotations, providing a foundation and resources for future exploration of comparative fungal mitogenomics.

Ahrendt, Steven R. [USDOE Joint Genome Institute (↗
DOE OSTI2013

ModBase, a database of annotated comparative protein structure models and associated resources

ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building and model assessment (http://salilab.org/modeller/). ModBase currently contains almost 30 million reliable models for domains in 4.7 million unique protein sequences. ModBase allows users to compute or update comparative models on demand, through an interface to the ModWeb modeling server (http://salilab.org/ modweb). ModBase models are also available through the Protein Model Portal (http://www.prote inmodelportal.org/). Recently developed associated resources include the AllosMod server for modeling ligand-induced protein dynamics (http://salilab.org/ allosmod), the AllosMod-FoXS server for predicting a structural ensemble that fits an SAXS profile (http://salilab.org/allosmod-foxs), the FoXSDock server for protein–protein docking filtered by an SAXS profile (http://salilab.org/foxsdock), the SAXS Merge server for automatic merging of SAXS profiles (http://salilab.org/saxsmerge) and the Pose & Rank server for scoring protein–ligand complexes (http://salilab.org/poseandrank). In this update, we also highlight two applications of ModBase: a PSI:Biology initiative to maximize the structural coverage of the human alpha-helical transmembrane proteome and a determination of structural determinants of human immunodeficiency virus-1 protease specificity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions

The discovery of structured non-coding RNAs (ncRNAs) in bacteria can reveal new facets of biology and biochemistry. Comparative genomics analyses executed by powerful computer algorithms have successfully been used to uncover many novel bacterial ncRNA classes in recent years. However, this general search strategy favors the discovery of more common ncRNA classes, whereas progressively rarer classes are correspondingly more difficult to identify. In the current study, we confront this problem by devising several methods to select subsets of intergenic regions that can concentrate these rare RNA classes, thereby increasing the probability that comparative sequence analysis approaches will reveal their existence. By implementing these methods, we discovered 224 novel ncRNA classes, which include ROOL RNA, an RNA class averaging 581 nt and present in multiple phyla, several highly conserved and widespread ncRNA classes with properties that suggest sophisticated biochemical functions and a multitude of putative cis-regulatory RNA classes involved in a variety of biological processes. We expect that further research on these newly found RNA classes will reveal additional aspects of novel biology, and allow for greater insights into the biochemistry performed by ncRNAs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

A Logical Model of Homology for Comparative Biology

There is a growing body of research on the evolution of anatomy in a wide variety of organisms. Discoveries in this field could be greatly accelerated by computational methods and resources that enable these findings to be compared across different studies and different organisms and linked with the genes responsible for anatomical modifications. Homology is a key concept in comparative anatomy; two important types are historical homology (the similarity of organisms due to common ancestry) and serial homology (the similarity of repeated structures within an organism). We explored how to most effectively represent historical and serial homology across anatomical structures to facilitate computational reasoning. We assembled a collection of homology assertions from the literature with a set of taxon phenotypes for the skeletal elements of vertebrate fins and limbs from the Phenoscape Knowledgebase. Using seven competency questions, we evaluated the reasoning ramifications of two logical models: the Reciprocal Existential Axioms (REA) homology model and the Ancestral Value Axioms (AVA) homology model. The AVA model returned all user-expected results in addition to the search term and any of its subclasses. The AVA model also returns any superclass of the query term in which a homology relationship has been asserted. The REA model returned the user-expected results for five out of seven queries. We identify some challenges of implementing complete homology queries due to limitations of OWL reasoning. This work lays the foundation for homology reasoning to be incorporated into other ontology-based tools, such as those that enable synthetic supermatrix construction and candidate gene discovery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

