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At least 1,027 records · Page 57
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Enhanced particle transport events approaching the density limit of the J-TEXT tokamak

Enhanced particle transport events are discovered and analyzed as the density limit of the J-TEXT tokamak is approached. Edge shear layer collapse is observed and the ratio of Reynolds power to turbulence production decreases. Simultaneously, the divergence of turbulence internal energy flux (i.e. turbulence spreading) increases, indicating that shear layer collapse triggers an outward spreading event. Studies of correlations show that the enhanced particle transport events are quasi-coherent, and manifested primarily in density fluctuations which exhibit positive skewness. Furthermore, electron adiabaticity emerges as the critical parameter which signals transport event onset. For α < 0.35 as density approaches the Greenwald density, both turbulence spreading and density fluctuations rise rapidly. Taken together, these results elucidate the connections between edge shear layer, density fluctuations, particle transport events, turbulence spreading and plasma edge cooling as the density limit is approached.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2018

Novel functional and distributed approaches to data analysis available in ROOT

The bright future of particle physics at the Energy and Intensity frontiers poses exciting challenges to the scientific software community. The traditional strategies for processing and analyzing data are evolving in order to (i) offer higher-level programming model approaches and (ii) exploit parallelism to cope with the ever increasing complexity and size of the datasets. This contribution describes how the ROOT framework, a cornerstone of software stacks dedicated to particle physics, is preparing to provide adequate solutions for the analysis of large amount of scientific data on parallel architectures. The functional approach to parallel data analysis provided with the ROOT TDataFrame interface is then characterized. The design choices behind this new interface are described also comparing with other widely adopted tools such as Pandas and Apache Spark. The programming model is illustrated highlighting the reduction of boilerplate code, composability of the actions and data transformations as well as the capabilities of dealing with different data sources such as ROOT, JSON, CSV or databases. Details are given about how the functional approach allows transparent implicit parallelization of the chain of operations specified by the user. The progress done in the field of distributed analysis is examined. In particular, the power of the integration of ROOT with Apache Spark via the PyROOT interface is shown. In addition, the building blocks for the expression of parallelism in ROOT are briefly characterized together with the structural changes applied in the building and testing infrastructure which were necessary to put them in production.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2015

NEOWISE OBSERVATIONS OF COMET C/2013 A1 (SIDING SPRING) AS IT APPROACHES MARS

The Near-Earth Object Wide-field Infrared Survey Explorer mission observed comet C/2013 A1 (Siding Spring) three times at 3.4 μm and 4.6 μm as the comet approached Mars in 2014. The comet is an extremely interesting target since its close approach to Mars in late 2014 will be observed by various spacecraft in situ. The observations were taken in 2014 January, July, and September when the comet was at heliocentric distances of 3.82 AU, 1.88 AU, and 1.48 AU. The level of activity increased significantly between the January and July visits but then decreased by the time of the observations in September, approximately four weeks prior to its close approach to Mars. In this work, we calculate Afρ values and CO/CO{sub 2} production rates.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Beyond quantum cluster theories: multiscale approaches for strongly correlated systems

The degrees of freedom that confer to strongly correlated systems their many intriguing properties also render them fairly intractable through typical perturbative treatments. For this reason, the mechanisms responsible for their technologically promising properties remain mostly elusive. Computational approaches have played a major role in efforts to fill this void. In particular, dynamical mean field theory and its cluster extension, the dynamical cluster approximation have allowed significant progress. However, despite all the insightful results of these embedding schemes, computational constraints, such as the minus sign problem in quantum Monte Carlo (QMC), and the exponential growth of the Hilbert space in exact diagonalization (ED) methods, still limit the length scale within which correlations can be treated exactly in the formalism. A recent advance aiming to overcome these difficulties is the development of multiscale many body approaches whereby this challenge is addressed by introducing an intermediate length scale between the short length scale where correlations are treated exactly using a cluster solver such QMC or ED, and the long length scale where correlations are treated in a mean field manner. At this intermediate length scale correlations can be treated perturbatively. This is the essence of multiscale many-body methods. Furthermore, we will review various implementations of these multiscale many-body approaches, the results they have produced, and the outstanding challenges that should be addressed for further advances.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Discriminative versus generative approaches to simulation-based inference

