Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “extensions”

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 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

SPT-SZ MCMF: an extension of the SPT-SZ catalogue over the DES region

We present an extension to a Sunyaev–Zel’dovich Effect (SZE) selected cluster catalogue based on observations from the South Pole Telescope (SPT); this catalogue extends to lower signal to noise than the previous SPT–SZ catalogue and therefore includes lower mass clusters. Optically derived redshifts, centres, richnesses, and morphological parameters together with catalogue contamination and completeness statistics are extracted using the multicomponent matched filter (MCMF) algorithm applied to the S/N > 4 SPT–SZ candidate list and the Dark Energy Survey (DES) photometric galaxy catalogue. The main catalogue contains 811 sources above S/N = 4, has 91 per cent purity, and is 95 per cent complete with respect to the original SZE selection. It contains in total 50 per cent more clusters and twice as many clusters above z = 0.8 in comparison to the original SPT-SZ sample. The MCMF algorithm allows us to define subsamples of the desired purity with traceable impact on catalogue completeness. As an example, we provide two subsamples with S/N > 4.25 and S/N > 4.5 for which the sample contamination and cleaning-induced incompleteness are both as low as the expected Poisson noise for samples of their size. The subsample with S/N > 4.5 has 98 per cent purity and 96 per cent completeness and is part of our new combined SPT cluster and DES weak-lensing cosmological analysis. We measure the number of false detections in the SPT-SZ candidate list as function of S/N, finding that it follows that expected from assuming Gaussian noise, but with a lower amplitude compared to previous estimates from simulations.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata

Viruses are widely recognized as critical members of all microbiomes. Metagenomics enables large-scale exploration of the global virosphere, progressively revealing the extensive genomic diversity of viruses on Earth and highlighting the myriad of ways by which viruses impact biological processes. IMG/VR provides access to the largest collection of viral sequences obtained from (meta)genomes, along with functional annotation and rich metadata. A web interface enables users to efficiently browse and search viruses based on genome features and/or sequence similarity. Here, for this work, we present the fourth version of IMG/VR, composed of >15 million virus genomes and genome fragments, a ≈6-fold increase in size compared to the previous version. These clustered into 8.7 million viral operational taxonomic units, including 231 408 with at least one high-quality representative. Viral sequences in IMG/VR are now systematically identified from genomes, metagenomes, and metatranscriptomes using a new detection approach (geNomad), and IMG standard annotation are complemented with genome quality estimation using CheckV, taxonomic classification reflecting the latest taxonomic standards, and microbial host taxonomy prediction. IMG/VR v4 is available at https://img.jgi.doe.gov/vr, and the underlying data are available to download at https://genome.jgi.doe.gov/portal/IMG_VR.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

MolViewSpec: a Mol* extension for describing and sharing molecular visualizations

Data visualization is a pivotal component of a structural biologist’s arsenal. The Mol* Viewer makes molecular visualizations available to broader audiences via most web browsers. While Mol* provides a wide range of functionality, it has a steep learning curve and is only available via a JavaScript interface. To enhance the accessibility and usability of web-based molecular visualization, we introduce MolViewSpec (molstar.org/mol-view-spec), a standardized approach for defining molecular visualizations that decouples the definition of complex molecular scenes from their rendering. Scene definition can include references to commonly used structural, volumetric, and annotation data formats together with a description of how the data should be visualized and paired with optional annotations specifying colors, labels, measurements, and custom 3D geometries. Developed as an open standard, this solution paves the way for broader interoperability and support across different programming languages and molecular viewers, enabling more streamlined, standardized, and reproducible visual molecular analyses. MolViewSpec is freely available as a Mol* extension and a standalone Python package.

Midlik, Adam [European Bioinformatics Institute (U↗
DOE OSTI2022

The Chlamydomonas Genome Project, version 6: reference assemblies for mating type plus and minus strains reveal extensive structural mutation in the laboratory

Five versions of the Chlamydomonas reinhardtii reference genome have been produced over the last two decades. Here we present version 6, bringing significant advances in assembly quality and structural annotations. PacBio-based chromosome-level assemblies for two laboratory strains, CC-503 and CC-4532, provide resources for the plus and minus mating type alleles. We corrected major misassemblies in previous versions and validated our assemblies via linkage analyses. Contiguity increased over ten-fold and >80% of filled gaps are within genes. We used Iso-Seq and deep RNA-seq datasets to improve structural annotations, and updated gene symbols and textual annotation of functionally characterized genes via extensive manual curation. We discovered that the cell wall-less classical reference strain CC-503 exhibits genomic instability potentially caused by deletion of the helicase RECQ3, with major structural mutations identified that affect >100 genes. We therefore present the CC-4532 assembly as the primary reference, although this strain also carries unique structural mutations and is experiencing rapid proliferation of a Gypsy retrotransposon. We expect all laboratory strains to harbor gene-disrupting mutations, which should be considered when interpreting and comparing experimental results. Collectively, the resources presented here herald a new era of Chlamydomonas genomics and will provide the foundation for continued research in this important reference organism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Building an extensible cell wall

