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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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All sources NASA NTRS DOE OSTI

DOE OSTI2022

Poisson hurdle model-based method for clustering microbiome features

Abstract Motivation High-throughput sequencing technologies have greatly facilitated microbiome research and have generated a large volume of microbiome data with the potential to answer key questions regarding microbiome assembly, structure and function. Cluster analysis aims to group features that behave similarly across treatments, and such grouping helps to highlight the functional relationships among features and may provide biological insights into microbiome networks. However, clustering microbiome data are challenging due to the sparsity and high dimensionality. Results We propose a model-based clustering method based on Poisson hurdle models for sparse microbiome count data. We describe an expectation–maximization algorithm and a modified version using simulated annealing to conduct the cluster analysis. Moreover, we provide algorithms for initialization and choosing the number of clusters. Simulation results demonstrate that our proposed methods provide better clustering results than alternative methods under a variety of settings. We also apply the proposed method to a sorghum rhizosphere microbiome dataset that results in interesting biological findings. Availability and implementation R package is freely available for download at https://cran.r-project.org/package=PHclust. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2008

Development and Application of an Integrated Approach toward NASA Airspace Systems Research

The National Aeronautics and Space Administration's (NASA) Airspace Systems Program is contributing air traffic management research in support of the 2025 Next Generation Air Transportation System (NextGen). Contributions support research and development needs provided by the interagency Joint Planning and Development Office (JPDO). These needs generally call for integrated technical solutions that improve system-level performance and work effectively across multiple domains and planning time horizons. In response, the Airspace Systems Program is pursuing an integrated research approach and has adapted systems engineering best practices for application in a research environment. Systems engineering methods aim to enable researchers to methodically compare different technical approaches, consider system-level performance, and develop compatible solutions. Systems engineering activities are performed iteratively as the research matures. Products of this approach include a demand and needs analysis, system-level descriptions focusing on NASA research contributions, system assessment and design studies, and common systemlevel metrics, scenarios, and assumptions. Results from the first systems engineering iteration include a preliminary demand and needs analysis; a functional modeling tool; and initial system-level metrics, scenario characteristics, and assumptions. Demand and needs analysis results suggest that several advanced concepts can mitigate demand/capacity imbalances for NextGen, but fall short of enabling three-times current-day capacity at the nation s busiest airports and airspace. Current activities are focusing on standardizing metrics, scenarios, and assumptions, conducting system-level performance assessments of integrated research solutions, and exploring key system design interfaces.

Barhydt, Richard↗

DOE OSTI2013

Exact-to-precision generalized perturbation for neutron transport calculation

This manuscript extends the exact-to-precision generalized perturbation theory (E{sub P}GPT), introduced previously, to neutron transport calculation whereby previous developments focused on neutron diffusion calculation only. The E{sub P}GPT collectively denotes new developments in generalized perturbation theory (GPT) that place premium on computational efficiency and defendable accuracy in order to render GPT a standard analysis tool in routine design and safety reactor calculations. EPGPT constructs a surrogate model with quantifiable accuracy which can replace the original neutron transport model for subsequent engineering analysis, e.g. functionalization of the homogenized few-group cross sections in terms of various core conditions, sensitivity analysis and uncertainty quantification. This is achieved by reducing the effective dimensionality of the state variable (i.e. neutron angular flux) by projection onto an active subspace. Confining the state variations to the active subspace allows one to construct a small number of what is referred to as the 'active' responses which are solely dependent on the physics model rather than on the responses of interest, the number of input parameters, or the number of points in the state phase space. (authors)

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

Dark Energy Survey Year 1 Results: Joint Analysis of Galaxy Clustering, Galaxy Lensing, and CMB Lensing Two-point Functions