Most of the fundamental, emergent, and phenomenological parameters of particle and nuclear physics are determined through parametric template fits. Simulations are used to populate histograms which are then matched to data. This approach is inherently lossy, since histograms are binned and low-dimensional. Deep learning has enabled unbinned and high-dimensional parameter estimation through neural likelihood(-ratio) estimation. We compare two approaches for neural simulation-based inference (NSBI): one based on discriminative learning (classification) and one based on generative modeling. These two approaches are directly evaluated on the same datasets, with a similar level of hyperparameter optimization in both cases. In addition to a Gaussian dataset, we study NSBI using a Higgs boson dataset from the FAIR Universe Challenge. We find that both the direct likelihood and likelihood ratio estimation are able to effectively extract parameters with reasonable uncertainties. For the numerical examples and within the set of hyperparameters studied, we found that the likelihood ratio method is more accurate and/or precise. Both methods have a significant spread from the network training and would require ensembling or other mitigation strategies in practice.

high energy physics↗
DOE OSTI2021

A New Approach to Evaluate and Reduce Uncertainty of Model-Based Biodiversity Projections for Conservation Policy Formulation

Biodiversity projections with uncertainty estimates under different climate, land-use, and policy scenarios are essential to setting and achieving international targets to mitigate biodiversity loss. Evaluating and improving biodiversity predictions to better inform policy decisions remains a central conservation goal and challenge. A comprehensive strategy to evaluate and reduce uncertainty of model outputs against observed measurements and multiple models would help to produce more robust biodiversity predictions. We propose an approach that integrates biodiversity models and emerging remote sensing and in-situ data streams to evaluate and reduce uncertainty with the goal of improving policy-relevant biodiversity predictions. In this work, we describe a multivariate approach to directly and indirectly evaluate and constrain model uncertainty, demonstrate a proof of concept of this approach, embed the concept within the broader context of model evaluation and scenario analysis for conservation policy, and highlight lessons from other modeling communities.

essential biodiversity variables↗
DOE OSTI2025

Inferring demographic and selective histories from population genomic data using a 2-step approach in species with coding-sparse genomes: an application to human data

Abstract The demographic history of a population, and the distribution of fitness effects (DFE) of newly arising mutations in functional genomic regions, are fundamental factors dictating both genetic variation and evolutionary trajectories. Although both demographic and DFE inference has been performed extensively in humans, these approaches have generally either been limited to simple demographic models involving a single population, or, where a complex population history has been inferred, without accounting for the potentially confounding effects of selection at linked sites. Taking advantage of the coding-sparse nature of the genome, we propose a 2-step approach in which coalescent simulations are first used to infer a complex multi-population demographic model, utilizing large non-functional regions that are likely free from the effects of background selection. We then use forward-in-time simulations to perform DFE inference in functional regions, conditional on the complex demography inferred and utilizing expected background selection effects in the estimation procedure. Throughout, recombination and mutation rate maps were used to account for the underlying empirical rate heterogeneity across the human genome. Importantly, within this framework it is possible to utilize and fit multiple aspects of the data, and this inference scheme represents a generalized approach for such large-scale inference in species with coding-sparse genomes.

