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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 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea

Ammonia-oxidizing archaea (AOA) are among the most abundant and ubiquitous microorganisms in the ocean, exerting primary control on nitrification and nitrogen oxides emission. Although united by a common physiology of chemoautotrophic growth on ammonia, a corresponding high genomic and habitat variability suggests tremendous adaptive capacity. Here, we compared 44 diverse AOA genomes, 37 from species cultivated from samples collected across diverse geographic locations and seven assembled from metagenomic sequences from the mesopelagic to hadopelagic zones of the deep ocean. Comparative analysis identified seven major marine AOA genotypic groups having gene content correlated with their distinctive biogeographies. Phosphorus and ammonia availabilities as well as hydrostatic pressure were identified as selective forces driving marine AOA genotypic and gene content variability in different oceanic regions. Notably, AOA methylphosphonate biosynthetic genes span diverse oceanic provinces, reinforcing their importance for methane production in the ocean. Together, our combined comparative physiological, genomic, and metagenomic analyses provide a comprehensive view of the biogeography of globally abundant AOA and their adaptive radiation into a vast range of marine and terrestrial habitats.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Fourier-based three-dimensional multistage transformer for aberration correction in multicellular specimens

High-resolution tissue imaging is often compromised by sample-induced optical aberrations that degrade resolution and contrast. Although wavefront sensor-based adaptive optics (AO) can measure these aberrations, such hardware solutions are typically complex, expensive to implement and slow when serially mapping spatially varying aberrations across large fields of view. Here we introduce AOViFT (adaptive optical vision Fourier transformer)—a machine learning-based aberration sensing framework built around a three-dimensional multistage vision transformer that operates on Fourier domain embeddings. AOViFT infers aberrations and restores diffraction-limited performance in puncta-labeled specimens with substantially reduced computational cost, training time and memory footprint compared to conventional architectures or real-space networks. We validated AOViFT on live gene-edited zebrafish embryos, demonstrating its ability to correct spatially varying aberrations using either a deformable mirror or postacquisition deconvolution. By eliminating the need for the guide star and wavefront sensing hardware and simplifying the experimental workflow, AOViFT lowers technical barriers for high-resolution volumetric microscopy across diverse biological samples.

Alshaabi, Thayer [Howard Hughes Medical Institute,↗
DOE OSTI2013

Marine Corps Base Camp Lejeune Avian Point Count Data 2011

Critical military training and testing on lands along the nation’s coastal and estuarine shorelines are increasingly placed at risk because of encroachment pressures in surrounding areas, impairments due to other anthropogenic disturbances, and changes in climate and sea level. The U.S. Department of Defense (DoD) intends to enhance and sustain its training and testing assets and also optimize its stewardship of natural resources through the development and application of an ecosystem-based management approach on DoD installations. To accomplish this goal, particularly for installations in estuarine/coastal environments, the Strategic Environmental Research and Development Program (SERDP) launched the Defense Coastal/Estuarine Research Program (DCERP) as a 10-year effort at Marine Corps Base Camp Lejeune (MCBCL) in North Carolina. The results of the second 5 years of the program (DCERP2) are presented in the DCERP2 Final Report.There were four overarching objectives of DCERP2. The first objective was to understand the effects of climate change impacts, including warming temperatures, variability in the hydrological cycle, storm events, and sea level rise on the coastal ecosystems at MCBCL from observations and measurements made over the 10-year program. The second objective was to understand the carbon cycle of the coastal and terrestrial ecosystems at MCBCL through a highly integrated sampling program. The third objective was to develop models, tools, and indicators to evaluate current and projected future ecosystem state changes and translate scientific findings into actionable information for installation managers. The last objective was to recommend adaptive management strategies to sustain ecosystem natural resources within the context of an active military installation.The census points were sampled in 2009 and again in 2010 and 2011 (2009 and 2010 data are in MARDIS). We used point counts to census birds following a methodology from Ralph et al. (1995) by Kirkpatrick et al. (2006). Surveys were conducted between April 10 and July 10 starting at sunrise and going no later than 10 a.m. (or 4 hours after dawn), on days without precipitation and with wind speeds less than 12 km/h (Ralph et al., 1995; Rosenstock et al., 2002). We recorded temperature (°C), wind speed (km/h), cloud cover, and background noise level. After initially arriving at a point, we waited for a 1-minute silent period, and then recorded any birds seen or heard for an 8-minute period (Farnsworth et 14-8 al., 2002; Rosenstock et al., 2002). We estimated the distance to each bird, using a Rangefinder whenever necessary (Buckland, 2001; Rosenstock et al., 2002).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Porting Adaptive Ensemble Molecular Dynamics Workflows to the Summit Supercomputer