Abstract This article recounts, from my perspective of four decades in this field, evolving paradigms of primary cell wall structure and the mechanism of surface enlargement of growing cell walls. Updates of the structures, physical interactions, and roles of cellulose, xyloglucan, and pectins are presented. This leads to an example of how a conceptual depiction of wall structure can be translated into an explicit quantitative model based on molecular dynamics methods. Comparison of the model’s mechanical behavior with experimental results provides insights into the molecular basis of complex mechanical behaviors of primary cell wall and uncovers the dominant role of cellulose–cellulose interactions in forming a strong yet extensible network.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

A comparison of the Caulobacter NA1000 and K31 genomes reveals extensive genome rearrangements and differences in metabolic potential

The genus Caulobacter is found in a variety of habitats and is known for its ability to thrive in low-nutrient conditions. K31 is a novel Caulobacter isolate that has the ability to tolerate copper and chlorophenols, and can grow at 4°C with a doubling time of 40 h. K31 contains a 5.5 Mb chromosome that codes for more than 5500 proteins and two large plasmids (234 and 178 kb) that code for 438 additional proteins. A comparison of the K31 and the Caulobacter crescentus NA1000 genomes revealed extensive rearrangements of gene order, suggesting that the genomes had been randomly scrambled. However, a careful analysis revealed that the distance from the origin of replication was conserved for the majority of the genes and that many of the rearrangements involved inversions that included the origin of replication. On a finer scale, numerous small indels were observed. K31 proteins involved in essential functions shared 80– 95% amino acid sequence identity with their C. crescentus homologues, while other homologue pairs tended to have lower levels of identity. In addition, the K31 chromosome contains more than 1600 genes with no homologue in NA1000.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Fast, differentiable, and extensible big bang nucleosynthesis package

Here, we introduce light isotope nucleosynthesis with JAX (LINX), a new differentiable public big bang nucleosynthesis code designed for fast parameter estimation. By leveraging JAX, LINX achieves both speed and differentiability, enabling the use of Bayesian inference, including gradient-based methods. We discuss the formalism used in LINX for rapid primordial elemental abundance predictions and give examples of how LINX can be used. When combined with differentiable cosmic microwave background power spectrum emulators, LINX can be used for joint cosmic microwave background and big bang nucleosynthesis analyses without requiring extensive computational resources, including on personal hardware.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Global description of $β$ – decay with the axially deformed Skyrme finite-amplitude method: Extension to odd-mass and odd-odd nuclei

Here we use the finite-amplitude method (FAM), an efficient implementation of the quasiparticle random phase approximation, to compute $β$-decay rates with Skyrme energy-density functionals for 3983 nuclei, essentially all the medium-mass and heavy isotopes on the neutron-rich side of stability. We employ an extension of the FAM that treats odd-mass and odd-odd nuclear ground states in the equal filling approximation. Our rates are in reasonable agreement both with experimental data where available and with rates from other global calculations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Pure quantum extension of the semiclassical Boltzmann-Uehling-Uhlenbeck equation

The Boltzmann equation is the traditional framework in which one extends the time-dependent mean field classical description of a many-body system to include the effect of particle-particle collisions in an approximate manner. A semiclassical extension of this approach to quantum many-body systems was suggested by Uehling and Uhlenbeck in 1933 for both Fermi and Bose statistics, and many further developments of this approach are known as the Boltzmann-Uehling-Uhlenbeck (BUU) equations. In this paper I introduce a pure quantum version of the BUU type of equations, which is mathematically equivalent to a generalized time-dependent density functional theory extended to superfluid systems. As expected, during nonequilibrium processes the quantum Boltzmann one-body entropy increases during evolution.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Anomalies in string-inspired nonlocal extensions of QED

We investigate anomalies in the class of nonlocal field theories that have been proposed as an ultraviolet completion of four-dimensional quantum field theory with generalizing the kinetic energy operators to an infinite series of higher derivatives inspired by the string field theory and ghost-free nonlocal approaches to quantum gravity. We explicitly calculate the vector and chiral anomalies in a string-inspired nonlocal extension of QED. We show that the vector anomaly vanishes as required by gauge invariance and the Ward identity. On the other hand, although the chiral anomaly vanishes to the leading order with massless fermions, it nonetheless does not vanish with the massive fermions and we calculate it to the leading order in the scale of nonlocality. We also calculate the nonlocal vector and axial currents explicitly and present an illustrative example by applying our results to the decay of π 0 → γ γ . Published by the American Physical Society 2024