Soni, Vivak (ORCID:0000000294969562)↗
DOE OSTI2022

A deep learning approach to identify missing is-a relations in SNOMED CT

Abstract Objective SNOMED CT is the largest clinical terminology worldwide. Quality assurance of SNOMED CT is of utmost importance to ensure that it provides accurate domain knowledge to various SNOMED CT-based applications. In this work, we introduce a deep learning-based approach to uncover missing is-a relations in SNOMED CT. Materials and Methods Our focus is to identify missing is-a relations between concept-pairs exhibiting a containment pattern (ie, the set of words of one concept being a proper subset of that of the other concept). We use hierarchically related containment concept-pairs as positive instances and hierarchically unrelated containment concept-pairs as negative instances to train a model predicting whether an is-a relation exists between 2 concepts with containment pattern. The model is a binary classifier leveraging concept name features, hierarchical features, enriched lexical attribute features, and logical definition features. We introduce a cross-validation inspired approach to identify missing is-a relations among all hierarchically unrelated containment concept-pairs. Results We trained and applied our model on the Clinical finding subhierarchy of SNOMED CT (September 2019 US edition). Our model (based on the validation sets) achieved a precision of 0.8164, recall of 0.8397, and F1 score of 0.8279. Applying the model to predict actual missing is-a relations, we obtained a total of 1661 potential candidates. Domain experts performed evaluation on randomly selected 230 samples and verified that 192 (83.48%) are valid. Conclusions The results showed that our deep learning approach is effective in uncovering missing is-a relations between containment concept-pairs in SNOMED CT.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Appendix Q: Recommendations for Developing Molecular Assays for Microbial Pathogen Detection Using Modern In Silico Approaches

We describe the use of in silico approaches to improve the process of molecular assay development and reduce time and cost by utilizing available databases of whole genome pathogen sequences combined with modern bioinformatics and physical modeling tools. Well-characterized assays are needed for accurately detecting pathogens in environmental and patient samples and also for evaluation of the efficacy of a medical countermeasure that may be administered to patients. The polymerase chain reaction (PCR) remains the gold standard for pathogen detection due to the simplicity of its instrumentation, low cost of reagents, and outstanding limit of detection (LOD), sensitivity, and specificity. However, creation of such PCR assays often involves iterations of design, preliminary testing, and thorough validation with clinical isolates and testing in relevant matrices, which can be time consuming, costly, and result in suboptimal assays. Since formal validation (e.g., for Emergency Use Authorization [EUA] or Food and Drug Administration [FDA] licensure) of an infectious disease assay can be very expensive and can require extensive time of development, having a well-designed assay up front is a critical first step. Yet, many assays described in the literature utilized limited design capabilities and many initially promising assays fail the validation process, resulting in increased costs and timelines for successful product development. While the computational approaches outlined in this document by no means obviate the need for wet lab testing, they can reduce the amount of effort wasted on empirical optimization and iterative redesigns and also guide validation studies. The proposed computational approaches also result in higher performing assays with better sensitivity, specificity, and lower LOD and reduce the possibility of assay failure due to signature erosion. To provide clarity, an extensive glossary of defined terms is provided.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Deep Learning Approach for High-accuracy Electron Counting of Monolithic Active Pixel Sensor-type Direct Electron Detectors at Increased Electron Dose

Abstract Electron counting can be performed algorithmically for monolithic active pixel sensor direct electron detectors to eliminate readout noise and Landau noise arising from the variability in the amount of deposited energy for each electron. Errors in existing counting algorithms include mistakenly counting a multielectron strike as a single electron event, and inaccurately locating the incident position of the electron due to lateral spread of deposited energy and dark noise. Here, we report a supervised deep learning (DL) approach based on Faster region-based convolutional neural network (R-CNN) to recognize single electron events at varying electron doses and voltages. The DL approach shows high accuracy according to the near-ideal modulation transfer function (MTF) and detector quantum efficiency for sparse images. It predicts, on average, 0.47 pixel deviation from the incident positions for 200 kV electrons versus 0.59 pixel using the conventional counting method. The DL approach also shows better robustness against coincidence loss as the electron dose increases, maintaining the MTF at half Nyquist frequency above 0.83 as the electron density increases to 0.06 e−/pixel. Thus, the DL model extends the advantages of counting analysis to higher dose rates than conventional methods.

