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At least 1,009 records · Page 56
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Improving precision and accuracy of genetic mapping with genotyping‐by‐sequencing data in outcrossing species

Abstract Genotyping‐by‐sequencing (GBS) is a widely used strategy for obtaining large numbers of genetic markers in model and non‐model organisms. In crop plants, GBS‐derived marker datasets are frequently used to perform quantitative trait locus (QTL) mapping. In some plant species, however, high heterozygosity and complex genome structure mean that researchers must use care in handling GBS data to conduct QTL mapping most effectively. Such outbred crops include most of the perennial grass and tree species used for bioenergy. To identify strategies for increasing accuracy and precision of QTL mapping using GBS data in outbred crops, we conducted an empirical study of SNP‐calling and genetic map‐building pipeline parameters in a Miscanthus sinensis population, and a complementary simulation study to estimate the relationship between genome‐wide error rate, read depth, and marker number. The bioenergy grass Miscanthus is an obligate outcrossing species with a recent (diploidized) whole‐genome duplication. For the study of empirical M. sinensis data, we compared two SNP‐calling methods (one non‐reference‐based and one reference‐based), a series of depth filters (12×, 20×, 30×, and 40×) and two map‐construction methods (i.e., marker ordering: linkage‐only and order‐corrected based on a reference genome). We found that correcting the order of markers on a linkage map by using a high‐quality reference genome improved QTL precision (shorter confidence intervals). For typical GBS datasets of between 1000 and 5000 markers to build a genetic map for biparental populations, a depth filter set at 30× to 40× applied to outbred populations provided a genome‐wide genotype‐calling error rate of less than 1%, improved accuracy of QTL point estimates and minimized type I errors for identifying QTL. Based on these results, we recommend using a reference genome to correct the marker order of genetic maps and a robust genotype depth filter to improve QTL mapping for outbred crops.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Measuring Young Stars in Space and Time. II. The Pre-main-sequence Stellar Content of N44

The Hubble Space Telescope survey Measuring Young Stars in Space and Time (MYSST) entails some of the deepest photometric observations of extragalactic star formation, capturing even the lowest-mass stars of the active star-forming complex N44 in the Large Magellanic Cloud. We employ the new MYSST stellar catalog to identify and characterize the content of young pre-main-sequence (PMS) stars across N44 and analyze the PMS clustering structure. To distinguish PMS stars from more evolved line of sight contaminants, a non-trivial task due to several effects that alter photometry, we utilize a machine-learning classification approach. This consists of training a support vector machine (SVM) and a random forest (RF) on a carefully selected subset of the MYSST data and categorize all observed stars as PMS or non-PMS. Combining SVM and RF predictions to retrieve the most robust set of PMS sources, we find ∼26,700 candidates with a PMS probability above 95% across N44. Employing a clustering approach based on a nearest neighbor surface density estimate, we identify 16 prominent PMS structures at 1σ significance above the mean density with sub-clusters persisting up to and beyond 3σ significance. The most active star-forming center, located at the western edge of N44's bubble, is a subcluster with an effective radius of ∼5.6 pc entailing more than 1100 PMS candidates. Furthermore, we confirm that almost all identified clusters coincide with known H ii regions and are close to or harbor massive young O stars or YSOs previously discovered by MUSE and Spitzer observations.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2020

NuSTAR Survey of Obscured Swift/BAT-selected Active Galactic Nuclei. II. Median High-energy Cutoff in Seyfert II Hard X-Ray Spectra

