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Results for “Bayesian retrieval”

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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26 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

PhaseT3M: 3D imaging at 1.6 Å resolution via electron cryo-tomography with nonlinear phase retrieval

Electron cryo-tomography (cryo-ET) enables 3D imaging of complex, radiation-sensitive structures with molecular detail. However, image contrast from the interference of scattered electrons is nonlinear with atomic density and multiple scattering further complicates interpretation. These effects degrade resolution, particularly in conventional reconstruction algorithms, which assume linearity. Particle averaging can reduce such issues but is unsuitable for heterogeneous or dynamic samples ubiquitous in biology, chemistry, and materials sciences. Here, we develop a phase retrieval-based cryo-ET method, PhaseT3M. We experimentally demonstrate its application to an approximately 7 nm Co3O4 nanoparticle on an approximately 30 nm carbon substrate, achieving a maximum resolution of 1.6 Å, surpassing conventional limits using standard cryo-TEM equipment. PhaseT3M uses a multislice model for multiple scattering and Bayesian optimization for alignment and computational aberration correction, with a positivity constraint to recover ‘missing wedge’ information. Applied directly to biological particles, it enhances reconstruction quality and reduces artifacts, establishing a standard for routine 3D imaging with phase contrast.

Biophysics↗
DOE OSTI2024

Methods for Incorporating Model Uncertainty into Exoplanet Atmospheric Analysis

A key goal of exoplanet spectroscopy is to measure atmospheric properties, such as abundances of chemical species, in order to connect them to our understanding of atmospheric physics and planet formation. In this new era of high-quality JWST data, it is paramount that these measurement methods are robust. When comparing atmospheric models to observations, multiple candidate models may produce reasonable fits to the data. Typically, conclusions are reached by selecting the best-performing model according to some metric. This ignores model uncertainty in favor of specific model assumptions, potentially leading to measured atmospheric properties that are overconfident and/or incorrect. In this paper, we compare three ensemble methods for addressing model uncertainty by combining posterior distributions from multiple analyses: Bayesian model averaging, a variant of Bayesian model averaging using leave-one-out predictive densities, and stacking of predictive distributions. We demonstrate these methods by fitting the Hubble Space Telescope (HST) + Spitzer transmission spectrum of the hot Jupiter HD 209458b using models with different cloud and haze prescriptions. All of our ensemble methods lead to uncertainties on retrieved parameters that are larger but more realistic and consistent with physical and chemical expectations. Since they have not typically accounted for model uncertainty, uncertainties of retrieved parameters from HST spectra have likely been underreported. We recommend stacking as the most robust model combination method. Our methods can be used to combine results from independent retrieval codes and from different models within one code. They are also widely applicable to other exoplanet analysis processes, such as combining results from different data reductions.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Accelerating quantum optics experiments with statistical learning

Quantum optics experiments, involving the measurement of low-probability photon events, are known to be extremely time-consuming. We present a methodology for accelerating such experiments using physically motivated ansatzes together with simple statistical learning techniques such as Bayesian maximum a posteriori estimation based on few-shot data. We show that it is possible to reconstruct time-dependent data using a small number of detected photons, allowing for fast estimates in under a minute and providing a one-to-two order of magnitude speed-up in data acquisition time. We test our approach using real experimental data to retrieve the second order intensity correlation function, G (2) ($τ$), as a function of time delay τ between detector counts, for thermal light as well as anti-bunched light emitted by a quantum dot driven by periodic laser pulses. The proposed methodology has a wide range of applicability and has the potential to impact the scientific discovery process across a multitude of domains.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Identification of a new circulating recombinant form of human immunodeficiency virus type 1, CRF124_cpx involving subtypes A, G, H, and CRF27_cpx in Angola

