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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 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Competitive Exclusion and Metabolic Dependency among Microorganisms Structure the Cellulose Economy of an Agricultural Soil

Microorganisms that degrade cellulose utilize extracellular reactions that yield free by-products which can promote interactions with noncellulolytic organisms. We hypothesized that these interactions determine the ecological and physiological traits governing the fate of cellulosic carbon (C) in soil. We performed comparative genomics with genome bins from a shotgun metagenomic-stable isotope probing experiment to characterize the attributes of cellulolytic and noncellulolytic taxa accessing 13 C from cellulose. We hypothesized that cellulolytic taxa would exhibit competitive traits that limit access, while noncellulolytic taxa would display greater metabolic dependency, such as signatures of adaptive gene loss. We tested our hypotheses by evaluating genomic traits indicative of competitive exclusion or metabolic dependency, such as antibiotic production, growth rate, surface attachment, biomass degrading potential, and auxotrophy. The most 13 C-enriched taxa were cellulolytic Cellvibrio (Gammaproteobacteria) and Chaetomium (Ascomycota), which exhibited a strategy of self-sufficiency (prototrophy), rapid growth, and competitive exclusion via antibiotic production. Auxotrophy was more prevalent in cellulolytic Actinobacteria than in cellulolytic Proteobacteria, demonstrating differences in dependency among cellulose degraders. Noncellulolytic taxa that accessed 13 C from cellulose (Planctomycetales, Verrucomicrobia, and Vampirovibrionales) were also more dependent, as indicated by patterns of auxotrophy and 13 C labeling (i.e., partial labeling or labeling at later stages). Major 13 C-labeled cellulolytic microbes (e.g., Sorangium, Actinomycetales, Rhizobiales, and Caulobacteraceae) possessed adaptations for surface colonization (e.g., gliding motility, hyphae, attachment structures) signifying the importance of surface ecology in decomposing particulate organic matter. Our results demonstrated that access to cellulosic C was accompanied by ecological trade-offs characterized by differing degrees of metabolic dependency and competitive exclusion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Discovery of an Antarctic Ascidian-Associated Uncultivated Verrucomicrobia with Antimelanoma Palmerolide Biosynthetic Potential

The Antarctic marine ecosystem harbors a wealth of biological and chemical innovation that has risen in concert over millennia since the isolation of the continent and formation of the Antarctic circumpolar current. Scientific inquiry into the novelty of marine natural products produced by Antarctic benthic invertebrates led to the discovery of a bioactive macrolide, palmerolide A, that has specific activity against melanoma and holds considerable promise as an anticancer therapeutic. While this compound was isolated from the Antarctic ascidian Synoicum adareanum, its biosynthesis has since been hypothesized to be microbially mediated, given structural similarities to microbially produced hybrid nonribosomal peptide-polyketide macrolides. Here, we describe a metagenome-enabled investigation aimed at identifying the biosynthetic gene cluster (BGC) and palmerolide A-producing organism. A 74-kbp candidate BGC encoding the multimodular enzymatic machinery (hybrid type I-trans-AT polyketide synthase-nonribosomal peptide synthetase and tailoring functional domains) was identified and found to harbor key features predicted as necessary for palmerolide A biosynthesis. Surveys of ascidian microbiome samples targeting the candidate BGC revealed a high correlation between palmerolide gene targets and a single 16S rRNA gene variant (R = 0.83 to 0.99). Through repeated rounds of metagenome sequencing followed by binning contigs into metagenome-assembled genomes, we were able to retrieve a nearly complete genome (10 contigs) of the BGC-producing organism, a novel verrucomicrobium within the Opitutaceae family that we propose here as “Candidatus Synoicihabitans palmerolidicus.” The refined genome assembly harbors five highly similar BGC copies, along with structural and functional features that shed light on the host-associated nature of this unique bacterium.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil

ABSTRACT Soil ecosystems harbor diverse microorganisms and yet remain only partially characterized as neither single-cell sequencing nor whole-community sequencing offers a complete picture of these complex communities. Thus, the genetic and metabolic potential of this “uncultivated majority” remains underexplored. To address these challenges, we applied a pooled-cell-sorting-based mini-metagenomics approach and compared the results to bulk metagenomics. Informatic binning of these data produced 200 mini-metagenome assembled genomes (sorted-MAGs) and 29 bulk metagenome assembled genomes (MAGs). The sorted and bulk MAGs increased the known phylogenetic diversity of soil taxa by 7.2% with respect to the Joint Genome Institute IMG/M database and showed clade-specific sequence recruitment patterns across diverse terrestrial soil metagenomes. Additionally, sorted-MAGs expanded the rare biosphere not captured through MAGs from bulk sequences, exemplified through phylogenetic and functional analyses of members of the phylum Bacteroidetes . Analysis of 67 Bacteroidetes sorted-MAGs showed conserved patterns of carbon metabolism across four clades. These results indicate that mini-metagenomics enables genome-resolved investigation of predicted metabolism and demonstrates the utility of combining metagenomics methods to tap into the diversity of heterogeneous microbial assemblages. IMPORTANCE Microbial ecologists have historically used cultivation-based approaches as well as amplicon sequencing and shotgun metagenomics to characterize microbial diversity in soil. However, challenges persist in the study of microbial diversity, including the recalcitrance of the majority of microorganisms to laboratory cultivation and limited sequence assembly from highly complex samples. The uncultivated majority thus remains a reservoir of untapped genetic diversity. To address some of the challenges associated with bulk metagenomics as well as low throughput of single-cell genomics, we applied flow cytometry-enabled mini-metagenomics to capture expanded microbial diversity from forest soil and compare it to soil bulk metagenomics. Our resulting data from this pooled-cell sorting approach combined with bulk metagenomics revealed increased phylogenetic diversity through novel soil taxa and rare biosphere members. In-depth analysis of genomes within the highly represented Bacteroidetes phylum provided insights into conserved and clade-specific patterns of carbon metabolism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Measurement of single top-quark production in association with a W boson in the single-lepton channel at $\sqrt{s} = 8\,\text {TeV}$ with the ATLAS detector

The production cross-section of a top quark in association with a W boson is measured using proton–proton collisions at √s = 8TeV. The dataset corresponds to an integrated luminosity of 20.2 fb –1 , and was collected in 2012 by the ATLAS detector at the Large Hadron Collider at CERN. The analysis is performed in the single-lepton channel. Events are selected by requiring one isolated lepton (electron or muon) and at least three jets. A neural network is trained to separate the tW signal from the dominant tt¯ background. The cross-section is extracted from a binned profile maximum-likelihood fit to a two-dimensional discriminant built from the neural-network output and the invariant mass of the hadronically decaying W boson. The measured cross-section is σ tW = 26 ± 7pb, in good agreement with the Standard Model expectation.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Improved measurement of the strong-phase difference $\delta _D^{K\pi }$ in quantum-correlated $D{\overline{D}}$ decays

The decay D → K - π + is studied in a sample of quantum-correlated D$\overline{D}$ pairs, based on a data set corresponding to an integrated luminosity of 2.93 fb -1 collected at the ψ(3770) resonance by the BESIII experiment. The asymmetry between CP-odd and CP-even eigenstate decays into K - π + is determined to be A Kπ = 0.132 ± 0.011 ± 0.007, where the first uncertainty is statistical and the second is systematic. This measurement is an update of an earlier study exploiting additional tagging modes, including several decay modes involving a $K^{0}_{L}$ meson. The branching fractions of the $K^{0}_{L}$ modes are determined as input to the analysis in a manner that is independent of any strong phase uncertainty. Using the predominantly CP-even tag D → π + π - π 0 and the ensemble of CP-odd eigenstate tags, the observable $A^{πππ^0}_{Kπ}$ is measured to be 0.130 ± 0.012 ± 0.008. The two asymmetries are sensitive to $r^{Kπ}_{D}$ cos $δ^{Kπ}_{D}$ where $r^{Kπ}_{D}$ and $δ^{Kπ}_{D}$ are the ratio of amplitudes and phase difference, respectively, between the doubly Cabibbo-suppressed and Cabibbo-favoured decays. In addition, events containing D → K - π + tagged by D → $K^{0}_{S,L}$π + π - are studied in bins of phase space of the three-body decays. This analysis has sensitivity to both $r^{Kπ}_{D}$ cos $δ^{Kπ}_{D}$ and $r^{Kπ}_{D}$, sin $δ^{Kπ}_{D}$. A fit to A Kπ , $A^{πππ^0}_{Kπ}$ and the phase-space distribution of the D → $K^{0}_{S,L}$π + π - tags yields $δ^{Kπ}_{D}$ = ($187.6^{+8.9+5.4}_{-9.7-6.4}$)°, where external constraints are applied for $r^{Kπ}_{D}$ and other relevant parameters. This is the most precise measurement of $δ^{Kπ}_{D}$ in quantum-correlated D$\overline{D}$ decays.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