Broadband X-ray spectroscopy of the X-ray emission produced in the coronae of active galactic nuclei (AGNs) can provide important insights into the physical conditions very close to their central supermassive black holes. The temperature of the Comptonizing plasma that forms the corona is manifested through a high-energy cutoff that has been difficult to directly constrain even in the brightest AGN because it requires high-quality data at energies above 10 keV. In this paper we present a large collection of coronal cutoff constraints for obscured AGNs based on a sample of 130 AGNs selected in the hard X-ray band with Swift/BAT and observed nearly simultaneously with NuSTAR and Swift/XRT. Additionally, we find that under a reasonable set of assumptions regarding partial constraints the median cutoff is well constrained to 290 ± 20 keV, where the uncertainty is statistical and given at the 68% confidence level. We investigate the sensitivity of this result to our assumptions and find that consideration of various known systematic uncertainties robustly places the median cutoff between 240 and 340 keV. The central 68% of the intrinsic cutoff distribution is found to be between about 140 and 500 keV, with estimated uncertainties of 20 and 100 keV, respectively. In comparison with the literature, we find no clear evidence that the cutoffs in obscured and unobscured AGNs are substantially different. Our analysis highlights the importance of carefully considering partial and potentially degenerate constraints on the coronal high-energy cutoff in AGNs.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

CMB-S4: Foreground-cleaning Pipeline Comparison for Measuring Primordial Gravitational Waves

We compare multiple foreground-cleaning pipelines for estimating the tensor-to-scalar ratio, r, using simulated maps of the planned CMB-S4 experiment within the context of the South Pole Deep Patch. To evaluate robustness, we analyze bias and uncertainty on r across various foreground suites using map-based simulations. The foreground-cleaning methods include: a parametric maximum likelihood approach applied to auto- and cross-power spectra between frequency maps; a map-based parametric maximum-likelihood method; and a harmonic-space internal linear combination using frequency maps. We summarize the conceptual basis of each method to highlight their similarities and differences. To better probe the impact of foreground residuals, we implement an iterative internal delensing step, leveraging a map-based pipeline to generate a lensing B-mode template from the large aperture telescope frequency maps. Our results show that the performance of the three approaches is comparable for simple and intermediate-complexity foregrounds, with σ(r) ranging from 3–5 ×10 −4 . However, biases at the 1σ–2σ level appear when analyzing more complex forms of foreground emission. By extending the baseline pipelines to marginalize over foreground residuals, we demonstrate that contamination can be reduced to within statistical uncertainties, albeit with a pipeline-dependent impact on σ(r), which translates to a detection significance between 2σ and 4σ for an input value of r = 0.003. These findings suggest varying levels of maturity among the tested pipelines, with the auto- and cross-spectra-based approach demonstrating the best stability and overall performance. Moreover, given the extremely low noise levels, mutual validation of independent foreground-cleaning pipelines is essential to ensure the robustness of any potential detection.

astronomy data analysis↗
NASA NTRS1975

Control optimization, stabilization and computer algorithms for aircraft applications

Research related to reliable aircraft design is summarized. Topics discussed include systems reliability optimization, failure detection algorithms, analysis of nonlinear filters, design of compensators incorporating time delays, digital compensator design, estimation for systems with echoes, low-order compensator design, descent-phase controller for 4-D navigation, infinite dimensional mathematical programming problems and optimal control problems with constraints, robust compensator design, numerical methods for the Lyapunov equations, and perturbation methods in linear filtering and control.

Source record↗
NASA NTRS1996

Durable High-Density Data Storage

The focus ion beam (FIB) micromilling process for data storage provides a new non-magnetic storage method for archiving large amounts of data. The process stores data on robust materials such as steel, silicon, and gold coated silicon. The storage process was developed to provide a method to insure the long term storage life of data. We estimate that the useful life of data written on silicon or gold-coated silicon to be on the order of a few thousand years without the need to rewrite the data every few years. The process uses an ion beam to carve material from the surface, much like stone cutters in ancient civilizations removed material from stone. The deeper the information is carved into the media, the longer the expected life of the information. The process can record information in three formats: (1) binary at densities of 23 Gbits/square inch, (2) alphanumeric at optical or non-optical density, and (3) graphical at optical and non-optical density. The formats can be mixed on the same media; and thus, it is possible to record, in a human-viewable format, instructions that can be read using an optical microscope. These instructions provide guidance on reading the remaining higher density information.

