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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 1,477 records · Page 82
All sourcesNASA NTRSDOE OSTI
NASA NTRS1993

The methodology of multi-viewpoint clustering analysis

One of the greatest challenges facing the software engineering community is the ability to produce large and complex computer systems, such as ground support systems for unmanned scientific missions, that are reliable and cost effective. In order to build and maintain these systems, it is important that the knowledge in the system be suitably abstracted, structured, and otherwise clustered in a manner which facilitates its understanding, manipulation, testing, and utilization. Development of complex mission-critical systems will require the ability to abstract overall concepts in the system at various levels of detail and to consider the system from different points of view. Multi-ViewPoint - Clustering Analysis MVP-CA methodology has been developed to provide multiple views of large, complicated systems. MVP-CA provides an ability to discover significant structures by providing an automated mechanism to structure both hierarchically (from detail to abstract) and orthogonally (from different perspectives). We propose to integrate MVP/CA into an overall software engineering life cycle to support the development and evolution of complex mission critical systems.

Mehrotra, Mala↗
DOE OSTI2023

RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure models of proteins

Recent advances in Artificial Intelligence and Machine Learning (e.g., AlphaFold, RosettaFold, and ESMFold) enable prediction of three-dimensional (3D) protein structures from amino acid sequences alone at accuracies comparable to lower-resolution experimental methods. These tools have been employed to predict structures across entire proteomes and the results of large-scale metagenomic sequence studies, yielding an exponential increase in available biomolecular 3D structural information. Given the enormous volume of this newly computed biostructure data, there is an urgent need for robust tools to manage, search, cluster, and visualize large collections of structures. Equally important is the capability to efficiently summarize and visualize metadata, biological/biochemical annotations, and structural features, particularly when working with vast numbers of protein structures of both experimental origin from the Protein Data Bank (PDB) and computationally-predicted models. Moreover, researchers require advanced visualization techniques that support interactive exploration of multiple sequences and structural alignments. This paper introduces a suite of tools provided on the RCSB PDB research-focused web portal RCSB. org, tailor-made for efficient management, search, organization, and visualization of this burgeoning corpus of 3D macromolecular structure data.

3D visualization↗
DOE OSTI2017

Diazotroph Community Characterization via a High-Throughput nifH Amplicon Sequencing and Analysis Pipeline

The dinitrogenase reductase gene ( nifH ) is the most widely established molecular marker for the study of nitrogen-fixing prokaryotes in nature. A large number of PCR primer sets have been developed for nifH amplification, and the effective deployment of these approaches should be guided by a rapid, easy-to-use analysis protocol. Bioinformatic analysis of marker gene sequences also requires considerable expertise. In this study, we advance the state of the art for nifH analysis by evaluating nifH primer set performance, developing an improved amplicon sequencing workflow, and implementing a user-friendly bioinformatics pipeline. Furthermore, the developed amplicon sequencing workflow is a three-stage PCR-based approach that uses established technologies for incorporating sample-specific barcode sequences and sequencing adapters. Based on our primer evaluation, we recommend the Ando primer set be used with a modified annealing temperature of 58°C, as this approach captured the largest diversity of nifH templates, including paralog cluster IV/V sequences. To improve nifH sequence analysis, we developed a computational pipeline which infers taxonomy and optionally filters out paralog sequences. In addition, we employed an empirical model to derive optimal operational taxonomic unit (OTU) cutoffs for the nifH gene at the species, genus, and family levels. A comprehensive workflow script named TaxADivA (TAXonomy Assignment and DIVersity Assessment) is provided to ease processing and analysis of nifH amplicons. Our approach is then validated through characterization of diazotroph communities across environmental gradients in beach sands impacted by the Deepwater Horizon oil spill in the Gulf of Mexico, in a peat moss-dominated wetland, and in various plant compartments of a sugarcane field. IMPORTANCE: Nitrogen availability often limits ecosystem productivity, and nitrogen fixation, exclusive to prokaryotes, comprises a major source of nitrogen input that sustains food webs. The nifH gene, which codes for the iron protein of the nitrogenase enzyme, is the most widely established molecular marker for the study of nitrogen-fixing microorganisms (diazotrophs) in nature. In this study, a flexible sequencing/analysis pipeline, named TaxADivA, was developed for nifH amplicons produced by Illumina paired-end sequencing, and it enables an inference of taxonomy, performs clustering, and produces output in formats that may be used by programs that facilitate data exploration and analysis. Diazotroph diversity and community composition are linked to ecosystem functioning, and our results advance the phylogenetic characterization of diazotroph communities by providing empirically derived nifH similarity cutoffs for species, genus, and family levels. Thus, the utility of our pipeline is validated for diazotroph communities in a variety of ecosystems, including contaminated beach sands, peatland ecosystems, living plant tissues, and rhizosphere soil.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2006

