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DOE OSTI2022

Single Gaussian process method for arbitrary tokamak regimes with a statistical analysis

Abstract Gaussian process regression is a Bayesian method for inferring profiles based on input data. The technique is increasing in popularity in the fusion community due to its many advantages over traditional fitting techniques including intrinsic uncertainty quantification and robustness to over-fitting. This work investigates the use of a new method, the change-point method, for handling the varying length scales found in different tokamak regimes. The use of the Student’s t-distribution for the Bayesian likelihood probability is also investigated and shown to be advantageous in providing good fits in profiles with many outliers. To compare different methods, synthetic data generated from analytic profiles is used to create a database enabling a quantitative statistical comparison of which methods perform the best. Using a full Bayesian approach with the change-point method, Matérn kernel for the prior probability, and Student’s t-distribution for the likelihood is shown to give the best results.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2

To investigate the evolutionary history of the recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China, a total of 70 genomes of virus strains from China and elsewhere with sampling dates between 24 December 2019 and 3 February 2020 were analyzed. To explore the potential intermediate animal host of the SARS-CoV-2 virus, we reanalyzed virome data sets from pangolins and representative SARS-related coronaviruses isolates from bats, with particular attention paid to the spike glycoprotein gene. We performed phylogenetic, split network, transmission network, likelihood-mapping, and comparative analyses of the genomes. Additionally, based on Bayesian time-scaled phylogenetic analysis using the tip-dating method, we estimated the time to the most recent common ancestor and evolutionary rate of SARS-CoV-2, which ranged from 22 to 24 November 2019 and 1.19 to 1.31 × 10 -3 substitutions per site per year, respectively. Our results also revealed that the BetaCoV/bat/Yunnan/RaTG13/2013 virus was more similar to the SARS-CoV-2 virus than the coronavirus obtained from the two pangolin samples (SRR10168377 and SRR10168378). We also identified a unique peptide (PRRA) insertion in the human SARS-CoV-2 virus, which may be involved in the proteolytic cleavage of the spike protein by cellular proteases, and thus could impact host range and transmissibility. Interestingly, the coronavirus carried by pangolins did not have the RRAR motif. Therefore, we concluded that the human SARS-CoV-2 virus, which is responsible for the recent outbreak of COVID-19, did not come directly from pangolins.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Single‐Particle Tracking for Understanding Polydisperse Nanoparticle Dispersions

Abstract Colloidal dispersions of nanomaterials are often polydisperse in size, significantly complicating their characterization. This is particularly true for materials early in their historical development due to synthetic control, dispersion efficiency, and instability during storage. Because a wide range of system properties and technological applications depend on particle dimensions, it remains an important problem in nanotechnology to identify a method for the routine characterization of polydispersity in nanoparticle samples, especially changes over time. Commonly employed methods such as dynamic light scattering or analytical ultracentrifugation (AUC) accurately estimate only the first moment of the distribution or are not routine. In this work, the use of single‐particle tracking (SPT) to probe size distributions of common nanoparticle dispersions, including polystyrene nanoparticles, single‐walled carbon nanotubes, graphene oxide, chitosan‐tripolyphosphate, acrylate, hexagonal boron nitride, and poly(lactic‐ co ‐glycolic acid), is proposed and explored. The analysis of particle tracks is conducted using a newly developed Bayesian algorithm that is called Maximum A posteriori Nanoparticle Tracking Analysis. By combining SPT and AUC techniques, it is shown that it is possible to independently estimate the mean aspect ratio of anisotropic particles, an important characterization property. It is concluded that SPT provides a facile, rapid analytical method for routine nanomaterials characterization.