Lamartine, Bruce C.↗
NASA NTRS2012

Deep Space Habitat Configurations Based On International Space Station Systems

A Deep Space Habitat (DSH) is the crew habitation module designed for long duration missions. Although humans have lived in space for many years, there has never been a habitat beyond low-Earth-orbit. As part of the Advanced Exploration Systems (AES) Habitation Project, a study was conducted to develop weightless habitat configurations using systems based on International Space Station (ISS) designs. Two mission sizes are described for a 4-crew 60-day mission, and a 4-crew 500-day mission using standard Node, Lab, and Multi-Purpose Logistics Module (MPLM) sized elements, and ISS derived habitation systems. These durations were selected to explore the lower and upper bound for the exploration missions under consideration including a range of excursions within the Earth-Moon vicinity, near earth asteroids, and Mars orbit. Current methods for sizing the mass and volume for habitats are based on mathematical models that assume the construction of a new single volume habitat. In contrast to that approach, this study explored the use of ISS designs based on existing hardware where available and construction of new hardware based on ISS designs where appropriate. Findings included a very robust design that could be reused if the DSH were assembled and based at the ISS and a transportation system were provided for its return after each mission. Mass estimates were found to be higher than mathematical models due primarily to the use of multiple ISS modules instead of one new large module, but the maturity of the designs using flight qualified systems have potential for improved cost, schedule, and risk benefits.

Smitherman, David↗
NASA NTRS2012

Deep Space Habitat Configurations Based on International Space Station Systems

A Deep Space Habitat (DSH) is the crew habitation module designed for long duration missions. Although humans have lived in space for many years, there has never been a habitat beyond low-Earth-orbit. As part of the Advanced Exploration Systems (AES) Habitation Project, a study was conducted to develop weightless habitat configurations using systems based on International Space Station (ISS) designs. Two mission sizes are described for a 4-crew 60-day mission, and a 4-crew 500-day mission using standard Node, Lab, and Multi-Purpose Logistics Module (MPLM) sized elements, and ISS derived habitation systems. These durations were selected to explore the lower and upper bound for the exploration missions under consideration including a range of excursions within the Earth-Moon vicinity, near earth asteroids, and Mars orbit. Current methods for sizing the mass and volume for habitats are based on mathematical models that assume the construction of a new single volume habitat. In contrast to that approach, this study explored the use of ISS designs based on existing hardware where available and construction of new hardware based on ISS designs where appropriate. Findings included a very robust design that could be reused if the DSH were assembled and based at the ISS and a transportation system were provided for its return after each mission. Mass estimates were found to be higher than mathematical models due primarily to the use of multiple ISS modules instead of one new large module, but the maturity of the designs using flight qualified systems have potential for improved cost, schedule, and risk benefits.

Smitherman, David↗
NASA NTRS2013

Simple Sensitivity Analysis for Orion Guidance Navigation and Control

The performance of Orion flight software, especially its GNC software, is being analyzed by running Monte Carlo simulations of Orion spacecraft flights. The simulated performance is analyzed for conformance with flight requirements, expressed as performance constraints. Flight requirements include guidance (e.g. touchdown distance from target) and control (e.g., control saturation) as well as performance (e.g., heat load constraints). The Monte Carlo simulations disperse hundreds of simulation input variables, for everything from mass properties to date of launch. We describe in this paper a sensitivity analysis tool ("Critical Factors Tool" or CFT) developed to find the input variables or pairs of variables which by themselves significantly influence satisfaction of requirements or significantly affect key performance metrics (e.g., touchdown distance from target). Knowing these factors can inform robustness analysis, can inform where engineering resources are most needed, and could even affect operations. The contributions of this paper include the introduction of novel sensitivity measures, such as estimating success probability, and a technique for determining whether pairs of factors are interacting dependently or independently. The tool found that input variables such as moments, mass, thrust dispersions, and date of launch were found to be significant factors for success of various requirements. Examples are shown in this paper as well as a summary and physics discussion of EFT-1 driving factors that the tool found.

