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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 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Kraken2 Metagenomic Virus Database

The Database: Kraken2 [1] database built from a classification tree containing over 700k metagenomic viruses from JGI IMG/VR [2]. (1) Wood, D. E., Lu, J., and Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome Biol., 20(1), 1–13. doi: 10.1186/s13059-019-1891-0 (2) Paez-Espino D, Chen I-MA, Palaniappan K, Ratner A, Chu K, Szeto E, et al. IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. Nucleic Acids Res. 2017;45:D457-65. For Paper: Title: A k-mer based approach for virus classification in metatranscriptomic and metagenomic samples identifies viral associations in the Populus phytobiome and autism brains Abstract Background Viruses are an underrepresented taxa in the study and identification of microbiome constituents; however, they play an important role in health, microbiome regulation, and transfer of genetic material. Only a few thousand viruses have been isolated, sequenced, and assigned a taxonomy, which further limits the ability to identify and quantify viruses in the microbiome. Additionally, the vast diversity of viruses represents a challenge for classification, not only in constructing a viral taxonomy, but also in identifying similarities between a virus' genotype and its phenotype. However, the diversity of viral sequences can be leveraged to classify their sequences in metagenomic and metatranscriptomic samples. Methods To identify viruses in transcriptomic and genomic samples, we developed a dynamic programming algorithm for creating a classification tree out of 715,672 metagenome viruses. To create the classification tree, we clustered proportional similarity scores generated from the k-mer profiles of each of the metagenome viruses. We then integrated the viral classification tree with the NCBI taxonomy for use with ParaKraken, a metagenomic/transcriptomic classifier. Results To illustrate the breadth of our utility for classifying viruses with ParaKraken, we analyzed data from a plant metagenome study identifying the differences between two Populus genotypes in three different compartments and on a human metatranscriptome study identifying the differences between Autism Spectrum Disorder patients and controls in post mortem brain biopsies. In the Populus study, we identified genotype and compartment specific viral signatures, while in the Autism study we identified a significant increased abundance of eight viral sequences in Autism brain biopsies. Conclusion Viruses represent an important aspect of the microbiome. The ability to classify viruses represents the first step in being able to better understand their role in the microbiome. The viral classification method presented here allows for more complete identification of viral sequences for use in identifying associations between viruses and the host and viruses and other microbiome members. Acknowledgements and Funding This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725. This research was also supported by the Plant-Microbe Interfaces Scientific Focus Area in the Genomic Science Program, the Office of Biological and Environmental Research (BER) in the U.S. Department of Energy Office of Science, and by the Department of Energy, Laboratory Directed Research and Development funding (ProjectID 8321), at the Oak Ridge National Laboratory. Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the US DOE under contract DE-AC05-00OR22725. This research used resources of the Compute and Data Environment for Science (CADES).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

A Simplified Multi-Path Event Tree for the Integral, Inherently-Safe Light Water Reactor (I{sup 2}S-LWR)

The Integral, Inherently-Safe Light Water Reactor (I{sup 2}S-LWR) concept aims to raise the bar for nuclear power plant safety while maintaining the economic advantages of large, gigawatt-scale plants.1 To obtain this goal, the project safety team seeks to eliminate initiating events where possible, maximize passivity of safety systems, and optimize a balance of redundancy, diversity, and simplicity of safety systems.2 Achievement of these objectives, particularly the last set, requires detailed, quantitative risk information from the earliest stages of development. Therefore, despite limited design information, we have constructed a preliminary probabilistic risk assessment (PRA) for I{sup 2}S-LWR. Safety implementation for I{sup 2}S-LWR, then, requires an iterative process involving system design, thermal-hydraulic (T/H) and neutronic deterministic analyses, and risk-informing PRA studies. Due to this parallelism, it is vital those team members without PRA expertise quickly and correctly understand preliminary PRA results. To this end, we have developed a method to condense the entire PRA into a single, multi-path event tree (MPET). (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2018

