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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 595 records · Page 33
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Rapid Divergence Followed by Adaptation to Contrasting Ecological Niches of Two Closely Related Columbine Species Aquilegia japonica and A. oxysepala

Elucidating the mechanisms underlying the genetic divergence between closely related species is crucial to understanding the origin and evolution of biodiversity. The genus Aquilegia L. has undergone rapid adaptive radiation, generating about 70 well-recognized species that are specialized to distinct habitats and pollinators. In this study, to address the underlying evolutionary mechanisms that drive the genetic divergence, we analyzed the whole genomes of two ecologically isolated Aquilegia species, A. oxysepala and A. japonica as well as their putative hybrid. Our comparative genomic analyses reveal that while the two species diverged only recently and experienced recurrent gene flow, a high level of genetic divergence is observed in their nuclear genomes. In particular, candidate genomic regions that show signature of selection differ dramatically between the two species. Given that the splitting time of the two species is broadly matched with the decrease in effective population sizes, we propose that allopatric isolation together with natural selection have preceded the interspecific gene flow in the process of speciation. The observed high genetic divergence is likely an outcome of combined effects of natural selection, genetic drift and divergent sorting of ancestral polymorphisms. Our study provides a genome-wide view of how genetic divergence has evolved between closely related species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Laminarin stimulates single cell rates of sulfate reduction whereas oxygen inhibits transcriptomic activity in coastal marine sediment

Abstract The chemical cycles carried out by bacteria and archaea living in coastal sediments are vital aspects of benthic ecology. These ecosystems are subject to physical disruption, which may allow for increased respiration and complex carbon consumption—impacting chemical cycling in this environment often thought to be a terminal place of deposition. We use the redox-enzyme sensitive probe RedoxSensor Green to measure rates of electron transfer physiology in individual sulfate reducer cells residing in anoxic sediment, subjected to transient exposure of oxygen and laminarin. We use index fluorescence activated cell sorting and single cell genomics sequencing to link those measurements to genomes of respiring cells. We measure per-cell sulfate reduction rates in marine sediments (0.01–4.7 fmol SO42− cell−1 h−1) and determine that cells within the Chloroflexota phylum are the most active in respiration. Chloroflexota respiration activity is also stimulated with the addition of laminarin, even in marine sediments already rich in organic matter. Evaluating metatranscriptomic data alongside this respiration-based technique, Chloroflexota genomes encode laminarinases indicating a likely ability to degrade laminarin. We also provide evidence that abundant Patescibacteria cells do not use electron transport pathways for energy, and instead likely carry out fermentation of polysaccharides. There is a decoupling of respiration-related activity rates from transcription, as respiration rates increase while transcription decreases with oxygen exposure. Overall, we reveal an active community of respiring Chloroflexota that cycles sulfate at potential rates of 23–40 nmol h−1 per cm3 sediment in incubation settings, and non-respiratory Patescibacteria that can cycle complex polysaccharides.

Lindsay, Melody R.↗
DOE OSTI2025

Climate warming enhances biodiversity and stability of grassland soil phosphorus-cycling microbial communities

Abstract Climate warming poses significant challenges to global phosphorus sustainability, an essential component of Earth biogeochemistry cycling and water-food-energy nexus. Despite the crucial role of polyphosphate-accumulating organism as key functional microbial agents in phosphorus cycling, the impacts of global climate warming on polyphosphate accumulating organism communities remain largely enigmatic. This study investigates the effects of climate warming on the taxonomic, network, and functional profiles of soil bacterial polyphosphate-accumulating organisms, leveraging fluorescence-activated cell sorting and single-cell Raman spectroscopy. Climate warming enhances both taxonomic and functional biodiversity of polyphosphate-accumulating organisms via biotic interactions and environmental filtering, with observed functionality-biodiversity relationships supporting the functional redundancy theory. Furthermore, polyphosphate-accumulating organism network complexity and stability rise under warming with strengthened positive relationships, supporting stress gradient hypothesis and the belief that complexity begets stability. Finally, polyphosphate-accumulating organisms are significantly correlated to key ecosystem functioning in carbon and phosphorus cycling under warming. Our study suggests that preserving polyphosphate-accumulating organism communities is crucial for maintaining soil ecosystem functioning and sustainable phosphorus management in a warming world and opens avenues for predicting the responses of other functional microbial groups to climate change, beneficially or maliciously.

