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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Inference of Transmission Network Structure from HIV Phylogenetic Trees

Phylogenetic inference is an attractive means to reconstruct transmission histories and epidemics. However, there is not a perfect correspondence between transmission history and virus phylogeny. Both node height and topological differences may occur, depending on the interaction between within-host evolutionary dynamics and between-host transmission patterns. To investigate these interactions, we added a within-host evolutionary model in epidemiological simulations and examined if the resulting phylogeny could recover different types of contact networks. To further improve realism, we also introduced patient-specific differences in infectivity across disease stages, and on the epidemic level we considered incomplete sampling and the age of the epidemic. Second, we implemented an inference method based on approximate Bayesian computation (ABC) to discriminate among three well-studied network models and jointly estimate both network parameters and key epidemiological quantities such as the infection rate. Our ABC framework used both topological and distance-based tree statistics for comparison between simulated and observed trees. Overall, our simulations showed that a virus time-scaled phylogeny (genealogy) may be substantially different from the between-host transmission tree. This has important implications for the interpretation of what a phylogeny reveals about the underlying epidemic contact network. In particular, we found that while the within-host evolutionary process obscures the transmission tree, the diversification process and infectivity dynamics also add discriminatory power to differentiate between different types of contact networks. We also found that the possibility to differentiate contact networks depends on how far an epidemic has progressed, where distance-based tree statistics have more power early in an epidemic. Finally, we applied our ABC inference on two different outbreaks from the Swedish HIV-1 epidemic.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Calibration verification for stochastic agent-based disease spread models

Accurate disease spread modeling is crucial for identifying the severity of outbreaks and planning effective mitigation efforts. To be reliable when applied to new outbreaks, model calibration techniques must be robust. However, current methods frequently forgo calibration verification (a stand-alone process evaluating the calibration procedure) and instead use overall model validation (a process comparing calibrated model results to data) to check calibration processes, which may conceal errors in calibration. In this work, we develop a stochastic agent-based disease spread model to act as a testing environment as we test two calibration methods using simulation-based calibration, which is a synthetic data calibration verification method. The first calibration method is a Bayesian inference approach using an empirically-constructed likelihood and Markov chain Monte Carlo (MCMC) sampling, while the second method is a likelihood-free approach using approximate Bayesian computation (ABC). Simulation-based calibration suggests that there are challenges with the empirical likelihood calculation used in the first calibration method in this context. These issues are alleviated in the ABC approach. Despite these challenges, we note that the first calibration method performs well in a synthetic data model validation test similar to those common in disease spread modeling literature. We conclude that stand-alone calibration verification using synthetic data may benefit epidemiological researchers in identifying model calibration challenges that may be difficult to identify with other commonly used model validation techniques.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Analysis of a Stabilized CNLF Method with Fast Slow Wave Splittings for Flow Problems

In this work, we study Crank-Nicolson leap-frog (CNLF) methods with fast-slow wave splittings for Navier-Stokes equations (NSE) with a rotation/Coriolis force term, which is a simplification of geophysical flows. We propose a new stabilized CNLF method where the added stabilization completely removes the method's CFL time step condition. A comprehensive stability and error analysis is given. We also prove that for Oseen equations with the rotation term, the unstable mode (for which u(n+1) + u(n-1) equivalent to 0) of CNLF is asymptotically stable. Numerical results are provided to verify the stability and the convergence of the methods.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Advanced Methods for Immersed Domain Multi-physics Computations

This is the final report on the project, and describes the main accomplishments in the development of the Shifted Boundary Method (SBM), a new computational framework for embedded/immersed computational mechanics applications.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Comprehensive uncertainty quantification (UQ) for full engineering models by solving probability density function (PDF) equation

This report details a new method for propagating parameter uncertainty (forward uncertainty quantification) in partial differential equations (PDE) based computational mechanics applications. The method provides full-field quantities of interest by solving for the joint probability density function (PDF) equations which are implied by the PDEs with uncertain parameters. Full-field uncertainty quantification enables the design of complex systems where quantities of interest, such as failure points, are not known apriori. The method, motivated by the well-known probability density function (PDF) propagation method of turbulence modeling, uses an ensemble of solutions to provide the joint PDF of desired quantities at every point in the domain. A small subset of the ensemble is computed exactly, and the remainder of the samples are computed with approximation of the driving (dynamics) term of the PDEs based on those exact solutions. Although the proposed method has commonalities with traditional interpolatory stochastic collocation methods applied directly to quantities of interest, it is distinct and exploits the parameter dependence and smoothness of the dynamics term of the governing PDEs. The efficacy of the method is demonstrated by applying it to two target problems: solid mechanics explicit dynamics with uncertain material model parameters, and reacting hypersonic fluid mechanics with uncertain chemical kinetic rate parameters. A minimally invasive implementation of the method for representative codes SPARC (reacting hypersonics) and NimbleSM (finite- element solid mechanics) and associated software details are described. For solid mechanics demonstration problems the method shows order of magnitudes improvement in accuracy over traditional stochastic collocation. For the reacting hypersonics problem, the method is implemented as a streamline integration and results show very good accuracy for the approximate sample solutions of re-entry flow past the Apollo capsule geometry at Mach 30.