Pressburger, Tom↗
NASA NTRS2013

Simple Sensitivity Analysis for Orion GNC

The performance of Orion flight software, especially its GNC software, is being analyzed by running Monte Carlo simulations of Orion spacecraft flights. The simulated performance is analyzed for conformance with flight requirements, expressed as performance constraints. Flight requirements include guidance (e.g. touchdown distance from target) and control (e.g., control saturation) as well as performance (e.g., heat load constraints). The Monte Carlo simulations disperse hundreds of simulation input variables, for everything from mass properties to date of launch.We describe in this paper a sensitivity analysis tool (Critical Factors Tool or CFT) developed to find the input variables or pairs of variables which by themselves significantly influence satisfaction of requirements or significantly affect key performance metrics (e.g., touchdown distance from target). Knowing these factors can inform robustness analysis, can inform where engineering resources are most needed, and could even affect operations. The contributions of this paper include the introduction of novel sensitivity measures, such as estimating success probability, and a technique for determining whether pairs of factors are interacting dependently or independently. The tool found that input variables such as moments, mass, thrust dispersions, and date of launch were found to be significant factors for success of various requirements. Examples are shown in this paper as well as a summary and physics discussion of EFT-1 driving factors that the tool found.

Monte Carlo Simulation↗
DOE OSTI2021

Convolutional Neural Networks for the CHIPS Neutrino Detector R&D Project.

The CHerenkov detectors In mine PitS (Chips) neutrino detector R&D project aims to develop novel strategies and technologies for very large yet ‘cheap as chips’ water Cherenkov neutrino detectors. Via deployment in a body of water, use of commercially available components, and instrumentation coverage optimisation for the study of exclusively accelerator beam neutrinos, Chips will enable megaton scale detectors to become a reality at the cost of $200k-$300k per kt of sensitive mass. During the summer of 2019 a prototype Chips detector, Chips-5, was deployed into the Wentworth 2W disused mine pit in northern Minnesota, 7 mrad off the NuMI beam axis. A novel data acquisition system was introduced using cheap single-board computers and open-source software. This work presents a novel approach to water Cherenkov neutrino detector event reconstruction and classification. Three forms of a Convolutional Neural Network, a type of deep learning algorithm, have been trained to reject cosmic muon events, classify beam events, and estimate neutrino energies, all using only the raw detector event as input. When evaluated on the expected distribution of Chips-5 events, this new approach is shown to be robust and explainable as well as providing a significant performance increase over the standard likelihood-based reconstruction and simple neural network classification. Promisingly, the performance presented here is comparable to the more complex (and expensive) neutrino oscillation experiments within the field.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

A Hybrid Data-Driven and Model-Based Anomaly Detection Scheme for DER Operation

This paper proposes a hybrid data and model-based anomaly detection scheme to secure the operation of distributed energy resources (DERs) in distribution grids. Data-driven autoencoders are set up at the edge device level and they use local DER operational data as inputs. The abnormal statuses are detected by analyzing reconstruction errors. In parallel, modelbased state estimation (SE) is set up at the central level and it uses system-wide models and measurements as data inputs. The anomalies are identified by analyzing measurement residuals. The hybrid scheme preserves the benefits of both data-driven and model-based analyses and thus improves the robustness and the accuracy of anomaly detection. Numerical tests based on the model of a real distribution feeder in Southern California highlight the proposed scheme's effectiveness and benefits.

anomaly detection↗
DOE OSTI2022

A Hybrid Data-Driven and Model-Based Anomaly Detection Scheme for DER Operation: Preprint