Environmental Sciences & Ecology↗
DOE OSTI2017

Transporters involved in pH and K + homeostasis affect pollen wall formation, male fertility, and embryo development

Flowering plant genomes encode multiple cation/H + exchangers (CHXs) whose functions are largely unknown. AtCHX17, AtCHX18, and AtCHX19 are membrane transporters that modulate K+ and pH homeostasis and are localized in the dynamic endomembrane system. Loss of function reduced seed set, but the particular phase(s) of reproduction affected was not determined. Pollen tube growth and ovule targeting of chx17chx18chx19 mutant pollen appeared normal, but reciprocal cross experiments indicate a largely male defect. Although triple mutant pollen tubes reach ovules of a wild-type pistil and a synergid cell degenerated, half of those ovules were unfertilized or showed fertilization of the egg or central cell, but not both female gametes. Fertility could be partially compromised by impaired pollen tube and/or sperm function as CHX19 and CHX18 are expressed in the pollen tube and sperm cell, respectively. When fertilization was successful in self-pollinated mutants, early embryo formation was retarded compared with embryos from wild-type ovules receiving mutant pollen. Thus CHX17 and CHX18 proteins may promote embryo development possibly through the endosperm where these genes are expressed. The reticulate pattern of the pollen wall was disorganized in triple mutants, indicating perturbation of wall formation during male gametophyte development. Lastly, as pH and cation homeostasis mediated by AtCHX17 affect membrane trafficking and cargo delivery, these results suggest that male fertility, sperm function, and embryo development are dependent on proper cargo sorting and secretion that remodel cell walls, plasma membranes, and extracellular factors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Dark Energy Survey Year 3 results: marginalization over redshift distribution uncertainties using ranking of discrete realizations

ABSTRACT Cosmological information from weak lensing surveys is maximized by sorting source galaxies into tomographic redshift subsamples. Any uncertainties on these redshift distributions must be correctly propagated into the cosmological results. We present hyperrank, a new method for marginalizing over redshift distribution uncertainties, using discrete samples from the space of all possible redshift distributions, improving over simple parametrized models. In hyperrank, the set of proposed redshift distributions is ranked according to a small (between one and four) number of summary values, which are then sampled, along with other nuisance parameters and cosmological parameters in the Monte Carlo chain used for inference. This approach can be regarded as a general method for marginalizing over discrete realizations of data vector variation with nuisance parameters, which can consequently be sampled separately from the main parameters of interest, allowing for increased computational efficiency. We focus on the case of weak lensing cosmic shear analyses and demonstrate our method using simulations made for the Dark Energy Survey (DES). We show that the method can correctly and efficiently marginalize over a wide range of models for the redshift distribution uncertainty. Finally, we compare hyperrank to the common mean-shifting method of marginalizing over redshift uncertainty, validating that this simpler model is sufficient for use in the DES Year 3 cosmology results presented in companion papers.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2018

IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes

The Integrated Microbial Genomes & Microbiomes system v.5.0 (IMG/M: https://img.jgi.doe.gov/m/) contains annotated datasets categorized into: archaea, bacteria, eukarya, plasmids, viruses, genome fragments, metagenomes, cell enrichments, single particle sorts, and metatranscriptomes. Source datasets include those generated by the DOE's Joint Genome Institute (JGI), submitted by external scientists, or collected from public sequence data archives such as NCBI. All submissions are typically processed through the IMG annotation pipeline and then loaded into the IMG data warehouse. IMG's web user interface provides a variety of analytical and visualization tools for comparative analysis of isolate genomes and metagenomes in IMG. IMG/M allows open access to all public genomes in the IMG data warehouse, while its expert review (ER) system (IMG/MER: https://img.jgi.doe.gov/mer/) enabled registered users to access their private genomes and to store their private datasets in workspace for sharing and for further analysis. IMG/M data content has increased by 60% since the last report published in the 2017 NAR Database Issue. IMG/M v.5.0 has a new and more powerful genome search feature, new statistical tools, and supports metagenome binning.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