A subleading power operator basis for the scalar quark current

Factorization theorems play a crucial role in our understanding of the strong interaction. For collider processes they are typically formulated at leading power and much less is known about power corrections in the λ << 1 expansion. Here we present a complete basis of power suppressed operators for a scalar quark current at O(λ 2 ) in the amplitude level power expansion in the Soft Collinear Effective Theory, demonstrating that helicity selection rules significantly simplify the construction. This basis applies for the production of any color singlet scalar in qq¯¯ annihilation (such as bb¯¯→H ). We also classify all operators which contribute to the cross section at O(λ 2 ) and perform matching calculations to determine their tree level Wilson coefficients. Furthermore, these results can be exploited to study power corrections in both resummed and fixed order perturbation theory, and for analyzing the factorization properties of gauge theory amplitudes and cross sections at subleading power.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Recovery of Rare Earth Elements (REEs) from Coal Mine Drainage, Phase 2

Phase 1 research identified a two-step refining train, acid leaching of AMD precipitate feed followed by solvent extraction (SX), to produce a 2% TREE product. For the Phase 2 bench scale system, the objective was to get the acid leaching step to operate in batch-mode with sufficient storage capacity to feed an aqueous, enriched REE liquor to a pilot SX plant operating in continuous-mode at a feed rate capable of producing 3 g/hr 2% TREE. Important process variables included feed rate, extractant makeup, flowsheet configuration, and stripping conditions. Operating parameters were optimized through a feedback-capable SCADA system configured for the SX bench scale plant. These conditions were met and exceeded. TREE grades approaching 90% were produced while our Techno-Economic Assessment indicated highly favorable economic returns. The project led to the design of a pilot facility for producing roughly 500 kg/TREE/year. That plant is now in the procurement stage with constructed expected to begin in late 2020.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2020

Recovery of Rare Earth Elements (REEs) from Coal Mine Drainage, Phase 2

Phase 1 research identified a two-step refining train, acid leaching of AMD precipitate feed followed by solvent extraction (SX), to produce a 2% TREE product. For the Phase 2 bench scale system, the objective was to get the acid leaching step to operate in batch-mode with sufficient storage capacity to feed an aqueous, enriched REE liquor to a pilot SX plant operating in continuous-mode at a feed rate capable of producing 3 g/hr 2% TREE. Important process variables included feed rate, extractant makeup, flowsheet configuration, and stripping conditions. Operating parameters were optimized through a feedback-capable SCADA system configured for the SX bench scale plant. These conditions were met and exceeded. TREE grades approaching 90% were produced while our Techno-Economic Assessment indicated highly favorable economic returns. The project led to the design of a pilot facility for producing roughly 500 kg/TREE/year. That plant is now in the procurement stage with constructed expected to begin in late 2020.

01 COAL, LIGNITE, AND PEAT↗
NASA NTRS1992

Recognition and characterization of hierarchical interstellar structure. II - Structure tree statistics

A new method of image analysis is described, in which images partitioned into 'clouds' are represented by simplified skeleton images, called structure trees, that preserve the spatial relations of the component clouds while disregarding information concerning their sizes and shapes. The method can be used to discriminate between images of projected hierarchical (multiply nested) and random three-dimensional simulated collections of clouds constructed on the basis of observed interstellar properties, and even intermediate systems formed by combining random and hierarchical simulations. For a given structure type, the method can distinguish between different subclasses of models with different parameters and reliably estimate their hierarchical parameters: average number of children per parent, scale reduction factor per level of hierarchy, density contrast, and number of resolved levels. An application to a column density image of the Taurus complex constructed from IRAS data is given. Moderately strong evidence for a hierarchical structural component is found, and parameters of the hierarchy, as well as the average volume filling factor and mass efficiency of fragmentation per level of hierarchy, are estimated. The existence of nested structure contradicts models in which large molecular clouds are supposed to fragment, in a single stage, into roughly stellar-mass cores.

Houlahan, Padraig↗
NASA NTRS2003

Subauditory Speech Recognition based on EMG/EPG Signals

Sub-vocal electromyogram/electro palatogram (EMG/EPG) signal classification is demonstrated as a method for silent speech recognition. Recorded electrode signals from the larynx and sublingual areas below the jaw are noise filtered and transformed into features using complex dual quad tree wavelet transforms. Feature sets for six sub-vocally pronounced words are trained using a trust region scaled conjugate gradient neural network. Real time signals for previously unseen patterns are classified into categories suitable for primitive control of graphic objects. Feature construction, recognition accuracy and an approach for extension of the technique to a variety of real world application areas are presented.

