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At least 487 records · Page 27

Adaptive Bayesian Inference for Prediction

Performing rigorous predictive simulation necessitates that all available data be incorporated into the modeling process in order to accurately quantify uncertainties in predictions of the model. Statistical Bayesian inference is the most commonly used approach for incorporating data into uncertainty estimates. Statistical Bayesian inference uses data and an assumed error model to inform posterior distributions of model input variables and model discrepancies. An explicit characterization of the posterior distribution is not formed, but rather methods such as Markov chain Monte-Carlo (MCMC) are used to draw samples from the posterior. These samples are then used to evaluate statistics, such as integrals, of predicted quantities of interest (QoI). Recently the authors have developed an alternative reformulation of Bayesian inference based upon a measure-theoretic inversion technique. Unlike traditional statistical Bayesian inference, this reformulation allows us to directly interrogate the posterior distribution and, consequently, to generate samples from the posterior without MCMC. In this work we use forward propagation uncertainty quantification techniques to reduce the cost of approximating the posterior distribution. Specifically we investigate goal-oriented adaptive sparse grid approximation methods. These adaptive methods concentrate high-fidelity model evaluations in regions of the parameter space that both significantly contribute to the uncertainty in specified QoI and are informed by the available data. Numerical results are presented to compare our approach with the standard statistical Bayesian approach and to demonstrate the effectiveness of the goal-oriented adaptivity.

97 MATHEMATICS AND COMPUTING↗

Isotope ratio characteristics and sensitivity for uranium determinations using a liquid sampling-atmospheric pressure glow discharge ion source coupled to an Orbitrap mass analyzer

Abstract The continued development of the liquid sampling-atmospheric pressure glow discharge (LS-APGD) microplasma as an ion source for diverse, elemental/isotopic analysis applications continues. To this end, characterization of the capabilities in performing precise and accurate isotope ratio (IR) determinations is essential. Based on past experience with the Thermo Exactive Orbitrap mass analyzer, the LS-APGD was interfaced with this instrument for these tests. While the Orbitrap platform has demonstrated excellent mass resolution and accuracy in “organic” mass spectrometry (MS) applications, work using an Orbitrap for IR analysis is very sparse. These efforts build off previous work in this coupling, where the importance of a few of the LS-APGD discharge parameters and Orbitrap data acquisition methods on IR precision and accuracy were probed. Presented here are the results of a study that evaluated the analytical precision for natural uranium sample (assumed 235U/238U = 0.0072) determinations. The instrumental parameters evaluated include the number of microscans and scans making up a data acquisition set, uranium concentration/signal level, sample make-up, and Fourier transform digitization window. Ultimately, a precision of 0.41% relative standard deviation (RSD) can be achieved for a single determination, with a reproducibility of 1.63 %RSD over 10 separate analytical measurements. A preliminary study of matrix effects on IR measurements of U is presented, highlighting the importance of pre-mass selection before injection into the Orbitrap. The analytical system sensitivity is suggested with the ability to produce a calibration function having an R2 value of >0.99 over a range of 4 orders of magnitude of concentration (~1 – 1000 ng mL-1). These efforts demonstrate the very promising pairing of the LS-APGD ionization source and the Orbitrap, pointing as well to definitive paths forward to better utilize both components in high quality isotope ratio mass spectrometry (IRMS).

Environmental Molecular Sciences Laboratory↗

Facile hermetic TEM grid preparation for molecular imaging of hydrated biological samples at room temperature

Abstract Although structures of vitrified supramolecular complexes have been determined at near-atomic resolution, elucidating in situ molecular structure in living cells remains a challenge. Here, we report a straightforward liquid cell technique, originally developed for real-time visualization of dynamics at a liquid-gas interface using transmission electron microscopy, to image wet biological samples. Due to the scattering effects from the liquid phase, the micrographs display an amplitude contrast comparable to that observed in negatively stained samples. We succeed in resolving subunits within the protein complex GroEL imaged in a buffer solution at room temperature. Additionally, we capture various stages of virus cell entry, a process for which only sparse structural data exists due to their transient nature. To scrutinize the morphological details further, we used individual particle electron tomography for 3D reconstruction of each virus. These findings showcase this approach potential as an efficient, cost-effective complement to other microscopy technique in addressing biological questions at the molecular level.