XRISM high-resolution X-ray spectroscopy of Cygnus X-1: Orbital and short-term variability of iron absorption

We present the first high-resolution spectroscopy of the black hole high-mass X-ray binary Cygnus X-1 with XRISM, including orbital-phase-resolved analyses and tentative evidence of short-term variability in the Fe K band on second timescales. Using data from the Performance Verification phase in 2024 April, we analyzed spectral variability across orbital phases with the Resolve microcalorimeter and the Xtend CCD imager. The unprecedented resolution of Resolve reveals variability in highly ionized Fe absorption lines. The absorption features show orbital-phase-dependent variability in column density, ionization state, and blueshifted velocity, suggesting structural variations in the focused stellar wind along the line of sight. We also find indications of subtle broadening of the neutral Fe emission profile. In addition, intensity-sorted spectroscopy during dip phases suggests possible variability on timescales of a few seconds in the absorption features, consistent with cooler, denser, and lower-ionized gas clumps. Although the statistical significance is limited, these results hint that the stellar wind and the X-rays from the accretion disk around the black hole may interact on timescales as short as a few seconds. These XRISM results constrain wind-fed accretion in Cyg X-1 and highlight Resolve’s capability to probe plasma environments in high-mass X-ray binaries.

Astronomy and AstroPhysics↗
DOE OSTI2020

The parallelism motifs of genomic data analysis

Genomic datasets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share these data with the research community, but some of these genomic data analysis problems require large-scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high-end parallel systems today and place different requirements on programming support, software libraries and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high-performance genomics analysis, including alignment, profiling, clustering and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or ‘motifs’ that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing. This article is part of a discussion meeting issue ‘Numerical algorithms for high-performance computational science’.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Characterization of Thylakoid Division Using Chloroplast Dividing Mutants in Arabidopsis

Here, chloroplasts are double membrane bound organelles that are found in plants and algae. Their division requires a number of proteins to assemble into rings along the center of the organelle and to constrict in synchrony. Chloroplasts possess a third membrane system, the thylakoids, which house the majority of proteins responsible for the light-dependent reactions. The mechanism that allows chloroplasts to sort out and separate the intricate thylakoid membrane structures during organelle division remain unknown. By characterizing the sizes of thylakoids found in a number of different chloroplast division mutants in Arabidopsis, we show that thylakoids do not divide independently of the chloroplast division cycle. More specifically, we show that thylakoid division requires the formation of both the inner and the outer contractile rings of the chloroplast.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Study of Oak Ridge soils using BONCAT-FACS-Seq reveals that a large fraction of the soil microbiome is active

The ability to link soil microbial diversity to soil processes requires technologies that differentiate active subpopulations of microbes from so-called relic DNA and dormant cells. Measures of microbial activity based on various techniques including DNA labelling have suggested that most cells in soils are inactive, a fact that has been difficult to reconcile with observed high levels of bulk soil activities. We hypothesized that measures of in situ DNA synthesis may be missing the soil microbes that are metabolically active but not replicating, and we therefore applied BONCAT (Bioorthogonal Non Canonical Amino Acid Tagging) i.e. a proxy for activity that does not rely on cell division, to measure translationally active cells in soils. We compared the active population of two soil depths from Oak Ridge (TN) incubated under the same conditions for up to seven days. Depending on the soil, a maximum of 25 – 70% of the cells were active, accounting for 3-4 million cells per gram of soil type, which is an order of magnitude higher than previous estimates. The BONCAT positive cell fraction was recovered by fluorescence activated cell sorting (FACS) and identified by 16S rDNA amplicon sequencing. The diversity of the active fraction was a selected subset of the bulk soil community. Excitingly, some of the same members of the community were recruited at both depths independently from their abundance rank. On average, 86% of sequence reads recovered from the active community shared >97% sequence similarity with cultured isolates from the field site. Our observations are in line with a recent report that, of the few taxa that are both abundant and ubiquitous in soil, 45% are also cultured – and indeed some of these ubiquitous microorganisms were found to be translationally active. The use of BONCAT on soil microbiomes provides evidence that a large portion of the soil microbes can be active simultaneously. We conclude that BONCAT coupled to FACS and sequencing is effective for interrogating the active fraction of soil microbiomes in situ and provides new perspectives to link metabolic capacity to overall soil ecological traits and processes.

