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At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Lower soil moisture and deep soil temperatures in thermokarst features increase old soil carbon loss after 10 years of experimental permafrost warming

Almost half of the global terrestrial soil carbon (C) is stored in the northern circumpolar permafrost region, where air temperatures are increasing two times faster than the global average. As climate warms, permafrost thaws and soil organic matter becomes vulnerable to greater microbial decomposition. Long-term soil warming of ice-rich permafrost can result in thermokarst formation that creates variability in environmental conditions. Consequently, plant and microbial proportional contributions to ecosystem respiration may change in response to long-term soil warming. Natural abundance δ 13 C and Δ 14 C of aboveground and belowground plant material, and of young and old soil respiration were used to inform a mixing model to partition the contribution of each source to ecosystem respiration fluxes. We employed a hierarchical Bayesian approach that incorporated gross primary productivity and environmental drivers to constrain source contributions. We found that long-term experimental permafrost warming introduced a soil hydrology component that interacted with temperature to affect old soil C respiration. Old soil C loss was suppressed in plots with warmer deep soil temperatures because they tended to be wetter. When soil volumetric water content significantly decreased in 2018 relative to 2016 and 2017, the dominant respiration sources shifted from plant aboveground and young soil respiration to old soil respiration. The proportion of ecosystem respiration from old soil C accounted for up to 39% of ecosystem respiration and represented a 30-fold increase compared to the wet-year average. Our findings show that thermokarst formation may act to moderate microbial decomposition of old soil C when soil is highly saturated. However, when soil moisture decreases, a higher proportion of old soil C is vulnerable to decomposition and can become a large flux to the atmosphere. Furthermore, as permafrost systems continue to change with climate, we must understand the thresholds that may propel these systems from a C sink to a source.

permafrost↗
DOE OSTI2015

Kullback--Leibler Approximation for Probability Measures on Infinite Dimensional Spaces

In a variety of applications it is important to extract information from a probability measure μ on an infinite dimensional space. Examples include the Bayesian approach to inverse problems and (possibly conditioned) continuous time Markov processes. It may then be of interest to find a measure ν, from within a simple class of measures, which approximates μ. Here, this problem is studied in the case where the Kullback–Leibler divergence is employed to measure the quality of the approximation. A calculus of variations viewpoint is adopted, and the particular case where ν is chosen from the set of Gaussian measures is studied in detail. Basic existence and uniqueness theorems are established, together with properties of minimizing sequences. Furthermore, parameterization of the class of Gaussians through the mean and inverse covariance is introduced, the need for regularization is explained, and a regularized minimization is studied in detail. The calculus of variations framework resulting from this work provides the appropriate underpinning for computational algorithms.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Designing optimal experiments: an application to proton Compton scattering

Interpreting measurements requires a physical theory, but the theory’s accuracy may vary across the experimental domain. To optimize experimental design, and so to ensure that the substantial resources necessary for modern experiments are focused on acquiring the most valuable data, both the theory uncertainty and the expected pattern of experimental errors must be considered. We develop a Bayesian approach to this problem, and apply it to the example of proton Compton scattering. Chiral Effective Field Theory (χEFT) predicts the functional form of the scattering amplitude for this reaction, so that the electromagnetic polarizabilities of the nucleon can be inferred from data. With increasing photon energy, both experimental rates and sensitivities to polarizabilities increase, but the accuracy of χEFT decreases. Our physics-based model of χEFT truncation errors is combined with present knowledge of the polarizabilities and reasonable assumptions about experimental capabilities at HI γ S and MAMI to assess the information gain from measuring specific observables at specific kinematics, i.e. to determine the relative amount by which new data are apt to shrink uncertainties. The strongest gains would likely come from new data on the spin observables Σ 2x and Σ 2x' at ω≃140 to 200 MeV and 40° to 120°. These would tightly constrain γ E1E1 –γ E1M2 . New data on the differential cross section between 100 and 200 MeV and over a wide angle range will substantially improve constraints on α E1 –β M1 , γ π and γ M1M1 –γ M1E2 . Good signals also exist around 160 MeV for Σ 3 and Σ 2z' . As a result, such data will be pivotal in the continuing quest to pin down the scalar polarizabilities and refine understanding of the spin polarizabilities.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Fully Bayesian Analysis With Model Inadequacy Correction For Nuclear Graphite Property Models With Hierarchical Variance Structure

Nuclear-grade graphites are extensively utilized in the core designs of various advanced nuclear reactors. Within the reactor environment, graphite is subjected to prolonged exposure to extreme conditions, including high temperatures, radiation, and potentially molten salt and oxygen. Such exposure can induce several degradation mechanisms in graphite, such as nonuniform volumetric strains caused by irradiation and thermal expansion, leading to stresses that may compromise the performance of graphite components. Assessing component integrity, forecasting component performance over the reactor's lifespan, and developing design standards necessitate robust tools for predicting fracture initiation and propagation in graphite structural components within nuclear reactors. This code enables the Bayesian calibration of properties for nuclear-grade graphites. Using a hierarchical Bayesian approach, multiple experimental data sources are combined to develop Gaussian process models for the properties. Using the Kennedy O'Hagan framework, the uncertainties due inadequacies in the model and the inherent spread in the experimental data are quantified.