We perform a joint analysis of the auto and cross-correlations between three cosmic fields: the galaxy density field, the galaxy weak lensing shear field, and the cosmic microwave background (CMB) weak lensing convergence field. These three fields are measured using roughly 1300 sq. deg. of overlapping optical imaging data from first year observations of the Dark Energy Survey and millimeter-wave observations of the CMB from both the South Pole Telescope Sunyaev-Zel'dovich survey and Planck. We present cosmological constraints from the joint analysis of the two-point correlation functions between galaxy density and galaxy shear with CMB lensing. We test for consistency between these measurements and the DES-only two-point function measurements, finding no evidence for inconsistency in the context of flat $\Lambda$CDM cosmological models. Performing a joint analysis of five of the possible correlation functions between these fields (excluding only the CMB lensing autospectrum) yields $S_{8}\equiv \sigma_8\sqrt{\Omega_{\rm m}/0.3} = 0.782^{+0.019}_{-0.025}$ and $\Omega_{\rm m}=0.260^{+0.029}_{-0.019}$. We test for consistency between these five correlation function measurements and the Planck-only measurement of the CMB lensing autospectrum, again finding no evidence for inconsistency in the context of flat $\Lambda$CDM models. Combining constraints from all six two-point functions yields $S_{8}=0.776^{+0.014}_{-0.021}$ and $\Omega_{\rm m}= 0.271^{+0.022}_{-0.016}$. These results provide a powerful test and confirmation of the results from the first year DES joint-probes analysis.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2015

Model Analysis ToolKit

MATK provides basic functionality to facilitate model analysis within the Python computational environment. Model analysis setup within MATK includes: - define parameters - define observations - define model (python function) - define samplesets (sets of parameter combinations) Currently supported functionality includes: - forward model runs - Latin-Hypercube sampling of parameters - multi-dimensional parameter studies - parallel execution of parameter samples - model calibration using internal Levenberg-Marquardt algorithm - model calibration using lmfit package - model calibration using levmar package - Markov Chain Monte Carlo using pymc package MATK facilitates model analysis using: - scipy - calibration (scipy.optimize) - rpy2 - Python interface to R

Harp, DylanR.↗

DOE OSTI2015

Model Analysis ToolKit

Harp, Dylan R.↗

DOE OSTI2011

Analysis of Casimir forces with window functions: Kramers-Kronig general approach for real measured dielectric data

In this work we describe how the window method, which has been used with ideal Kramers-Kroning (K-K) consistent dielectric functions, is affected by real optical data where some degree of K-K inconsistency is always present. Analysis using measured data of the frequency-dependent dielectric function for gold and phase-change materials shows that the window method can in some cases amplify the errors introduced in the calculation of the Casimir force due to K-K inconsistency instead of minimizing them. The latter indicates that caution is required for the proper choice of the window function for dielectric data analysis and Casmir force calculations.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

NASA NTRS1984

Predictability experiments using a low order empirically corrected dynamical model

It is generally accepted that day to day weather variations possess a finite range of predictability estimated to be approximately two weeks (e.g., Lorenz, 1965). However, considerable observational evidence points to the existence of a number of low frequency flow regimes which are potentially predictable beyond this limit. These include blocking events and teleconnection patterns such as those described in Wallace and Gutzler (1981). The problem of the predictability of such modes is addressed by employing a highly simplified dynamical model projected onto the modes of interest. These modes are computed from an empirical orthogonal function (EOF) analysis of 10-day averaged anomalies (deviations from the mean seasonal cycle) of the 500 mb stream function for the winters of 1967-76. The first three EOF's are associated with an index cycle and some of the teleconnection patterns. The fourth and ninth are related to North Pacific and North Atlantic blocking, respectively.

Schubert, S.↗

DOE OSTI2022

Molecular-based analysis of nanoparticle solvation: Classical density functional approach

Proper statistical mechanics understanding of nanoparticle solvation processes requires an accurate description of the molecular structure of the solvent. Achieving this goal with standard molecular dynamics (MD) simulation methods is challenging due to large length scales. An alternative approach to this problem can be formulated using classical density functional theory (cDFT), where a full configurational description of the positions of all the atoms is replaced by collective atomic site densities in the molecule. Using an example of the negatively charged silica-like system in an aqueous polar environment represented by a two-site water model, we demonstrate here that cDFT can reproduce MD data at a fraction of the computational cost. An important implication of this result is the ability to understand how the solvent molecular features may affect the system’s properties at the macroscopic scale. A concrete example highlighted in this work is the analysis of nanoparticle interactions with sizes of up to 100 nm in diameter.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Illustrated formalisms for total scattering data: a guide for new practitioners