Reconfigurable Software for Controlling Formation Flying

Software for a system to control the trajectories of multiple spacecraft flying in formation is being developed to reflect underlying concepts of (1) a decentralized approach to guidance and control and (2) reconfigurability of the control system, including reconfigurability of the software and of control laws. The software is organized as a modular network of software tasks. The computational load for both determining relative trajectories and planning maneuvers is shared equally among all spacecraft in a cluster. The flexibility and robustness of the software are apparent in the fact that tasks can be added, removed, or replaced during flight. In a computational simulation of a representative formation-flying scenario, it was demonstrated that the following are among the services performed by the software: Uploading of commands from a ground station and distribution of the commands among the spacecraft, Autonomous initiation and reconfiguration of formations, Autonomous formation of teams through negotiations among the spacecraft, Working out details of high-level commands (e.g., shapes and sizes of geometrically complex formations), Implementation of a distributed guidance law providing autonomous optimization and assignment of target states, and Implementation of a decentralized, fuel-optimal, impulsive control law for planning maneuvers.

Mueller, Joseph B.↗
NASA NTRS1998

NCSTRL+: Adding Multi-Discipline and Multi-Genre Support to the Dienst Protocol Using Clusters and Buckets

We describe NCSTRL+, a unified, canonical digital library for scientific and technical information (STI). NCSTRL+ is based on the Networked Computer Science Technical Report Library (NCSTRL), a World Wide Web (WWW) accessible digital library (DL) that provides access to over 100 university departments and laboratories. NCSTRL+ implements two new technologies: cluster functionality and publishing buckets. We have extended Dienst, the protocol underlying NCSTRL, to provide the ability to cluster independent collections into a logically centralized digital library based upon subject category classification, type of organization, and genres of material. The bucket construct provides a mechanism for publishing and managing logically linked entities with multiple data forms as a single object. The NCSTRL+ prototype DL contains the holdings of NCSTRL and the NASA Technical Report Server (NTRS). The prototype demonstrates the feasibility of publishing into a multi-cluster DL, searching across clusters, and storing and presenting buckets of information.

Nelson, Michael L.↗
DOE OSTI2016

Probing electronic wave functions of sodium-doped clusters: Dyson orbitals, anisotropy parameters, and ionization cross-sections

We apply high-level ab initio methods to describe the electronic structure of small clusters of ammonia and dimethylether (DME) doped with sodium, which provide a model for solvated electrons. We investigate the effect of the solvent and cluster size on the electronic states. We consider both energies and properties, with a focus on the shape of the electronic wave function and the related experimental observables such as photoelectron angular distributions. The central quantity in modeling photoionization experiments is the Dyson orbital, which describes the difference between the initial N-electron and final (N-1)-electron states of a system. Dyson orbitals enter the expression of the photoelectron matrix element, which determines total and partial photoionization cross-sections. We compute Dyson orbitals for the Na(NH3)n and Na(DME)m clusters using correlated wave functions (obtained with equation-of-motion coupled-cluster model for electron attachment with single and double substitutions) and compare them with more approximate Hartree-Fock and Kohn-Sham orbitals. As a result, we also analyze the effect of correlation and basis sets on the shapes of Dyson orbitals and the experimental observables.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

