Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “marcelling”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Iterative reconstruction excursions for Baryon Acoustic Oscillations and beyond

ABSTRACT The density field reconstruction technique has been widely used for recovering the baryon acoustic oscillation (BAO) feature in galaxy surveys that has been degraded due to non-linearities. Recent studies advocated adopting iterative steps to improve the recovery much beyond that of the standard technique. In this paper, we investigate the performance of a few selected iterative reconstruction techniques focusing on the BAO and the broad-band shape of the two-point clustering. We include redshift-space distortions, halo bias, and shot noise and inspect the components of the reconstructed field in Fourier space and in configuration space using both density field-based reconstruction and displacement field-based reconstruction. We find that the displacement field reconstruction becomes quickly challenging in the presence of non-negligible shot noise and therefore present surrogate methods that can be practically applied to a much more sparse field such as galaxies. For a galaxy field, implementing a debiasing step to remove the Lagrangian bias appears crucial for the displacement field reconstruction. We show that the iterative reconstruction does not substantially improve the BAO feature beyond an aggressively optimized standard reconstruction with a small smoothing kernel. However, we find taking iterative steps allows us to use a small smoothing kernel more ‘stably’, i.e. without causing a substantial deviation from the linear power spectrum on large scales. In one specific example we studied, we find that a deviation of 13 per cent in $P(k\sim 0.1\, h{\rm \,\,Mpc^{-1}})$ with an aggressive standard reconstruction can reduce to 3–4 per cent with iterative steps.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

FLAMINGO: combining kinetic SZ effect and galaxy–galaxy lensing measurements to gauge the impact of feedback on large-scale structure

Energetic feedback processes associated with accreting supermassive black holes can expel gas from massive haloes and significantly alter various measures of clustering on $\sim$Mpc scales, potentially biasing the values of cosmological parameters inferred from analyses of large-scale structure (LSS) if not modelled accurately. Here, we use the state-of-the-art FLAMINGO suite of cosmological hydrodynamical simulations to gauge the impact of feedback on large-scale structure by comparing to Planck + ACT stacking measurements of the kinetic Sunyaev–Zel’dovich (kSZ) effect of SDSS BOSS galaxies. We make careful like-with-like comparisons to the observations, aided by high precision KiDS and DES galaxy–galaxy lensing measurements of the BOSS galaxies to inform the selection of the simulated galaxies. In qualitative agreement with several recent studies using dark matter only simulations corrected for baryonic effects, we find that the kSZ effect measurements prefer stronger feedback than predicted by simulations which have been calibrated to reproduce the gas fractions of low redshift X-ray-selected groups and clusters. We find that the increased feedback can help to reduce the so-called $S_8$ tension between the observed and CMB-predicted clustering on small scales as probed by cosmic shear (although at the expense of agreement with the X-ray group measurements). However, the increased feedback is only marginally effective at reducing the reported offsets between the predicted and observed clustering as probed by the thermal SZ (tSZ) effect power spectrum and tSZ effect – weak lensing cross-spectrum, both of which are sensitive to higher halo masses than cosmic shear.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

The IMG/M data management and analysis system v.7: content updates and new features

The Integrated Microbial Genomes & Microbiomes system at the Department of Energy (DOE) Joint Genome Institute (JGI) continues to provide support for users to perform comparative analysis of isolate and single cell genomes, metagenomes, and metatranscriptomes. In addition to datasets produced by the JGI, IMG v.7 also includes datasets imported from public sources such as NCBI Genbank, SRA, and the DOE National Microbiome Data Collaborative (NMDC), or submitted by external users. In the past couple years, we have continued our effort to help the user community by improving the annotation pipeline, upgrading the contents with new reference database versions, and adding new analysis functionalities such as advanced scaffold search, Average Nucleotide Identity (ANI) for high-quality metagenome bins, new cassette search, improved gene neighborhood display, and improvements to metatranscriptome data display and analysis. Here, we also extended the collaboration and integration efforts with other DOE-funded projects such as NMDC and DOE Biology Knowledgebase (KBase).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata

Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They drive horizontal gene transfer, impacting ecological and evolutionary processes within microbial communities, and hold substantial importance in human health and biotechnology. To support plasmid research and provide scientists with data of an unprecedented diversity of plasmid sequences, we introduce the IMG/PR database, a new resource encompassing 699 973 plasmid sequences derived from genomes, metagenomes and metatranscriptomes. IMG/PR is the first database to provide data of plasmid that were systematically identified from diverse microbiome samples. IMG/PR plasmids are associated with rich metadata that includes geographical and ecosystem information, host taxonomy, similarity to other plasmids, functional annotation, presence of genes involved in conjugation and antibiotic resistance. The database offers diverse methods for exploring its extensive plasmid collection, enabling users to navigate plasmids through metadata-centric queries, plasmid comparisons and BLAST searches. The web interface for IMG/PR is accessible at https://img.jgi.doe.gov/pr. Plasmid metadata and sequences can be downloaded from https://genome.jgi.doe.gov/portal/IMG_PR.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Altering translation allows E. coli to overcome G-quadruplex stabilizers