Molecular dynamics (MD) simulations must take very small (femtosecond) integration steps in simulation-time to avoid numerical errors. Efficient use of parallel programming models and accelerators in state-of-the art MD programs now is pushing Moore’s limit for time-per-MD step. As a result, directly simulating timescales beyond milliseconds will not be attainable directly, even at exascale. However, concepts from statistical physics can be used to combine many parallel simulations to provide information about longer timescales and to adequately sample the simulation space, while preserving details about the dynamics of the system. Implementing such an approach requires a workflow program that allows adaptable steering of task assignments based on extensive statistical analysis of intermediate results. Here we report the implementation of such an adaptable workflow program to drive simulations on the Summit IBM Power System AC922, a pre-exascale supercomputer at the Oak Ridge Leadership Computing Facility (OLCF). We compare to experiences on Titan, Summit’s predecessor, report the performance of the workflow and its components, and describe the porting process. We find that using a workflow program managed by a Mongo database can provide the fault tolerance, scalable performance, task dispatch rate, and reconfigurability required for robust and portable implementation of ensemble simulations such as are used in enhanced-sampling molecular dynamics. This type of workflow generator can also be used to provide adaptive steering of ensemble simulations for other applications in addition to MD.

Ossyra, John R.↗
DOE OSTI2024

Fine-scale contemporary recombination variation and its fitness consequences in adaptively diverging stickleback fish

Despite deep evolutionary conservation, recombination rates vary greatly across the genome and among individuals, sexes and populations. Yet the impact of this variation on adaptively diverging populations is not well understood. Here we characterized fine-scale recombination landscapes in an adaptively divergent pair of marine and freshwater populations of threespine stickleback from River Tyne, Scotland. Through whole-genome sequencing of large nuclear families, we identified the genomic locations of almost 50,000 crossovers and built recombination maps for marine, freshwater and hybrid individuals at a resolution of 3.8 kb. We used these maps to quantify the factors driving variation in recombination rates. We found strong heterochiasmy between sexes but also differences in recombination rates among ecotypes. Hybrids showed evidence of significant recombination suppression in overall map length and in individual loci. Recombination rates were lower not only within individual marine–freshwater-adaptive loci, but also between loci on the same chromosome, suggesting selection on linked gene ‘cassettes’. Through temporal sampling along a natural hybrid zone, we found that recombinants showed traits associated with reduced fitness. Our results support predictions that divergence in cis-acting recombination modifiers, whose functions are disrupted in hybrids, may play an important role in maintaining differences among adaptively diverging populations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Parallel multiple-chain DRAM MCMC for large-scale geosteering inversion and uncertainty quantification

Geosteering is the proactive control of a wellbore placement based on the downhole measurements, aiming at maximizing economic production from the well. We report the recent development of azimuthal resistivity logging-whiledrilling (LWD) tools have a much larger depth of detection, thus sets higher demands for geosteering inversion as more unknown parameters need to be taken into account in the earth model to be inverted. For complicated nonlinear problems, traditional deterministic inversion methods are more likely to be trapped near local optima. In general, Markov chain Monte Carlo (MCMC) inversion methods are more capable of finding the global optimal solution and providing additional uncertainty analyses by sampling from the target distribution. However, MCMC methods usually have the problem of slow convergence. Even though optimization methods like delayed rejection (DR) and adaptive Metropolis (AM) were proposed to speed up the convergence, using MCMC methods to solve geosteering inversion problems may still incur unacceptable time cost. To reduce the sampling cost of MCMC methods, we use parallel multiple-chain DRAM MCMC methods to solve geosteering inverse problems and estimate the corresponding uncertainty. A clustering method, density-based spatial clustering of applications with noise (DBSCAN), is applied to select the best solution among many results. Lastly, the simulation results show that running many relatively short MCMC chains for one problem can obtain a similar result as running a long single chain. Besides, avoiding communications between multiple Markov chains during the sampling process yields almost linear scalability.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Adaptive Reweighted Variance Estimation for Monte Carlo Eigenvalue Simulations