Jorgensen, Charles↗
DOE OSTI2025

The Analysis Description Language Ecosystem: Latest developments and physics applications

We present latest developments in Analysis Description Language (ADL), a declarative domain-specific language describing the physics algorithm of a HEP data analysis decoupled from software frameworks. Analyses written in ADL can be integrated into any framework for various tasks. ADL is a multipurpose construct with uses ranging from analysis design to preservation, reinterpretation, queries, visualisation, combination, etc. The most advanced infrastructure to execute ADL on events is the CutLang runtime interpreter. Recent technical developments include an automated interface with different data types, generation of the abstract syntax tree, a visualization tool that that auto-converts analysis flows to graphs, incorporation of trained machine learning models and a Jupyter-based plotting tool. We also report physics implications including a large scale LHC analysis implementation and validation effort for beyond the standard model reinterpretation purposes and studies with ATLAS and CMS open data.

Sekmen, Sezen [Kyungpook National Univ., Daegu (Ko↗
DOE OSTI2021

The Last Journey. II. SMACC—Subhalo Mass-loss Analysis Using Core Catalogs

Here we introduce Subhalo Mass-loss Analysis using Core Catalogs (SMACC). SMACC adds a mass model to substructure merger trees based on halo "core tracking." Our approach avoids the need for running expensive subhalo finding algorithms and instead uses subhalo mass-loss modeling to assign masses to halo cores. We present details of the SMACC methodology and demonstrate its excellent performance in describing halo substructure and its evolution. Validation of the approach is carried out using cosmological simulations at significantly different resolutions. We apply SMACC to the 1.24-trillion-particle Last Journey simulation and construct core catalogs with the additional mass information. These catalogs can be readily used as input to semianalytic models or subhalo abundance matching approaches to determine approximate galaxy distributions, as well as for in-depth studies of small-scale structure evolution.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS2020

Mapping tall shrub biomass in Alaska at landscape scale using structure-from-motion photogrammetry and lidar

Warming in arctic and boreal regions is increasing shrub cover and biomass. In southcentral Alaska, willow (Salix spp.) and alder (Alnus spp.) shrubs grow taller than many tree species and account for a substantial proportion of aboveground biomass, yet they are not individually measured as part of the operational Forest Inventory and Analysis (FIA) Program. The goal of this research was to test methods for landscape-scale mapping of tall shrub biomass in upper montane and subalpine environments using FIA-type plot measurements (n = 51) and predictor variables from imagery-based structure-from-motion (SfM) and airborne lidar. Specifically, we compared biomass models constructed from imagery acquired by unmanned aerial vehicle (UAV; ~1.7 cm pixels), imagery from the NASA Goddard's Lidar, Hyperspectral, and Thermal Airborne Imager (G-LiHT; ~3.1 cm pixels), and concomitant G-LiHT small-footprint lidar. Tall shrub biomass was most accurately predicted at 5 m resolution (R^2 = 0.81, RMSE = 1.09 kg/sq. m) using G-LiHT SfM color and structure variables. Lidar-only models had lower precision (R^2 = 0.74, RMSE = 1.26 kg/sq. m), possibly due to reduced model information content from variable multicollinearity or lower data density. Separate models for upper montane zones with trees and shrubs and subalpine zones with only shrubs were always chosen over single models based on minimization of Akaike's Information Criterion, indicating the need for variable sets robust to overhanging tree canopy. Decreasing point density from UAV (5000–8000 pts./sq. m) to the G-LiHT SfM point cloud (500–2000 pts./sq. m) had little impact on model fit, suggesting that high-resolution airborne imagery can extend SfM approaches well beyond line-of-sight restrictions for UAV platforms. Overall, our results confirmed that SfM from high-resolution imagery is a viable approach to estimate shrub biomass in the boreal region, especially when an existing lidar terrain model and local field calibration data are available to quantify uncertainty in the SfM point cloud and landscape-scale estimates of shrub biomass.