59 BASIC BIOLOGICAL SCIENCES↗

Model-measurement consistency and limits of bioaerosol abundance over the continental United States

Abstract. Due to low concentrations and chemical complexity, in situ observations of bioaerosol are geographically and temporally sparse, and this limits the accuracy of current emissions inventories. In this study, we apply a new methodology, including corrections for misidentification of mineral dust, to measurements of single particles over four airborne sampling campaigns to derive vertical profiles of bioaerosol over the continental United States. The new methodology is based on single-particle mass spectrometry (SPMS); it can extend historic datasets to include measurements of bioaerosol, it allows comparisons to other techniques, and it generally agrees with a global aerosol model. In the locations sampled, bioaerosols were at least a factor of 10 less abundant than mineral dust. Below 2 km, bioaerosol concentrations were measured between 6×103 and 2×104 m−3. Between 2 and 8 km, bioaerosol concentrations were between 0 and 2×104 m−3, and above 8 km, bioaerosol concentrations were between 0 and 1×103 m−3. Between 30 % and 80 % of single bioaerosol particles detected were internally mixed with dust. A direct comparison of the SPMS methodology with a co-located wideband integrated bioaerosol sensor (WIB) fluorescence sensor on a mountaintop site showed agreement to within a factor of 3 over the common size range.

54 ENVIRONMENTAL SCIENCES↗

Climatic Analysis of Oceanic Water Vapor Transports Based on Satellite E-P Datasets

Understanding the climatically varying properties of water vapor transports from a robust observational perspective is an essential step in calibrating climate models. This is tantamount to measuring year-to-year changes of monthly- or seasonally-averaged, divergent water vapor transport distributions. This cannot be done effectively with conventional radiosonde data over ocean regions where sounding data are generally sparse. This talk describes how a methodology designed to derive atmospheric water vapor transports over the world oceans from satellite-retrieved precipitation (P) and evaporation (E) datasets circumvents the problem of inadequate sampling. Ultimately, the method is intended to take advantage of the relatively complete and consistent coverage, as well as continuity in sampling, associated with E and P datasets obtained from satellite measurements. Independent P and E retrievals from Special Sensor Microwave Imager (SSM/I) measurements, along with P retrievals from Tropical Rainfall Measuring Mission (TRMM) measurements, are used to obtain transports by solving a potential function for the divergence of water vapor transport as balanced by large scale E - P conditions.

Smith, Eric A.↗

Modeling Sound Propagation Through Non-Axisymmetric Jets

A method for computing the far-field adjoint Green's function of the generalized acoustic analogy equations under a locally parallel mean flow approximation is presented. The method is based on expanding the mean-flow-dependent coefficients in the governing equation and the scalar Green's function in truncated Fourier series in the azimuthal direction and a finite difference approximation in the radial direction in circular cylindrical coordinates. The combined spectral/finite difference method yields a highly banded system of algebraic equations that can be efficiently solved using a standard sparse system solver. The method is applied to test cases, with mean flow specified by analytical functions, corresponding to two noise reduction concepts of current interest: the offset jet and the fluid shield. Sample results for the Green's function are given for these two test cases and recommendations made as to the use of the method as part of a RANS-based jet noise prediction code.

Leib, Stewart J.↗

Karyotypes of Human Lymphocytes Exposed to High-Energy Iron Ions

Chromosomal aberrations were analyzed using multicolor fluorescence in situ hybridization (mFISH) in human peripheral blood lymphocytes after in vitro exposure to gamma rays or accelerated (56)Fe ions (1 GeV/nucleon, 145 keV/microm) at Brookhaven National Laboratory (Upton, NY). Doses of 0.3 and 3 Gy were used for both radiation types. Chromosomes were prematurely condensed by a phosphatase inhibitor (calyculin A) to avoid the population selection bias observed at metaphase as a result of the severe cell cycle delays induced by heavy ions. A total of 1053 karyotypes (G(2) and M phases) were analyzed in irradiated lymphocytes. Results revealed different distribution patterns for chromosomal aberrations after low- and high-LET radiation exposures: Heavy ions induced a much higher fraction of cells with multiple aberrations, while the majority of the aberrant cells induced by low doses of gamma rays contained a single aberration. The high fraction of complex-type exchanges after heavy ions leads to an overestimation of simple-type asymmetrical interchanges (dicentrics) from analysis of Giemsa-stained samples. However, even after a dose of 3 Gy iron ions, about 30% of the cells presented no complex-type exchanges. The involvement of individual chromosomes in exchanges was similar for densely and sparsely ionizing radiation, and no statistically significant evidence of a nonrandom involvement of specific chromosomes was detected.