Monte Carlo (MC) simulation is used to solve the eigenvalue form of the Boltzmann transport equation to estimate various parameters such as fuel pin flux distributions that are crucial for the safe and efficient operation of nuclear systems (e.g., a nuclear reactor). Monte Carlo eigenvalue simulation uses a sample mean over many stationary cycles (iterations) to estimate various parameters important to nuclear systems. A variance estimate of the sample mean is often used for calculating the confidence intervals. However, MC eigenvalue simulation variance estimators that ignore the intercycle correlation underestimate the true variance of the estimated quantity. This paper presents novel data-adaptive approaches based on a simple autoregressive (AR) model and sigmoid functions to improve MC variance estimation. The standard MC sample-based variance estimator (or naïve estimator) and the spectral density–based MC variance estimator are enhanced by adding data-adaptive components that reduce their bias and improve performance. By investigating the frequency pattern of the AR(1) (order 1) model, two adaptive spectral estimators and one adaptive naïve estimator are proposed. The proposed estimators manifest superior performance when applied to three test problems compared to the standard spectral density–based estimator previously introduced by the authors. In conclusion, these new estimators are straightforward, as they use online algorithms and do not require storage of tallies from all active cycles.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2014

SIMPLIFIED PREDICTIVE MODELS FOR CO₂ SEQUESTRATION PERFORMANCE ASSESSMENT RESEARCH TOPICAL REPORT ON TASK #3 STATISTICAL LEARNING BASED MODELS

We compare two approaches for building a statistical proxy model (metamodel) for CO₂ geologic sequestration from the results of full-physics compositional simulations. The first approach involves a classical Box-Behnken or Augmented Pairs experimental design with a quadratic polynomial response surface. The second approach used a space-filling maxmin Latin Hypercube sampling or maximum entropy design with the choice of five different meta-modeling techniques: quadratic polynomial, kriging with constant and quadratic trend terms, multivariate adaptive regression spline (MARS) and additivity and variance stabilization (AVAS). Simulations results for CO₂ injection into a reservoir-caprock system with 9 design variables (and 97 samples) were used to generate the data for developing the proxy models. The fitted models were validated with using an independent data set and a cross-validation approach for three different performance metrics: total storage efficiency, CO₂ plume radius and average reservoir pressure. The Box-Behnken–quadratic polynomial metamodel performed the best, followed closely by the maximin LHS–kriging metamodel.

Mishra, Srikanta↗
DOE OSTI2013

Minimal multi-element stochastic collocation for uncertainty quantification of discontinuous functions

We propose a multi-element stochastic collocation method that can be applied in high-dimensional parameter space for functions with discontinuities lying along manifolds of general geometries. The key feature of the method is that the parameter space is decomposed into multiple elements defined by the discontinuities and thus only the minimal number of elements are utilized. On each of the resulting elements the function is smooth and can be approximated using high-order methods with fast convergence properties. The decomposition strategy is in direct contrast to the traditional multi-element approaches which define the sub-domains by repeated splitting of the axes in the parameter space. Such methods are more prone to the curse-of-dimensionality because of the fast growth of the number of elements caused by the axis based splitting. The present method is a two-step approach. Firstly a discontinuity detector is used to partition parameter space into disjoint elements in each of which the function is smooth. The detector uses an efficient combination of the high-order polynomial annihilation technique along with adaptive sparse grids, and this allows resolution of general discontinuities with a smaller number of points when the discontinuity manifold is low-dimensional. After partitioning, an adaptive technique based on the least orthogonal interpolant is used to construct a generalized Polynomial Chaos surrogate on each element. The adaptive technique reuses all information from the partitioning and is variance-suppressing. We present numerous numerical examples that illustrate the accuracy, efficiency, and generality of the method. When compared against standard locally-adaptive sparse grid methods, the present method uses many fewer number of collocation samples and is more accurate.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Multiscale graph neural network autoencoders for interpretable scientific machine learning

The goal of this work is to address two limitations in autoencoder-based models: latent space interpretability and compatibility with unstructured meshes. This is accomplished here with the development of a novel graph neural network (GNN) autoencoding architecture with demonstrations on complex fluid flow applications. To address the first goal of interpretability, the GNN autoencoder achieves reduction in the number nodes in the encoding stage through an adaptive graph reduction procedure. Further, this reduction procedure essentially amounts to flowfieldconditioned node sampling and sensor identification, and produces interpretable latent graph representations tailored to the flowfield reconstruction task in the form of so-called masked fields. These masked fields allow the user to (a) visualize where in physical space a given latent graph is active, and (b) interpret the time-evolution of the latent graph connectivity in accordance with the time-evolution of unsteady flow features (e.g. recirculation zones, shear layers) in the domain. To address the goal of unstructured mesh compatibility, the autoencoding architecture utilizes a series of multi-scale message passing (MMP) layers, each of which models information exchange among node neighborhoods at various lengthscales. The MMP layer, which augments standard single-scale message passing with learnable coarsening operations, allows the decoder to more efficiently reconstruct the flowfield from the identified regions in the masked fields. Analysis of latent graphs produced by the autoencoder for various model settings are conducted using unstructured snapshot data sourced from large-eddy simulations in a backward-facing step (BFS) flow configuration with an OpenFOAM-based flow solver at high Reynolds numbers.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Polynomial chaos expansions on principal geodesic Grassmannian submanifolds for surrogate modeling and uncertainty quantification