Abu-Ajamieh, Fayez↗
DOE OSTI2017

Light sterile neutrinos, dark matter, and new resonances in a U ( 1 ) extension of the MSSM

We present $ψ$'MSSM, a model based on a $U(1)$ $ψ$' extension of the minimal supersymmetric standard model. The gauge symmetry $U(1)$ $ψ$' , also known as $U(1)$ $N$ , is a linear combination of the $U(1)$ $χ$ and $U(1)$ $ψ$ subgroups of $E$ 6 . The model predicts the existence of three sterile neutrinos with masses ≲ 0.1 eV, if the $U(1)$ $ψ$' breaking scale is of order 10 TeV. Their contribution to the effective number of neutrinos at nucleosynthesis is $ΔN$ $ν$ ≃ 0.29. The model can provide a variety of possible cold dark matter candidates including the lightest sterile sneutrino. If the $U(1)$ $ψ$' breaking scale is increased to 10 3 TeV, the sterile neutrinos, which are stable on account of a $Z$ 2 symmetry, become viable warm dark matter candidates. The observed value of the standard model Higgs boson mass can be obtained with relatively light stop quarks thanks to the D-term contribution from $U(1)$ $ψ$' . The model predicts diquark and diphoton resonances which may be found at an updated LHC. The well-known $µ$ problem is resolved, and the observed baryon asymmetry of the universe can be generated via leptogenesis. The breaking of $U(1)$ $ψ'$ produces superconducting strings that may be present in our galaxy. In conclusion, a $U(1)$ R symmetry plays a key role in keeping the proton stable and providing the light sterile neutrinos.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Freely jointed chain models with extensible links

We report analytical relations for the mechanical response of single polymer chains are valuable for modeling purposes, on both the molecular and the continuum scale. These relations can be obtained using statistical thermodynamics and an idealized single-chain model, such as the freely jointed chain model. To include bond stretching, the rigid links in the freely jointed chain model can be made extensible, but this almost always renders the model analytically intractable. Here, an asymptotically correct statistical thermodynamic theory is used to develop analytic approximations for the single-chain mechanical response of this model. The accuracy of these approximations is demonstrated using several link potential energy functions. This approach can be applied to other single-chain models, and to molecular stretching in general.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Black Holes in an Effective Field Theory Extension of General Relativity

Effective field theory methods suggest that some rather general extensions of general relativity include, or are mimicked by, certain higher-order curvature corrections, with coupling constants expected to be small but otherwise arbitrary. Thus, the tantalizing prospect to test the fundamental nature of gravity with gravitational-wave observations, in a systematic way, emerges naturally. Here, we build black hole solutions in such a framework and study their main properties. Once rotation is included, we find the first purely gravitational example of geometries without Z 2 symmetry. Despite the higher-order operators of the theory, we show that linearized fluctuations of such geometries obey second-order differential equations. We find nonzero tidal Love numbers. We study and compute the quasinormal modes of such geometries. These results are of interest to gravitational-wave science but also potentially relevant for electromagnetic observations of the galactic center or x-ray binaries.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Denoising and Extension of Response Functions in the Time Domain

Response functions of quantum systems, such as electron Green’s functions, magnetic, or charge susceptibilities, describe the response of a system to an external perturbation. They are the central objects of interest in field theories and quantum computing and measured directly in experiment. Further, response functions are intrinsically causal. In equilibrium and steady-state systems, they correspond to a positive spectral function in the frequency domain. Since response functions define an inner product on a Hilbert space and thereby induce a positive definite function, the properties of this function can be used to reduce noise in measured data and, in equilibrium and steady state, to construct positive definite extensions for data known on finite time intervals, which are then guaranteed to correspond to positive spectra.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Extension of the sasCIF format and its applications for data processing and deposition