This paper proposes a hybrid data and model-based anomaly detection for securing the operation of distributed energy resources (DERs) in distribution grids. Data-driven autoencoders (AE) are set up at the edge level by taking local DER data and detect anomalous operations by leveraging the reconstruction ability. In parallel, model-based state estimation (SE) is running at the system level by taking system models and measurements, the anomalies are identified by analyzing the measurements residual. The hybrid scheme preserves the benefits of both data-driven and model-based analysis and thus improves the robustness and accuracy of anomaly detection. It can be established by getting full use of the existing infrastructures in distribution grids. Numerical tests on a realistic distribution feeder in Southern California highlight the effectiveness as well as benefits of the proposed scheme.

anomaly detection↗
DOE OSTI2020

Affinity propagation clustering of full-field, high-spatial-dimensional measurements for robust output-only modal identification: A proof-of-concept study

Determination of the model order is a challenging problem in system identification, especially in output-only or operational modal identification where some modes are weakly excited. While existing methods such as the stabilization diagram method (spectral information) are effective, they do not scale to high-dimensional data, which is usually needed for high-fidelity characterization of structural dynamics and has been made available in the emerging full-field measurement techniques using optical methods such as photogrammetry and laser vibrometers. In this proof-of-concept study we present a new non-parametric, data-driven approach for robust output-only identification of high-spatial-dimensional modal parameters of basic structures by efficiently processing and interactively exploiting the full-field measurement (i.e., very dense spatial measurement points). Specifically, we first over-estimate the system model once, producing a pool of candidate modes associated with their modal frequencies and full-field, high-spatial-dimensional mode shapes. This is accomplished by a data-driven method termed affinity propagation clustering (APC), where the active clusters, which are the active modes in our formulations, emerge from the "message-passing" procedure and does not require a pre-determination of the cluster number (mode or model order). Next, rather than using the spectral information to distinguish the physical and spurious modes in the stabilization diagram method, we exploit and visualize the spatial, full-field mode shape associated with each candidate mode to do so. We conduct extensive experiments on basic structural models with comparisons to a few existing methods. The results indicate that the new method is computationally efficient for identifying high-spatial-dimensional modal parameters, and robust to identify weak modes by exploiting the full-field measurement. We also discuss its applicability and limitations for structures with complex geometry (shapes).

42 ENGINEERING↗
DOE OSTI2023

An ICA-Based HVAC Load Disaggregation Method Using Smart Meter Data

This paper presents an independent component analysis (ICA) based unsupervised-learning method for heat, ventilation, and air-conditioning (HVAC) load disaggregation using row-resolution (i.e., 15 minutes) smart meter data. We first demonstrate that the electricity consumption profiles on mild-temperature days can be used to approximate the base load on hot days. A residual load profile can then be calculated by subtracting the mild-day load profile from the hot-day load profile. The residual load profiles are processed using ICA for HVAC load extraction. An optimization-based algorithm is proposed for post-adjustment of the ICA results, considering two bounding factors for enhancing the robustness of the ICA algorithm. First, we use the hourly HVAC energy bounds computed from the relationship between HVAC load and temperature to remove unrealistic HVAC load spikes. Second, we exploit the dependency between the daily nocturnal and diurnal loads extracted from historical meter data to smooth the base load profile. Pecan Street data with sub-metered HVAC data were used to test and verify the proposed methods. Simulation results demonstrated that the proposed method is computationally efficient and robust across multiple customers.

