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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 973 records · Page 54
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

The Target-Matrix Optimization Paradigm for High-Order Meshes

Here, we describe a framework for controlling and improving the quality of high-order finite element meshes based on extensions of the Target-Matrix Optimization Paradigm (TMOP) of [P. Knupp, Eng. Comput., 28 (2012), pp. 419--429]. This approach allows high-order applications to have a very precise control over local mesh quality, while still improving the mesh globally. We address the adaption of various TMOP components to the settings of general isoparametric element mappings, including the mesh quality metric in 2D and 3D, the selection of sample points and the solution of the resulting mesh optimization problem. We also investigate additional practical concerns, such as tangential relaxation and restricting the deviation from the original mesh. The benefits of the new high-order TMOP algorithms are illustrated on a number of test problems and examples from a high-order arbitrary Lagrangian--Eulerian (ALE) application [BLAST: High-order curvilinear finite elements for shock hydrodynamics, http://www.llnl.gov/CASC/blast]. Our implementation is freely available in an open-source library form [MFEM: Modular parallel finite element methods library, http://mfem.org].

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Measurement of deuteron spectra and elliptic flow in Pb–Pb collisions at $\sqrt{s_{\mathrm {NN}}}$ = 2.76 TeV at the LHC

The transverse momentum (p T ) spectra and elliptic flow coefficient (v 2 ) of deuterons and anti-deuterons at mid-rapidity (|y|<0.5) are measured with the ALICE detector at the LHC in Pb–Pb collisions at $\sqrt{s}$ NN = 2.76 TeV. The measurement of the p T spectra of (anti-)deuterons is done up to 8 GeV/c in 0–10% centrality class and up to 6 GeV/c in 10–20% and 20–40% centrality classes. The v 2 is measured in the 0.8 < p T < 5 GeV/c interval and in six different centrality intervals (0–5, 5–10, 10–20, 20–30, 30–40 and 40–50%) using the scalar product technique. Measured π ± , K ± and p+$\bar{p}$ transverse-momentum spectra and v 2 are used to predict the deuteron p T spectra and v 2 within the Blast-Wave model. The predictions are able to reproduce the v 2 coefficient in the measured p T range and the transverse-momentum spectra for p T > 1.8 GeV/c within the experimental uncertainties. The measurement of the coalescence parameter B 2 is performed, showing a p T dependence in contrast with the simplest coalescence model, which fails to reproduce also the measured v 2 coefficient. Finally, in addition, the coalescence parameter B 2 and the elliptic flow coefficient in the 20–40% centrality interval are compared with the AMPT model which is able, in its version without string melting, to reproduce the measured v 2 (p T ) and the B 2 (p T ) trend.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Measurement of Λ(1520) production in pp collisions at $\sqrt{s}$ = 7 TeV and p–Pb collisions at $\sqrt{s}$$_ {NN}$ = 5.02

The production of the Λ(1520) baryonic resonance has been measured at midrapidity in inelastic pp collisions at $\sqrt{s}$=7 TeV and in p–Pb collisions at $\sqrt{s}$$_ {NN}$=5.02 TeV for non-single diffractive events and in multiplicity classes. The resonance is reconstructed through its hadronic decay channel Λ(1520) →pK - and the charge conjugate with the ALICE detector. The integrated yields and mean transverse momenta are calculated from the measured transverse momentum distributions in pp and p–Pb collisions. The mean transverse momenta follow mass ordering as previously observed for other hyperons in the same collision systems. A Blast-Wave function constrained by other light hadrons (π, K, K$^0_S$, p, Λ) describes the shape of the Λ(1520) transverse momentum distribution up to 3.5 GeV/c in p–Pb collisions. In the framework of this model, this observation suggests that the Λ(1520) resonance participates in the same collective radial flow as other light hadrons. The ratio of the yield of Λ(1520) to the yield of the ground state particle Λ remains constant as a function of charged-particle multiplicity, suggesting that there is no net effect of the hadronic phase in p–Pb collisions on the Λ(1520) yield.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