COMPARATIVE COMPUTATIONAL MODELING OF AIRFLOWS AND VAPOR DOSIMETY IN THE RESPIRATORY TRACTS OF RAT, MONKEY, AND HUMAN

Coupling computational fluid dynamics (CFD) with physiologically based pharmacokinetic (PBPK) models is useful for predicting site-specific dosimetry of airborne materials in the respiratory tract and elucidating the importance of species differences in anatomy, physiology, and breathing patterns. Historically, these models were limited to discrete regions of the respiratory system. CFD/PBPK models have now been developed for the rat, monkey, and human that encompass airways from the nose or mouth to the lung. A PBPK model previously developed to describe acrolein uptake in nasal tissues was adapted to the extended airway models as an example application. Model parameters for each anatomic region were obtained from the literature, measured directly, or estimated from published data. Airflow and site-specific acrolein uptake patterns were determined under steadystate inhalation conditions to provide direct comparisons with prior data and nasalonly simulations. Results confirmed that regional uptake was dependent upon airflow rates and acrolein concentrations with nasal extraction efficiencies predicted to be greatest in the rat, followed by the monkey, then the human. For human oral-breathing simulations, acrolein uptake rates in oropharyngeal and laryngeal tissues were comparable to nasal tissues following nasal breathing under the same exposure conditions. For both breathing modes, higher uptake rates were predicted for lower tracheo-bronchial tissues of humans than either the rat or monkey. These extended airway models provide a unique foundation for comparing dosimetry across a significantly more extensive range of conducting airways in the rat, monkey, and human than prior CFD models.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Comparative validation of the D. melanogaster modENCODE transcriptome annotation

Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data. Since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function, we have performed large-scale interspecific comparisons to increase confidence in predicted annotations. To support comparative genomics, we filled in divergence gaps in the Drosophila phylogeny by generating draft genomes for eight new species. For comparative transcriptome analysis, we generated mRNA expression profiles on 81 samples from multiple tissues and developmental stages of 15 Drosophila species, and we performed cap analysis of gene expression in D. melanogaster and D. pseudoobscura. We also describe conservation of four distinct core promoter structures composed of combinations of elements at three positions. Overall, each type of genomic feature shows a characteristic divergence rate relative to neutral models, highlighting the value of multispecies alignment in annotating a target genome that should prove useful in the annotation of other high priority genomes, especially human and other mammalian genomes that are rich in noncoding sequences. We report that the vast majority of elements in the annotation are evolutionarily conserved, indicating that the annotation will be an important springboard for functional genetic testing by the Drosophila community.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Comparing, optimizing, and benchmarking quantum-control algorithms in a unifying programming framework

For paving the way to novel applications in quantum simulation, computation, and technology, increasingly large quantum systems have to be steered with high precision. It is a typical task amenable to numerical optimal control to turn the time course of pulses, i.e., piecewise constant control amplitudes, iteratively into an optimized shape. Here, we present a comparative study of optimal-control algorithms for a wide range of finite-dimensional applications. We focus on the most commonly used algorithms: GRAPE methods which update all controls concurrently, and Krotov-type methods which do so sequentially. Guidelines for their use are given and open research questions are pointed out. Moreover, we introduce a unifying algorithmic framework, DYNAMO (dynamic optimization platform), designed to provide the quantum-technology community with a convenient matlab-based tool set for optimal control. In addition, it gives researchers in optimal-control techniques a framework for benchmarking and comparing newly proposed algorithms with the state of the art. It allows a mix-and-match approach with various types of gradients, update and step-size methods as well as subspace choices. Open-source code including examples is made available at http://qlib.info.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2020

Comparative many-body study of Pr 4 Ni 3 O 8 and NdNiO 2

We study the many-body electronic structure of the stoichiometric and electron-doped trilayer nickelate Pr4Ni 3 O 8 in comparison to that of the stoichiometric and hole-doped infinite layer nickelate NdNiO 2 within the framework of density functional plus dynamical mean field theory, noting that Pr4Ni 3 O 8 has the same nominal carrier concentration as NdNiO2 doped to a level of 1/3 holes/Ni. In this work, we find that the correlated Ni-3$\textit{d}$ shells of both of these low valence nickelates have similar many-body configurations with correlations dominated by the $d_{x^2 - y^2}$ orbital. Additionally, when compared at the same nominal carrier concentration, the materials exhibit similar many-body electronic structures, self energies, and correlation strengths, but differ in Fermiology. Compared to cuprates, these materials are closer to the Mott-Hubbard regime due to their larger charge transfer energies. Moreover, doping involves the charge reservoir provided by the rare earth 5$\textit{d}$ electrons, as opposed to cuprates where it is realized via the oxygen 2$\textit{p}$ electrons.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Comparative determinant quantum Monte Carlo study of the acoustic and optical variants of the Su-Schrieffer-Heeger model