Recent advances in small-angle scattering (SAS) experimental facilities and data analysis methods have prompted a dramatic increase in the number of users and of projects conducted, causing an upsurge in the number of objects studied, experimental data available and structural models generated. To organize the data and models and make them accessible to the community, the Task Forces on SAS and hybrid methods for the International Union of Crystallography and the Worldwide Protein Data Bank envisage developing a federated approach to SAS data and model archiving. Within the framework of this approach, the existing databases may exchange information and provide independent but synchronized entries to users. At present, ways of exchanging information between the various SAS databases are not established, leading to possible duplication and incompatibility of entries, and limiting the opportunities for data-driven research for SAS users. In this work, a solution is developed to resolve these issues and provide a universal exchange format for the community, based on the use of the widely adopted crystallographic information framework (CIF). The previous version of the sasCIF format, implemented as an extension of the core CIF dictionary, has been available since 2000 to facilitate SAS data exchange between laboratories. The sasCIF format has now been extended to describe comprehensively the necessary experimental information, results and models, including relevant metadata for SAS data analysis and for deposition into a database. Processing tools for these files ( sasCIFtools ) have been developed, and these are available both as standalone open-source programs and integrated into the SAS Biological Data Bank, allowing the export and import of data entries as sasCIF files. Software modules to save the relevant information directly from beamline data-processing pipelines in sasCIF format are also developed. Lastly, this update of sasCIF and the relevant tools are an important step in the standardization of the way SAS data are presented and exchanged, to make the results easily accessible to users and to promote further the application of SAS in the structural biology community.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2016

Atomic resolution experimental phase information reveals extensive disorder and bound 2-methyl-2,4-pentanediol in Ca 2+ -calmodulin

Calmodulin (CaM) is the primary calcium signaling protein in eukaryotes and has been extensively studied using various biophysical techniques. Prior crystal structures have noted the presence of ambiguous electron density in both hydrophobic binding pockets of Ca 2+ -CaM, but no assignment of these features has been made. In addition, Ca 2+ -CaM samples many conformational substates in the crystal and accurately modeling the full range of this functionally important disorder is challenging. In order to characterize these features in a minimally biased manner, a 1.0 Å resolution single-wavelength anomalous diffraction data set was measured for selenomethionine-substituted Ca 2+ -CaM. Density-modified electron-density maps enabled the accurate assignment of Ca 2+ -CaM main-chain and side-chain disorder. These experimental maps also substantiate complex disorder models that were automatically built using low-contour features of model-phased electron density. Furthermore, experimental electron-density maps reveal that 2-methyl-2,4-pentanediol (MPD) is present in the C-terminal domain, mediates a lattice contact between N-terminal domains and may occupy the N-terminal binding pocket. The majority of the crystal structures of target-free Ca 2+ -CaM have been derived from crystals grown using MPD as a precipitant, and thus MPD is likely to be bound in functionally critical regions of Ca 2+ -CaM in most of these structures. The adventitious binding of MPD helps to explain differences between the Ca 2+ -CaM crystal and solution structures and is likely to favor more open conformations of the EF-hands in the crystal.

Lin, Jiusheng↗
DOE OSTI2018

Skluma: An extensible metadata extraction pipeline for disorganized data

To mitigate the effects of high-velocity data expansion and to automate the organization of filesystems and data repositories, we have developed Skluma-a system that automatically processes a target filesystem or repository, extracts content-and context-based metadata, and organizes extracted metadata for subsequent use. Skluma is able to extract diverse metadata, including aggregate values derived from embedded structured data; named entities and latent topics buried within free-text documents; and content encoded in images. Skluma implements an overarching probabilistic pipeline to extract increasingly specific metadata from files. It applies machine learning methods to determine file types, dynamically prioritizes and then executes a suite of metadata extractors, and explores contextual metadata based on relationships among files. The derived metadata, represented in JSON, describes probabilistic knowledge of each file that may be subsequently used for discovery or organization. Skluma's architecture enables it to be deployed both locally and used as an on-demand, cloud-hosted service to create and execute dynamic extraction workflows on massive numbers of files. It is modular and extensible-allowing users to contribute their own specialized metadata extractors. Thus far we have tested Skluma on local filesystems, remote FTP-accessible servers, and publicly-accessible Globus endpoints. We have demonstrated its efficacy by applying it to a scientific environmental data repository of more than 500,000 files. We show that we can extract metadata from those files with modest cloud costs in a few hours.

data swamp↗
DOE OSTI2021

Phasor Based Control with the Distributed, Extensible Grid Control Platform

This paper describes how to implement Phasor Based Control (PBC) using the Distributed, Extensible Grid Control (DEGC) Platform. PBC is a novel method for controlling distributed energy resources (DER) that coordinates a centralized optimization with distributed feedback controllers to enforce voltage phasor targets. DEGC is an open source software and communication platform designed for general DER control. We deployed PBC at Lawrence Berkeley Lab's FLEXLAB test site, conducting multiple hardware-in-the-loop test runs. Here, we describe how DEGC was used to implement PBC on hardware, and results demonstrating successful deployment.

24 POWER TRANSMISSION AND DISTRIBUTION↗