$K^{*}(892)^0$ meson production in inelastic p+p interactions at 40 and 80 $\text{ GeV }\!/\!c$ beam momenta measured by NA61/SHINE at the CERN SPS

Measurements of $K^{*}(892)^0$ resonance production via its $K^{+}\pi ^{-}$ decay mode in inelastic p+p collisions at beam momenta 40 and 80 $\text{ GeV }\!/\!c$ ($\sqrt{s_{NN}}=8.8$ and 12.3 $\text{ GeV }$) are presented. The data were recorded by the NA61/SHINE hadron spectrometer at the CERN Super Proton Synchrotron. The template method was used to extract the $K^{*}(892)^0$ signal. Transverse momentum and rapidity spectra were obtained. The mean multiplicities of $K^{*}(892)^0$ mesons were found to be $(35.1 \pm 1.3 \mathrm {(stat)} \pm 3.6 \mathrm {(sys))} \cdot 10^{-3}$ at 40 $\text{ GeV }\!/\!c$ and $(58.3 \pm 1.9 \mathrm {(stat)} \pm 4.9 \mathrm {(sys))} \cdot 10^{-3}$ at 80 $\text{ GeV }\!/\!c$. The NA61/SHINE results are compared with the Epos1.99 and Hadron Resonance Gas models as well as with world data. The transverse mass spectra of $K^{*}(892)^0$ mesons and other particles previously reported by NA61/SHINE were fitted within the Blast-Wave model. The transverse flow velocities are close to 0.1–0.2 of the speed of light and are significantly smaller than the ones determined in heavy nucleus-nucleus interactions at the same beam momenta.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Constraining the $\overline{K}$N coupled channel dynamics using femtoscopic correlations at the LHC

The interaction of K – with protons is characterised by the presence of several coupled channels, systems like $\overline{K}$ 0 n and πΣ with a similar mass and the same quantum numbers as the K – p state. The strengths of these couplings to the K – p system are of crucial importance for the understanding of the nature of the Λ(1405) resonance and of the attractive K – p strong interaction. In this article, we present measurements of the K – p correlation functions in relative momentum space obtained in pp collisions at $\sqrt{s}$=13 Te, in p–Pb collisions at $\sqrt{s_{NN}}$= 5.02 Te, and (semi)peripheral Pb–Pb collisions at $\sqrt{s_{NN}}$= 5.02 Te. The emitting source size, composed of a core radius anchored to the K + p correlation and of a resonance halo specific to each particle pair, varies between 1 and 2 fm in these collision systems. The strength and the effects of the $\overline{K}$ 0 n and πΣ inelastic channels on the measured K – p correlation function are investigated in the different colliding systems by comparing the data with state-of-the-art models of chiral potentials. A novel approach to determine the conversion weights ω, necessary to quantify the amount of produced inelastic channels in the correlation function, is presented. In this method, particle yields are estimated from thermal model predictions, and their kinematic distribution from blast-wave fits to measured data. The comparison of chiral potentials to the measured K – p interaction indicates that, while the πΣ –K – p dynamics is well reproduced by the model, the coupling to the $\overline{K}$ 0 n channel in the model is currently underestimated.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Modeling a High-Temperature Electrochemically Driven Water-Gas-Shift Process Using a Mixed-Conducting Membrane without External Electrical Power

This paper develops a model to predict and interpret the performance of an elevated-temperature, electrochemical, membrane-assisted, water-gas-shift process. The process uses separated feed streams of H 2 O and CO to produce separated streams of H 2 and CO 2 , without an external electrical power source. The dense ceramic membrane is mixed ionic-electronic-conducting (MIEC) gadolinium-doped ceria (GDC) and the porous composite electrodes are Ni-YSZ. At elevated temperature, GDC conducts both oxygen ions and small polarons. The present process uses chemical potential to drive the process. Electrochemical oxidation of CO proceeds within the composite anode and H 2 O reduction proceeds within the composite cathode. At high temperature (e.g., T > 700 °C), GDC has significant electronic leakage in the form of a reduced-cerium small polaron, which supports the charge-transfer reactions. In a typical electrolyzer or fuel cell, this leakage is significantly problematic. However, the present process depends on the leakage current to complete the electrochemical circuit. Model development and validation is based on measured material properties and reactor performance. Potential applications include using CO-rich blast-furnace off gases in steel processing, producing separated streams of H 2 and CO 2 .