58 GEOSCIENCES↗
DOE OSTI2018

From powerhouse to processing plant: conserved roles of mitochondrial outer membrane proteins in tRNA splicing

The mitochondrial cytoplasmic surface serves as a processing site for numerous RNAs from budding yeast to metazoans. We report that budding yeast mitochondrial outer membrane (MOM) proteins that are subunits of the translocase of the outer mitochondrial membrane (Tom70 and Tom 22) and sorting and assembly machinery (Sam37) are required for efficient pretransfer RNA (pre-tRNA) splicing. Defective pre-tRNA splicing in MOM mutants is due not to loss of respiratory metabolism but instead inefficient targeting/tethering of tRNA splicing endonuclease (SEN) subunits to mitochondria. Schizosaccharomyces pombe SEN subunits also localize to mitochondria, and Tom70 is required for this localization and pre-tRNA splicing. Thus, the role of MOM protein in targeting/tethering SEN subunits to mitochondria has been conserved for >500 million years.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Primordial black holes and their mass spectra: The effects of mergers and accretion within stasis cosmologies

A variety of processes in the very early Universe can give rise to a population of primordial black holes (PBHs) with an extended mass spectrum. For certain mass spectra of this sort, it has been shown that the evaporation of these PBHs into radiation can drive the universe toward an epoch of cosmological stasis which can persist for a significant number of 𝑒-folds of cosmological expansion. However, in general, the initial mass spectrum which characterizes a population of PBHs at the time of production can subsequently be distorted by processes such as mergers and accretion. Here, in this paper, we examine the effects that these processes have on the spectra that lead to a PBH-induced stasis. Within such stasis models, we find that mergers have only a negligible effect on these spectra within the regime of interest for stasis. We likewise find that the effect of accretion is negligible in many cases of interest. However, we find that the effect of accretion on the PBH mass spectrum is non-negligible in situations in which this spectrum is particularly broad. In such situations, the stasis epoch is abridged or, in extreme cases, does not occur at all. Thus accretion plays a nontrivial role in constraining the emergence of stasis within scenarios which lead to extended PBH mass spectra.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

Nature and impact of stripe freezing in La 1.67 Sr 0.33 NiO 4

La 1.67 Sr 0.33 NiO 4 develops charge and spin stripe orders at temperatures of roughly 200 K, with modulation wave vectors that are temperature independent. Here, various probes of spin and charge response have provided independent evidence for some sort of change below ~50 K. In combination with a new set of neutron scattering measurements, we propose a unified interpretation of all of these observations in terms of a freezing of Ni-centered charges stripes, together with a glassy ordering of the spin stripes that shows up in neutron scattering as a slight rotation of the average spin direction.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Multigap electron-phonon superconductivity in the quasi-one-dimensional pnictide K 2 Mo 3 As 3

In this work, we show, using density functional calculations, that quasi-one-dimensional K 2 Mo 3 As 3 , which is closely related to K 2 Cr 3 As 3 and has very similar superconducting properties, is not close to magnetism and has conventional s wave electron-phonon superconductivity. This superconductivity is of multigap character due to different coupling on different Fermi surface sheets. This is discussed in relation to the properties of this family of quasi-one-dimensional pnictide superconductors. The results show that this family of superconductors provides a unique opportunity for studying the interplay of spin fluctuations and electron-phonon superconductivity in transition metal pnictides, and offer a path for sorting out the different proposed superconducting scenarios in this fascinating family of pnictide superconductors.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Natural anomaly mediation from the landscape with implications for LHC SUSY searches

