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At least 775 records · Page 43
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Quartet-based inference is statistically consistent under the unified duplication-loss-coalescence model

Abstract Motivation The classic multispecies coalescent (MSC) model provides the means for theoretical justification of incomplete lineage sorting-aware species tree inference methods. This has motivated an extensive body of work on phylogenetic methods that are statistically consistent under MSC. One such particularly popular method is ASTRAL, a quartet-based species tree inference method. Novel studies suggest that ASTRAL also performs well when given multi-locus gene trees in simulation studies. Further, Legried et al. recently demonstrated that ASTRAL is statistically consistent under the gene duplication and loss model (GDL). GDL is prevalent in evolutionary histories and is the first core process in the powerful duplication-loss-coalescence evolutionary model (DLCoal) by Rasmussen and Kellis. Results In this work, we prove that ASTRAL is statistically consistent under the general DLCoal model. Therefore, our result supports the empirical evidence from the simulation-based studies. More broadly, we prove that the quartet-based inference approach is statistically consistent under DLCoal. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Quantifying leaf symptoms of sorghum charcoal rot in images of field‐grown plants using deep neural networks

Abstract Charcoal rot of sorghum (CRS) is a significant disease affecting sorghum crops, with limited genetic resistance available. The causative agent, Macrophomina phaseolina (Tassi) Goid, is a highly destructive fungal pathogen that targets over 500 plant species globally, including essential staple crops. Utilizing field image data for precise detection and quantification of CRS could greatly assist in the prompt identification and management of affected fields and thereby reduce yield losses. The objective of this work was to implement various machine learning algorithms to evaluate their ability to accurately detect and quantify CRS in red‐green‐blue images of sorghum plants exhibiting symptoms of infection. EfficientNet‐B3 and a fully convolutional network emerged as the top‐performing models for image classification and segmentation tasks, respectively. Among the classification models evaluated, EfficientNet‐B3 demonstrated superior performance, achieving an accuracy of 86.97%, a recall rate of 0.71, and an F1 score of 0.73. Of the segmentation models tested, FCN proved to be the most effective, exhibiting a validation accuracy of 97.76%, a recall rate of 0.68, and an F1 score of 0.66. As the size of the image patches increased, both models’ validation scores increased linearly, and their inference time decreased exponentially. This trend could be attributed to larger patches containing more information, improving model performance, and fewer patches reducing the computational load, thus decreasing inference time. The models, in addition to being immediately useful for breeders and growers of sorghum, advance the domain of automated plant phenotyping and may serve as a foundation for drone‐based or other automated field phenotyping efforts. Additionally, the models presented herein can be accessed through a web‐based application where users can easily analyze their own images.

Gonzalez, Emmanuel M.↗
NASA NTRS1985

Curie isotherm surfaces inferred from high-altitude magnetic anomaly data

Two-dimensional Curie depth models along two sections across the western United States are derived using an equivalent layer magnetization model derived from Magsat data, and the results are used to constrain finite element thermal models developed by Mayhew and Majer (1980). Regional heat flow variations predicted by the models compare favorably with those inferred from direct measurements. The methodology is applied to upward-continued aeromagnetic data, and the results are found to be in good agreement with previous Curie depth estimates and average measured heat flow.