Zhu, Huayang↗
DOE OSTI2025

Choline Chloride-Based Water-in-Salt Electrolyte for Efficient Iron Electrodeposition

Electrochemical production of iron is a promising low-cost and modular approach to replace the traditional blast furnace. Aqueous electrolytes for iron electrolysis are advantageous as they can be operated at near-ambient temperatures, but they suffer from inefficiencies due to the parasitic hydrogen evolution reaction. In this work, we identify a new water-in-salt electrolyte (WiSE) based on choline chloride (ChCl) for high coulombic efficiency (>85%) iron deposition. Electrochemical analysis of the partial current densities of iron plating and hydrogen co-evolution revealed that, at optimal WiSE compositions, water reduction is kinetically suppressed resulting in an increase in the Fe plating efficiency. Decreased coordination of water and increased coordination of choline’s alcohol group with the Fe 2+ ion were observed through 1 H NMR providing evidence that water reduction is kinetically suppressed in WiSE. Additionally, Raman spectroscopy revealed that complexation effects (with Cl – ) reduce Fe 2+ diffusion coefficients and corresponding limiting currents as the ChCl concentration is increased. This results in an optimal WiSE composition (4 M ChCl + 1 M FeCl 2 ) that provides kinetic suppression of HER but also low transport resistance to Fe plating yielding 85% coulombic efficiency at high current densities.

Sinclair, Nicholas Scott [Case Western Reserve Uni↗
DOE OSTI2025

Stable, Efficient Iron Electrodeposition via Anion-Directed Control of Fe(II) Coordination

Traditional steelmaking processes consume about 7% of the world’s energy supply, with reduction of iron oxides into iron via blast furnaces representing the most energy-demanding and capital-intensive step. To economize and modularize iron reduction processes, we aim to develop an electrodeposition technique to reduce aqueous iron ions to metallic iron. However, the hydrogen reduction reaction (HER) occurs at a more positive standard reduction potential than the iron reduction reaction. In addition, aqueous Fe(II) cations easily precipitate at mildly acidic conditions (pH ≥ 3), which limits the deposition efficiency and degrades deposit quality. To address these challenges, we first search for anions that have intermediate coordination strength with Fe(II) based on the hard-soft acid-base theory, trading a slightly more negative Fe(II) reduction potential for a considerably broader pH stability range. We select citrate with predicted intermediate coordination strength, in combination with more weakly coordinating anions (e.g., SO 4 2- , Cl - ) to control the coordination structure of Fe 2+ for improved electrolyte stability and electrodeposition behavior. We find that citrate coordination stabilizes Fe 2+ -based electrolytes at higher pH conditions (4.8–5.5), significantly extending their shelf life while also suppressing HER during Fe electrodeposition by orders of magnitude. To measure Faradaic efficiencies (FE), we developed a straightforward, titration-based methodology to quantify the amount of deposited iron regardless of the rate of concurrent HER. Although coordination between citrate and Fe 2+ decreases the reduction potential of Fe(II), high FE (≥98%) was achieved at 10 mA cm -2 . FE and achievable deposition rates are tunable by both concentration and the ratio of Fe 2+ to citrate. In all cases, Raman spectroscopy and X-ray diffraction (XRD) reveal that iron deposition in citrate-containing electrolytes suppresses iron oxide/hydroxide precipitation, in contrast to deposits generated in citrate-free electrolytes. Altogether, this work demonstrates that citrate-mediated anion coordination enables high-purity iron electrodeposition with increased FE, high current density, and improved electrolyte stability. This multi-anion coordination strategy provides a versatile framework for designing stable electrolyte and efficient metal electrodeposition.