The total scattering method is the simultaneous study of both the real- and reciprocal-space representations of diffraction data. While conventional Bragg-scattering analysis (employing methods such as Rietveld refinement) provides insight into the average structure of the material, pair distribution function (PDF) analysis allows for a more focused study of the local atomic arrangement of a material. Generically speaking, a PDF is generated by Fourier transforming the total measured reciprocal-space diffraction data (Bragg and diffuse) into a real-space representation. However, the details of the transformation employed and, by consequence, the resultant appearance and weighting of the real-space representation of the system can vary between different research communities. As the worldwide total scattering community continues to grow, these subtle differences in nomenclature and data representation have led to conflicting and confusing descriptions of how the PDF is defined and calculated. This paper provides a consistent derivation of many of these different forms of the PDF and the transformations required to bridge between them. Some general considerations and advice for total scattering practitioners in selecting and defining the appropriate choice of PDF in their own research are presented. This contribution aims to benefit people starting in the field or trying to compare their results with those of other researchers.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Orientational analysis of atomic pair correlations in nanocrystalline indium oxide thin films

The application of grazing-incidence total X-ray scattering (GITXS) for pair distribution function (PDF) analysis using >50 keV X-rays from synchrotron light sources has created new opportunities for structural characterization of supported thin films with high resolution. Compared with grazing-incidence wide-angle X-ray scattering, which is only useful for highly ordered materials, GITXS/PDFs expand such analysis to largely disordered or nanostructured materials by examining the atomic pair correlations dependent on the direction relative to the surface of the supporting substrate. A characterization of nanocrystalline In 2 O 3 -derived thin films is presented here with in-plane-isotropic and out-of-plane-anisotropic orientational ordering of the atomic structure, each synthesized using different techniques. The atomic orientations of such films are known to vary based on the synthetic conditions. Here, an azimuthal orientational analysis of these films using GITXS with a single incident angle is shown to resolve the markedly different orientations of the atomic structures with respect to the planar support and the different degrees of long-range order, and hence, the terminal surface chemistries. It is anticipated that orientational analysis of GITXS/PDF data will offer opportunities to extend structural analyses of thin films by providing a means to qualitatively determine the major atomic orientation within nanocrystalline and, eventually, non-crystalline films.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2011

Matter induced bimetric actions for gravity

Research Highlights: > Gravitational effective action in the bimetric truncation. > RG flow in the large N limit of matter coupled to gravity. > Asymptotically safe theory found in the large N expansion. - Abstract: The gravitational effective average action is studied in a bimetric truncation with a nontrivial background field dependence, and its renormalization group flow due to a scalar multiplet coupled to gravity is derived. Neglecting the metric contributions to the corresponding beta functions, the analysis of its fixed points reveals that, even on the new enlarged theory space which includes bimetric action functionals, the theory is asymptotically safe in the large N expansion.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2018

Sub-picomolar Inhibition of HIV-1 Protease with a Boronic Acid

Boronic acids have been typecast as moieties for covalent complexation and are employed only rarely as agents for non-covalent recognition. By exploiting the profuse ability of a boronic acid group to form hydrogen bonds, we have developed an inhibitor of HIV-1 protease with extraordinary affinity. Specifically, we find that replacing an aniline moiety in darunavir with a phenylboronic acid leads to 20-fold greater affinity for the protease. X-ray crystallography demonstrates that the boronic acid group participates in three hydrogen bonds, more than the amino group of darunavir or any other analog. Importantly, the boronic acid maintains its hydrogen bonds and its affinity for the drug-resistant D30N variant of HIV-1 protease. The BOH···OC hydrogen bonds between the boronic acid hydroxy group and Asp30 (or Asn30) of the protease are short (r O···O = 2.2 Å), and density functional theory analysis reveals a high degree of covalency. Furthermore, these data highlight the utility of boronic acids as versatile functional groups in the design of small-molecule ligands.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Fatty acid capped, metal oxo clusters as the smallest conceivable nanocrystal prototypes