Mayhew, M. A.↗
DOE OSTI2021

Finding Liebig’s law of the minimum

Abstract Liebig’s law of the minimum (LLM) is often used to interpret empirical biological growth data and model multiple substrates co‐limited growth. However, its mechanistic foundation is rarely discussed, even though its validity has been questioned since its introduction in the 1820s. Here we first show that LLM is a crude approximation of the law of mass action, the state of art theory of biochemical reactions, and the LLM model is less accurate than two other approximations of the law of mass action: the synthesizing unit model and the additive model. We corroborate this conclusion using empirical data sets of algae and plants grown under two co‐limiting substrates. Based on our analysis, we show that when growth is modeled directly as a function of substrate uptake, the LLM model improperly restricts the organism to be of fixed elemental stoichiometry, making it incapable of consistently resolving biological adaptation, ecological evolution, and community assembly. When growth is modeled as a function of the cellular nutrient quota, the LLM model may obtain good results at the risk of incorrect model parameters as compared to those inferred from the more accurate synthesizing unit model. However, biogeochemical models that implement these three formulations are needed to evaluate which formulation is acceptably accurate and their impacts on predicted long‐term ecosystem dynamics. In particular, studies are needed that explore the extent to which parameter calibration can rescue model performance when the mechanistic representation of a biogeochemical process is known to be deficient.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Ligand Many-Body Expansion as a General Approach for Accelerating Transition Metal Complex Discovery

Methods that accelerate the evaluation of molecular properties are essential for chemical discovery. While some degree of ligand additivity has been established for transition metal complexes, it is underutilized in asymmetric complexes, such as the square pyramidal coordination geometries highly relevant to catalysis. To develop predictive methods beyond simple additivity, we apply a many-body expansion to octahedral and square pyramidal complexes and introduce a correction based on adjacent ligands (i.e., the cis interaction model). We first test the cis interaction model on adiabatic spin-splitting energies of octahedral Fe(II) complexes, predicting DFT-calculated values of unseen binary complexes to within an average of 1.4 kcal/mol. Uncertainty analysis reveals the optimal basis, comprising the homoleptic and mer symmetric complexes. We next show that the cis model (i.e., the cis interaction model solved for the optimal basis) infers both DFT- and CCSD(T)-calculated model catalytic reaction energies to within 1 kcal/mol on average. The cis model predicts low-symmetry complexes with reaction energies outside the range of binary complex reaction energies. We observe that trans interactions are unnecessary for most monodentate systems but can be important for some combinations of ligands, such as complexes containing a mixture of bidentate and monodentate ligands. Lastly, we demonstrate that the cis model may be combined with Δ-learning to predict CCSD(T) reaction energies from exhaustively calculated DFT reaction energies and the same fraction of CCSD(T) reaction energies needed for the cis model, achieving around 30% of the error from using the CCSD(T) reaction energies in the cis model alone.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRSDate not supplied

Introduction to our COSPAR-Sponsored Session: Space-Observation Contributions Supporting Climate Action

• The challenge for us at COSPAR in putting this program together was that we are primarily a scientifically oriented organization. “Climate Action,” as it is often expressed publicly, tends to be the domain of “activists.” As scientists, on the other hand, to retain our credibility – and for the contributions we make to continue carrying the weight of scientific truth – it is critical that we remain even-handed in our analysis and our reporting of results. • COSPAR is the Committee on Space Research, and fortunately, much of what we observe from space bears objectively on the attributes of the Earth System and how it is evolving. We can measure from space changes in the cryosphere, in the oceans, the land surface and the atmosphere, frequently, on a global scale, to a degree that is generally not possible any other way. And we have been making such observations, in increasing detail, scope, and precision, for about 60 years. • These data help us characterize the current state and identify patterns of change in the Earth System that allow us to infer processes and to improve climate models. With modeling we can test and refine our inferences, and make some predictions. The results can then inform policy and decision-makers, the public in general, as well as those taking direct action. • So, for today’s session we have invited 7 15-minute presentations spanning a broad range of climate-related topics, covering observations from space that can inform climate-related decision-making – from sea-ice extent and sea-level rise, to land surface properties and land-based water resources, to interactions between land or water surfaces and the atmosphere, to severe events in the atmosphere itself. • We begin with an overview of the observations contributed by one of the premier space agencies, given by NASA Chief Scientist and Senior Climate Advisor Dr. Kate Calvin, which will be followed by talks on what we are learning about specific attributes of the Earth System from space-based measurements that can inform climate-related policy and action.