The W40 region in the gould belt: An embedded cluster and H II region at the junction of filaments

We present a multiwavelength study of the W40 star-forming region using infrared (IR) observations in the UKIRT JHK bands, Spitzer Infrared Array Camera bands, and Herschel PACS bands, 2.12 μm H{sub 2} narrowband imaging, and radio continuum observations from GMRT (610 and 1280 MHz), in a field of view (FoV) of ∼34' × 40'. Archival Spitzer observations in conjunction with near-IR observations are used to identify 1162 Class II/III and 40 Class I sources in the FoV. The nearest-neighbor stellar surface density analysis shows that the majority of these young stellar objects (YSOs) constitute the embedded cluster centered on the high-mass source IRS 1A South. Some YSOs, predominantly the younger population, are distributed along and trace the filamentary structures at lower stellar surface density. The cluster radius is measured to be 0.44 pc—matching well with the extent of radio emission—with a peak density of 650 pc{sup –2}. The JHK data are used to map the extinction in the region, which is subsequently used to compute the cloud mass—126 M {sub ☉} and 71 M {sub ☉} for the central cluster and the northern IRS 5 region, respectively. H{sub 2} narrowband imaging shows significant emission, which prominently resembles fluorescent emission arising at the borders of dense regions. Radio continuum analysis shows that this region has a blister morphology, with the radio peak coinciding with a protostellar source. Free-free emission spectral energy distribution analysis is used to obtain physical parameters of the overall photoionized region and the IRS 5 sub-region. This multiwavelength scenario is suggestive of star formation having resulted from the merging of multiple filaments to form a hub. Star formation seems to have taken place in two successive epochs, with the first epoch traced by the central cluster and the high-mass star(s)—followed by a second epoch that is spreading into the filaments as uncovered by the Class I sources and even younger protostellar sources along the filaments. The IRS 5 H II region displays indications of swept-up material that has possibly led to the formation of protostars.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Preparing NERSC users for Cori, a Cray XC40 system with Intel many integrated cores

The newest NERSC supercomputer Cori is a Cray XC40 system consisting of 2,388 Intel Xeon Haswell nodes and 9,688 Intel Xeon-Phi “Knights Landing” (KNL) nodes. Compared to the Xeon-based clusters NERSC users are familiar with, optimal performance on Cori requires consideration of KNL mode settings; process, thread, and memory affinity; fine-grain parallelization; vectorization; and use of the high-bandwidth MCDRAM memory. This paper describes our efforts preparing NERSC users for KNL through the NERSC Exascale Science Application Program, Web documentation, and user training. We discuss how we configured the Cori system for usability and productivity, addressing programming concerns, batch system configurations, and default KNL cluster and memory modes. Here, system usage data, job completion analysis, programming and running jobs issues, and a few successful user stories on KNL are presented.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2013

PULSATING B-TYPE STARS IN THE OPEN CLUSTER NGC 884: FREQUENCIES, MODE IDENTIFICATION, AND ASTEROSEISMOLOGY

Recent progress in the seismic interpretation of field β Cep stars has resulted in improvements of the physical description in the stellar structure and evolution model computations of massive stars. Further asteroseismic constraints can be obtained from studying ensembles of stars in a young open cluster, which all have similar age, distance, and chemical composition. We present an observational asteroseismology study based on the discovery of numerous multi-periodic and mono-periodic B stars in the open cluster NGC 884. We describe a thorough investigation of the pulsational properties of all B-type stars in the cluster. Overall, our detailed frequency analysis resulted in 115 detected frequencies in 65 stars. We found 36 mono-periodic, 16 bi-periodic, 10 tri-periodic, and 2 quadru-periodic stars and one star with nine independent frequencies. We also derived the amplitudes and phases of all detected frequencies in the U, B, V, and I filter, if available. We achieved unambiguous identifications of the mode degree for 12 of the detected frequencies in nine of the pulsators. Imposing the identified degrees and measured frequencies of the radial, dipole, and quadrupole modes of five pulsators led to a seismic cluster age estimate of log (age/yr) = 7.12-7.28 from a comparison with stellar models. Our study is a proof-of-concept for and illustrates the current status of ensemble asteroseismology of a young open cluster.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Surface-supported cluster catalysis: Ensembles of metastable states run the show