NASA Center JSC↗

Mangrove Carbon Stocks in Pongara National Park, Gabon

Mangroves are recognized for their valued ecosystem services to coastal areas, and the functional linkages between those services and ecosystem carbon stocks have been established. However, spatially explicit inventories are necessary to facilitate management and protection of mangroves, as well as providing a foundation for payment for ecosystem service programs such as REDD+. We conducted an inventory of carbon stocks in mangroves within Pongara National Park (PNP), Gabon using a stratified random sampling design based on forest canopy height derived from TanDEM-X remote sensing data. Ecosystem carbon pools, including aboveground and belowground biomass and necromass, and soil carbon to a depth of 2 m were assessed using measurements and samples from plots distributed among three canopy height classes within the park. There were two mangrove species within the inventory area in PNP, Rhizophora racemosa and R. harrisonii. R. harrisonii was predominant in the sparse, low-stature stands that dominated the west side of the park. In the east side of the park, both species occurred in tall-stature stands, with tree height often exceeding 30 m. Canopy height was an effective means to stratify the inventory area, as biomass was significantly different among the height classes. Despite those differences in aboveground biomass, the soil carbon density was not significantly different among height classes. Soils were the main component of the ecosystem carbon stock, accounting for over 84% of the total. The ecosystem carbon density ranged from 644 to 943 Mg C ha−1 among the three height classes. The ecosystem carbon stock within PNP is estimated to be 40,588 Gg C. The combination of pre-inventory information about stand conditions and their spatial distribution within the assessment area obtained from remote sensing data and a spatial decision support system were fundamental to implementing this relatively large-scale field inventory. This work exemplifies how mangrove carbon stocks can be quantified to augment national C reporting statistics, provide a baseline for projects involving monitoring, reporting and verification (i.e., MRV), and provide data on the forest composition and structure for sustainable management and conservation practices.

Carl C Trettin↗

Uncertainty and Sensitivity Analysis of TREAT Transient Test no. 15

The U.S. Department of Energy (DOE) is preparing for the resumption of transient testing using the Transient Reactor Test Facility (TREAT) located at the Idaho National Laboratory (INL). In order to support the analysis of TREAT operation and experiment planning, the MAMMOTH reactor physics team has recently begun development of uncertainty and sensitivity analysis for the TREAT core simulated via MAMMOTH. MAMMOTH is a high-fidelity three-dimensional transient multi-physics code developed at INL under the DOE-NE Advanced Modeling and Simulation program (NEAMS). This research is part of the development presenting some initial uncertainty and sensitivity analysis of TREAT Transient Test no. 15. In this summary, we employ the Sobol sampling strategy implemented in RAVEN to efficiently perform the sensitivity and uncertainty analysis. The idea is using Sobol functional decomposition with generalized polynomial chaos (gPC) expansions to estimate the responses of interest. The gPC coefficients are then computed via the sparse grid spectral projection method. In addition, this strategy includes evaluation of the second or higher order sensitivity indices, allowing the study of interactions between several input variables. The principal focus of this analysis is to quantify the uncertainties in the total power and maximum fuel temperatures with respect to uncertainties in the initial transient conditions, such as rated power, fuel temperature, graphite fuel density and control rod boron concentration. In addition, both the first order and second order time-dependent sensitivity indices are computed and analyzed. The results show that the interactions between initial control rod boron concentration and the rated power will contribute at most 1% to the total uncertainty of the power peak.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Pushing the size limit of de novo structure ensemble prediction guided by sparse SDSL-EPR restraints to 200 residues: The monomeric and homodimeric forms of BAX

Structure determination remains a challenge for many biologically important proteins. In particular, proteins that adopt multiple conformations often evade crystallization in all biologically relevant states. Although computational de novo protein folding approaches often sample biologically relevant conformations, the selection of the most accurate model for different functional states remains a formidable challenge, in particular, for proteins with more than about 150 residues. Electron paramagnetic resonance (EPR) spectroscopy can obtain limited structural information for proteins in well-defined biological states and thereby assist in selecting biologically relevant conformations. The present study demonstrates that de novo folding methods are able to accurately sample the folds of 192-residue long soluble monomeric Bcl-2-associated X protein (BAX). The tertiary structures of the monomeric and homodimeric forms of BAX were predicted using the primary structure as well as 25 and 11 EPR distance restraints, respectively. The predicted models were subsequently compared to respective NMR/X-ray structures of BAX. EPR restraints improve the protein-size normalized root-mean-square-deviation (RMSD100) of the most accurate models with respect to the NMR/crystal structure from 5.9 Å to 3.9 Å and from 5.7 Å to 3.3 Å, respectively. Additionally, the model discrimination is improved, which is demonstrated by an improvement of the enrichment from 5% to 15% and from 13% to 21%, respectively.