coordination↗
DOE OSTI2014

Compare Gene Profiles

Compare Gene Profiles (CGP) performs pairwise gene content comparisons among a relatively large set of related bacterial genomes. CGP performs pairwise BLAST among gene calls from a set of input genome and associated annotation files, and combines the results to generate lists of common genes, unique genes, homologs, and genes from each genome that differ substantially in length from corresponding genes in the other genomes. CGP is implemented in Python and runs in a Linux environment in serial or parallel mode.

Source record↗
DOE OSTI2017

Mercat

Mercat is a highly scalable property software package for robust of analysis of features in next-generation sequencing data and observed unique peptides from metaproteomic data. Mercat is offered in python 3.5/anaconda3, is multiparellel and is easily installed using bioconda/conda recipes. Mercat inputs include assembled contigs, raw sequence reads from any platform, and unique peptide files obtained from proteomics with feature abundance counts tables. Mercat is the only software available that allows for direct analysis of data properties without a data-dependent search tools such as BLAST or diamond for compositional analysis of whole community shotgun sequencing (e.g. metagenomes and/or metatranscriptomes) or metaproteomic data.

Source record↗
DOE OSTI2012

Aquatic Acoustic Metrics Interface

Fishes and marine mammals may suffer a range of potential effects from exposure to intense underwater sound generated by anthropogenic activities such as pile driving, shipping, sonars, and underwater blasting. Several underwater sound recording (USR) devices have been built to acquire samples of the underwater sound generated by anthropogenic activities. Software becomes indispensable for processing and analyzing the audio files recorded by these USRs. The new Aquatic Acoustic Metrics Interface Utility Software (AAMI) is specifically designed for analysis of underwater sound recordings to provide data in metrics that facilitate evaluation of the potential impacts of the sound on aquatic animals. In addition to the basic functions, such as loading and editing audio files recorded by USRs and batch processing of sound files, the software utilizes recording system calibration data to compute important parameters in physical units. The software also facilitates comparison of the noise sound sample metrics with biological measures such as audiograms of the sensitivity of aquatic animals to the sound, integrating various components into a single analytical frame.

Source record↗
DOE OSTI2025

GenomeDepot v1.0

GenomeDepot is a web-based platform for annotation, management, and comparative analysis of microbial genomic sequences and associated data including ortholog families, protein domains, operons, regulatory interactions, strain taxonomy, and sample metadata. GenomeDepot supports rapid creation of web-sites for user-defined genome collections that include bioinformatic tools for interactive genome browsing, BLAST search, annotation search, comparative genomic neighborhood visualization, and sequence download. Gene function annotations are generated by a customizable annotation pipeline. The pipeline runs annotation tools in Conda environments and can be easily extended with additional user-specified tools.

Kazakov, Alexey [Lawrence Berkeley National Labora↗
DOE OSTI2024

Poplar

SAND2025-00683O Poplar is a software tool that generates a phylogenetic tree from input gene and genome sequences. It integrates established tools to identify genes within genomes, group sequences, construct gene trees, and infer a species tree. Poplar processes nucleotide sequences, identifies similar sequences using Nucleotide BLAST, groups them with DBSCAN, aligns sequences with MAFFT, constructs gene trees with RAxML-NG, and infers a species tree using ASTRAL-Pro3. This pipeline provides a structured approach to phylogenetic analysis, facilitating the study of evolutionary relationships among species. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Krishnakumar, Raga↗
DOE OSTI2026