Michael Alonzo↗
DOE OSTI2025

Smooth splitting and zeros from on-shell recursion

We describe a new approach to understanding the origins of recently discovered “hidden zeros” and “smooth splitting” of tree-level amplitudes in Tr ϕ 3 , Non-Linear Sigma Model (NLSM), Yang-Mill-Scalar (YMS) and the special Galileon. Introducing a new type of linear shift in kinematic space we demonstrate that the mysterious splitting formulae follow from a simple contour integration argument in the style of on-shell recursion. The argument makes use of only standard notions of tree-level factorization on propagators, but assumes improved UV behavior in the form of the absence of a residue at infinity. In the case of Tr ϕ 3 and NLSM this is proven by identifying our shift as a special case of a more general construction called a g-vector shift; in the case of YMS it remains an unproven conjecture. This recursive perspective leads to numerous new results: we derive generalizations of the splitting formulae on more relaxed near-zero kinematics, including interesting new kinematic limits in which the amplitude splits into a triple-product; we also demonstrate that the uncolored special Galileon model has improved UV scaling and hence also splits. We also investigate the possible realization of hidden zeros in four dimensions. The conditions under which the dimensionality constraints are compatible with zero kinematics is investigated in detail for Tr ϕ 3 and YMS; for the latter we find they can be realized only with certain restrictions on external helicity states. The realizable 4d zeros are proven by a similar recursive argument based on BCFW and is found to generalize to a new class of intrinsically 4d “helicity zeros” present in all sectors of YM and also gravity.

effective field theories↗
DOE OSTI2021

Root lateral interactions drive water uptake patterns under water limitation

The plasticity of root water uptake determines the maintenance of transpiration during periods of water limitation and drought. However, the mechanistic basis of plant water uptake, as well as the implications of water uptake strategies at the individual and ecosystem scale remain elusive. We model three-dimensional root water uptake under variably saturated conditions for a one-hectare temperate forest plot for a growing season with a pronounced mid-season dry period. Variations in root architecture, hydraulic properties, and degree of lateral interaction between root systems produce divergent local responses to water limitation and provide insights on individual and community response to meteorological conditions. Results demonstrate the plasticity of ecosystem-scale responses to surface drying, where interacting roots shift regions of active uptake to deeper soil layers with less abundant root biomass. These shifts, a product of both root system and soil hydraulic properties, illustrate intimate links between root and soil hydraulics in determining plant water sourcing. Furthermore, we demonstrate that root lateral interactions are beneficial at the ecosystem-scale, even when trees compete for water. Specifically, a more spatially extensive root system facilitates access to a larger soil water reservoir, often ameliorating water limitation and reducing sharp water potential gradients. While the reduction of water stress is a benefit, it can be offset by increased root construction and maintenance costs associated with the larger rooting system. A plausible “viability” region of root communal co-existence is therefore implied where competitive pressures and root production costs are balanced by a potential water benefit.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

On positive geometry and scattering forms for matter particles

We initiate the study of positive geometry and scattering forms for tree-level amplitudes with matter particles in the (anti-)fundamental representation of the color/flavor group. As a toy example, we study the bi-color scalar theory, which supplements the bi-adjoint theory with scalars in the (anti-)fundamental representations of both groups. Using a recursive construction we obtain a class of unbounded polytopes called open associahedra (or associahedra with certain facets at infinity) whose canonical form computes amplitudes in bi-color theory, for arbitrary number of legs and flavor assignments. In addition, we discuss the duality between color factors and wedge products, or "color is kinematics", for amplitudes with matter particles as well.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
NASA NTRS2009

Developing Large-Scale Bayesian Networks by Composition: Fault Diagnosis of Electrical Power Systems in Aircraft and Spacecraft

In this paper, we investigate the use of Bayesian networks to construct large-scale diagnostic systems. In particular, we consider the development of large-scale Bayesian networks by composition. This compositional approach reflects how (often redundant) subsystems are architected to form systems such as electrical power systems. We develop high-level specifications, Bayesian networks, clique trees, and arithmetic circuits representing 24 different electrical power systems. The largest among these 24 Bayesian networks contains over 1,000 random variables. Another BN represents the real-world electrical power system ADAPT, which is representative of electrical power systems deployed in aerospace vehicles. In addition to demonstrating the scalability of the compositional approach, we briefly report on experimental results from the diagnostic competition DXC, where the ProADAPT team, using techniques discussed here, obtained the highest scores in both Tier 1 (among 9 international competitors) and Tier 2 (among 6 international competitors) of the industrial track. While we consider diagnosis of power systems specifically, we believe this work is relevant to other system health management problems, in particular in dependable systems such as aircraft and spacecraft. (See CASI ID 20100021910 for supplemental data disk.)