Biochemistry & Molecular Biology↗

Sparse optimization of two-dimensional terahertz spectroscopy

Two-dimensional terahertz spectroscopy (2DTS) is a low-frequency analog of two-dimensional optical spectroscopy that is rapidly maturing as a probe of a wide variety of condensed matter systems. However, a persistent problem with 2DTS is the long experimental acquisition times, which prevent its broader adoption. A potential solution, requiring no increase in experimental complexity, is signal reconstruction via compressive sensing. In this work, we apply the sparse exponential mode analysis (SEMA) technique to 2DTS of a cuprate superconductor. We benchmark the performance of the algorithm in reconstructing terahertz nonlinearities and find that SEMA reproduces the asymmetric photon echo line shapes at sampling rates as low as 10%, reaching the reconstruction noise floor at sampling rates beyond 20%–30%. The success of SEMA in reproducing such subtle, asymmetric line shapes confirms compressive sensing as a general method to accelerate 2DTS and multidimensional spectroscopies more broadly.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Restoring the discontinuous heat equation source using sparse boundary data and dynamic sensors

Abstract This study focuses on addressing the inverse source problem associated with the parabolic equation. We rely on sparse boundary flux data as our measurements, which are acquired from a restricted section of the boundary. While it has been established that utilizing sparse boundary flux data can enable source recovery, the presence of a limited number of observation sensors poses a challenge for accurately tracing the inverse quantity of interest. To overcome this limitation, we introduce a sampling algorithm grounded in Langevin dynamics that incorporates dynamic sensors to capture the flux information. Furthermore, we propose and discuss two distinct dynamic sensor migration strategies. Remarkably, our findings demonstrate that even with only two observation sensors at our disposal, it remains feasible to successfully reconstruct the high-dimensional unknown parameters.

Mathematics↗

UHF coplanar-slot antenna for aircraft-to-satellite data communications

The initiative for starting the Aircraft-to-Satellite Data Relay (ASDAR) Program came from a recognition that much of the world's weather originates in the data sparse area of the tropics which are primarily ocean. The ASDAR system consists of (1) a data acquisition and control unit to acquire, store and format these data; (2) a clock to time the data sampling and transmission periods; and (3) a transmitter and low-profile upper hemisphere coverage antenna to relay the formatted data via satellite to the National Weather Service ground stations, as shown schematically. The low-profile antenna is a conformal antenna based on the coplanar-slot approach. The antenna is circular polarized and has an on-axis gain of nearly 2.5 dB and a HPBW greater than 90 deg. The discussion covers antenna design, radiation characteristics, flight testing, and system performance.

Myhre, R. W.↗

Systems and methods for active learning from sparse training data

A method for active learning using sparse training data can include training a machine learning model using less than ten first training data points to generate a candidate machine learning model. The method can include performing a Monte Carlo process to sample one or more first outputs of the candidate machine learning model. The method can include testing the one or more first outputs to determine if each of the one or more first outputs satisfy a respective convergence condition. The method can include, responsive to at least one first output not satisfying the respective convergence condition, training the candidate machine learning model using at least one second training data point corresponding to the at least one first output. The method can include, responsive to the one or more first outputs each satisfying the respective convergence condition, outputting the candidate machine learning model.

Sankaranarayanan, Subramanian↗

Efficient mapping between void shapes and stress fields using Deep Convolutional Neural Networks with sparse data

Establishing fast and accurate structure-to-property relationships is an important component in the design and discovery of advanced materials. Physics-based simulation models like the finite element method (FEM) are often used to predict deformation, stress, and strain fields as a function of material microstructure in material and structural systems. Such models may be computationally expensive and time intensive if the underlying physics of the system is complex. This limits their application to solve inverse design problems and identify structures that maximize performance. In such scenarios, surrogate models are employed to make the forward mapping computationally efficient to evaluate. However, the high dimensionality of the input microstructure and the output field of interest often renders such surrogate models inefficient, especially when dealing with sparse data. Deep convolutional neural network (CNN) based surrogate models have shown great promise in handling such high-dimensional problems. In this paper, a single ellipsoidal void structure under a uniaxial tensile load represented by a linear elastic, high-dimensional and expensive-to-query, FEM model. We consider two deep CNN architectures, a modified convolutional autoencoder framework with a fully connected bottleneck and a UNet CNN, and compare their accuracy in predicting the von Mises stress field for any given input void shape in the FEM model. Additionally, a sensitivity analysis study is performed using the two approaches, where the variation in the prediction accuracy on unseen test data is studied through numerical experiments by varying the number of training samples from 20 to 100.