G-quadruplex (G4) structures can form in guanine-rich DNA or RNA and have been found to modulate cellular processes, including replication, transcription, and translation. Many studies on the cellular roles of G4s have focused on eukaryotic systems, with far fewer probing bacterial G4s. Using a chemical-genetic approach, we identified genes in Escherichia coli that are important for growth in G4-stabilizing conditions. Reducing levels of translation elongation factor Tu or slowing translation initiation or elongation with kasugamycin, chloramphenicol, or spectinomycin suppress the effects of G4-stabilizing compounds. In contrast, reducing the expression of specific translation termination or ribosome recycling proteins is detrimental to growth in G4-stabilizing conditions. Proteomic and transcriptomic analyses reveal decreased protein and transcript levels, respectively, for ribosome assembly factors and proteins associated with translation in the presence of G4 stabilizer. Our results support a model in which reducing the rate of translation by altering translation initiation, translation elongation, or ribosome assembly can compensate for G4-related stress in E. coli.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

SEED LIPID DROPLET PROTEIN1, SEED LIPID DROPLET PROTEIN2, and LIPID DROPLET PLASMA MEMBRANE ADAPTOR mediate lipid droplet–plasma membrane tethering

Membrane contact sites (MCSs) are interorganellar connections that allow for the direct exchange of molecules, such as lipids or Ca 2+ between organelles, but can also serve to tether organelles at specific locations within cells. Here, we identified and characterized three proteins of Arabidopsis thaliana that form a lipid droplet (LD)–plasma membrane (PM) tethering complex in plant cells, namely LD-localized SEED LD PROTEIN (SLDP) 1 and SLDP2 and PM-localized LD-PLASMA MEMBRANE ADAPTOR (LIPA). Using proteomics and different protein–protein interaction assays, we show that both SLDPs associate with LIPA. Disruption of either SLDP1 and SLDP2 expression, or that of LIPA, leads to an aberrant clustering of LDs in Arabidopsis seedlings. Ectopic co-expression of one of the SLDPs with LIPA is sufficient to reconstitute LD–PM tethering in Nicotiana tabacum pollen tubes, a cell type characterized by dynamically moving LDs in the cytosolic streaming. Furthermore, confocal laser scanning microscopy revealed both SLDP2.1 and LIPA to be enriched at LD–PM contact sites in seedlings. These and other results suggest that SLDP and LIPA interact to form a tethering complex that anchors a subset of LDs to the PM during post-germinative seedling growth in Arabidopsis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Regioselectivity mechanism of the Thunbergia alata Δ 6 -16:0-acyl carrier protein desaturase

Plant plastidial acyl–acyl carrier protein (ACP) desaturases are a soluble class of diiron-containing enzymes that are distinct from the diiron-containing integral membrane desaturases found in plants and other organisms. The archetype of this class is the stearoyl-ACP desaturase which converts stearoyl-ACP into oleoyl (18:1Δ 9 cis )-ACP. Several variants expressing distinct regioselectivity have been described including a Δ 6 -16:0-ACP desaturase from black-eyed Susan vine ( Thunbergia alata ). We solved a crystal structure of the T. alata desaturase at 2.05 Å resolution. Using molecular dynamics (MD) simulations, we identified a low-energy complex between 16:0-ACP and the desaturase that would position C6 and C7 of the acyl chain adjacent to the diiron active site. The model complex was used to identify mutant variants that could convert the T. alata Δ 6 desaturase to Δ 9 regioselectivity. Additional modeling between ACP and the mutant variants confirmed the predicted regioselectivity. Furthermore, to validate the in-silico predictions, we synthesized two variants of the T. alata desaturase and analyzed their reaction products using gas chromatography-coupled mass spectrometry. Assay results confirmed that mutants designed to convert T. alata Δ 6 to Δ 9 selectivity exhibited the predicted changes. In complementary experiments, variants of the castor desaturase designed to convert Δ 9 to Δ 6 selectivity lost some of their Δ9 desaturation ability and gained the ability to desaturate at the Δ 6 position. The computational workflow for revealing the mechanistic understanding of regioselectivity presented herein lays a foundation for designing acyl-ACP desaturases with novel selectivities to increase the diversity of monoenes available for bioproduct applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Impact of Soil Salinity on the Cowpea Nodule-Microbiome and the Isolation of Halotolerant PGPR Strains to Promote Plant Growth under Salinity Stress