Dhulipala, Som Lakshmi NarasimhaLakshmi Narasimha ↗
DOE OSTI2022

Sequentially calibrating a Bayesian microsimulation model to incorporate new information and assumptions

Background: Microsimulation models are mathematical models that simulate event histories for individual members of a population. They are useful for policy decisions because they simulate a large number of individuals from an idealized population, with features that change over time, and the resulting event histories can be summarized to describe key population-level outcomes. Model calibration is the process of incorporating evidence into the model. Calibrated models can be used to make predictions about population trends in disease outcomes and effectiveness of interventions, but calibration can be challenging and computationally expensive. Methods: This paper develops a technique for sequentially updating models to take full advantage of earlier calibration results, to ultimately speed up the calibration process. A Bayesian approach to calibration is used because it combines different sources of evidence and enables uncertainty quantification which is appealing for decision-making. We develop this method in order to re-calibrate a microsimulation model for the natural history of colorectal cancer to include new targets that better inform the time from initiation of preclinical cancer to presentation with clinical cancer (sojourn time), because model exploration and validation revealed that more information was needed on sojourn time, and that the predicted percentage of patients with cancers detected via colonoscopy screening was too low. Results: The sequential approach to calibration was more efficient than recalibrating the model from scratch. Incorporating new information on the percentage of patients with cancers detected upon screening changed the estimated sojourn time parameters significantly, increasing the estimated mean sojourn time for cancers in the colon and rectum, providing results with more validity. Conclusions: A sequential approach to recalibration can be used to efficiently recalibrate a microsimulation model when new information becomes available that requires the original targets to be supplemented with additional targets.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Radiation Source Mapping with Bayesian Inverse Methods

In this work, we present a method to map the spectral and spatial distributions of radioactive sources using a limited number of detectors. Locating and identifying radioactive materials is important for border monitoring, in accounting for special nuclear material in processing facilities, and in cleanup operations following a radioactive material spill. Most methods to analyze these types of problems make restrictive assumptions about the distribution of the source. In contrast, the source mapping method presented here allows an arbitrary three-dimensional distribution in space and a gamma peak distribution in energy. To apply the method, the problem is cast as an inverse problem where the system’s geometry and material composition are known and fixed, while the radiation source distribution is sought. A probabilistic Bayesian approach is used to solve the resulting inverse problem since the system of equations is ill-posed. The posterior is maximized with a Newton optimization method. The probabilistic approach also provides estimates of the confidence in the final source map prediction. A set of adjoint, discrete ordinates flux solutions, obtained in this work by the Denovo code, is required to efficiently compute detector responses from a candidate source distribution. These adjoint fluxes form the linear mapping from the state space to the response space. The test of the method’s success is simultaneously locating a set of 137 Cs and 60 Co gamma sources in a room. This test problem is solved using experimental measurements that we collected for this purpose. Because of the weak sources available for use in the experiment, some of the expected photopeaks were not distinguishable from the Compton continuum. However, by supplanting 14 flawed measurements (out of a total of 69) with synthetic responses computed by MCNP, the proof-of-principle source mapping was successful. The locations of the sources were predicted within 25 cm for two of the sources and 90 cm for the third, in a room with an ~4-x 4-m floor plan. Finally, the predicted source intensities were within a factor of ten of their true value.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2023

BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale

Metabolic fluxes, the number of metabolites traversing each biochemical reaction in a cell per unit time, are crucial for assessing and understanding cell function. 13 C Metabolic Flux Analysis ( 13 C MFA) is considered to be the gold standard for measuring metabolic fluxes. 13 C MFA typically works by leveraging extracellular exchange fluxes as well as data from 13 C labeling experiments to calculate the flux profile which best fit the data for a small, central carbon, metabolic model. However, the nonlinear nature of the 13 C MFA fitting procedure means that several flux profiles fit the experimental data within the experimental error, and traditional optimization methods offer only a partial or skewed picture, especially in “non-gaussian” situations where multiple very distinct flux regions fit the data equally well. Here, we present a method for flux space sampling through Bayesian inference (BayFlux), that identifies the full distribution of fluxes compatible with experimental data for a comprehensive genome-scale model. This Bayesian approach allows us to accurately quantify uncertainty in calculated fluxes. We also find that, surprisingly, the genome-scale model of metabolism produces narrower flux distributions (reduced uncertainty) than the small core metabolic models traditionally used in 13 C MFA. The different results for some reactions when using genome-scale models vs core metabolic models advise caution in assuming strong inferences from 13 C MFA since the results may depend significantly on the completeness of the model used. Based on BayFlux, we developed and evaluated novel methods (P- 13 C MOMA and P- 13 C ROOM) to predict the biological results of a gene knockout, that improve on the traditional MOMA and ROOM methods by quantifying prediction uncertainty.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Mechanistic within-host mathematical model of inhalational anthrax

We present a mathematical model of the dynamics of Bacillus anthracis bacteria within the lymph nodes and blood of a host, following inhalation of an initial dose of spores. We also incorporate the dynamics of protective antigen, which is the binding component of the anthrax toxin produced by the bacteria. The model offers a mechanistic description of the early infection dynamics of inhalational anthrax, while its stochastic nature allows us to study the probabilities of different outcomes (for example, how likely it is that the infection will be cleared for a given inhaled dose of spores) in order to explain dose-response data for inhalational anthrax. The model is calibrated via a Bayesian approach, using in vivo data from New Zealand white rabbit and guinea pig infection studies, enabling within-host parameters to be estimated. We also leverage incubation-period data from the Sverdlovsk 1979 anthrax outbreak to show that the model can accurately describe human time-to-symptoms data under reasonable parameter regimes. Finally, we derive a simple approximate formula for the probability of symptom onset before time t, assuming that the number of inhaled spores has a Poisson distribution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Phylogenetic diversity of 200+ isolates of the ectomycorrhizal fungus Cenococcum geophilum associated with Populus trichocarpa soils in the Pacific Northwest, USA and comparison to globally distributed representatives

The ectomycorrhizal fungal symbiont Cenococcum geophilum is of high interest as it is globally distributed, associates with many plant species, and has resistance to multiple environmental stressors. C . geophilum is only known from asexual states but is often considered a cryptic species complex, since extreme phylogenetic divergence is often observed within nearly morphologically identical strains. Alternatively, C . geophilum may represent a highly diverse single species, which would suggest cryptic but frequent recombination. Here we describe a new isolate collection of 229 C . geophilum isolates from soils under Populus trichocarpa at 123 collection sites spanning a ~283 mile north-south transect in Western Washington and Oregon, USA (PNW). To further understanding of the phylogenetic relationships within C . geophilum , we performed maximum likelihood and Bayesian phylogenetic analyses to assess divergence within the PNW isolate collection, as well as a global phylogenetic analysis of 789 isolates with publicly available data from the United States, Japan, and European countries. Phylogenetic analyses of the PNW isolates revealed three distinct phylogenetic groups, with 15 clades that strongly resolved at >80% bootstrap support based on a GAPDH phylogeny and one clade segregating strongly in two principle component analyses. The abundance and representation of PNW isolate clades varied greatly across the North-South range, including a monophyletic group of isolates that spanned nearly the entire gradient at ~250 miles. A direct comparison between the GAPDH and ITS rRNA gene region phylogenies, combined with additional analyses revealed stark incongruence between the ITS and GAPDH gene regions, consistent with intra-species recombination between PNW isolates. In the global isolate collection phylogeny, 34 clades were strongly resolved using Maximum Likelihood and Bayesian approaches (at >80% MLBS and >0.90 BPP respectively), with some clades having intra- and intercontinental distributions. Together these data are highly suggestive of divergence within multiple cryptic species, however additional analyses such as higher resolution genotype-by-sequencing approaches are needed to distinguish potential species boundaries and the mode and tempo of recombination patterns.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Developing a Comprehensive Risk Assessment Framework for Geological Storage CO 2