Gong, Xun↗

DOE OSTI2018

Quarkonium in-medium properties from realistic lattice NRQCD

Here, we present the final results of our high statistics study on the properties of bottomonium and charmonium at finite temperature. We focus on the temperature range around the crossover transition 150 ≤ T ≤ 410MeV, relevant for current heavy ion collision experiments. The QCD medium degrees of freedom, which consist of dynamical u,d, and s quarks and gluons are captured by realistic state-of-the art (m π ≈ 161MeV) lattice QCD simulations of the HotQCD collaboration. For the heavy quarks we deploy the non-relativistic effective field theory of QCD, NRQCD. The in-medium properties of quarkonium are deduced from their spectral functions, which are reconstructed using improved and novel Bayesian approaches. Through a systematic analysis we shed light on the origin of the discrepancies in melting temperatures previously reported in the literature, showing that they are owed to underestimated methods uncertainties of the deployed spectral reconstructions. Our simulations corroborate a picture of sequential in-medium modification, ordered according to the vacuum binding energy of the states. As a central quantitative result, our study reveals how the mass of the heavy quarkonium ground state reduces as temperature increases. The observed spectral modifications are interpreted in the light of, and compared to previous studies based on the complex lattice potential for heavy quarkonium. Furthermore for the first time we provide a robust picture of in-medium heavy quarkonium modification in the quark-gluon plasma consistent among different non-relativistic methods. We also critically discuss the perspectives for improving on these results.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2023

BeyondPlanck: XV. Limits on large-scale polarized anomalous microwave emission from Planck LFI and WMAP

We constrained the level of polarized anomalous microwave emission (AME) on large angular scales using Planck Low-Frequency Instrument (LFI) and WMAP polarization data within a Bayesian cosmic microwave background (CMB) analysis framework. We modeled synchrotron emission with a power-law spectral energy distribution, as well as the sum of AME and thermal dust emission through linear regression with the Planck High-Frequency Instrument (HFI) 353 GHz data. This template-based dust emission model allowed us to constrain the level of polarized AME while making minimal assumptions on its frequency dependence. We neglected CMB fluctuations, but show through simulations that these fluctuations have a minor impact on the results. We find that the resulting AME polarization fraction confidence limit is sensitive to the polarized synchrotron spectral index prior. In addition, for prior means β s < -3.1 we find an upper limit of p AME max ≲ 0.6% (95% confidence). In contrast, for means β s = -3.0, we find a nominal detection of p AME = 2.5 ± 1.0% (95% confidence). These data are thus not strong enough to simultaneously and robustly constrain both polarized synchrotron emission and AME, and our main result is therefore a constraint on the AME polarization fraction explicitly as a function of β s . Combining the current Planck and WMAP observations with measurements from high-sensitivity low-frequency experiments such as C-BASS and QUIJOTE will be critical to improve these limits further.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

BEYONDPLANCK III. Commander3

We describe the computational infrastructure for end-to-end Bayesian cosmic microwave background (CMB) analysis implemented by the BeyondPlanck Collaboration. The code is called Commander3. It provides a statistically consistent framework for global analysis of CMB and microwave observations and may be useful for a wide range of legacy, current, and future experiments. The paper has three main goals. Firstly, we provide a high-level overview of the existing code base, aiming to guide readers who wish to extend and adapt the code according to their own needs or re-implement it from scratch in a different programming language. Secondly, we discuss some critical computational challenges that arise within any global CMB analysis framework, for instance in-memory compression of time-ordered data, fast Fourier transform optimization, and parallelization and load-balancing. Thirdly, we quantify the CPU and RAM requirements for the current BEYONDPLANCK analysis, finding that a total of 1.5 TB of RAM is required for efficient analysis and that the total cost of a full Gibbs sample for LFI is 170 CPU-hrs, including both low-level processing and high-level component separation, which is well within the capabilities of current low-cost computing facilities. The existing code base is made publicly available under a GNU General Public Library (GPL) license.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Fingerprints of hydrogen bonding in the terahertz dynamics of ethanol and water: An inelastic x-ray scattering study

Here, we used inelastic x-ray scattering methods to measure the terahertz spectrum of density fluctuations of ethanol in both liquid and solid phases. The results of a Bayesian inference-based lineshape analysis with a multiple excitation model and the comparison with a previous similar analysis on water indicate that the different structures induced by hydrogen bonds in ethanol and water have a profound influence on the respective dynamic responses, the latter being characterized by longer living and better resolved high-frequency acoustic excitations. In addition, we compare these findings with those obtained with an alternative approach based on the exponential expansion theory and ensuring sum rules fulfillment, demonstrating that the model’s choice directly impacts the number of spectral modes detected.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Cosmic ray spectrum of protons plus helium nuclei between 6 and 158 TeV from HAWC data