We compare the acoustic Su–Schrieffer–Heeger (SSH) model with two of its optical variants where the phonons are defined on either on the sites or bonds of the system. First, we discuss how to make fair comparisons between these models in any dimension by ensuring their dimensionless coupling λ and relevant phonon energies are the same. We then use determinant quantum Monte Carlo to perform nonperturbative and sign-problem-free simulations of all three models on one-dimensional chains at and away from half-filling. By comparing the results obtained from each model, we demonstrate that the optical and acoustic models produce near identical results within error bars for suitably chosen phonon energies and λ at half-filling. In contrast, the bond model has quantitatively different behavior due to its coupling to the q = 0 phonon mode. These differences also manifest in the total length of the chain, which shrinks for the bond model but not for the acoustic and optical models when λ ≠ 0. Furthermore, our results have important implications for quantum Monte Carlo modeling of SSH-like interactions, where these models are sometimes regarded as being interchangeable.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Comparative study of the superconductivity in the Holstein and optical Su-Schrieffer-Heeger models

Theoretical studies suggest that Su-Schrieffer-Heeger-like electron-phonon (e-ph) interactions can mediate high-temperature bipolaronic superconductivity that is robust against repulsive electron-electron interactions. Here we present a comparative analysis of the pairing and competing charge/bond correlations in the two-dimensional Holstein and optical Su-Schrieffer-Heeger (SSH) models using numerically exact determinant quantum Monte Carlo. We find that the SSH interactions support light bipolarons and strong superconducting correlations out to relatively large values of the e-ph coupling λ and densities near half-filling, while the Holstein interaction does not due to the formation of heavy bipolarons and competing charge-density-wave order. We further find that the Holstein and SSH models have comparable pairing correlations in the weak coupling limit for carrier concentrations < n > <<1, where competing orders and polaronic effects are absent. These results support the proposal that SSH (bi)polarons can support superconductivity to larger values of λ in comparison to the Holstein polaron, but that the resulting T c gains are small in the weak coupling limit. We also find that the SSH model's pairing correlations are suppressed after including a weak on-site Hubbard repulsion. Furthermore, these results have important implications for identifying and engineering bipolaronic superconductivity.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Polarized 𝐽/𝜓 production in semi-inclusive DIS at large 𝑄 2 : Comparing quark fragmentation and photon-gluon fusion

We compare the relative importance of different mechanisms for polarized 𝐽/𝜓 production in semi-inclusive deep inelastic scattering processes at large 𝑄 2 . The transverse momentum dependent (TMD) factorization framework and nonrelativistic quantum chromodynamics are used to study the leading contributions from light quark fragmentation to polarized 𝐽/𝜓, and compared to direct production via photon-gluon fusion, which can proceed through color-singlet as well as color-octet mechanisms. We identify kinematic regimes where light quark fragmentation dominates, allowing for the extraction of the 3 𝑆$^{[8]}_{1}$ matrix element, as well as regimes where photon gluon fusion dominates, suggesting that the gluon TMD parton distribution function can be probed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2018

Comparing fully general relativistic and Newtonian calculations of structure formation

In the standard approach to studying cosmological structure formation, the overall expansion of the Universe is assumed to be homogeneous, with the gravitational effect of inhomogeneities encoded entirely in a Newtonian potential. A topic of ongoing debate is to what degree this fully captures the dynamics dictated by general relativity, especially in the era of precision cosmology. To quantitatively assess this, in this paper we directly compare standard N-body Newtonian calculations to full numerical solutions of the Einstein equations, for cold matter with various magnitude initial inhomogeneities on scales comparable to the Hubble horizon. We analyze the differences in the evolution of density, luminosity distance, and other quantities defined with respect to fiducial observers. This is carried out by reconstructing the effective spacetime and matter fields dictated by the Newtonian quantities, and by taking care to distinguish effects of numerical resolution. We find that the fully general relativistic and Newtonian calculations show excellent agreement, even well into the nonlinear regime. Finally, they only notably differ in regions where the weak gravity assumption breaks down, which arise when considering extreme cases with perturbations exceeding standard values.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

First-principles comparative study of Cr migration in O3 and O/P hybrid-phased NaCrO 2

