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All sourcesNASA NTRSDOE OSTI
NASA NTRS2012

VESGEN Software for Mapping and Quantification of Vascular Regulators

VESsel GENeration (VESGEN) Analysis is an automated software that maps and quantifies effects of vascular regulators on vascular morphology by analyzing important vessel parameters. Quantification parameters include vessel diameter, length, branch points, density, and fractal dimension. For vascular trees, measurements are reported as dependent functions of vessel branching generation. VESGEN maps and quantifies vascular morphological events according to fractal-based vascular branching generation. It also relies on careful imaging of branching and networked vascular form. It was developed as a plug-in for ImageJ (National Institutes of Health, USA). VESGEN uses image-processing concepts of 8-neighbor pixel connectivity, skeleton, and distance map to analyze 2D, black-and-white (binary) images of vascular trees, networks, and tree-network composites. VESGEN maps typically 5 to 12 (or more) generations of vascular branching, starting from a single parent vessel. These generations are tracked and measured for critical vascular parameters that include vessel diameter, length, density and number, and tortuosity per branching generation. The effects of vascular therapeutics and regulators on vascular morphology and branching tested in human clinical or laboratory animal experimental studies are quantified by comparing vascular parameters with control groups. VESGEN provides a user interface to both guide and allow control over the users vascular analysis process. An option is provided to select a morphological tissue type of vascular trees, network or tree-network composites, which determines the general collections of algorithms, intermediate images, and output images and measurements that will be produced.

Parsons-Wingerter, Patricia A.↗
DOE OSTI2020

Model-based Reconstruction for Single Particle Cryo-Electron Microscopy

Single particle cryo-electron microscopy is a vital tool for 3D characterization of protein structures. A typical workflow involves acquiring projection images of a collection of randomly oriented particles, picking and classifying individual particle projections by orientation, and finally using the individual particle projections to reconstruct a 3D map of the electron density profile. The reconstruction is challenging because of the low signal-to-noise ratio of the data, the unknown orientation of the particles, and the sparsity of data especially when dealing with flexible proteins where there may not be sufficient data corresponding to each class to obtain an accurate reconstruction using standard algorithms. In this paper we present a model-based image reconstruction technique that uses a regularized cost function to reconstruct the 3D density map by assuming known orientations for the particles. Our method casts the reconstruction as minimizing a cost function involving a novel forward model term that accounts for the contrast transfer function of the microscope, the orientation of the particles and the center of rotation offsets. We combine the forward model term with a regularizer that enforces desirable properties in the volume to be reconstructed. Using simulated data, we demonstrate how our method can significantly improve upon the typically used approach.

Venkatakrishnan, Singanallur↗
NASA NTRS2000

Charon Message-Passing Toolkit for Scientific Computations

Charon is a library, callable from C and Fortran, that aids the conversion of structured-grid legacy codes-such as those used in the numerical computation of fluid flows-into parallel, high- performance codes. Key are functions that define distributed arrays, that map between distributed and non-distributed arrays, and that allow easy specification of common communications on structured grids. The library is based on the widely accepted MPI message passing standard. We present an overview of the functionality of Charon, and some representative results.

VanderWijngaart, Rob F.↗
DOE OSTI2022

tapir: A tool for topologies, amplitudes, partial fraction decomposition and input for reductions

The demand for precision predictions in the field of high energy physics has dramatically increased over recent years. Experiments conducted at the LHC, as well as precision measurements at the intensity frontier such as Belle II require equally precise theoretical predictions to make full use of the acquired data. To match the experimental precision, second-, third- and, for certain quantities, even higher-order calculations in perturbative quantum field theory are required. To facilitate such calculations, computer software automating as many steps as possible is required. Yet, each calculation poses different challenges and thus, a high level of configurability is required. In this context we present tapir: a tool for identification, manipulation and minimization of Feynman integral families. It is designed to integrate in toolchains based on the computer algebra system FORM, the use of which is common practice in the field. tapir can be used to reduce the complexity of multi-loop problems with cut-filters, topology mapping, partial fraction decomposition and alike. Program Title:tapir CPC Library link to program files:https://doi.org/10.17632/ptc9t46xyn.1 Developer's repository link:https://gitlab.com/tapir-devs/tapir Licensing provisions: GPLv3 Programming language:python 3, C++ Nature of problem: Multi-loop computations require the automatization of a large number of different tasks related to Feynman integral topologies. Among them are the identification and minimization of integral topologies, partial fraction decomposition of topologies in the case of linearly dependent propagators as well as mapping scalar products of loop momenta to scalar functions. Solution method: The minimization of topologies is performed by comparison of their respective Nickel indices [1], even further minimization utilizes Pak's algorithm [2]. To efficiently map scalar products of loop momenta to scalar functions FORM [3] code is generated. Additional comments including restrictions and unusual features: Minimization based on Pak's algorithm slows down for many lines and scales. A coarser minimization using the Nickel indices, however, is still possible. [1]B. Nickel, D. Meiron, G.A.J. Baker, Compilation of 2-pt and 4-pt graphs for continuous spin model, Report, University of Guelph, 1977.[2]A. Pak, J. Phys. Conf. Ser. 368 (2012) 012049, https://doi.org/10.1088/1742-6596/368/1/012049, arXiv:1111.0868.[3]B. Ruijl, T. Ueda, J. Vermaseren, FORM version 4.2, arXiv:1707.06453, 7 2017.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Fourier Neural Networks as Function Approximators and Differential Equation Solvers