surrogate modeling; convolutional neural networks;↗

Bayesian sparse learning with preconditioned stochastic gradient MCMC and its applications

Deep neural networks have been successfully employed in an extensive variety of research areas, including solving partial differential equations. Despite its significant success, there are some challenges in effectively training DNN, such as avoiding overfitting in over-parameterized DNNs and accelerating the optimization in DNNs with pathological curvature. Here, we propose a Bayesian type sparse deep learning algorithm. The algorithm utilizes a set of spike-and-slab priors for the parameters in the deep neural network. The hierarchical Bayesian mixture will be trained using an adaptive empirical method. That is, one will alternatively sample from the posterior using preconditioned stochastic gradient Langevin Dynamics (PSGLD), and optimize the latent variables via stochastic approximation. The sparsity of the network is achieved while optimizing the hyperparameters with adaptive searching and penalizing. A popular SG-MCMC approach is Stochastic gradient Langevin dynamics (SGLD). However, considering the complex geometry in the model parameter space in nonconvex learning, updating parameters using a universal step size in each component as in SGLD may cause slow mixing. To address this issue, we apply a computationally manageable preconditioner in the updating rule, which provides a step-size parameter to adapt to local geometric properties. Moreover, by smoothly optimizing the hyperparameter in the preconditioning matrix, our proposed algorithm ensures a decreasing bias, which is introduced by ignoring the correction term in the preconditioned SGLD. According to the existing theoretical framework, we show that the proposed algorithm can asymptotically converge to the correct distribution with a controllable bias under mild conditions. Numerical tests are performed on both synthetic regression problems and learning solutions of elliptic PDE, which demonstrate the accuracy and efficiency of the present work.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Comparison of sparse domain approaches for 4D SPECT dynamic image reconstruction

Purpose: Dynamic imaging (DI) provides additional diagnostic information in emission tomography in comparison to conventional static imaging at the cost of being computationally more challenging. Dynamic single photon emission computed tomography (SPECT) reconstruction is particularly difficult because of the limitations in the sampling geometry present in most existing scanners. We have developed an algorithm Spline Initialized Factor Analysis of Dynamic Structures (SIFADS) that is a matrix factorization method for reconstructing the dynamics of tracers in tissues and blood directly from the projections in dynamic cardiac SPECT, without first resorting to any 3D reconstruction. Methods: SIFADS is different from "pure" factor analysis in dynamic structures (FADS) in that it employs a dedicated spline-based pre-initialization. In this paper, we analyze the convergence properties of SIFADS and FADS using multiple metrics. The performances of the two approaches are evaluated for numerically simulated data and for real dynamic SPECT data from canine and human subjects. Results: For SIFADS, metrics analyzed for reconstruction algorithm convergence show better features of the metric curves vs iterations. In addition, SIAFDS provides better tissue segmentations than that from pure FADS. Measured computational times are also typically better for SIFADS implementations than those with pure FADS. Conclusion: The analysis supports the utility of the pre-initialization of a factorization algorithm for better dynamic SPECT image reconstruction.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Atom probe tomography characterization of ion and neutron irradiated Alloy 800H

Alloy 800H is a high temperature and creep resistant alloy, and is considered as a candidate alloy for use in Generation IV nuclear reactor systems. To clarify the alloy's behavior under irradiation, samples were subjected to single ion irradiations up to 20 dpa at 440°C, a dual ion/He irradiation to 17 dpa at 460°C, and a neutron irradiation to 17 dpa at 385°C. The irradiated microstructures were characterized using atom probe tomography to complement previously published transmission electron microscopy studies. Additionally, after single ion irradiation, sparse fine Al and Ti clusters were observed after 1dpa, while high number densities of nanoscale Ni-Al-Ti clusters, Cr-Ti rich carbides, and Si-decorated dislocation loops developed after 10 and 20 dpa. The microstructure formed during single ion irradiation exhibited a strong depth dependence. No significant differences were observed between the single and dual ion irradiations. While Ni-Al-Ti clusters, Cr-Ti rich carbides, and Si-decorated dislocation loops were also observed after neutron irradiation, the neutron-irradiated microstructure differed from those found in the ion-irradiated samples.

36 MATERIALS SCIENCE↗