Materials Science↗
DOE OSTI2022

A novel approach for calculating galaxy rotation curves using spaxel cross-correlation and iterative smoothing

ABSTRACT Precise measurements of the internal dynamics of galaxies have proven of great importance for understanding the internal dark matter distribution of galaxies. We present a novel method for measuring the line-of-sight (LOS) velocities across the face of galaxies by cross-correlation of spectral pixels (spaxels) and an iterative method of smoothing. On simulated data the method can accurately recover the input LOS velocities for different types of spectra (absorption-line dominated, emission-line dominated, and differing shapes of the continuum), and can handle stellar population radial gradients. Most important of all, it continues to provide reliable measurements of LOS velocities with reasonable uncertainties even when the spectra are very low signal-to-noise ratio (approaching ∼1), which is a challenge for traditional template-fitting approaches. We apply our method to data from a real MaNGA galaxy as a demonstration and find promising results with good precision. This novel approach can be complementary to existing methods primarily based on template fitting.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

A pooling-based approach to mapping genetic variants associated with DNA methylation

DNA methylation is an epigenetic modification that plays a key role in gene regulation. Previous studies have investigated its genetic basis by mapping genetic variants that are associated with DNA methylation at specific sites, but these have been limited to microarrays that cover <2% of the genome and cannot account for allele-specific methylation (ASM). Other studies have performed whole-genome bisulfite sequencing on a few individuals, but these lack statistical power to identify variants associated with DNA methylation. We present a novel approach in which bisulfite-treated DNA from many individuals is sequenced together in a single pool, resulting in a truly genome-wide map of DNA methylation. Compared to methods that do not account for ASM, our approach increases statistical power to detect associations while sharply reducing cost, effort, and experimental variability. As a proof of concept, we generated deep sequencing data from a pool of 60 human cell lines; we evaluated almost twice as many CpGs as the largest microarray studies and identified more than 2000 genetic variants associated with DNA methylation. Here we found that these variants are highly enriched for associations with chromatin accessibility and CTCF binding but are less likely to be associated with traits indirectly linked to DNA, such as gene expression and disease phenotypes. In summary, our approach allows genome-wide mapping of genetic variants associated with DNA methylation in any tissue of any species, without the need for individual-level genotype or methylation data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Interference in nonlinear Compton scattering using a Schrödinger-equation approach

The interference between Compton scattering and nonlinear Compton scattering from a two-color field in the X-ray regime is theoretically examined for bound electrons. Here, the underlying phase shifts are analyzed using a perturbative approach in the incoming classical field. The perturbative approach is bench marked with a non-perturbative approach in the classical field. The interference for different combinations of linear polarization of the two fields is examined when the Compton and the nonlinear Compton scattered waves have the same wave vector and polarization. Only two cases exhibit interference. When there is interference, the calculations reveal an intrinsic phase difference between the Compton scattered wave function and the nonlinear Compton scattered wave function of either 0 or pi depending on the scattering angle.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Alternative approach to quantum imaginary time evolution

There is increasing interest in quantum algorithms (QAs) that are based on the imaginary time evolution (ITE), a successful classical numerical approach to obtain ground states. However, most of the proposals so far require heavy postprocessing computational steps on a classical computer, such as solving linear equations. Here we provide an alternative approach to implement ITE. A key feature in our approach is the use of an orthogonal basis set: the propagated state is efficiently expressed in terms of orthogonal basis states at every step of the evolution. We argue that the number of basis states needed at those steps to achieve an accurate solution can be kept on the order of n , the number of qubits, by controlling the precision (number of significant digits) and the imaginary time increment. The number of quantum gates per imaginary time step is estimated to be polynomial in n . Additionally, while in many QAs the locality of the Hamiltonian is a key assumption, in our algorithm this restriction is not required. This characteristic of our algorithm renders it useful for studying highly nonlocal systems, such as the occupation-representation nuclear shell model. Here, we illustrate our algorithm through numerical implementation on an IBM quantum simulator.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Diffusion quantum Monte Carlo approach to the polaritonic ground state