Angola, located in Central Africa, has around 320,000 (270,000–380,000) people living with human immunodeficiency virus (HIV)/AIDS, equivalent to 1% of the country’s population at the end of 2021. A previous study conducted in 2012, using Angolan samples collected between 2008 and 2010 revealed a high prevalence of HIV-1 recombinants, around 42% of sequences, with 21% showing the same UH profile in partial pol region which were grouped into a monophyletic cluster with high bootstrap support. Thus, the objective of the present work was to obtain complete genomes of those sequences and characterize them, aiming at a description of a new circulating recombinant form (CRF). Whole blood from nine HIV-1 UH pol -infected individuals had their genomic DNA extracted, and nested PCR was used to amplify seven overlapping fragments targeting the full-length HIV-1 genome. The final classification was based on maximum likelihood trees, and recombination analyses were performed using a bootscan from the Simplot program. BLAST and Los Alamos Database inspections were used to search other similar H-like pol sequences. Complete genome amplification was possible for three samples, partial genomes were obtained for the other three, and only pol was available for the remaining three sequences. Bootscan analysis of the two whole-genome and three partial genome sequences retrieved from people living with HIV/AIDS (PLHIVA) without epidemiological linkage showed the same complex recombination profile involving HIV-1 subtypes A/G/H/CRF27_cpx, with a total of six recombinant breakpoints, aiming to classify a new HIV-1 CRF124_cpx. We found no other full-length HIV-1 genomes with the same mosaic profile; however, we identified 33 partial pol sequences, mainly sampled from Angola between 2001 to 2019, with the same H-like profile. Bayesian analysis of H and H-like pol sequences indicates that CRF124_cpx probably originated in Angola at mid-1970s, indicating that this CRF has been circulating in the country for a long time. In summary, our study describes a new CRF circulating principally in Angola and highlights the importance of continuing molecular surveillance studies, especially in countries with high molecular diversity of HIV.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Assessing the design of integrated methane sensing networks

Abstract While methane is the second largest contributor to global warming after carbon dioxide, it has a larger warming effect over a much shorter lifetime. Despite accelerated technological efforts to radically reduce global carbon dioxide emissions, rapid reductions in methane emissions are needed to limit near-term warming. Being primarily emitted as a byproduct from agricultural activities and energy extraction, methane is currently monitored via bottom–up (i.e. activity level) or top–down (via airborne or satellite retrievals) approaches. However, significant methane leaks remain undetected and emission rates are challenging to characterize with current monitoring frameworks. In this paper, we study the design of a layered monitoring approach that combines bottom–up and top–down approaches as an integrated sensing network. By recognizing that varying meteorological conditions and emission rates impact the efficacy of bottom–up monitoring, we develop a probabilistic approach to optimal sensor placement in its bottom–up network. Subsequently, we derive an inverse Bayesian framework to quantify the improvement that a design-optimized integrated framework has on emission-rate quantifications and their uncertainties. We find that under realistic meteorological conditions, the overall error in estimating the true emission rates is approximately 1.3 times higher, with their uncertainties being approximately 2.4 times higher, when using a randomized network over an optimized network, highlighting the importance of optimizing the design of integrated methane sensing networks. Further, we find that optimized networks can improve scenario coverage fractions by more than a factor of 2 over experimentally-studied networks, and identify a budget threshold beyond which the rate of optimized-network coverage improvement exhibits diminishing returns, suggesting that strategic sensor placement is also crucial for maximizing network efficiency.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

ARES. II. Characterizing the Hot Jupiters WASP-127 b, WASP-79 b, and WASP-62b with the Hubble Space Telescope