42 ENGINEERING↗
DOE OSTI2021

Overview of Algorithms for Using Particle Morphology in Pre-Detonation Nuclear Forensics

A major goal in pre-detonation nuclear forensics is to infer the processing conditions and/or facility type that produced radiological material. This review paper focuses on analyses of particle size, shape, texture (“morphology”) signatures that could provide information on the provenance of interdicted materials. For example, uranium ore concentrates (UOC or yellowcake) include ammonium diuranate (ADU), ammonium uranyl carbonate (AUC), sodium diuranate (SDU), magnesium diuranate (MDU), and others, each prepared using different salts to precipitate U from solution. Once precipitated, UOCs are often dried and calcined to remove adsorbed water. The products can be allowed to react further, forming uranium oxides UO3, U3O8, or UO2 powders, whose surface morphology can be indicative of precipitation and/or calcination conditions used in their production. This review paper describes statistical issues and approaches in using quantitative analyses of measurements such as particle size and shape to infer production conditions. Statistical topics include multivariate t tests (Hotelling’s T 2 ), design of experiments, and several machine learning (ML) options including decision trees, learning vector quantization neural networks, mixture discriminant analysis, and approximate Bayesian computation (ABC). ABC is emphasized as an attractive option to include the effects of model uncertainty in the selected and fitted forward model used for inferring processing conditions.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
DOE OSTI2021

Quantification of Type I Interferon Inhibition by Viral Proteins: Ebola Virus as a Case Study

Type I interferons (IFNs) are cytokines with both antiviral properties and protective roles in innate immune responses to viral infection. They induce an antiviral cellular state and link innate and adaptive immune responses. Yet, viruses have evolved different strategies to inhibit such host responses. One of them is the existence of viral proteins which subvert type I IFN responses to allow quick and successful viral replication, thus, sustaining the infection within a host. We propose mathematical models to characterise the intra-cellular mechanisms involved in viral protein antagonism of type I IFN responses, and compare three different molecular inhibition strategies. We study the Ebola viral protein, VP35, with this mathematical approach. Approximate Bayesian computation sequential Monte Carlo, together with experimental data and the mathematical models proposed, are used to perform model calibration, as well as model selection of the different hypotheses considered. Finally, we assess if model parameters are identifiable and discuss how such identifiability can be improved with new experimental data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

The chemical homogeneity of open clusters

Determining the level of chemical homogeneity in open clusters is of fundamental importance in the study of the evolution of star-forming clouds and that of the Galactic disk. Yet limiting the initial abundance spread in clusters has been hampered by difficulties in obtaining consistent spectroscopic abundances for different stellar types. Without reference to any specific model of stellar photospheres, a model for a homogeneous cluster is that it forms a one-dimensional sequence, with any differences between members due to variations in stellar mass and observational uncertainties. I present a novel method for investigating the abundance spread in open clusters that tests this one-dimensional hypothesis at the level of observed stellar spectra, rather than constraining homogeneity using derived abundances as is traditionally done. Using high-resolution APOGEE spectra for 49 giants in M67, NGC 6819, and NGC 2420 I demonstrate that these spectra form one-dimensional sequences for each cluster. With detailed forward modeling of the spectra and Approximate Bayesian Computation, I derive strong limits on the initial abundance spread of 15 elements: <0.01 (0.02) dex for C and Fe, ≲0.015 (0.03) dex for N, O, Mg, Si, and Ni, ≲0.02 (0.03) dex for Al, Ca, and Mn, and ≲0.03 (0.05) dex for Na, S, K, Ti, and V (at 68% and 95% confidence, respectively). The strong limits on C and O imply that no pollution by massive core-collapse supernovae occurred during star formation in open clusters, which, thus, need to form within ≲6 Myr. Further development of this and related techniques will bring the power of differential abundances to stars other than solar twins in large spectroscopic surveys and will help unravel the history of star formation and chemical enrichment in the Milky Way through chemical tagging.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2018

A New Method to Measure the Post-reionization Ionizing Background from the Joint Distribution of Ly α and Ly β Forest Transmission