In this work we introduce a manifold learning-based surrogate modeling framework for uncertainty quantification in high-dimensional stochastic systems. Our first goal is to perform data mining on the available simulation data to identify a set of low-dimensional (latent) descriptors that efficiently parameterize the response of the high-dimensional computational model. To this end, we employ Principal Geodesic Analysis on the Grassmann manifold of the response to identify a set of disjoint principal geodesic submanifolds, of possibly different dimension, that captures the variation in the data. Since operations on the Grassmann require the data to be concentrated, we propose an adaptive algorithm based on Riemannian K-means and the minimization of the sample Fréchet variance on the Grassmann manifold to identify “local” principal geodesic submanifolds that represent different system behavior across the parameter space. Polynomial chaos expansion is then used to construct a mapping between the random input parameters and the projection of the response on these local principal geodesic submanifolds. Here, the method is demonstrated on four test cases, a toy-example that involves points on a hypersphere, a Lotka-Volterra dynamical system, a continuous-flow stirred-tank chemical reactor system, and a two-dimensional Rayleigh-Bénard convection problem.

42 ENGINEERING↗
DOE OSTI2015

Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers

Many microbial communities are characterized by high genetic diversity. 16S ribosomal RNA sequencing can determine community members, and metagenomics can determine the functional diversity, but resolving the functional role of individual cells in high throughput remains an unsolved challenge. Here, we describe epicPCR (Emulsion, Paired Isolation and Concatenation PCR), a new technique that links functional genes and phylogenetic markers in uncultured single cells, providing a throughput of hundreds of thousands of cells with costs comparable to one genomic library preparation. We demonstrate the utility of our technique in a natural environment by profiling a sulfate-reducing community in a freshwater lake, revealing both known sulfate reducers and discovering new putative sulfate reducers. Our method is adaptable to any conserved genetic trait and translates genetic associations from diverse microbial samples into a sequencing library that answers targeted ecological questions. Potential applications include identifying functional community members, tracing horizontal gene transfer networks and mapping ecological interactions between microbial cells.

Environmental Sciences & Ecology↗
DOE OSTI2021

Lytic archaeal viruses infect abundant primary producers in Earth’s crust

The continental subsurface houses a major portion of life’s abundance and diversity, yet little is known about viruses infecting microbes that reside there. Here, we use a combination of metagenomics and virus-targeted direct-geneFISH (virusFISH) to show that highly abundant carbon-fixing organisms of the uncultivated genus Candidatus Altiarchaeum are frequent targets of previously unrecognized viruses in the deep subsurface. Analysis of CRISPR spacer matches display resistances of Ca. Altiarchaea against eight predicted viral clades, which show genomic relatedness across continents but little similarity to previously identified viruses. Based on metagenomic information, we tag and image a putatively viral genome rich in protospacers using fluorescence microscopy. VirusFISH reveals a lytic lifestyle of the respective virus and challenges previous predictions that lysogeny prevails as the dominant viral lifestyle in the subsurface. CRISPR development over time and imaging of 18 samples from one subsurface ecosystem suggest a sophisticated interplay of viral diversification and adapting CRISPR-mediated resistances of Ca. Altiarchaeum. We conclude that infections of primary producers with lytic viruses followed by cell lysis potentially jump-start heterotrophic carbon cycling in these subsurface ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

In situ flame chemistry tracing by imaging photoelectron photoion coincidence spectroscopy

Adaptation of a low-pressure flat flame burner with a flame-sampling interface to the imaging photoelectron photoion coincidence spectrometer (iPEPICO) of the VUV beamline at the Swiss Light Source is presented. The combination of molecular-beam mass spectrometry and iPEPICO provides a new powerful analytical tool for the detailed investigation of reaction networks in flames. First results demonstrate the applicability of the new instrument to comprehensive flame diagnostics and the potentially high impact for reaction mechanism development for conventional and alternative fuels. Isomer specific identification of stable and radical flame species is demonstrated with unrivaled precision. Radical detection and identification is achieved for the initial H-abstraction products of fuel molecules as well as for the reaction controlling H, O, and OH radicals. Furthermore, quantitative evaluation of changing species concentrations during the combustion process and the applicability of respective results for kinetic model validation are demonstrated. Utilization of mass-selected threshold photoelectron spectra is shown to ensure precise signal assignment and highly reliable spatial profiles.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Comparison of Nb 3 Sn Insulation Systems With as Received and De-Sized Glass

Epoxy cracking has been the main suspected contributor to training in Nb 3 Sn magnets for some time, as it leads to energy release and magnet quenching. Cracking in a superconducting composite can occur from several modes, and the likelihood of these modes is not well understood. Failure has been observed between insulation systems and the superconducting cable itself rather than within the cable or insulation. To target the behavior at the interface, samples have been fabricated and tested for Mode I fracture toughness in an adapted version of ASTM D5528. This work seeks to better characterize the fracture toughness of this interface to better understand how to model and design insulation systems.