Supersymmetric models with the anomaly-mediated supersymmetry (SUSY) breaking (AMSB) form for soft SUSY breaking terms arise in two different settings: (1) extra-dimensional models where SUSY breaking occurs in a sequestered sector, and (2) 4 − d models with dynamical SUSY breaking in a hidden sector where scalars gain masses of order the gravitino mass m 3 / 2 , but gaugino masses and trilinear soft terms are assumed to be of the AMSB form. Both models run into serious conflicts with (1) LHC sparticle and Higgs mass constraints, (2) constraints from winolike weakly interacting massive particle dark matter searches, and (3) bounds from naturalness. These conflicts may be avoided by introducing minor changes to the underlying phenomenological models consisting of nonuniversal bulk scalar Higgs masses and A terms, providing a setting for natural anomaly mediation (nAMSB). In nAMSB, the wino is still expected to be the lightest of the gauginos, but the Higgsinos are expected to be the lightest electroweakinos (EWinos) in accord with naturalness. We examine what sorts of spectra are expected to emerge when nAMSB arises from a string landscape setting: While model 2 can only be natural for a Higgs mass m h ≲ 123 GeV , model 1 can accommodate naturalness along with m h ∼ 125 GeV while still respecting LHC bounds on sparticle masses. We explore the LHC phenomenology of nAMSB models where we find that for Higgsino pair production, typically larger dilepton mass gaps arise from the soft dilepton-plus-jets signature than in models with gaugino mass unification. For wino-pair production, the higher m 3 / 2 portion of nAMSB parameter space is excluded by recent LHC bounds from gaugino pair production searches. We characterize the dominant LHC signatures arising from the remaining lower m 3 / 2 ∼ 90 – 200 TeV range of parameter space, which should be fully testable at high-luminosity LHC via EWino pair production searches. Published by the American Physical Society 2024

Astronomy & Astrophysics↗
DOE OSTI2024

Fuzzy gauge theory for quantum computers

Continuous gauge theories, because of their bosonic degrees of freedom, have an infinite-dimensional local Hilbert space. Encoding these degrees of freedom on qubit-based hardware demands some sort of “qubitization” scheme, where one approximates the behavior of a theory while using only finitely many degrees of freedom. We propose a novel qubitization strategy for gauge theories, called “fuzzy gauge theory,” building on the success of the fuzzy σ -model in earlier work. We provide arguments that the fuzzy gauge theory lies in the same universality class as regular gauge theory, in which case its use would obviate the need of any further limit besides the usual spatial continuum limit. Furthermore, we demonstrate that these models are relatively resource-efficient for quantum simulations. Published by the American Physical Society 2024

Astronomy & Astrophysics↗
DOE OSTI2022

Redundantly Amplified Information Suppresses Quantum Correlations in Many-Body Systems

We establish bounds on quantum correlations in many-body systems. They reveal what sort of information about a quantum system can be simultaneously recorded in different parts of its environment. Specifically, independent agents who monitor environment fragments can eavesdrop only on amplified and redundantly disseminated—hence, effectively classical—information about the decoherence-resistant pointer observable. We also show that the emergence of classical objectivity is signaled by a distinctive scaling of the conditional mutual information, bypassing hard numerical optimizations. Our results validate the core idea of quantum Darwinism: objective classical reality does not need to be postulated and is not accidental, but rather a compelling emergent feature of quantum theory that otherwise—in the absence of decoherence and amplification—leads to “quantum weirdness.” In particular, a lack of consensus between agents that access environment fragments is bounded by the information deficit, a measure of the incompleteness of the information about the system.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Computational prediction of nanostructured alloys with enhanced thermoelectric properties

The Materials Genome Initiative calls for a dramatic increase in the rate of materials discovery and development. High-throughput (HT) calculations can advance this goal by efficiently screening a large search space for candidate materials to study in more depth. Thermoelectric materials (TEs) are prime candidates for such HT calculations: The properties required to achieve good performance are known, but systematic ways of improving these properties are scarce. Furthermore, known HT methods for TEs only address bulk crystals—screening realistic multicomponent alloys for their TE properties has yet to be accomplished. In this paper, we use a density functional theory driven HT screening-and-sorting procedure to search for new multicomponent bulk-nanostructured thermoelectric materials. We make maximum use of minimal calculations to obtain eight descriptors of the thermodynamics and TE performance of five-element semiconductor alloy systems from combinations of ternary additions in binary compounds. We use these descriptors to reduce a search space of 29 700 five-element systems to a set of 130 candidates. Lastly, we screen these candidates using TE descriptors to identify several existing high-performance thermoelectrics as well as promising new material systems awaiting further experimental verification.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