Ralph Kahn↗
DOE OSTI2023

Robust inference of ecosystem soil water stress from eddy covariance data

Eddy covariance data are invaluable for determining ecosystem water use strategies under soil water stress. However, existing stress inference methods require numerous subjective data processing and model specification assumptions whose effect on the inferred soil water stress signal is rarely quantified. These uncertainties may confound the stress inference and the generalization of ecosystem water use strategies across multiple sites and studies. In this research, we quantify the sensitivity of soil water stress signals inferred from eddy covariance data to the prevailing data and modeling assumptions (i.e., their robustness) to compile a comprehensive list of sites with robust soil water stress signals and assess the performance of current stress inference methods. To accomplish this, we identify the most prevalent assumptions from the literature and perform a digital factorial experiment to extract probability distributions of plausible soil water stress signals and model performance at 151 FLUXNET2015 and AmeriFlux-FLUXNET sites. Here, we develop a new framework that summarizes these probability distributions to classify and rank the robustness of each site’s soil water stress signal, which we display with a user-friendly heat map. We estimate that only 5%–36% of sites exhibit a robust soil water stress signal due to deficient model performance and poorly constrained ecosystem water use parameters. We also find that the lack of robustness is site-specific, which undermines grouping stress signals by broad ecosystem categories or comparing results across studies with differing assumptions. Lastly, existing stress inference methods appear better suited for eddy covariance sites with grass/annual vegetation. Our findings call for more careful and consistent inference of ecosystem water stress from eddy covariance data.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Circumstellar dust around AGB stars and implications for infrared emission from galaxies

Stellar population synthesis (SPS) models are used to infer many galactic properties including star formation histories, metallicities, and stellar and dust masses. However, most SPS models neglect the effect of circumstellar dust shells around evolved stars and it is unclear to what extent they impact the analysis of spectral energy distributions (SEDs). To overcome this shortcoming we have created a new set of circumstellar dust models, using the radiative transfer code DUSTY, for asymptotic giant branch (AGB) stars and incorporated them into the Flexible Stellar Population Synthesis code. The circumstellar dust models provide a good fit to individual AGB stars as well as the IR color–magnitude diagrams of the Large and Small Magellanic Clouds. IR luminosity functions from the Large and Small Magellanic Clouds are not well-fit by the 2008 Padova isochrones when coupled to our circumstellar dust models and so we adjusted the lifetimes of AGB stars in the models to provide a match to the data. We show, in agreement with previous work, that circumstellar dust from AGB stars can make a significant contribution to the IR (≳4 μm) emission from galaxies that contain relatively little diffuse dust, including low-metallicity and/or non-star-forming galaxies. Our models provide a good fit to the mid-IR spectra of early-type galaxies. Circumstellar dust around AGB stars appears to have a small effect on the IR SEDs of metal-rich star-forming galaxies (i.e., when A{sub V} ≳ 0.1). Stellar population models that include circumstellar dust will be needed to accurately interpret data from the James Webb Space Telescope and other IR facilities.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2018

Modeling the immune response to HIV infection

The interplay between immune response and HIV is intensely studied via mathematical modeling, with significant insights but few direct answers. Here in this short review, we highlight advances and knowledge gaps across different aspects of immunity. In particular, we identify the innate immune response and its role in priming the adaptive response as ripe for modeling. The latter have been the focus of most modeling studies, but we also synthesize key outstanding questions regarding effector mechanisms of cellular immunity and development of broadly neutralizing antibodies. Thus far, most modeling studies aimed to infer general immune mechanisms; we foresee that significant progress will be made next by detailed quantitative fitting of models to data, and prediction of immune responses.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Modeling the Formation of the Family of the Dwarf Planet Haumea