Making and using polaritonic states (i.e., hybrid electron-photon states) for chemical applications has recently become one of the most prominent and active fields that connects the communities of chemistry and quantum optics. Modeling of such polaritonic phenomena using ab initio approaches calls for new methodologies, leading to the reinvention of many commonly used electronic structure methods, such as Hartree-Fock, density functional, and coupled cluster theories. Here in this work, we explore the formally exact diffusion quantum Monte Carlo approach to obtain numerical solutions to the polaritonic ground state during the dissociation of the H 2 molecular system. Here, we examine various electron-nuclear-photon properties throughout the dissociation, such as changes to the minimum of the cavity Born-Oppenheimer surface, the localization of the electronic wave function, and the average mode occupation. Finally, we directly compare our results to that obtained with state-of-the-art, yet approximate, polaritonic coupled cluster approaches.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2016

Variational approach to extracting the phonon mean free path distribution from the spectral Boltzmann transport equation

The phonon Boltzmann transport equation (BTE) is a powerful tool for studying nondiffusive thermal transport. Here, we develop a new universal variational approach to solving the BTE that enables extraction of phonon mean free path (MFP) distributions from experiments exploring nondiffusive transport. By utilizing the known Fourier heat conduction solution as a trial function, we propose a direct approach to calculating the effective thermal conductivity from the BTE. We reveal this technique on the transient thermal grating experiment, which is a useful tool for studying nondiffusive thermal transport and probing the MFP distribution of materials. We obtain a closed form expression for a suppression function that is materials dependent, successfully addressing the nonuniversality of the suppression function used in the past, while providing a general approach to studying thermal properties in the nondiffusive regime.

42 ENGINEERING↗
DOE OSTI2019

New approach to determining radiative capture reaction rates at astrophysical energies

Radiative capture reactions play a crucial role in stellar nucleosynthesis but have proved challenging to determine experimentally. In particular, the large uncertainty (≈100%) in the measured rate of the 12 C(α,γ) 16 O reaction is the largest source of uncertainty in any stellar evolution model. With development of high-current energy-recovery linear accelerators (ERLs) and high-density gas targets, measurement of the 16 O(e,e'α) 12 C reaction close to threshold using detailed balance allows a new approach to determine the 12 C(α,γ) 16 O reaction rate with significantly increased precision (<20%). We present the formalism to relate photo- and electrodisintegration reactions and consider the design of an optimal experiment to deliver increased precision. Furthermore, once the new ERLs come online, an experiment to validate the approach we propose should be carried out. This approach has broad applicability to radiative capture reactions in astrophysics.

6 ≤ A ≤ 19↗
DOE OSTI2013

Unified ab initio approach to bound and unbound states: No-core shell model with continuum and its application to 7 He

In this study, we introduce a unified approach to nuclear bound and continuum states based on the coupling of the no-core shell model (NCSM), a bound-state technique, with the no-core shell model/resonating group method (NCSM/RGM), a nuclear scattering technique. This new ab initio method, no-core shell model with continuum (NCSMC), leads to convergence properties superior to either NCSM or NCSM/RGM while providing a balanced approach to different classes of states. In the NCSMC, the ansatz for the many-nucleon wave function includes (i) a square-integrable A-nucleon component expanded in a complete harmonic oscillator basis and (ii) a binary-cluster component with asymptotic boundary conditions that can properly describe weakly bound states, resonances, and scattering. The Schrödinger equation is transformed into a system of coupled-channel integral-differential equations that we solve using a modified microscopic R-matrix formalism within a Lagrange mesh basis. We demonstrate the usefulness of the approach by investigating the unbound 7 He nucleus.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