A study of $CP$ violation in the decays $B^±$ → [$K^+ K^-π^+π^-$]$_Dh^±$ ($h$ = $K, π$) and $B^±$ → [$π^+π^-π^+π^-$]$_Dh^±$

The first study of CP violation in the decay mode $B^±$ → [$K^+ K^-π^+π^-$]$_Dh^±$, with $h$ = $K, π$, is presented, exploiting a data sample of proton–proton collisions collected by the LHCb experiment that corresponds to an integrated luminosity of 9 fb -1 . The analysis is performed in bins of phase space, which are optimised for sensitivity to local CP asymmetries. CP-violating observables that are sensitive to the angle γ of the Unitarity Triangle are determined. The analysis requires external information on charm-decay parameters, which are currently taken from an amplitude analysis of LHCb data, but can be updated in the future when direct measurements become available. Measurements are also performed of phase-space integrated observables for $B^±$ → [$K^+ K^-π^+π^-$]$_Dh^±$ and $B^±$ → [$π^+π^-π^+π^-$]$_Dh^±$ decays.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Measurement of the CKM angle $\gamma $ in the ${{{B} ^0} \rightarrow {D} {{K} ^{*0}}}$ channel using self-conjugate ${D} \rightarrow {{K} ^0_{\textrm{S}}} h^+ h^-$ decays

A model-independent study of $C\!P$ violation in ${{B} ^0} \rightarrow {D} {{K} ^{*0}}$ decays is presented using data corresponding to an integrated luminosity of 9 fb -1 collected by the LHCb experiment at centre-of-mass energies of $\sqrt{s}=7, \, 8$ and 13 TeV. The CKM angle $\gamma$ is determined by examining the distributions of signal decays in phase-space bins of the self-conjugate ${D} \rightarrow {{K} ^0_{\textrm{S}}} h^+ h^-$ decays, where $h = \pi , K$. Observables related to $C\!P$ violation are measured and the angle $\gamma$ is determined to be $\gamma =(49^{+ 22}_{-19})^\circ$. Measurements of the amplitude ratio and strong-phase difference between the favoured and suppressed ${B} ^0$ decays are also presented.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Measurement of the associated production of a top-antitop-quark pair and a Higgs boson decaying into a $b\bar{b}$ pair in pp collisions at $\sqrt{s} = 13$ TeV using the ATLAS detector at the LHC

This paper reports the measurement of Higgs boson production in association with a $t\bar{t}$ pair in the $H$ → $b\bar{b}$ decay channel. The analysis uses 140 fb -1 of 13 TeV proton–proton collision data collected with the ATLAS detector at the Large Hadron Collider. The final states with one or two electrons or muons are employed. An excess of events over the expected background is found with an observed (expected) significance of 4.6 (5.4) standard deviations. The $t\bar{t}$ $H$ cross-section is $σ_{t\bar{t} H}$ = $411^{+101}_{-92}$ fb = $411 ± 54$ (stat.) $^{+85}_{-75}$ (syst.) fb for a Higgs boson mass of 125.09 GeV, consistent with the prediction of the Standard Model of $507^{+35}_{-75}$ fb. The cross-section is also measured differentially in bins of the Higgs boson transverse momentum within the simplified template cross-section framework.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2026

A practical guide to unbinned unfolding

Unfolding, in the context of high-energy particle physics, refers to the process of removing detector distortions in experimental data. The resulting unfolded measurements are straightforward to use for direct comparisons between experiments and a wide variety of theoretical predictions. For decades, popular unfolding strategies were designed to operate on data formatted as one or more binned histograms. In recent years, new strategies have emerged that use machine learning to unfold datasets in an unbinned manner, allowing for higher-dimensional analyses and more flexibility for current and future users of the unfolded data. This guide comprises recommendations and practical considerations from researchers across a number of major particle physics experiments who have recently put these techniques into practice on real data.