Mengshoel, Ole Jakob↗
DOE OSTI2020

Estimating rates and patterns of diversification with incomplete sampling: a case study in the rosids

Premise Recent advances in generating large‐scale phylogenies enable broad‐scale estimation of species diversification. These now common approaches typically are characterized by (1) incomplete species coverage without explicit sampling methodologies and/or (2) sparse backbone representation, and usually rely on presumed phylogenetic placements to account for species without molecular data. We used empirical examples to examine the effects of incomplete sampling on diversification estimation and provide constructive suggestions to ecologists and evolutionary biologists based on those results. Methods We used a supermatrix for rosids and one well‐sampled subclade (Cucurbitaceae) as empirical case studies. We compared results using these large phylogenies with those based on a previously inferred, smaller supermatrix and on a synthetic tree resource with complete taxonomic coverage. Finally, we simulated random and representative taxon sampling and explored the impact of sampling on three commonly used methods, both parametric (RPANDA and BAMM) and semiparametric (DR). Results We found that the impact of sampling on diversification estimates was idiosyncratic and often strong. Compared to full empirical sampling, representative and random sampling schemes either depressed or inflated speciation rates, depending on methods and sampling schemes. No method was entirely robust to poor sampling, but BAMM was least sensitive to moderate levels of missing taxa. Conclusions We suggest caution against uncritical modeling of missing taxa using taxonomic data for poorly sampled trees and in the use of summary backbone trees and other data sets with high representative bias, and we stress the importance of explicit sampling methodologies in macroevolutionary studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Unitarity methods in AdS/CFT

We develop a systematic unitarity method for loop-level AdS scattering amplitudes, dual to non-planar CFT correlators, from both bulk and boundary perspectives. We identify cut operators acting on bulk amplitudes that put virtual lines on shell, and show how the conformal partial wave decomposition of the amplitudes may be efficiently computed by gluing lower-loop amplitudes. A central role is played by the double discontinuity of the amplitude, which has a direct relation to these cuts. We then exhibit a precise, intuitive map between the diagrammatic approach in the bulk using cutting and gluing, and the algebraic, holographic unitarity method of [1] that constructs the non-planar correlator from planar CFT data. Our analysis focuses mostly on four-point, one-loop diagrams — we compute cuts of the scalar bubble, triangle and box, as well as some one-particle reducible diagrams — in addition to the five-point tree and four-point double-ladder. Analogies with S-matrix unitarity methods are drawn throughout.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

spot_bt_ros v.0.1.0

SAND2024-08478O The spot_bt_ros tool allows users to easily construct complex autonomous behaviors for Boston Dynamic's Spot robot without having to overly rely on the Spot software development kit (SDK). This package specifically allows a user to run the Robot Operating System 2 alongside the SDK. Using a form-of-state machine called a "behavior tree,” the software develops different "leaves" or actions that the robot undergoes. Attaching multiple actions in sequence creates a "branch" and several of these make up the "tree." 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.

Kakish, Zahi↗
DOE OSTI2025

Fully gauge-fixed SU(2) Hamiltonian for quantum simulations

Here, we demonstrate how to construct a fully gauge-fixed lattice Hamiltonian for a pure SU(2) gauge theory. Our work extends upon previous work, where a formulation of an SU(2) lattice gauge theory was developed that is efficient to simulate at all values of the gauge coupling. That formulation utilized maximal-tree gauge, where all local gauge symmetries are fixed and a residual global gauge symmetry remains. By using the geometric picture of an SU(2) lattice gauge theory as a system of rotating rods, we demonstrate how to fix the remaining global gauge symmetry. In particular, the quantum numbers associated with total charge can be isolated by rotating between the lab and body frames using the three Euler angles. The Hilbert space in this new “sequestered” basis partitions cleanly into sectors with differing total angular momentum, which makes gauge-fixing to a particular total charge sector trivial, particularly for the charge-zero sector. In addition to this sequestered basis inheriting the property of being efficient at all values of the coupling, we show that, despite the global nature of the final gauge-fixing procedure, this Hamiltonian can be simulated using quantum resources scaling only polynomially with the lattice volume.

Lattice gauge theory↗