Here, a measurement with high statistics of the differential energy spectrum of light elements in cosmic rays, in particular, of primary H plus He nuclei, is reported. The spectrum is presented in the energy range from 6 to 158 TeV per nucleus. Data was collected with the High Altitude Water Cherenkov (HAWC) Observatory between June 2015 and June 2019. The analysis was based on a Bayesian unfolding procedure, which was applied on a subsample of vertical HAWC data that was enriched to 82% of events induced by light nuclei. To achieve the mass separation, a cut on the lateral age of air shower data was set guided by predictions of CORSIKA/QGSJET-II-04 simulations. The measured spectrum is consistent with a broken power-law spectrum and shows a kneelike feature at around E = 24.0$^{+3.6}_{-3.1}$ TeV , with a spectral index γ = -2.51 ± 0.02 before the break and with γ = -2.83 ± 0.02 above it. The feature has a statistical significance of 4.1σ. Within systematic uncertainties, the significance of the spectral break is 0.8σ.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

HEPfit: a code for the combination of indirect and direct constraints on high energy physics models

HEPfit is a flexible open-source tool which, given the Standard Model or any of its extensions, allows to (i) fit the model parameters to a given set of experimental observables; (ii) obtain predictions for observables. HEPfit can be used either in Monte Carlo mode, to perform a Bayesian Markov Chain Monte Carlo analysis of a given model, or as a library, to obtain predictions of observables for a given point in the parameter space of the model, allowing HEPfit to be used in any statistical framework. In the present version, around a thousand observables have been implemented in the Standard Model and in several new physics scenarios. In this paper, we describe the general structure of the code as well as models and observables implemented in the current release.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Risk-informed Predictive Analytics To Achieve Cost-effective Condition-based Monitoring And Maintenance Strategy

The research involves developing risk-informed predictive analytic capabilities to achieve condition-based monitoring and maintenance strategies to reduce overall maintenance costs. The research utilizes data (real-time data, periodic data, and institutional knowledge) related to a particular plant asset from a specific nuclear plant site to develop risk-informed predictive analytic algorithms. The developed algorithms and codes are used to optimize the maintenance strategy and estimate/forecast generation costs based on the state of health of the plant asset. Developed codes specifically include 1. Parameter estimation code based on Bayesian inference 2. Statistical data analysis code 3. Feature engineering code 4. Health classifier code 5. Diagnosis code 6. Prognosis code 7. Hazard code 8. Generation risk code 9. Economic code

Agarwal, Vivek↗

DOE OSTI2018

24.1.3.3 Quarterly Report FY18 Q1

Here, we will develop an enhanced statistical framework to evaluate environmental swipe samples collected at nuclear facilities with the goal of identifying anomalies associated with potential undeclared activities. Our approach will be based on Bayesian methodology and time series analysis. This overall framework should result in a more cost effective and operationally effective approach to environmental swipe sample analysis and interpretation.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

DOE OSTI2018

Statistical Methods for Improved Evaluation of Environmental Sample Data quarterly FY18Q2

We will develop an enhanced statistical framework to evaluate environmental swipe samples collected at nuclear facilities with the goal of identifying anomalies associated with potential undeclared activities. Our approach will be based on Bayesian methodology and time series analysis. This overall framework should result in a more cost effective and operationally effective approach to environmental swipe sample analysis and interpretation.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Machine Learning Model Geotiffs - Applications of Machine Learning Techniques to Geothermal Play Fairway Analysis in the Great Basin Region, Nevada

This submission contains geotiffs, supporting shapefiles and readmes for the inputs and output models of algorithms explored in the Nevada Geothermal Machine Learning project, meant to accompany the final report. Layers include: Artificial Neural Network (ANN), Extreme Learning Machine (ELM), Bayesian Neural Network (BNN), Principal Component Analysis (PCA/PCAk), Non-negative Matrix Factorization (NMF/NMFk), input rasters of feature sets, and positive/negative training sites. See readme .txt files and final report for additional metadata. A submission linking the full codebase for generating machine learning output models is available under "related resources" on this page.