The operational risks for CCS projects include: risks of capturing, compressing, transporting and injecting CO₂; risks of well blowouts; risk that CO 2 will leak into shallow aquifers and contaminate potable water; and risk that sequestered CO 2 will leak into the atmosphere. This report examines these risks by using information on the risks associated with analogue activities such as CO 2 based enhanced oil recovery (CO 2 -EOR), natural gas storage and acid gas disposal. We have developed a new analysis of pipeline risk based on Bayesian statistical analysis. Bayesian theory probabilities may describe states of partial knowledge, even perhaps those related to non-repeatable events. The Bayesian approach enables both utilizing existing data and at the same time having the capability to adsorb new information thus to lower uncertainty in our understanding of complex systems. Incident rates for both natural gas and CO 2 pipelines have been widely used in papers and reports on risk of CO 2 pipelines as proxies for the individual risk created by such pipelines. Published risk studies of CO 2 pipelines suggest that the individual risk associated with CO2 pipelines is between 10 -3 and 10 -4 , which reflects risk levels approaching those of mountain climbing, which many would find unacceptably high. This report concludes, based on a careful analysis of natural gas pipeline failures, suggests that the individual risk of CO 2 pipelines is likely in the range of 10-6 to 10-7, a risk range considered in the acceptable to negligible range in most countries. If, as is commonly thought, pipelines represent the highest risk component of CCS outside of the capture plant, then this conclusion suggests that most (if not all) previous quantitative- risk assessments of components of CCS may be orders of magnitude to high. The potential lethality of unexpected CO 2 releases from pipelines or wells are arguably the highest risk aspects of CO 2 enhanced oil recovery (CO2-EOR), carbon capture, and storage (CCS). Assertions in the CCS literature, that CO 2 levels of 10% for ten minutes, or 20 to 30% for a few minutes are lethal to humans, are not supported by the available evidence. The results of published experiments with animals exposed to CO 2 , from mice to monkeys, at both normal and depleted oxygen levels, suggest that lethal levels of CO 2 toxicity are in the range 50 to 60%. These experiments demonstrate that CO 2 does not kill by asphyxia, but rather is toxic at high concentrations. It is concluded that quantitative risk assessments of CCS have overestimated the risk of fatalities by using values of lethality a factor two to six lower than the values estimated in this paper. In many dispersion models of CO 2 releases from pipelines, no fatalities would be predicted if appropriate levels of lethality for CO 2 had been used in the analysis.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

Statistical Modeling Efforts for Headspace Gas

The purpose of this document is to describe the statistical modeling effort for gas concentrations in WIPP storage containers. The concentration (in ppm) of CO 2 in the headspace volume of standard waste box (SWB) 68685 is shown. A Bayesian approach and an adaptive Metropolis-Hastings algorithm were used.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2017

Multi-scale modeling of carbon capture systems

The development and scale up of cost effective carbon capture processes is of paramount importance to enable the widespread deployment of these technologies to significantly reduce greenhouse gas emissions. The U.S. Department of Energy initiated the Carbon Capture Simulation Initiative (CCSI) in 2011 with the goal of developing a computational toolset that would enable industry to more effectively identify, design, scale up, operate, and optimize promising concepts. The first half of the presentation will introduce the CCSI Toolset consisting of basic data submodels, steady-state and dynamic process models, process optimization and uncertainty quantification tools, an advanced dynamic process control framework, and high-resolution filtered computationalfluid- dynamics (CFD) submodels. The second half of the presentation will describe a high-fidelity model of a mesoporous silica supported, polyethylenimine (PEI)-impregnated solid sorbent for CO 2 capture. The sorbent model includes a detailed treatment of transport and amine-CO 2 - H 2 O interactions based on quantum chemistry calculations. Using a Bayesian approach for uncertainty quantification, we calibrate the sorbent model to Thermogravimetric (TGA) data.

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

Uncertainty Quantification in High Explosives Equations of State [Slides]

In order to fit models to data, we need a way to simulate the data given a model. Our projects involved simulators for the Manganin gauge experiment and for cylinder tests, which we use to calibrate models to experiments. We call the parameters we seek to optimize the degrees of freedom (DOF). We use a Bayesian approach with its associated UQ benefits.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
DOE OSTI2015

Probabilistic methods for sensitivity analysis and calibration in the NASA challenge problem

In this study, a series of algorithms are proposed to address the problems in the NASA Langley Research Center Multidisciplinary Uncertainty Quantification Challenge. A Bayesian approach is employed to characterize and calibrate the epistemic parameters based on the available data, whereas a variance-based global sensitivity analysis is used to rank the epistemic and aleatory model parameters. A nested sampling of the aleatory–epistemic space is proposed to propagate uncertainties from model parameters to output quantities of interest.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

High contrast imaging with Spitzer: constraining the frequency of giant planets out to 1000 au separations