Cowpea is one of the major legumes cultivated in arid and semiarid regions of the world. Four soil-microbial samples (SS-1 through SS-4) collected from semiarid soils in Punjab, Pakistan were planted with cowpea (Vigna unguiculata) crops, which were grown under salinity stress to analyze bacterial composition in the rhizosphere and within nodules using cultivation-dependent and -independent methods. Two varieties, 603 and the salt-tolerant CB 46, were each inoculated with or without the four different native soil samples or grown in medium either N-deficient (-N) or supplemented with N (+N). Plants inoculated with soil samples SS-2 and SS-4 grew better than plants inoculated with SS-1- and SS-3 and grew comparably with the +N controls. Environmental DNA (eDNA) was isolated from SS-1 and SS-4, and, by 16S ribosomal RNA sequencing, the soil microbiomes consisted mainly of Actinobacteria, Firmicutes, Proteobacteria, and other nonproteobacterial genera. However, analysis of eDNA isolated from cowpea nodules established by the trap plants showed that the nodule microbiome consisted almost exclusively of proteobacterial sequences, particularly species of Bradyrhizobium. Bacteria were isolated from both soils and nodules, and 34 of the 51 isolates tested positive for plant-growth-promoting rhizobacteria traits in plate assays. Many could serve as future inocula for crops in arid soils. The discrepancy between the types of bacteria isolated by culturing bacteria isolated from surface-sterilized cowpea nodules (proteobacteria and nonproteobacteria) versus those detected by sequencing DNA isolated from the nodules (proteobacteria) from cowpea nodules (proteobacteria and nonproteobacteria) versus those detected in the nodule microbiome (proteobacteria) needs further study.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Isolation of potential plant growth-promoting bacteria from nodules of legumes grown in arid Botswana soil

As the world population increases, improvements in crop growth and yield will be needed to meet rising food demands, especially in countries that have not developed agricultural practices optimized for their own soils and crops. In many African countries, farmers improve agricultural productivity by applying synthetic fertilizers and pesticides to crops, but their continued use over the years has had serious environmental consequences including air and water pollution as well as loss of soil fertility. To reduce the overuse of synthetic amendments, we are developing inocula for crops that are based on indigenous soil microbes, especially those that enhance plant growth and improve agricultural productivity in a sustainable manner. We first isolated environmental DNA from soil samples collected from an agricultural region to study the composition of the soil microbiomes and then used Vigna unguiculata (cowpea), an important legume crop in Botswana and other legumes as “trap” plants using the collected soil to induce nitrogen-fixing nodule formation. We have identified drought-tolerant bacteria from Botswana soils that stimulate plant growth; many are species of Bacillus and Paenibacillus . In contrast, the cowpea nodule microbiomes from plants grown in these soils house mainly rhizobia particularly Bradyrhizobium , but also Methylobacterium spp. Hence, the nodule microbiome is much more limited in non-rhizobial diversity compared to the soil microbiome, but also contains a number of potential pathogenic bacteria.

Kosty, Melissa↗
DOE OSTI2026

Third moments of nucleon unpolarized, polarized, and transversity parton distribution functions from physical-point lattice QCD

Using forward matrix elements of local leading-twist operators, we present a determination of the isovector third Mellin moments ⟨𝑥 2 ⟩ of nucleon unpolarized, polarized, and transversity parton distribution functions. Two lattice QCD ensembles at the physical pion mass are used, which were generated using a tree-level Symanzik-improved gauge action and 2+1 flavor tree-level improved Wilson Clover fermions coupling via 2-level HEX-smearing. Leveraging a wide set of operators, two extraction methods for the matrix elements, and the automatic inclusion of model uncertainties via bootstrapped model averages, we extract values of the third Mellin moments. Furthermore, this is the first direct calculation of these observables performed at the physical pion mass.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

Laser-driven production of the antihydrogen molecular ion

The feasibility of producing the molecular antihydrogen anion H 2 – in the laboratory is investigated here. Utilizing reaction rates calculated here involving the interaction of laser excited-state antihydrogen atoms held in magnetic minimum traps, key processes are identified that could lead to anion production, as well as competing effects leading to anti-atom loss. These are discussed in the context of present-day and near-future experimental capabilities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Pulse shaping in strong-field ionization: Theory and experiments