The dwarf planet (136108) Haumea has an intriguing combination of unique physical properties: near-breakup spin, two regular satellites, and an unexpectedly compact family. While these properties point toward formation by a collision, there is no self-consistent and reasonably probable formation hypothesis that can connect the unusually rapid spin and low relative velocities of Haumea family members (“Haumeans”). We explore and test the proposed formation hypotheses (catastrophic collision, graze-and-merge, and satellite collision) in detail. We flexibly parameterize the properties of the collision (e.g., the collision location) and use simple models for the unique three-dimensional velocity ejection field expected from each model to generate simulated families. These are then compared to the observed Kuiper Belt objects using Bayesian parameter inference, including a mixture model that robustly allows for interlopers from the background population. After testing our methodology, we find that the best match to the observed Haumeans is an essentially isotropic ejection field with a typical velocity of 150 m s{sup −1}. The graze-and-merge formation hypothesis—in which Haumeans are shed due to excess angular momentum—is clearly disfavored because the observed Haumeans are not oriented in a plane. The satellite collision model is also disfavored. Including these new constraints, we present a detailed discussion of the formation hypotheses, including variations, some of which are tested. Some new hypotheses are proposed (a cratering collision and a collision where Haumea’s upper layers are “missing”) and scrutinized. We do not identify a satisfactory formation hypothesis, but we do propose several avenues of additional investigation. In the process of these analyses, we identify many new candidate Haumeans and dynamically confirm seven of them as consistent with the observed family. We also confirm that Haumeans have a shallow size distribution and discuss implications for the discovery and identification of new Haumeans.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

U.S. stock market interaction network as learned by the Boltzmann machine

Here, we study historical dynamics of joint equilibrium distribution of stock returns in the U.S. stock market using the Boltzmann distribution model being parametrized by external fields and pairwise couplings. Within Boltzmann learning framework for statistical inference, we analyze historical behavior of the parameters inferred using exact and approximate learning algorithms. Since the model and inference methods require use of binary variables, effect of this mapping of continuous returns to the discrete domain is studied. The presented results show that binarization preserves the correlation structure of the market. Properties of distributions of external fields and couplings as well as the market interaction network and industry sector clustering structure are studied for different historical dates and moving window sizes. We demonstrate that the observed positive heavy tail in distribution of couplings is related to the sparse clustering structure of the market. We also show that discrepancies between the model’s parameters might be used as a precursor of financial instabilities.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Thermal Decomposition Kinetics of 4,6‐Diamino‐5,7‐dinitro‐benzo‐furazan

This experimental study investigated the thermal decomposition kinetics of 4,6-diamino-5,7-dinitro-benzo-furazan (referred to as F1 hereafter)—an important decomposition product of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB—a prototypical insensitive high explosive). Simultaneous differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), and mass spectrometry (MS) measurements were employed to determine the decomposition kinetics of F1 and to track the evolution of product gases. The DSC profiles were measured at 10 different heating rates between 0.025°C/min and 10°C/min. The measured exotherms were influenced by F1 melting at heating rates above 0.25°C/min, and corresponding changes in decomposition enthalpy and TGA mass-loss-rate profiles indicated a transition from solid-to-gas decomposition to an increasing contribution from liquid-to-gas decomposition. Analysis of low-heating-rate DSC data between 0.025°C/min and 0.17°C/min with the extended Prout–Tompkins model yielded an activation energy of 305 kJ/mol for solid-to-gas F1 decomposition, higher than previous values inferred from TATB decomposition models involving F1. This study provides the first direct experimental determination of the energy barrier for F1 decomposition. MS measurements showed that the major gaseous products matched species previously reported for TATB decomposition (e.g., CO 2 , HCN, C 2 N 2 , etc.), with water identified as the dominant product. Furthermore, these results provide important experimental constraints for improving chemical kinetics models of TATB decomposition and for predicting the reactivity, stability, and safety of TATB-based high explosives under long-term aging conditions and abnormal thermal environments.