We report results of a re-analysis of archival Spitzer IRAC direct imaging surveys encompassing a variety of nearby stars. Our sample is generated from the combined observations of 73 young stars (median age, distance, spectral type = 85 Myr, 23.3 pc, G5) and 48 known exoplanet host stars with unconstrained ages (median distance, spectral type = 22.6 pc, G5). While the small size of Spitzer provides a lower resolution than 8 m class AO-assisted ground-based telescopes, which have been used for constraining the frequency of 0.5–13 M {sub J} planets at separations of 10–10{sup 2} au, its exquisite infrared sensitivity provides the ability to place unmatched constraints on the planetary populations at wider separations. Here we apply sophisticated high-contrast techniques to our sample in order to remove the stellar point-spread function and to open up sensitivity to planetary mass companions down to 5″ separations. This enables sensitivity to 0.5–13 M {sub J} planets at physical separations on the order of 10{sup 2}–10{sup 3} au, allowing us to probe a parameter space that has not previously been systematically explored to any similar degree of sensitivity. Based on a color and proper motion analysis, we do not record any planetary detections. Exploiting this enhanced survey sensitivity, employing Monte Carlo simulations with a Bayesian approach, and assuming a mass distribution of dn/dm∝m{sup −1.31}, we constrain (at 95% confidence) a population of 0.5–13 M {sub J} planets at separations of 100–1000 au with an upper frequency limit of 9%.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

A BAYESIAN ESTIMATE OF THE CMB–LARGE-SCALE STRUCTURE CROSS-CORRELATION

Evidences for late-time acceleration of the universe are provided by multiple probes, such as Type Ia supernovae, the cosmic microwave background (CMB), and large-scale structure (LSS). In this work, we focus on the integrated Sachs–Wolfe (ISW) effect, i.e., secondary CMB fluctuations generated by evolving gravitational potentials due to the transition between, e.g., the matter and dark energy (DE) dominated phases. Therefore, assuming a flat universe, DE properties can be inferred from ISW detections. We present a Bayesian approach to compute the CMB–LSS cross-correlation signal. The method is based on the estimate of the likelihood for measuring a combined set consisting of a CMB temperature and galaxy contrast maps, provided that we have some information on the statistical properties of the fluctuations affecting these maps. The likelihood is estimated by a sampling algorithm, therefore avoiding the computationally demanding techniques of direct evaluation in either pixel or harmonic space. As local tracers of the matter distribution at large scales, we used the Two Micron All Sky Survey galaxy catalog and, for the CMB temperature fluctuations, the ninth-year data release of the Wilkinson Microwave Anisotropy Probe ( WMAP 9). The results show a dominance of cosmic variance over the weak recovered signal, due mainly to the shallowness of the catalog used, with systematics associated with the sampling algorithm playing a secondary role as sources of uncertainty. When combined with other complementary probes, the method presented in this paper is expected to be a useful tool to late-time acceleration studies in cosmology.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

ACCESS: Ground-based Optical Transmission Spectroscopy of the Hot Jupiter WASP-4b

We present an optical transmission spectrum of the atmosphere of WASP-4b obtained through observations of four transits with Magellan/IMACS, as part of the Arizona-CfA-Católica-Carnegie Exoplanet Spectroscopy Survey (ACCESS). Using a Bayesian approach to atmospheric retrieval, we find no evidence for scattering or absorption features in our transit spectrum. Our models include a component to model the transit light source effect (spectral contamination from unocculted spots on the stellar photosphere), which we show can have a marked impact on the observed transmission spectrum for reasonable spot-covering fractions (<5%); this is the first such analysis for WASP-4b. We are also able to fit for the size and temperature contrast of spots observed during the second and third transits, finding evidence for both small, cool and large, warm spot-like features on the photosphere. Finally, we compare our results to those published by Huitson et al. using Gemini/GMOS and May et al. using IMACS, and we find that our data are in agreement.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

A Catalog of Distance Determinations for the LAMOST DR8 K Giants in the Galactic Halo

We present a catalog of distances for 19,544 K giants drawn from Large Sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST) DR8. Most of them are located in the halo of the Milky Way up to ~120 kpc. There are 15% K giants without Sloan Digital Sky Survey (SDSS) photometry, for which we supplements with Pan-STARRS1 (PS1) photometry calibrated to SDSS photometric system. The possible contamination of the red clumps/horizontal branch are removed according to metallicities and colors before the distance determination. Combining the LAMOST spectroscopic metallicities with the SDSS/PS1 photometry, we estimate the absolute magnitudes in the SDSS r band, the distance moduli, and the corresponding uncertainties through an Bayesian approach devised by Xue et al. for the Sloan Extension for Galactic understanding and exploration halo K giants. The typical distance precision is about 11%. The stars in the catalog lie in a region of 4–126 kpc from the Galactic center, of which with 6320 stars beyond 20 kpc and 273 stars beyond 50 kpc, forming the largest spectroscopic sample of distant tracers in the Milky Way halo so far.

79 ASTRONOMY AND ASTROPHYSICS↗