We present a Fourier neural network (FNN) that can be mapped directly to the Fourier decomposition. The choice of activation and loss function yields results that replicate a Fourier series expansion closely while preserving a straightforward architecture with a single hidden layer. The simplicity of this network architecture facilitates the integration with any other higher-complexity networks, at a data pre- or postprocessing stage. We validate this FNN on naturally periodic smooth functions and on piecewise continuous periodic functions. We showcase the use of this FNN for modeling or solving partial differential equations with periodic boundary conditions. The main advantages of the current approach are the validity of the solution outside the training region, interpretability of the trained model, and simplicity of use.

Fourier decomposition↗
NASA NTRS1976

Computer simulation and evaluation of edge detection algorithms and their application to automatic path selection

The construction of an autonomous roving vehicle requires the development of complex data-acquisition and processing systems, which determine the path along which the vehicle travels. Thus, a vehicle must possess algorithms which can (1) reliably detect obstacles by processing sensor data, (2) maintain a constantly updated model of its surroundings, and (3) direct its immediate actions to further a long range plan. The first function consisted of obstacle recognition. Obstacles may be identified by the use of edge detection techniques. Therefore, the Kalman Filter was implemented as part of a large scale computer simulation of the Mars Rover. The second function consisted of modeling the environment. The obstacle must be reconstructed from its edges, and the vast amount of data must be organized in a readily retrievable form. Therefore, a Terrain Modeller was developed which assembled and maintained a rectangular grid map of the planet. The third function consisted of directing the vehicle's actions.

Longendorfer, B. A.↗
NASA NTRS1996

Report on 3 and 4-point correlation statistics in the COBE DMR anisotrophy maps

As part of the work performed under NASA contract # NAS5-32648, we have computed the 3-point and 4-point correlation functions of the COBE-DNIR 2-year and 4-year anisotropy maps. The motivation for this study was to search for evidence of non-Gaussian statistical fluctuations in the temperature maps: skewness or asymmetry in the case of the 3-point function, kurtosis in the case of the 4-point function. Such behavior would have very significant implications for our understanding of the processes of galaxy formation, because our current models of galaxy formation predict that non-Gaussian features should not be present in the DMR maps. The results of our work showed that the 3-point correlation function is consistent with zero and that the 4-point function is not a very sensitive probe of non-Gaussian behavior in the COBE-DMR data. Our computation and analysis of 3-point correlations in the 2-year DMR maps was published in the Astrophysical Journal Letters, volume 446, page L67, 1995. Our computation and analysis of 3-point correlations in the 4-year DMR maps will be published, together with some additional tests, in the June 10, 1996 issue of the Astrophysical Journal Letters. Copies of both of these papers are attached as an appendix to this report.

Hinshaw, Gary↗
DOE OSTI2025

Mixed quantum-classical methods for polaron spectral functions

In this work, using two distinct semiclassical approaches—namely, the mean-field Ehrenfest method and the mapping approach to surface hopping—we investigate the spectral function of a single charge interacting with phonons on a lattice. This quantity is relevant for the description of angle-resolved photoemission experiments. Focusing on the one-dimensional Holstein model, we compare the performance of these approaches across a range of coupling strengths and lattice sizes, exposing the relative strengths and weaknesses of each. We demonstrate that these approaches can be efficiently applied with reasonable accuracy to ab initio polaron models. Furthermore, our work provides a route to the calculation of spectral properties in realistic electron–phonon-coupled systems in a computationally inexpensive manner with encouraging accuracy.