This paper presents the atmospheric characterization of three large, gaseous planets: WASP-127 b, WASP-79 b, and WASP-62 b. We analyzed spectroscopic data obtained with the G141 grism (1.088–1.68 μm) of the Wide Field Camera 3 on board the Hubble Space Telescope using the Iraclis pipeline and the TauREx3 retrieval code, both of which are publicly available. For WASP-127 b, which is the least dense planet discovered so far and is located in the short-period Neptune desert, our retrieval results found strong water absorption corresponding to an abundance of log(H{sub 2}O) = −2.71{sub −1.05}{sup +0.78} and absorption compatible with an iron hydride abundance of log(FeH) = −5.25{sub −1.10}{sup +0.88}, with an extended cloudy atmosphere. We also detected water vapor in the atmospheres of WASP-79 b and WASP-62 b, with best-fit models indicating the presence of iron hydride, too. We used the Atmospheric Detectability Index as well as Bayesian log evidence to quantify the strength of the detection and compared our results to the hot Jupiter population study by Tsiaras et al. While all the planets studied here are suitable targets for characterization with upcoming facilities such as the James Webb Space Telescope and Ariel, WASP-127 b is of particular interest due to its low density, and a thorough atmospheric study would develop our understanding of planet formation and migration.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

A Bayesian Approach for Statistical–Physical Bulk Parameterization of Rain Microphysics. Part II: Idealized Markov Chain Monte Carlo Experiments

Observationally informed development of a new framework for bulk rain microphysics, the Bayesian Observationally Constrained Statistical–Physical Scheme (BOSS; described in Part I of this study), is demonstrated. This scheme’s development is motivated by large uncertainties in cloud and weather simulations associated with approximations and assumptions in existing microphysics schemes. Here, a proof-of-concept study is introduced using a Markov chain Monte Carlo sampling algorithm with BOSS to probabilistically estimate microphysical process rates and parameters directly from a set of synthetically generated rain observations. The framework utilized is an idealized steady-state one-dimensional column rainshaft model with specified column-top rain properties and a fixed thermodynamical profile. Different configurations of BOSS—flexibility being a key feature of this approach—are constrained via synthetic observations generated from a traditional three-moment bulk microphysics scheme. The ability to retrieve correct parameter values when the true parameter values are known is illustrated. For cases when there is no set of true parameter values, the accuracy of configurations of BOSS that have different levels of complexity is compared. It is found that addition of the sixth moment as a prognostic variable improves prediction of the third moment (proportional to bulk rain mass) and rain rate. In contrast, increasing process rate formulation complexity by adding more power terms has little benefit—a result that is explained using further-idealized experiments. BOSS rainshaft simulations are shown to well estimate the true process rates from constraint by bulk rain observations, with the further benefit of rigorously quantified uncertainty of these estimates.

58 GEOSCIENCES↗
DOE OSTI2024

Deriving cloud droplet number concentration from surface-based remote sensors with an emphasis on lidar measurements

Abstract. Given the importance of constraining cloud droplet number concentrations (Nd) in low-level clouds, we explore two methods for retrieving Nd from surface-based remote sensing that emphasize the information content in lidar measurements. Because Nd is the zeroth moment of the droplet size distribution (DSD), and all remote sensing approaches respond to DSD moments that are at least 2 orders of magnitude greater than the zeroth moment, deriving Nd from remote sensing measurements has significant uncertainty. At minimum, such algorithms require the extrapolation of information from two other measurements that respond to different moments of the DSD. Lidar, for instance, is sensitive to the second moment (cross-sectional area) of the DSD, while other measures from microwave sensors respond to higher-order moments. We develop methods using a simple lidar forward model that demonstrates that the depth to the maximum in lidar-attenuated backscatter (Rmax⁡) is strongly sensitive to Nd when some measure of the liquid water content vertical profile is given or assumed. Knowledge of Rmax⁡ to within 5 m can constrain Nd to within several tens of percent. However, operational lidar networks provide vertical resolutions of > 15 m, making a direct calculation of Nd from Rmax⁡ very uncertain. Therefore, we develop a Bayesian optimal estimation algorithm that brings additional information to the inversion such as lidar-derived extinction and radar reflectivity near the cloud top. This statistical approach provides reasonable characterizations of Nd and effective radius (re) to within approximately a factor of 2 and 30 %, respectively. By comparing surface-derived cloud properties with MODIS satellite and aircraft data collected during the MARCUS and CAPRICORN II campaigns, we demonstrate the utility of the methodology.

54 ENVIRONMENTAL SCIENCES↗