Intense ultrafast pulses cause dissociative ionization and shaping the pulses may allow control of both electronic and nuclear dynamics that determine ion yields. We report on a combined experimental and theoretical effort to determine how shaped laser pulses affect tunnel ionization, the process that precedes many strong-field phenomena. We carried out experiments on Ar, N 2 , H 2 O, and O 2 using a phase-step function of amplitude 3/4π that is scanned across the spectrum of the pulse. In addition, we changed the amount of chirp in the pulses. Semiclassical as well as fully quantum mechanical time-dependent Schrödinger equation calculations are found to be in excellent agreement with experimental results. We find that precise knowledge of the field parameters in the time and frequency domains is essential to afford reproducible results and quantitative theory and experiment comparisons.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Bayesian optimization of the beam injection process into a storage ring

We have evaluated the data-efficient Bayesian optimization method for the specific task of injection tuning in a circular accelerator. In this paper, we describe the implementation of this method at the Karlsruhe Research Accelerator with up to nine tuning parameters, including the determination of the associated hyperparameters. We show that the Bayesian optimization method outperforms manual tuning and the commonly used Nelder-Mead optimization algorithm in both simulation and experiment. The algorithm was also successfully used to ease the commissioning phase after the installation of new injection magnets and is regularly used during accelerator operations. We demonstrate that the introduction of context variables that include intrabunch scattering effects, such as the Touschek effect, further improves the control and robustness of the injection process.

43 PARTICLE ACCELERATORS↗
DOE OSTI2020

Above-threshold multiphoton photoemission from noble metal surfaces

Exciting solids with intense femtosecond laser pulses prompts electrons of the interrogated material to respond in a highly nonlinear manner, as is evident in the emission of high-order harmonic radiation and photoelectrons with kinetic energies well above that of the driving photons. Such high-field interactions can be resolved, for example, in above-threshold multiphoton photoemission (ATP) spectroscopy. In this work, we interrogate the nonlinear photoelectric responses of the pristine copper, silver, and gold noble metal surfaces in (111) and (100) crystal orientations in the perturbative regime. Using multiphoton photoemission spectroscopy (mPP) excited by finely tuned optical fields, we characterize enhancement of the mPP and ATP yields from (111) surfaces in selected k||-momentum ranges when the occupied Shockley surface (SS) states are (near-)resonantly coupled by multiphoton transitions to image potential (IP) intermediate states in the excitation process. The ATP signal from the IP states of (111) surfaces is largely defined by their formation through polarization of SS electrons; this observation is contrasted with ATP experiments from the Ag(100) surface, for which the SS becomes an unoccupied resonance and the IP states can only be excited from bands with significantly more bulk character. In addition, based on the optical power and nonlinear order-dependent mPP spectra, we provide evidence for ATP being a one-step, rather than a sequential process, as previously postulated.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Plasmonically assisted channels of photoemission from metals

We analyze recently measured nonlinear photoemission spectra from Ag surfaces that reveal resonances whose energies do not scale with the applied photon energy but stay pinned to multiples of bulk plasmon energy $\hbar$ω p above the Fermi level. To elucidate these unexpected and peculiar features we investigate the spectra of plasmons generated in a solid by the optically pumped electronic polarization and their effect on photoemission. By combining quadratic response formalism for calculations of photoemission yield, a nonperturbative approach to inelastic electron scattering, and first-principles calculations for the electronic structure, we demonstrate the dependence of probability amplitude for single- and multiplasmon excitations on the basic parameters characterizing the photon pulse and the system. The resulting multiexcitation spectrum evolves towards a truncated plasmonic coherent state. Analogous concept is extrapolated to interpret plasmon generation by multiphoton excited electronic polarization. Based on this we elaborate a scenario that the thus created real plasmons act as supplementary frequency-locked pump field for non-Einsteinian plasmonically assisted channels of photoemission from metals. The established paradigm enables assignment and assessment of the observed linear $\hbar$ω p and nonlinear 2$\hbar$ω p electron yields from Ag. Such effects may be exploited for selective filtering of optical energy conversion in electronic systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Flexocaloric effect near a ferroelastic transition

A Ginzburg-Landau model embedded into a vibrational model is used to study the flexocaloric effect in a beam near a ferroelastic transition. The caloric response upon bending is characterized by the isothermal entropy change and the adiabatic temperature change of the beam. Here, we obtain a larger response relative to the strength of the applied forces at temperatures slightly above the transition temperature. It is also obtained that the maximum caloric response is almost linear with the bending angle of the beam, whereas the relation between the bending angle and the applied forces is highly nonlinear. Small hysteresis associated with the phase transition is obtained for sufficiently large bending forces due to the existence of a critical point in the temperature-stress phase diagram of the ferroelastic material. Finally, the microstructure changes with bending in the beam are consistent with previous experimental observations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