Atomic and molecular spectra↗
DOE OSTI2024

Primordial non-Gaussianities with weak lensing: information on non-linear scales in the Ulagam full-sky simulations

Abstract Primordial non-Gaussianities (PNGs) are signatures in the density field that encode particle physics processes from the inflationary epoch. Such signatures have been extensively studied using the Cosmic Microwave Background, through constraining their amplitudes,f X NL , with future improvements expected from large-scale structure surveys; specifically, the galaxy correlation functions. We show that weak lensing fields can be used to achieve competitive and complementary constraints. This is shown via theUlagamsuite of N-body simulations, a subset of which evolves primordial fields with four types of PNGs. We create full-sky lensing maps and estimate the Fisher information from three summary statistics measured on the maps: the moments, the cumulative distribution function, and the 3-point correlation function. We find that the year 10 sample from the Rubin Observatory Legacy Survey of Space and Time (LSST) can constrain PNGs toσ(f NL eq ) ≈ 110,σ(f NL or, lss ) ≈ 120,σ(f NL loc ) ≈ 40. For the former two, this is better than or comparable to expected galaxy clustering-based constraints from the Dark Energy Spectroscopic Instrument (DESI). The PNG information in lensing fields is on non-linear scales and at low redshifts (z≲ 1.25), with a clear origin in the evolution history of massive halos. The constraining power degrades by ∼60% under scale cuts of ≳ 20 Mpc, showing there is still significant information on scales mostly insensitive to small-scale systematic effects (e.g., baryons). We publicly release theUlagamsuite to enable more survey-focused analyses.

Astronomy & Astrophysics↗
DOE OSTI2020

Opportunities and challenges for assigning cofactors in cryo-EM density maps of chlorophyll-containing proteins

Abstract The accurate assignment of cofactors in cryo-electron microscopy maps is crucial in determining protein function. This is particularly true for chlorophylls (Chls), for which small structural differences lead to important functional differences. Recent cryo-electron microscopy structures of Chl-containing protein complexes exemplify the difficulties in distinguishing Chl b and Chl f from Chl a . We use these structures as examples to discuss general issues arising from local resolution differences, properties of electrostatic potential maps, and the chemical environment which must be considered to make accurate assignments. We offer suggestions for how to improve the reliability of such assignments.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1993

NASA Lewis 8- by 6-foot supersonic wind tunnel user manual

The 8- by 6-Foot Supersonic Wind Tunnel (SWT) at Lewis Research Center is available for use by qualified researchers. This manual contains tunnel performance maps which show the range of total temperature, total pressure, static pressure, dynamic pressure, altitude, Reynolds number, and mass flow as a function of test section Mach number. These maps are applicable for both the aerodynamic and propulsion cycle. The 8- by 6-Foot Supersonic Wind Tunnel is an atmospheric facility with a test section Mach number range from 0.36 to 2.0. General support systems (air systems, hydraulic system, hydrogen system, infrared system, laser system, laser sheet system, and schlieren system are also described as are instrumentation and data processing and acquisition systems. Pretest meeting formats are outlined. Tunnel user responsibility and personal safety requirements are also stated.

Soeder, Ronald H.↗
DOE OSTI2021

Spatiotemporal mapping of mesoscopic liquid dynamics

The study of liquid dynamics at mesoscopic scales is still strewn with difficulty due to limitations in theory and experiment. Historically, significant attention has been given to the analysis of space-time correlation functions and their frequency-Fourier transforms at a few discrete wave numbers. The massive computing power afforded by modern high performance computing clusters and the advent of a wide-angle neutron spin-echo spectrometer, however, have unlocked a more intuitive and fruitful approach to this problem. Using molecular dynamics simulations, here we demonstrate the benefits of spatiotemporally mapping intermediate scattering functions on a dense grid of correlation times and wave numbers. Four model systems are investigated: a Lennard-Jones liquid, a coarse-grained bead-spring polymer, a molten sodium chloride, and a poly(ethylene oxide) melt. We show that the spatiotemporal mapping approach is particularly useful for elucidating the mesoscopic dynamics in these liquids, where several underlying mechanisms, such as molecular relaxations, hydrodynamic modes, and nonhydrodynamic excitations, are potentially at play. Therefore, compared to the traditional method, direct visualization of density space-time correlation functions on two-dimensional color maps permits appraisals of complicated dynamical behavior at mesoscales in a global manner. For example, the scaling relations between space and time for different types of molecular motions can be straightforwardly identified on these plots, without any model-dependent analysis. Additionally, we show how theoretical ideas regarding collective mesoscopic dynamics, such as the classical hydrodynamic theory, the convolution approximation, and a recently proposed phenomenological model, can be discussed in terms of the global features of spatiotemporal maps of intermediate scattering functions. The new perspective offered by the spatiotemporal mapping method should prove useful for the study of liquid dynamics in general.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NASA NTRS1999