Canelli, Florencia [Univ. of Zurich (Switzerland)]↗
DOE OSTI2020

Algorithms for Efficient Reproducible Floating Point Summation

We define “reproducibility” as getting bitwise identical results from multiple runs of the same program, perhaps with different hardware resources or other changes that should not affect the answer. Many users depend on reproducibility for debugging or correctness. However, dynamic scheduling of parallel computing resources, combined with nonassociative floating point addition, makes reproducibility challenging even for summation, or operations like the BLAS. We describe a “reproducible accumulator” data structure (the “binned number”) and associated algorithms to reproducibly sum binary floating point numbers, independent of summation order. We use a subset of the IEEE Floating Point Standard 754-2008 and bitwise operations on the standard representations in memory. Our approach requires only one read-only pass over the data, and one reduction in parallel, using a 6-word reproducible accumulator (more words can be used for higher accuracy), enabling standard tiling optimization techniques. Summing n words with a 6-word reproducible accumulator requires approximately 9 n floating point operations (arithmetic, comparison, and absolute value) and approximately 3 n bitwise operations. The final error bound with a 6-word reproducible accumulator and our default settings can be up to 2 29 times smaller than the error bound for conventional (recursive) summation on ill-conditioned double-precision inputs.

Computer Science↗
DOE OSTI2025

eCounter: Inline Per-IP Network Monitoring at Millisecond Resolution via eBPF

Scientific data acquisition (SciDAQ) systems are shifting from archive-based workflows to streaming paradigms, where real-time, fine-grained network monitoring becomes essential. While P4-enabled devices offer per-packet in-band observability, they require specialized switches and routers. Host-side tools like Prometheus exporters lack sufficient temporal granularity. To bridge this gap, we present eCounter, a lightweight, hardware-agnostic, inline telemetry agent built on extended Berkeley Packet Filter (eBPF). eCounter captures per-interface ingress and egress traffic, categorized by IP address and protocol, at millisecond to sub-millisecond resolution. In a 100 Gbps environment, it continuously exports up to 3,257 time-series bins per second with only 4% CPU utilization at a 35¿KiB/s data rate. We evaluate eCounter across diverse NIC MTU settings, hook types, CPU architectures and operating systems, and observed negligible impact on concurrent high-throughput streaming applications. Complexity analysis confirms that it can be readily scaled to distributed SciDAQ deployments.

Mei, Xinxin [Computational Sciences and Technology↗
DOE OSTI2021

becquerel (bq) v0.4.0

Becquerel is a Python package for analyzing nuclear spectroscopic measurements. The core functionalities are reading and writing different spectrum file types, fitting spectral features, rebinning spectrum counts to different bin edges, performing detector calibrations and interpreting measurement results. It also includes tools for visualizing radiation spectra and fits of different spectral features, as well as convenient access to tabulated nuclear data both from remote servers and local caches. It relies heavily on the standard scientific Python stack of numpy, scipy, matplotlib, pandas, and numba. It is intended to be general-purpose enough that it can be useful to anyone from an undergraduate taking a laboratory course to the advanced

Bandstra, Mark↗
DOE OSTI2020

RODeO (Revenue Operation and Device Optimization Model) [SWR 20-67]

The Revenue, Operation, and Device Optimization (RODeO) model explores optimal system design and operation considering different levels of grid integration, equipment cost, operating limitations, financing, and credits and incentives. RODeO is a price-taker model formulated as a mixed-integer linear programming (MILP) model in the GAMS modeling platform. The objective is to maximizes the net revenue for a collection of equipment at a given site. The equipment includes generators (e.g., gas turbine, steam turbine, solar, wind, hydro, fuel cells, etc.), storage systems (batteries, pumped hydro, gas-fired compressed air energy storage, long-duration systems, hydrogen), and flexible loads (e.g., electric vehicles, electrolyzers, flexible building loads). The input data required by RODeO can be classified into three bins: 1) utility service data, which refers to retail utility rate information (meter cost, energy and demand charges), 2) electricity market data, which include energy and reserve prices, 3) other inputs, which refer to additional electrical demand, product output demand, technological assumptions, financial properties, and operational parameters.