It has recently been demonstrated that the dynamic behaviour of surface-supported nanocluster catalysts in realistic reaction conditions defies conventional models used in catalysis. This opens new doors in catalysis by giving more leverage in catalyst design, but also requires a major revision of the understanding of how dynamic heterogeneous catalytic interfaces operate, as well as of the computational approaches of catalyst modelling, and experimental methods of catalyst characterization. Key aspects of the new paradigm include the collective action of many catalyst states that form a statistical ensemble in reacting conditions, the catalytic activity and selectivity being driven by rare and metastable catalyst states, reaction thermodynamics and kinetics being controlled by different states of the catalyst, broken scaling relationships, non-Arrhenius behaviours, and catalyst dynamic restructuring being an essential part of the reaction mechanism. For computation, this complexity means the departure from the standard DFT calculations of reaction mechanisms on a single catalyst structure. For experiment, it calls for the development of operando characterization tools with the per-site resolution and the ability to find the minority sites that govern the catalytic activity. For catalyst design, the goal becomes the creation of the catalyst state (geometric and electronic) that might not be present in the as-prepared catalyst, but would develop in the reaction conditions and would have the desired activity then. While cluster catalysts are the most dramatic in their dynamic fluxionality, other amorphous interfaces also exhibit some of it, and thus are also subject to similar paradigm revision.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Computing the dipole polarizability of Ca 48 with increased precision

Here, we compute the electric dipole polarizability of 48 Ca with an increased precision by including more correlations than in previous studies. Employing the coupled-cluster method we go beyond single and double excitations and include leading-order three-particle-three-hole (3p-3h) excitations for the ground state, excited states, and the similarity-transformed operator. We study electromagnetic sum rules, such as the bremsstrahlung sum rule m 0 and the polarizability sum rule αD using interactions from chiral effective field theory. To gauge the quality of our coupled-cluster approximations we perform several benchmarks with the effective interaction hyperspherical harmonics approach in 4 He and with self consistent Green's function in 16 O. We compute the dipole polarizability of 48 Ca employing the chiral interaction N 2 LO sat and the 1.8/2.0 (EM). We find that the effect of 3p-3h excitations in the ground state is small for 1.8/2.0 (EM) but non-negligible for N 2 LO sat . The addition of these new correlations allows us to improve the precision of our 48 Ca calculations and reconcile the recently reported discrepancy between coupled-cluster results based on these interactions and the experimentally determined αD from proton inelastic scattering in 48 Ca. For the computation of electromagnetic and polarizability sum rules, the inclusion of leading-order 3p-3h excitations in the ground state is important, while it is less so for the excited states and the similarity-transformed dipole operator.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Linear-scaling quadruple excitations in local pair natural orbital coupled-cluster theory

Here, we present a fast, asymptotically linear-scaling implementation of the perturbative quadruples energy correction in coupled-cluster theory using local natural orbitals. Our work follows the domain-based local pair natural orbital (DLPNO) approach previously applied to lower levels of excitations in coupled-cluster theory. Our DLPNO-CCSDT(Q) algorithm uses converged doubles and triples amplitudes from a preceding DLPNO-CCSDT computation to compute the quadruples amplitude and energy in the quadruples natural orbital (QNO) basis. We demonstrate the compactness of the QNO space, showing that more than 95% of the (Q) correction can be recovered using relatively loose natural orbital cutoffs, compared to the tighter cutoffs used in pair and triples natural orbitals at lower levels of coupled-cluster theory. We also highlight the accuracy of our algorithm in the computation of relative energies, which yields deviations of sub-kJ mol −1 in relative energy compared to the canonical CCSDT(Q). Timings are conducted on a series of growing linear alkanes (up to 10 carbons and 608 basis functions) and water clusters (up to 49 water molecules and 2842 basis functions) to establish the asymptotic linear-scaling of our DLPNO-(Q) algorithm.