NASA Glenn 1-by 1-Foot Supersonic Wind Tunnel User Manual

This manual describes the NASA Glenn Research Center's 1 - by 1 -Foot Supersonic Wind Tunnel and provides information for customers who wish to conduct experiments in this facility. Tunnel performance envelopes of total pressure, total temperature, and dynamic pressure as a function of test section Mach number are presented. For each Mach number, maps are presented of Reynolds number per foot as a function of the total air temperature at the test section inlet for constant total air pressure at the inlet. General support systems-such as the service air, combustion air, altitude exhaust system, auxiliary bleed system, model hydraulic system, schlieren system, model pressure-sensitive paint, and laser sheet system are discussed. In addition, instrumentation and data processing, acquisition systems are described, pretest meeting formats and schedules are outlined, and customer responsibilities and personnel safety are addressed.

Seablom, Kirk D.↗
NASA NTRS2002

Oxidation and Volatilization of Silica-Formers in Water Vapor

At high temperatures SiC and Si3N4 react with water vapor to form a silica scale. Silica scales also react with water vapor to form a volatile Si(OH)4 species. These simultaneous reactions, one forming silica and the other removing silica, are described by paralinear kinetics. A steady state, in which these reactions occur at the same rate, is eventually achieved, After steady state is achieved, the oxide found on the surface is a constant thickness and recession of the underlying material occurs at a linear rate. The steady state oxide thickness, the time to achieve steady state, and the steady state recession rate can all be described in terms of the rate constants for the oxidation and volatilization reactions. In addition, the oxide thickness, the time to achieve steady state, and the recession rate can also be determined from parameters that describe a water vapor-containing environment. Accordingly, maps have been developed to show these steady state conditions as a function of reaction rate constants, pressure, and gas velocity. These maps can be used to predict the behavior of silica formers in water-vapor containing environments such as combustion environments. Finally, these maps are used to explore the limits of the paralinear oxidation model for SiC and Si3N4

Opila, E. J.↗
DOE OSTI2025

Tracking seasonal variability in plant traits from spaceborne PRISMA and NEON AOP across forest types and ecoregions

Plant traits serve as critical indicators of how plants adapt to environmental changes and influence ecosystem functions. While airborne hyperspectral remote sensing effectively maps plant traits through detailed reflectance properties, it is limited by cost and scale, making large-scale and temporal studies challenging. The recently launched spaceborne hyperspectral imager, PRecursore IperSpettrale della Missione Applicativa (PRISMA), offers frequent, large scale and high-fidelity observations on a spatial resolution of 30 m and a revisit time of around 29 days, making it suitable for large-scale seasonal trait mapping. However, their potential remains largely unexplored. This study developed a multi-stage framework by leveraging the PRISMA spaceborne hyperspectral data and National Ecological Observatory Network (NEON) Airborne Observation Platform (AOP) hyperspectral data to investigate the seasonal dynamics of four key plant traits — chlorophyll content, carotenoid content, equivalent water thickness, and nitrogen content — across eleven NEON sites representing diverse forest types and ecoregions in the contiguous U.S. Our results demonstrated that PRISMA hyperspectral data can reliably track seasonal variability in plant traits, achieving overall R 2 values ranging from 0.78 to 0.88 and normalized root mean square error (NRMSE) values ranging from 5.4% to 8.4% for the four traits. Seasonal patterns revealed bell-shaped trajectories for chlorophyll and carotenoids, while equivalent water thickness decreased steadily across most sites, driven by structural changes during leaf maturation and senescence. Nitrogen content exhibited less pronounced seasonal variation but followed expected nutrient resorption patterns. Analysis of environmental drivers showed that seasonal variability is primarily controlled by solar radiation and day length in northern sites, vapor pressure in semi-arid regions, and temperature in mid-southeastern sites. Spatial variability, meanwhile, was primarily driven by soil properties, particularly during the peak growing season. However, the influence of soil variables slightly declines toward the end of the season at several sites, as climatic factors become more prominent. This study highlights the capability of PRISMA, and potentially other similar spaceborne hyperspectral data for large-scale, time-series plant trait mapping and provides valuable insights into the interactions between plant traits and environmental factors. In conclusion, these findings contribute to advancing our understanding of plant functional ecology and improving predictions of ecosystem responses to environmental changes.