Guerra Fernandez, Omar Jose↗
DOE OSTI2021

BLINK v1

We introduce the Binned Large Interval Network Kernel approach for scoring fragmentation mass spectra similarity which takes advantage of sparse matrix multiplication. This enables BLINK to perform 100 million comparisons while maintaining 98% accuracy in 2.2 seconds making it over 1,000 times faster than the current implementations.

Bowen, Benjamin↗
DOE OSTI2023

NuDustC++

NuDustc++ is a nucleating and sputtering dust code. It takes in the temperature-density profiles, abundance data, and chemistry network. It creates a binned size distribution from user input data to track certain grain sizes. NuDustc++ loads the data and calculates where and when a shock is detected in the input data. Using a runge-Kutta DoPri 5 integrator, it calculates nucleation and growth of grains by solving a system of coupled non-linear ODEs. It calculates sputtering based on the presence or lack of a shock by either integrating over energy or summing up the sputtering yield contributions per gas species. It is used to determine and track dust grain nucleation, growth, and erosion (sputtering) in gaseous systems to determine characteristics of the produced grain distribution.

Stangl, Sarah↗
DOE OSTI2025

becquerel (bq) v0.7.0

Becquerel is a Python package for analyzing nuclear spectroscopic measurements. The core functionalities are reading and writing different spectrum file types, fitting spectral features, rebinning spectrum counts to different bin edges, performing detector calibrations and interpreting measurement results. It also includes tools for visualizing radiation spectra and fits of different spectral features, as well as convenient access to tabulated nuclear data both from remote servers and local caches. It relies heavily on the standard scientific Python stack of numpy, scipy, matplotlib, pandas, and numba. It is intended to be general-purpose enough that it can be useful to anyone from an undergraduate taking a laboratory course to the advanced researcher.

Bandstra, Mark [Lawrence Berkeley National Laborat↗
DOE OSTI2023

ShadeLab/PAPER_Howe_2023_switchgrass_MetaT

The raw data (metagenomes and metatranscriptomes) for this study are available in the Joint Genomes Institute Genome Portal (https://genome.jgi.doe.gov/portal/ Project ID 503249) with projects designated by year and product type. The MAG genomes analyzed in this paper are available on NCBI, as bioproject PRJNA800073. Plants and microorganisms form beneficial associations. Understanding plant-microbe interactions will inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify ecologically important leaf microbiome members on field-grown switchgrass and miscanthus and to quantify their activities for switchgrass over two growing seasons. We integrate metagenome and metatranscriptome sequencing from 192 leaf samples collected over representative time points in crop phenology. We curated 40 medium- and high-quality metagenome-assembled-genomes (MAGs) and focused analysis on seasonal transcript recruitment to them. Classes represented by these focal MAGs (Actinomycetia, Alpha- and Gamma- Proteobacteria, and Bacteroidota) were active and had increases in transcripts for short-chain dehydrogenase, molybdopterin oxidoreductase, and polyketide cyclase in the late season. The majority of MAGs had activated stress-associated pathways, including trehalose metabolism, indole acetic acid degradation, betaine biosynthesis, and reactive oxygen species degradation, suggesting direct engagement with the host environment. We also detected seasonally activated biosynthetic pathways for terpenes (carotenoids and isoprenoids) and for various non-ribosomal peptide pathways that were poorly annotated. Overall, this study overcame laboratory and bioinformatic challenges associated with field-based leaf metatranscriptome analysis to inform both general and likely specialized activities of these phyllosphere populations. These activities collectively support that leaf-associated bacterial populations are seasonally dynamic, responsive to host cues, and interactively engage in feedback with the plant. This analysis represented quality filtering of metagenomes and metatranscriptomes (data-preparation folder), metagenome assemblies (metagenome-assembly folder) and metagenome-assembled genome binning, curation, refinement, annotation (mag-evaluation folder). Abundances of sequencing libraries were calculated based on reads mapped (mapping folder). Additionallly, analysis of our annotated results are also included (analysis folder).

Howe, Adina↗