Krave, Steven T. [Fermilab] (ORCID:000000021752145↗
DOE OSTI2013

A prototype fan-beam optical CT scanner for 3D dosimetry

Purpose: The objective of this work is to introduce a prototype fan-beam optical computed tomography scanner for three-dimensional (3D) radiation dosimetry. Methods: Two techniques of fan-beam creation were evaluated: a helium-neon laser (HeNe, {lambda} = 543 nm) with line-generating lens, and a laser diode module (LDM, {lambda} = 635 nm) with line-creating head module. Two physical collimator designs were assessed: a single-slot collimator and a multihole collimator. Optimal collimator depth was determined by observing the signal of a single photodiode with varying collimator depths. A method of extending the dynamic range of the system is presented. Two sample types were used for evaluations: nondosimetric absorbent solutions and irradiated polymer gel dosimeters, each housed in 1 liter cylindrical plastic flasks. Imaging protocol investigations were performed to address ring artefacts and image noise. Two image artefact removal techniques were performed in sinogram space. Collimator efficacy was evaluated by imaging highly opaque samples of scatter-based and absorption-based solutions. A noise-based flask registration technique was developed. Two protocols for gel manufacture were examined. Results: The LDM proved advantageous over the HeNe laser due to its reduced noise. Also, the LDM uses a wavelength more suitable for the PRESAGE{sup TM} dosimeter. Collimator depth of 1.5 cm was found to be an optimal balance between scatter rejection, signal strength, and manufacture ease. The multihole collimator is capable of maintaining accurate scatter-rejection to high levels of opacity with scatter-based solutions (T < 0.015%). Imaging protocol investigations support the need for preirradiation and postirradiation scanning to reduce reflection-based ring artefacts and to accommodate flask imperfections and gel inhomogeneities. Artefact removal techniques in sinogram space eliminate streaking artefacts and reduce ring artefacts of up to {approx}40% in magnitude. The flask registration technique was shown to achieve submillimetre and subdegree placement accuracy. Dosimetry protocol investigations emphasize the need to allow gel dosimeters to cool gradually and to be scanned while at room temperature. Preliminary tests show that considerable noise reduction can be achieved with sinogram filtering and by binning image pixels into more clinically relevant grid sizes. Conclusions: This paper describes a new optical CT scanner for 3D radiation dosimetry. Tests demonstrate that it is capable of imaging both absorption-based and scatter-based samples of high opacities. Imaging protocol and gel dosimeter manufacture techniques have been adapted to produce optimal reconstruction results. These optimal results will require suitable filtering and binning techniques for noise reduction purposes.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2013

Hierarchy-Direction Selective Approach for Locally Adaptive Sparse Grids

We consider the problem of multidimensional adaptive hierarchical interpolation. We use sparse grids points and functions that are induced from a one dimensional hierarchical rule via tensor products. The classical locally adaptive sparse grid algorithm uses an isotropic refinement from the coarser to the denser levels of the hierarchy. However, the multidimensional hierarchy provides a more complex structure that allows for various anisotropic and hierarchy selective refinement techniques. We consider the more advanced refinement techniques and apply them to a number of simple test functions chosen to demonstrate the various advantages and disadvantages of each method. While there is no refinement scheme that is optimal for all functions, the fully adaptive family-direction-selective technique is usually more stable and requires fewer samples.

Stoyanov, Miroslav K↗
DOE OSTI2023

Interlaminar Fracture Toughness Testing of Nb3Sn Insulation Systems

Epoxy cracking has been the main suspected contributor to training in Nb3Sn magnets for some time, as it leads to energy release and magnet quenching. Cracking in a superconducting composite can occur from several modes, and the likelihood of these modes is not well understood. Failure has been observed between insulation systems and the superconducting cable itself rather than within the cable or insulation. To target the behavior at the interface, samples have been fabricated and tested for mode I fracture toughness in an adapted version of ASTM D5528. This work seeks to better characterize the fracture toughness of this interface to better understand how to model and design insulation systems.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