15 GEOTHERMAL ENERGY↗

DOE OSTI2024

Improved Statistical Analysis for the Neutrinoless Double-Beta Decay Matrix Element of 136Xe

Neutrinoless double beta decay nuclear matrix element (M0ν) for 136Xe was recently analyzed using a statistical approach (Phys. Rev. C 107, 045501 (2023)). In the analysis, three initial shell model effective Hamiltonians were randomly altered, and their results for 23 measured observables were used to infer credibility for the M0ν nuclear matrix element (NME) based on a Bayesian Model Averaging approach. In that analysis, a reasonable Gamow-Teller quenching factor of 0.7 was assumed for each starting effective Hamiltonian. Given that the result of the statistical analysis was sensible to this choice, we are here improving that analysis by assuming that the Gamow-Teller quenching factor is also randomly chosen within reasonabe limits for all three starting Hamiltonians. The outcomes are slightly higher expectation values and uncertainties for the M0ν NME.

Astronomy & Astrophysics↗

DOE OSTI2025

Benchmarking optimization methods for materials research: Gradient descent and Bayesian optimization for lithium-ion battery aging diagnostics

Accurate and efficient parameter estimation is essential for battery diagnostics and aging analysis. Here, in this study, we compare two optimization-based approaches—gradient descent and Bayesian optimization—for extracting parameters from differential voltage analysis in lithium-ion batteries. While these techniques are widely used, their relative strengths and limitations for this application are not well understood. The study evaluates the trade-offs between these methods in terms of result quality, computational cost, and reliability within this specific application. The diagnostic results from our battery data suggest adopting gradient descent as an initial method for rapid and efficient analysis, while employing more stable optimization techniques, such as Bayesian optimization, as a verification step to mitigate potential instability. Comparing the two methods provides information on algorithmic choice, while inspiring further discussions on selecting appropriate techniques for specific research tasks.

Zhao, Ziqing [Boston Univ., MA (United States)] (O↗

DOE OSTI2021

On the analysis of signal peaks in pulse-height spectra

The estimation of the signal location and intensity of a peak in a pulse height spectrum is important for X- ray and γ-ray spectroscopy, charged-particle spectrometry, liquid chromatography, and many other subfields. However, both the ‘‘centroid’’ and ‘‘signal intensity’’ of a peak in a pulse-height spectrum are ill-defined quantities and different methods of analysis will yield different numerical results. Here, we apply three methods of analysis. Method A is based on simple count summation and is likely the technique most frequently applied in practice. The analysis is straightforward and fast, and does not involve any statistical modeling. We find that it provides reliable results only for high signal-to-noise data, but has severe limitations in all other cases. Method B employs a Bayesian model to extract signal counts and centroid from the measured total and background counts. The resulting values are derived from the respective posteriors and, therefore, have a rigorous statistical meaning. The method makes no assumptions about the peak shape. It yields reliable and relatively small centroid uncertainties. However, it provides relatively large signal count uncertainties. Method C makes a strong assumption regarding the peak shape by fitting a Gaussian function to the data. Furthermore, the fit is based again on a Bayesian model. Although Method C requires careful consideration of the Gaussian width (usually given by the detector resolution) used in the fitting, it provides reliable values and relatively small uncertainties both for the signal counts and the centroid.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2021

Particle transport constraints via Bayesian spectral fitting of multiple atomic lines

Optimized operation of fusion devices demands detailed understanding of plasma transport, a problem that must be addressed with advances in both measurement and data analysis techniques. In this work, we adopt Bayesian inference methods to determine experimental particle transport, leveraging opportunities from high-resolution He-like ion spectra in a tokamak plasma. The Bayesian spectral fitting code is used to analyze resonance (w), forbidden (z), intercombination (x, y), and satellite (k, j) lines of He-like Ca following laser blow-off injections on Alcator C-Mod. This offers powerful transport constraints since these lines depend differently on electron temperature and density, but also differ in their relation to Li-like, He-like, and H-like ion densities, often the dominant Ca charge states over most of the C-Mod plasma radius. Using synthetic diagnostics based on the AURORA package, we demonstrate improved effectiveness of impurity transport inferences when spectroscopic data from a progressively larger number of lines are included.

47 OTHER INSTRUMENTATION↗

DOE OSTI2021

Particle transport constraints via Bayesian spectral fitting of multiple atomic lines

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