Kim, Hyeonjin↗
DOE OSTI2025

Low- n stability and plasma response to RMP in various STEP scenarios

The low-n (n is the toroidal mode number) magnetohydrodynamic (MHD) stability and plasma response are numerically investigated for various scenarios designed for STEP, that are relevant for the H-mode pedestal analysis. Control of the edge-localized modes (ELMs) with externally applied resonant magnetic perturbations (RMPs) is considered. Optimization of the ELM control coil current configuration, based on the computed plasma MHD response and well-established figures of merit validated on present-day experiments, finds reasonable robustness of a fixed coil phasing (for a given n-number) to control ELMs in all five STEP plasmas considered. Based on certain semi-empirical criteria, the required coil current to achieve ELM suppression is estimated to be about 10–20 kAt with the n = 1 or 2 RMP configuration and about 100–200 kAt for the n = 4 RMP. Systematic linear stability calculations are used to map out stability windows for the low-n kink-peeling modes, in terms of the ideal-wall location and variation of the edge safety factor q 95 with respect to the target design. The kink-peeling stability boundary is found to be generally sensitive to the q 95 variation, which has implications for achieving the quiescent H-mode regime in STEP. Full toroidal quasilinear initial-value simulations for these STEP plasmas find that generation of the edge-harmonic oscillations (EHOs) depends sensitively on the plasma scenario, the initial linear stability of the kink-peeling modes, the initial plasma toroidal flow and q 95 . In general, it is easier (more robust) to access the EHO-regime for two of the cases considered with smaller plasma volume and higher on-axis safety factor. Finally, quasilinear simulations find robust density pumpout due to applied RMPs in these STEP plasmas, but the effect on the plasma toroidal flow varies among different cases.

EHO↗
DOE OSTI2024

Robust inference of the Galactic Centre gamma-ray excess spatial properties

ABSTRACT The gamma-ray Fermi-LAT Galactic Centre excess (GCE) has puzzled scientists for over 15 yr. Despite ongoing debates about its properties, and especially its spatial distribution, its nature remains elusive. We scrutinize how the estimated spatial morphology of this excess depends on models for the Galactic diffuse emission, focusing particularly on the extent to which the Galactic plane and point sources are masked. Our main aim is to compare a spherically symmetric morphology – potentially arising from the annihilation of dark matter (DM) particles – with a boxy morphology – expected if faint unresolved sources in the Galactic bulge dominate the excess emission. Recent claims favouring a DM-motivated template for the GCE are shown to rely on a specific Galactic bulge template, which performs worse than other templates for the Galactic bulge. We find that a non-parametric model of the Galactic bulge derived from the VISTA Variables in the Via Lactea survey results in a significantly better fit for the GCE than DM-motivated templates. This result is independent of whether a galprop-based model or a more non-parametric ring-based model is used to describe the diffuse Galactic emission. This conclusion remains true even when additional freedom is added in the background models, allowing for non-parametric modulation of the model components and substantially improving the fit quality. When adopted, optimized background models provide robust results in terms of preference for a boxy bulge morphology for the GCE, regardless of the mask applied to the Galactic plane.

Astronomy & Astrophysics↗
DOE OSTI2023

Fully Implicit Conjugate Heat Transfer Analysis of the ARC-Class Vacuum Vessel

The coupled simulation of fusion reactor blankets including neutronics, thermal-hydraulics and thermo-mechanics is expected to speed up the design cycle of fusion reactor design concepts. In this work we demonstrate tight implicit coupling of conjugate heat transfer using the open-source Computational Fluid Dynamics software OpenFOAM for thermo-fluid mechanics and Diablo for thermo-solid mechanics. The heat transfer analysis is augmented by volumetric energy deposition from neutronic calculations using the Monte Carlo N-particle code on both solid and fluid parts of the vacuum vessel. An additional heat flux is imposed on the first wall estimated from the design power of the reactor. The tight coupling is realized through the open-source coupling library, preCICE, and tested on the vacuum vessel of the affordable, robust, compact reactor design by Commonwealth Fusion Systems. The features of the coupling and the influence of different coupling parameters such as coupling schemes, acceleration techniques and convergence criterion are discussed. The coupled simulation results are compared to a thermal-hydraulics simulation which includes only the fluid domains (the liquid immersion molten salt blanket and cooling channel) to demonstrate usefulness of a coupled simulation. Further analysis is performed to identify regions of hot spots for subsequent design improvement. This introduces the outline for integrating conjugate electromagnetics and fluid/solid mechanics (e.g., allow for deformation of the cooling channel walls) with our present approach for future analysis.

Sircar, Arpan↗