Environmental drivers↗
NASA NTRS1977

Three-dimensional modelling in magnetotelluric and magnetic variational sounding

The Galerkin finite-element method is used to obtain approximate solutions for the three-dimensional induction problem. A rectangular conductive prism is considered as an example, and solutions are obtained for linear and circularly polarized incident plane-wave fields. Magnetotelluric tensor impedances and magnetic transfer functions are computed. Polar diagrams of the tensor impedances and magnetic transfer functions along with their amplitude contour maps are presented. The dimensionality parameter, skew, is contoured at the surface of the earth. It is shown that the relative amplitudes and shapes of the additional and principal impedance polar diagrams can be used to determine the dimensionality of geoelectrical structures. Stations with skew values greater than 0.2 are significantly influenced by the three-dimensionality of the geoelectric structure. The amplitudes of the magnetic transfer function and the orientations of its polar diagrams exhibit large anomalies in the vicinity of the intersection of the lateral contacts.

Reddy, I. K.↗
NASA NTRS2001

Seismic Study of the Dynamics of the Solar Subsurface from SoHO Observations

In collaboration with Dr. Baudin, we have developed and refined the new observational methodology for local helioseismology known as time-distance analysis. Global helioseismology study the solar oscillations as a superposition of resonant modes, whose properties (mode frequencies) reflect the global structure of the sun (sound speed stratification, rotation rate, etc). In contrast, local helioseismology look at the solar oscillations as wave packets whose propagation will be affected by perturbations of the media sampled. These local perturbations (sound speed or velocity flows) will modify the propagation time, that in turn can be used as a diagnostic tool for a given region. From a data reduction perspective, the processing of solar dopplergrams that result in time-distance maps, i.e. propagation times as a function of distance between bounces at the surface, is radically different from the methodology used for global mode analysis. We have, in a first step, further develop the programs needed to carry out such analysis. We have then applied them to NMI data set, and explore the trade-off between various averaging and filtering approaches - steps required to improve the signal-to-noise ratio of correlation maps - and the resulting stability and precision of the fitted propagation times. While excessive averaging (whether over space, propagation distance, or time) will reduce the diagnostic potential of the method, insufficient averaging lead to unstable fits, or uncertainties so large as to hide the information we seek. In a second phase, we have developed the analysis methodology required to infer local properties from perturbation in time propagation. Namely, we have developed time-distance inversion techniques, with an emphasis on inferences of velocity flows from time anomalies. Note also that during the period covered by this grant, all the investigators on this proposal (i.e., Drs. Baudin, Eff-Darwich, Korzennik, and Noyes) took part in the organization of the SOHO 6 /GONG 99 Workshop: Structure and Dynamics of the Interior of the Sun and Sunlike Stars, held on June 1-4 1999 at the Boston Park Plaza Hotel in Boston, Massachusetts, USA. it was very well attended by more than 160 participants from 26 countries from all over the world. The proceedings were published in two volumes as ESA SP-418, with Sessions I-III in Volume 1, and Sessions IV-VI in Volume 2 (1,000 pages in total). The complete contents are also included in digital form on a CD-ROM included with Volume 1. This CD-ROM also contains additional multi-media material that complements some of the contributions.

Korzennik, Sylvain G.↗
NASA NTRS1994

A quantitative analysis of IRAS maps of molecular clouds

We present an analysis of IRAS maps of five molecular clouds: Orion, Ophiuchus, Perseus, Taurus, and Lupus. For the classification and description of these astrophysical maps, we use a newly developed technique which considers all maps of a given type to be elements of a pseudometric space. For each physical characteristic of interest, this formal system assigns a distance function (a pseudometric) to the space of all maps: this procedure allows us to measure quantitatively the difference between any two maps and to order the space of all maps. We thus obtain a quantitative classification scheme for molecular clouds. In this present study we use the IRAS continuum maps at 100 and 60 micrometer(s) to produce column density (or optical depth) maps for the five molecular cloud regions given above. For this sample of clouds, we compute the 'output' functions which measure the distribution of density, the distribution of topological components, the self-gravity, and the filamentary nature of the clouds. The results of this work provide a quantitative description of the structure in these molecular cloud regions. We then order the clouds according to the overall environmental 'complexity' of these star-forming regions. Finally, we compare our results with the observed populations of young stellar objects in these clouds and discuss the possible environmental effects on the star-formation process. Our results are consistent with the recently stated conjecture that more massive stars tend to form in more 'complex' environments.

Wiseman, Jennifer J.↗