Metal oxo clusters of the type M 6 O 4 (OH) 4 (OOCR) 12 (M = Zr or Hf) are valuable building blocks for materials science. Here, we synthesize a series of zirconium and hafnium oxo clusters with ligands that are typically used to stabilize oxide nanocrystals (fatty acids with long and/or branched chains). The fatty acid capped oxo clusters have a high solubility but do not crystallize, precluding traditional purification and single-crystal XRD analysis. We thus develop alternative purification strategies and we use X-ray total scattering and Pair Distribution Function (PDF) analysis as our main method to elucidate the structure of the cluster core. We identify the correct structure from a series of possible clusters (Zr3, Zr4, Zr6, Zr12, Zr10, and Zr26). Excellent refinements are only obtained when the ligands are part of the structure model. Further evidence for the cluster composition is provided by nuclear magnetic resonance (NMR), infrared spectroscopy (FTIR), thermogravimetry analysis (TGA), and mass spectrometry (MS). We find that hydrogen bonded carboxylic acid is an intrinsic part of the oxo cluster. Using our analytical tools, we elucidate the conversion from a Zr6 monomer to a Zr12 dimer (and vice versa), induced by carboxylate ligand exchange. Finally, we compare the catalytic performance of Zr12-oleate clusters with oleate capped, 5.5 nm zirconium oxide nanocrystals in the esterification of oleic acid with ethanol. The oxo clusters present a five times higher reaction rate, due to their higher surface area. Since the oxo clusters are the lower limit of downscaling oxide nanocrystals, we present them as appealing catalytic materials, and as atomically precise model systems. In addition, the lessons learned regarding PDF analysis are applicable to other areas of cluster science as well, from semiconductor and metal clusters, to polyoxometalates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Analysis of tumor-immune functional responses in a mathematical model of neoantigen cancer vaccines

Cancer neoantigen vaccines have emerged as a promising approach to stimulating the immune system to fight cancer. We propose a simple model including key elements of cancer-immune interactions and conduct a phase plane analysis to understand the immunological mechanisms of cancer neoantigen vaccines. Analytical results are obtained for two widely used functional forms that represent the killing rate of tumor cells by immune cells: the law of mass action (LMA) and the dePillis-Radunskaya Law (LPR). Using the LMA, our results reveal that a slowly growing tumor can escape the immune surveillance and that there is a unique periodic solution. The LPR offers richer dynamics, in which tumor elimination and uncontrolled tumor growth are both present. We show that tumor elimination requires sufficient number of initial activated T cells in relationship to the malignant cells, which lends support to using the neoantigen cancer vaccine as an adjuvant therapy after the primary tumor is surgically removed or treated using radiotherapy. We also derive a sufficient condition for uncontrolled tumor growth under the assumption of the LPR. Here, the juxtaposition of analyses with these two different choices for the killing rate function highlights their importance on model behavior and biological implications, by which we hope to spur further theoretical and experimental work to understand mechanisms underlying different functional forms for the killing rate.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

Analysis of electron energy distribution function in the Linac4 H{sup −} source

To understand the Electron Energy Distribution Function (EEDF) in the Radio Frequency Inductively Coupled Plasmas (RF-ICPs) in hydrogen negative ion sources, the detailed analysis of the EEDFs using numerical simulation and the theoretical approach based on Boltzmann equation has been performed. It is shown that the EEDF of RF-ICPs consists of two parts, one is the low energy part which obeys Maxwellian distribution and the other is high energy part deviated from Maxwellian distribution. These simulation results have been confirmed to be reasonable by the analytical approach. The results suggest that it is possible to enhance the dissociation of molecules and the resultant H{sup −} negative ion production by reducing the gas pressure.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

NASA NTRS1985

Building a functional, integrated GIS/remote sensing resource analysis and planning system

To be an effective tool for resource analysis and planning, a geographic information system (GIS) needs to be integrated with a digital remote sensing capability. To be truly functional, the paired system must be driven by grass roots local needs. A case study couched in a Soil Conservation District in northern Utah is presented. Agency representatives determined that the most fundamental data sets to be entered into the GIS system analysis system in the first round were: land use/land cover; geomorphic/soil unit data; hydrologic unit data; and digital terrain. The least expensive and best ways to obtain these data were determined. Data were acquired and formatted to enter the state's PRIME/ARC-INFO GIS, and are being interrogated for resource management decisions related to such issues as agricultural preservation, urban expansion, soil erosion control, and dam siting.

Ridd, M. K.↗

DOE OSTI2025

Oxygen Defect Configurations in Single-Phase UO 2.15

Hyperstoichiometric UO 2.15 was characterized by neutron total scattering at high temperature in the single-phase UO 2+x region of the U/O phase diagram. The diffraction data confirmed a single-phase fluorite structure at high temperature. Analysis of the short-range data showed that the same structural model does not fit the pair distribution functions well. Instead, structural models containing specific configurations of oxygen defect clusters best represent the local atomic arrangement. In conclusion, prevalent defect clusters previously proposed were fit to the experimental data, and moderately distorted oxygen cuboctahedra hypothesized by recent molecular dynamics simulations fit the data most accurately.

neutron pair-distribution function analysis↗