Auxiliary functions↗
DOE OSTI2018

Detecting Anomalies from End-to-End Internet Performance Measurements (PingER) Using Cluster Based Local Outlier Factor

PingER (Ping End-to-End Reporting) is a worldwide end-to-end Internet performance measurement framework. It was developed by the SLAC National Accelerator Laboratory, Stanford, USA and running from the last 20 years. It has more than 700 monitoring agents and remote sites which monitor the performance of Internet links around 170 countries of the world. At present, the size of the compressed PingER data set is about 60 GB comprising of 100,000 flat files. The data is publicly available for valuable Internet performance analyses. However, the data sets suffer from missing values and anomalies due to congestion, bottleneck links, queuing overflow, network software misconfiguration, hardware failure, cable cuts, and social upheavals. Therefore, the objective of this paper is to detect such performance drops or spikes labeled as anomalies or outliers for the PingER data set. In the proposed approach, the raw text files of the data set are transformed into a PingER dimensional model. The missing values are imputed using the k-NN algorithm. The data is partitioned into similar instances using the k-means clustering algorithm. Afterward, clustering is integrated with the Local Outlier Factor (LOF) using the Cluster Based Local Outlier Factor (CBLOF) algorithm to detect the anomalies or outliers from the PingER data. Lastly, anomalies are further analyzed to identify the time frame and location of the hosts generating the major percentage of the anomalies in the PingER data set ranging from 1998 to 2016.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Clustering VoIP caller for SPIT identification

Abstract The number of unsolicited and advertisement telephony calls over traditional and Internet telephony has rapidly increased over recent few years. Every year, the telecommunication regulators, law enforcement agencies and telecommunication operators receive a very large number of complaints against these unsolicited, unwanted calls. These unwanted calls not only bring financial loss to the users of the telephony but also annoy them with unwanted ringing alerts. Therefore, it is important for the operators to block telephony spammers at the edge of the network so to gain trust of their customers. In this paper, we propose a novel spam detection system by incorporating different social network features for combating unwanted callers at the edge of the network. To this extent the reputation of each caller is computed by processing call detailed records of user using three social network features that are the frequency of the calls between caller and the callee, the duration between caller and the callee and the number of outgoing partners associated with the caller. Once the reputation of the caller is computed, the caller is then places in a spam and non‐spam clusters using unsupervised machine learning. The performance of the proposed approach is evaluated using a synthetic dataset generated by simulating the social behaviour of the spammers and the non‐spammers. The evaluation results reveal that the proposed approach is highly effective in blocking spammer with 2% false positive rate under a large number of spammers. Moreover, the proposed approach does not require any change in the underlying VoIP network architecture, and also does not introduce any additional signalling delay in a call set‐up phase. Copyright © 2016 John Wiley & Sons, Ltd.

Azad, Muhammad Ajmal↗
DOE OSTI2021

Photoelectron Spectroscopic and ab Initio Computational Studies of the Anion, HThO –

The synergetic combination of anion photoelectron spectroscopy and high-level relativistic coupled-cluster calculations was employed to study the anion, HThO-. The atomic connectivity of this anion was found to be HThO- and not ThOH-. Vibrational and electronic energy spacings in the HThO- photoelectron spectrum were measured and calculated, with good agreement between them being found. Computations yielded electronic energies and equilibrium structures as well as enabling orbital analyses. The adiabatic electron affinity of HThO was determined to be 1.297 ± 0.035 eV.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

MemXCT: Design, Optimization, Scaling, and Reproducibility of X-Ray Tomography Imaging