CHEQUP v0.1

CHEQUP (Castro-based Hofi Expansion with QUasineutral Plasma) is a simulation code for modeling the formation of hydrodynamic optical-field-ionized (HOFI) plasma channels, which are used as waveguides in laser-plasma acceleration experiments. This includes experiments performed at LBNL's BELLA facility as well as other laser facilities across the world. CHEQUP extends the open-source Castro hydrodynamics framework with physics modules tailored for modeling HOFI plasma channels -- including multi-species ionization and three-body recombination for mixtures of hydrogen, nitrogen, helium, and argon ; a two-temperature model tracking electron and heavy-species temperatures separately ; and coupling with other codes of the BLAST ecosystem (https://blast.lbl.gov/) such as WarpX, via the openPMD standard. CHEQUP inherits from Castro the ability to run on modern GPU architectures (NVIDIA CUDA, AMD HIP) and supports adaptive mesh refinement (AMR) for efficient multi-scale resolution. Compared to existing tools, CHEQUP would be, to our knowledge, the first open-source code implementing the full HOFI channel formation physics, and the first implementation capable of running on GPUs. This enables significantly faster, large-scale parameter scans critical for the design of next-generation LPA-based accelerators and light sources.

Lehe, Remi [Lawrence Berkeley National Laboratory ↗
DOE OSTI2013

PoPLAR: Portal for Petascale Lifescience Applications and Research

Background: We are focusing specifically on fast data analysis and retrieval in bioinformatics that will have a direct impact on the quality of human health and the environment. The exponential growth of data generated in biology research, from small atoms to big ecosystems, necessitates an increasingly large computational component to perform analyses. Novel DNA sequencing technologies and complementary high-throughput approaches–such as proteomics, genomics, metabolomics, and meta-genomics–drive data-intensive bioinformatics. While individual research centers or universities could once provide for these applications, this is no longer the case. Today, only specialized national centers can deliver the level of computing resources required to meet the challenges posed by rapid data growth and the resulting computational demand. Consequently, we are developing massively parallel applications to analyze the growing flood of biological data and contribute to the rapid discovery of novel knowledge. Methods: The efforts of previous National Science Foundation (NSF) projects provided for the generation of parallel modules for widely used bioinformatics applications on the Kraken supercomputer. We have profiled and optimized the code of some of the scientific community’s most widely used desktop and small-cluster-based applications, including BLAST from the National Center for Biotechnology Information (NCBI), HMMER, and MUSCLE; scaled them to tens of thousands of cores on high-performance computing (HPC) architectures; made them robust and portable to next-generation architectures; and incorporated these parallel applications in science gateways with a web-based portal. Results: This paper will discuss the various developmental stages, challenges, and solutions involved in taking bioinformatics applications from the desktop to petascale with a front-end portal for very-large-scale data analysis in the life sciences. Conclusions: This research will help to bridge the gap between the rate of data generation and the speed at which scientists can study this data. The ability to rapidly analyze data at such a large scale is having a significant, direct impact on science achieved by collaborators who are currently using these tools on supercomputers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

VESPA: Software to Facilitate Genomic Annotation of Prokaryotic Organisms Through Integration of Proteomic and Transcriptomic Data

Visual Exploration and Statistics to Promote Annotation (VESPA) is an interactive visual analysis software tool that facilitates the discovery of structural mis-annotations in prokaryotic genomes. VESPA integrates high-throughput peptide-centric proteomics data and oligo-centric or RNA-Seq transcriptomics data into a genomic context. The data may be interrogated via visual analysis across multiple levels of genomic resolution, linked searches, exports and interaction with BLAST to rapidly identify location of interest within the genome and evaluate potential mis-annotations.

Peterson, Elena S.↗
DOE OSTI2012

Genetic diversity within the genus Francisella as revealed by comparative analyses of the genomes of two North American isolates from environmental sources