The amplitude of the ionizing background that pervades the intergalactic medium (IGM) at the end of the epoch of reionization provides a valuable constraint on the emissivity of the sources that reionized the universe. While measurements of the ionizing background at lower redshifts rely on a simulation-calibrated mapping between the photoionization rate and the mean transmission of the Lyα forest, at z ≳ 6 the IGM becomes increasingly opaque and transmission arises solely in narrow spikes separated by saturated Gunn–Peterson troughs. In this regime, the traditional approach of measuring the average transmission over large ~50 Mpc/h regions is less sensitive and suboptimal. In addition, the five times smaller oscillator strength of the Lyβ transition implies that the Lyβ forest is considerably more transparent at z ≳ 6, even in the presence of contamination by foreground z ~ 5 Lyα forest absorption. We present a novel statistical approach to analyze the joint distribution of transmission spikes in the cospatial z ~ 6 Lyα and Lyβ forests. Our method relies on approximate Bayesian computation (ABC), which circumvents the necessity of computing the intractable likelihood function describing the highly correlated Lyα and Lyβ transmission. We apply ABC to mock data generated from a large-volume hydrodynamical simulation combined with a state-of-the-art model of ionizing background fluctuations in the post-reionization IGM and show that it is sensitive to higher IGM neutral hydrogen fractions than previous techniques. As a proof of concept, we apply this methodology to a real spectrum of a z = 6.54 quasar and measure the ionizing background from 5.4 ≤ z ≤ 6.4 along this sightline with ~0.2 dex statistical uncertainties.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1973

Estimation of dipole-quadrupole dispersion energies.

The calculation of the dipole-quadrupole dispersion coefficient is discussed through a perturbation and a variation method. Accurate combination rules are obtained from both methods, one new and one already known. Further approximations permit computations in terms of accessible parameters. Values are calculated for the interactions of atomic pairs formed from hydrogen, alkali, and rare-gas atoms. A new relation giving the dipole-quadrupole coefficient in terms of the dipole-dipole coefficient and the dipole and quadrupole polarizabilities seems accurate, but needs further testing.

Alvarez-Rizzatti, M.↗
NASA NTRS1973

An interactive NASTRAN preprocessor

A Langley Research Center version of NASTRAN Level 15.1.0 designed to provide the analyst with an added tool for debugging massive NASTRAN input data is described. The program checks all NASTRAN input data cards and displays on a CRT the graphic representation of the undeformed structure. In addition, the program permits the display and alteration of input data and allows reexecution without physically resubmitting the job. Core requirements on the CDC 6000 computer are approximately 77,000 octal words of central memory.

Smith, W. W.↗
NASA NTRS1976

Methods of analyzing wind-tunnel data for dynamic flight conditions

The effects of power on the stability and the control characteristics of an airplane are discussed and methods of analysis are given for evaluating certain dynamic characteristics of the airplane that are not directly discernible from wind tunnel tests alone. Data are presented to show how the characteristics of a model tested in a wind tunnel are affected by power. The response of an airplane to a rolling and a yawing disturbance is discussed, particularly in regard to changes in wing dihedral and fin area. Solutions of the lateral equations of motion are given in a form suitable for direct computations. An approximate formula is developed that permits the rapid estimation of the accelerations produced during pull-up maneuvers involving abrupt elevator deflections.

Donlan, C. J.↗
NASA NTRS1978

Combustion of hydrogen in a two-dimensional duct with step fuel injectors

An investigation of the combustion of hydrogen perpendicularly injected from step fuel injectors into a Mach 2.72, 2100 K vitiated test gas was conducted. The model simulated the flow between the center and side struts of an integrated scramjet module at Mach 7 flight and an altitude of 29 km. Parametric variation included equivalence ratio, fuel dynamic pressure ratio, and area distribution of the model. The overall area ratio of the model was held constant at 2.87. The data analysis indicated that no measurable improvement in mixing or combustion efficiency was obtained by varying the fuel dynamic pressure ratio from 0.79 to 2.45. Computations indicated approximately 80 percent of the fuel was mixed so that it could react; however, only approximately 50 percent of the mixed fuel actually reacted in two test configurations, and 74 percent in later tests where less area expansion of the flow occurred.

Eggers, J. M.↗
NASA NTRS1978

The role of atmospheric shear, turbulence and a ground plane on the dissipation of aircraft vortex wakes

Enhanced dispersion of two-dimensional trailed vortex pairs within simplified neutral atmospheric backgrounds is studied numerically for three conditions: when the pair is imbedded in a constant turbulent bath (constant dissipation); when the pair is subjected to a mean cross-wind shear; and when the pair is near the ground. Turbulent transport is modeled using second-order closure turbulent transport theory. The turbulent background fields are constructed using a superequilibrium approximation. The computed results allow several general conclusions to be drawn with regard to the reduction in circulation of the vortex pair and the rolling moment induced on a following aircraft: (1) the rate of decay of a vortex pair increases with increasing background dissipation rate; (2) cross-wind shear disperses the vortex whose vorticity is opposite to the background; and (3) the proximity of a ground plane reduces the hazard of the pair by scrubbing. The phenomenon of vortex bounce is explained in terms of secondary vorticity produced at the ground plane. Qualitative comparisons are made with available experimental data, and inferences of these results upon the persistence of aircraft trailing vortices are discussed.

Bilanin, A. J.↗