In layered Na transition-metal (TM) oxides, TM migration usually occurs at highly charged states and severely deteriorates the capacity and reversibility. Meanwhile, the formation of hybrid phases with the intergrowth of octahedral (O-type) and prismatic (P-type) Na layers also takes place at highly charged states. These hybrid phases are often more stable than simple O3 or P3 stackings. However, little is known about the mechanism and impact of TM migration in these hybrid phases. In this work, a comparative first-principles study is performed to understand the connections between structural changes and Cr migration in layered O3 and hybrid-phased NaCrO 2 . After Cr migration, the hybrid-phased NaCrO 2 suffers from greater layer shrinkage than the O3 phase. Three factors affect the Cr migration energy E mig : the Na concentration, local 3D configurations, and 2D in-plane geometries. Low Na concentrations and certain local 3D configurations facilitate the Cr migration. The Cr migration barriers in both O3 and hybrid-phased NaCrO 2 are positively correlated with the Cr E mig . The Cr migration in 17 doped O3 and hybrid-phased NaCrO 2 is surveyed. In these doped NaCrO 2 , a more uniform distribution of the Cr–O bond lengths usually suggests suppressed Cr migration. Optimal dopants for suppressing Cr migration are identified by considering E mig for both Cr and the dopant. Finally, our comparative study on Cr migration in O3 and hybrid-phased NaCrO 2 reveals the significant role of hybrid-phased structures in the development of layered cathode materials.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Comparative Investigation of System-Level Optimized Power Conversion System Architectures to Reduce LCOE for Large-Scale PV-Plus-Storage Farms

PV-plus-storage (PVS) has become a prevalent configuration for newly commissioned large-scale solar projects. However, the optimal power conversion system (PCS) architecture has not been investigated yet. This paper first validates the limited impact of inverter cost on LCOE and then explores a system-level optimized PCS architecture with extended LCOE reduction to proliferate large-scale dispatchable solar energy. Two state-of-the-art architectures including central inverters (CI), traditional 480/600 V string inverters (SI) are compared with newly proposed medium voltage string inverters (MVSI) and multiport DC transformer (MDCT). With verified layouts and single line diagrams (SLDs) of 20 MW PVS plants, the losses and costs breakdown of different architectures are extracted and the PCS related LCOEs are derived. In this analysis, all electrical bill of materials (EBOS) elements, inverters, battery storage and its associated components, are included, whose losses and costs are obtained from markets, manufacturers, and literature. Besides, the sensitivities of PCS-related LCOEs to Inverter-Loading-Ratio (ILR) are also investigated. Here, the results show that compared with CI and SI with 1.5 kV PV, 4 kV MVSI and 34 kV MDCT present an extended LCOE reduction across all ILR from 1.0 to 3.0, making them economically favorable candidates for PVS farms.

14 SOLAR ENERGY↗
DOE OSTI2023

Towards a Comparative Assessment of Data-Driven Process Models in Health Information Technology

Process mining for conformance analysis focuses on comparing a reference process model against a data-driven process model that is generated via log files from information technology systems. While this approach is helpful when there is an existing process model in an organization, it leaves the question of what to do in the absence of a complete reference process model unanswered. In this paper, we present a comparative assessment approach that combines process mining, process mapping for dimensionality reduction, and statistical analysis. Our goal is to find similarities and dissimilarities in data-driven process models among U.S. Veterans Health Administration (VHA) facilities to assess process conformance among different healthcare facilities, which can help assess the standardization of care. We illustrate our approach by applying it to two clinical radiology order process models generated by two similar facilities. Our results demonstrate statistical similarities in the standardization of care among those two facilities.

Klasky, Hilda↗
DOE OSTI2024

Comparative Study of Large Language Model Architectures on Frontier

Large language models (LLMs) have garnered significant attention in both the AI community and beyond. Among these, the Generative Pre-trained Transformer (GPT) has emerged as the dominant architecture, spawning numerous variants. However, these variants have undergone pre-training under diverse conditions, including variations in input data, data preprocessing, and training methodologies, resulting in a lack of controlled comparative studies. Here we meticulously examine two prominent open-sourced GPT architectures, GPT-NeoX and LLaMA, leveraging the computational power of Frontier, the world’s first Exascale supercomputer. Employing the same materials science text corpus and a comprehensive end-to-end pipeline, we conduct a comparative analysis of their training and downstream performance. Our efforts culminate in achieving state-of-the-art performance on a challenging materials science benchmark. Furthermore, we investigate the computation and energy efficiency, and propose a computationally efficient method for architecture design. To our knowledge, these pre-trained models represent the largest available for materials science. Our findings provide practical guidance for building LLMs on HPC platforms.

Yin, Junqi↗