4,6-Diamino-5,7-dinitro-benzo-furazan↗
DOE OSTI2026

Delving into the depths of NGC 3783 with XRISM

Using XRISM/Resolve 439 ks time-averaged spectra of the well-known Seyfert-1.5 active galactic nucleus (AGN) in NGC 3783, we investigated the nature of the Fe Kα emission line at 6.4 keV, the strongest and most common X-ray line observed in AGNs. Even the narrow component of the line is resolved with evident Fe Kα 1 (6.404 keV) and Kα 2 (6.391 keV) contributions with a 2:1 flux ratio, fully consistent with a neutral gas with negligible bulk velocity. The narrow and intermediate-width components have a full width at half maximum of 350 ± 50 km/s and 3510 ± 470 km/s, respectively, suggesting that they arise in the outer disk/torus and/or broad line region. We detect a 10% excess flux around 4–7 keV that is not described well by a symmetric Gaussian line but is consistent with a relativistically broadened emission line. In this study we took the simplest approach, modelling the asymmetric line as a single emission line (assuming neutral, He-like, or H-like iron) convolved with a relativistic disk line model. As expected, the inferred inclination angle (i) is highly sensitive to the assumed ionisation state and ranges between 17 and 44°. This model also constrains the black hole spin via the extent of the red wing: the required gravitational redshift in the fitted disk-line profile disfavours a non-spinning (Schwarzschild) black hole. The derived inner radius is close to the radius of the innermost stable circular orbit (rISCO) and is strongly correlated with the black hole spin. To better constrain the spin, we fixed the inner radius to r ISCO and derived a lower limit on the spin of a ≥ 0.29 at the 3σ confidence level. A Compton shoulder is detected in our data as well as a 2–3σ detection of the Cr Kα and Ni Kα lines.

Astronomy and AstroPhysics↗
DOE OSTI2026

Quantum Computing for AI-based Design and Optimization of Electric Motors

Knowledge-based artificial intelligence and hierarchical fuzzy logic offer an interpretable framework for electricvehicle motor preliminary design, but their computational burden grows with linguistic granularity and coupled design-space size. This paper presents a reduced quantum reformulation of the hierarchical fuzzy inference of air-gap flux density, a representative level-one motor-design parameter. Starting from the published electric-vehicle motor-design framework, a three-term fuzzy prototype is constructed from the original inference structure. The reduced model is then reformulated as a modular quantum register-oracle system, in which each hierarchical subrelation is encoded as a block oracle and evaluated through superpositionbased candidate-label testing. The proposed modular quantum formulation reproduces the reduced classical prototype after block fusion. A resource analysis shows that the reduced modular system requires seven qubits per block and twenty-two qubits in a straightforward four-block implementation. Finally, a crossovercomplexity model is derived to identify the regime in which quantum candidate search may become favorable relative to hierarchical fuzzy inference. The results show that no quantum advantage should be claimed for the present one-output reduced benchmark, but that a plausible crossover emerges for larger joint candidate spaces and higher linguistic granularity. The work therefore establishes a technically consistent starting point for future quantum-assisted electric-vehicle motor-design optimization.

Kumar, Praveen [ORNL] (ORCID:0000000291877857)↗
NASA NTRS1982

Evaluation and development of satellite inferences of convective storm intensity using combined case study and thunderstorm model simulations

Observational requirements for predicting convective storm development and intensity as suggested by recent numerical experiments are examined. Recent 3D numerical experiments are interpreted with regard to the relationship between overshooting tops and surface wind gusts. The development of software for emulating satellite inferred cloud properties using 3D cloud model predicted data and the simulation of Heymsfield (1981) Northern Illinois storm are described as well as the development of a conceptual/semi-quantitative model of eastward propagating, mesoscale convective complexes forming to the lee of the Rocky Mountains.