Background: Francisella tularensis is an intracellular pathogen that causes tularemia in humans and the public health importance of this bacterium has been well documented in recent history. Francisella philomiragia, a distant relative of F. tularensis, is thought to constitute an environmental lineage along with Francisella novicida. Nevertheless, both F. philomiragia and F. novicida have been associated with human disease, primarily in immune-compromised individuals. To understand the genetic relationships and evolutionary contexts among different lineages within the genus Francisella, the genome of Francisella spp. strain TX07-7308 was sequenced and compared to the genomes of F. philomiragia strains ATCC 25017 and 25015, F. novicida strain U112, and F. tularensis strain Schu S4. Results: The size of strain ATCC 25017 chromosome was 2,045,775 bp and contained 1,983 protein-coding genes. The size of strain TX07-7308 chromosome was 2,035,931 bp and contained 1,980 protein-coding genes. Pairwise BLAST comparisons indicated that strains TX07-7308 and ATCC 25017 contained 1,700 protein coding genes in common. NUCmer analyses revealed that the chromosomes of strains TX07-7308 and ATCC 25017 were mostly collinear except for a few gaps, translocations, and/or inversions. Using the genome sequence data and comparative analyses with other members of the genus Francisella (e.g., F. novicida strain U112 and F. tularensis strain Schu S4), several strain-specific genes were identified. Strains TX07-7308 and ATCC 25017 contained an operon with six open reading frames encoding proteins related to enzymes involved in thiamine biosynthesis that was absent in F. novicida strain U112 and F. tularensis strain Schu S4. Strain ATCC 25017 contained an operon putatively involved in lactose metabolism that was absent in strain TX07-7308, F. novicida strain U112, and F. tularensis strain Schu S4. In contrast, strain TX07-7308 contained an operon putatively involved in glucuronate metabolism that was absent in the genomes of strain ATCC 25017, F. novicida strain U112, and F. tularensis strain Schu S4. The polymorphic nature of polysaccharide biosynthesis/modification gene clusters among different Francisella strains was also evident from genome analyses. Conclusions: From genome comparisons, it appeared that genes encoding novel functions have contributed to the metabolic enrichment of the environmental lineages within the genus Francisella. The inability to acquire new genes coupled with the loss of ancestral traits and the consequent reductive evolution may be a cause for, as well as an effect of, niche selection of F. tularensis. Sequencing and comparison of the genomes of more isolates are required to obtain further insights into the ecology and evolution of different species within the genus Francisella.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2012

Rapid phylogenetic and functional classification of short genomic fragments with signature peptides

Background: Classification is difficult for shotgun metagenomics data from environments such as soils, where the diversity of sequences is high and where reference sequences from close relatives may not exist. Approaches based on sequence-similarity scores must deal with the confounding effects that inheritance and functional pressures exert on the relation between scores and phylogenetic distance, while approaches based on sequence alignment and tree-building are typically limited to a small fraction of gene families. We describe an approach based on finding one or more exact matches between a read and a precomputed set of peptide 10-mers. Results: At even the largest phylogenetic distances, thousands of 10-mer peptide exact matches can be found between pairs of bacterial genomes. Genes that share one or more peptide 10-mers typically have high reciprocal BLAST scores. Among a set of 403 representative bacterial genomes, some 20 million 10-mer peptides were found to be shared. We assign each of these peptides as a signature of a particular node in a phylogenetic reference tree based on the RNA polymerase genes. We classify the phylogeny of a genomic fragment (e.g., read) at the most specific node on the reference tree that is consistent with the phylogeny of observed signature peptides it contains. Using both synthetic data from four newly-sequenced soil-bacterium genomes and ten real soil metagenomics data sets, we demonstrate a sensitivity and specificity comparable to that of the MEGAN metagenomics analysis package using BLASTX against the NR database. Phylogenetic and functional similarity metrics applied to real metagenomics data indicates a signal-to-noise ratio of approximately 400 for distinguishing among environments. Our method assigns ~6.6 Gbp/hr on a single CPU, compared with 25 kbp/hr for methods based on BLASTX against the NR database. Conclusions: Classification by exact matching against a precomputed list of signature peptides provides comparable results to existing techniques for reads longer than about 300 bp and does not degrade severely with shorter reads. Orders of magnitude faster than existing methods, the approach is suitable now for inclusion in analysis pipelines and appears to be extensible in several different directions.

59 BASIC BIOLOGICAL SCIENCES↗