Here, this work extends our previous research entitled "MemXCT: Memory-centric X-ray CT Reconstruction with Massive Parallelization" that was originally published at SC19 conference (Hidayetoglu et al., 2019) with reproducibility of the computational imaging performance. X-ray computed tomography (XCT) is regularly used at synchrotron light sources to study the internal morphology of materials at high resolution. However, experimental constraints, such as radiation sensitivity, can result in noisy or undersampled measurements. Further, depending on the resolution, sample size and data acquisition rates, the resulting noisy dataset can be in the order of terabytes. Advanced iterative reconstruction techniques can produce high-quality images from noisy measurements, but their computational requirements have made their use an exception rather than the rule. We propose a novel memory-centric approach that avoids redundant computations at the expense of additional memory complexity. We develop a memory-centric iterative reconstruction system, MemXCT, that uses an optimized SpMV implementation with two-level pseudo-Hilbert ordering and multi-stage input buffering. We evaluate MemXCT on various supercomputer architectures involving KNL and GPU. MemXCT can reconstruct a large (11Kx11K) mouse brain tomogram in 10 seconds using 4096 KNL nodes (256K cores). The results presented in our original article at the SC19 were based on large-scale supercomputing resources. The MemXCT application was selected for the Student Cluster Competition (SCC) Reproducibility Challenge and evaluated on a variety of cloud computing resources by universities around the world in the SC20 conference. We summarize the results of the top-ranked SCC Reproducibility Challenge teams and identify the most pertinent measures for ensuring the reproducibility of our experiments in this article.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Interpreting the Operando XANES of Surface-Supported Subnanometer Clusters: When Fluxionality, Oxidation State, and Size Effect Fight.

X-ray absorption near edge structure (XANES) spectroscopy is widely used for operando catalyst characterization. We show that, for highly fluxional supported nanoclusters, the customary extraction of the oxidation state of the metal from the XANES data by fitting to the bulk standards is highly questionable. The XANES signatures as well as the apparent oxidation state for such clusters arise from a complex combination of many factors, and not only from the chemical composition in reaction conditions (e.g., oxygen content in oxidizing atmosphere). The thermally accessible isomerization and population of several structurally distinct cluster forms, cluster-support interaction, and intrinsic size effects all impact the metal oxidation state and XANES signal. We demonstrate this on copper oxide clusters with different compositions, Cu4Ox(x = 2-5) and Cu5Oy (y = 3, 5), deposited on amorphous alumina and ultrananocrystalline diamond, for which we computed the XANES spectra and compare the results to the experiment. We show in addition that fitting the experimental spectrum to calculated spectra of supported clusters can, in contrast, provide good agreement and insight into the spectrum-composition-structure relation. Experimental XANES interpreted using the proposed fitting scheme shows the partial reduction of Cu oxide clusters at rising temperatures, and pinpoints the specific stoichiometries that dominate in the ensemble of cluster states as the temperature changes.

Zandkarimi, Borna↗
DOE OSTI2024

Electromagnetic observables of open-shell nuclei from coupled-cluster theory

Here we develop a new method to describe electromagnetic observables of open-shell nuclei with two nucleons outside a closed shell. This approach combines the equation-of-motion coupled-cluster method for such systems and the Lorentz integral transform technique, expanding the applicability of coupled-cluster theory for electromagnetic observables beyond closed-(sub)shell nuclei. To validate this new approach, we compute the non-energy-weighted dipole sum rule and the dipole polarizability of 16,24 ⁢O in both the closed-(sub)shell and the new equation-of-motion coupled-cluster frameworks, finding agreement within error bars. We then analyze the evolution of the dipole polarizability along the oxygen and calcium isotopic chains. Our predictions agree well with available experimental data and other available theoretical calculations for the closed-(sub)shell 16,22 ⁢O and the open-shell 18 O. In the calcium isotopes, we observe that our dipole polarizability predictions for open-shell nuclei are lower than those of closed-(sub)shell nuclei. We expect that our predictions for 24 O and 54,56 ⁢Ca will motivate future experimental studies at the drip line.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