Cotton, W. R.↗
DOE OSTI2019

Optimization of process models for determining volatility distribution and viscosity of organic aerosols from isothermal particle evaporation data

The composition of organic aerosol under different ambient conditions as well as their phase state have been a subject of intense study in recent years. One way to study particle properties is to measure the particle size shrinkage in a diluted environment at isothermal conditions. From these measurements it is possible to separate the fraction of low-volatility compounds from high-volatility compounds. In this work, we analyse and evaluate a method for obtaining particle composition and viscosity from measurements using process models coupled with input optimization algorithms. Two optimization methods, the Monte Carlo genetic algorithm and Bayesian inference, are used together with process models describing the dynamics of particle evaporation. The process model optimization scheme in inferring particle composition in a volatility-basis-set sense and composition-dependent particle viscosity is tested with artificially generated data sets and real experimental data. Optimizing model input so that the output matches these data yields a good match for the estimated quantities. Both optimization methods give equally good results when they are used to estimate particle composition to artificially test data. Finally, the timescale of the experiments and the initial particle size are found to be important in defining the range of values that can be identified for the properties from the optimization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Secular outflows from 3D MHD hypermassive neutron star accretion disc systems

Magnetized hypermassive neutron stars (HMNSs) have been proposed as a way for neutron star mergers to produce high electron fraction, high-velocity ejecta, as required by kilonova models to explain the observed light curve of GW170817. The HMNS drives outflows through neutrino energy deposition and mechanical oscillations, and raises the electron fraction of outflows through neutrino interactions before collapsing to a black hole (BH). Here, in this study, we perform 3D numerical simulations of HMNS–torus systems in ideal magnetohydrodynamics, using a leakage/absorption scheme for neutrino transport, the nuclear APR equation of state, and Newtonian self-gravity, with a pseudo-Newtonian potential added after BH formation. Due to the uncertainty in the HMNS collapse time, we choose two different parametrized times to induce collapse. We also explore two initial magnetic field geometries in the torus, and evolve the systems until the outflows diminish significantly ($\sim\!\! 1\!\! - \!\!2\ \mathrm{s}$). We find bluer, faster outflows as compared to equivalent BH–torus systems, producing M ∼ 10 −3 M ⊙ of ejecta with Y e ≥ 0.25 and v ≥ 0.25c by the simulation end. Approximately half the outflows are launched in disc winds at times $t\lesssim 500 \ \mathrm{ms}$, with a broad distribution of electron fractions and velocities, depending on the initial condition. The remaining outflows are thermally driven, characterized by lower velocities and electron fractions. Nucleosynthesis with tracer particles shows patterns resembling solar abundances in all models. Although outflows from our simulations do not match those inferred from two-component modelling of the GW170817 kilonova, self-consistent multidimensional detailed kilonova models are required to determine whether our outflows can power the blue kilonova.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS2025

Shock-Stationary Application of Pseudoshock Models During High-Amplitude Combustion-Driven Unsteadiness

The isolator pseudo-shock provides necessary compression within a dual-mode scramjet engine and buffers the engine system against unstart. Quasi-1D flux-conserved models are the state-of-the-art reduced-order model for optimization and online control of dual-mode scramjet engines. The stability and efficacy of this modeling approach is evaluated against data from a combustor-driven direct-connect experiment. The experiment exhibited strong combustor-driven unsteadiness that produced upstream propagating weak shocks into the isolator, interacting with the pseudo-shock. While this configuration resulted in unsteadiness that is atypical of standard operation, the experiment provided an opportunity to evaluate the modeling techniques in highly transient states. Such transients could occur during maneuvering or result from unexpected combustor events. A flexible quasi-1D formulation, the Fievet flux-conserved model is fit using Bayesian inference in the laboratory and shock-stationary reference frames. Model performance is analyzed using the Bayesian posteriors and model evaluations over the measured shock train speed range. It is concluded that to produce consistent isolator pressure profile estimates in this unsteady environment, the model must be implemented in a shock-stationary reference frame. Implementing this conclusion in model-based engine controllers may reduce needed unstart safety margins and increase maximum performance.

Bayesian↗