Search NASA⌕ Search

SEARCH · Search NASA

Results for “functional Principal Component Analysis”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 235 records · Page 13

EVIDENCE FOR THE INTERMEDIATE BROAD-LINE REGION OF REVERBERATION-MAPPED ACTIVE GALACTIC NUCLEUS PG 0052+251

We study the properties of the broad-line region (BLR) of a well-known reverberation-mapped active galactic nucleus (AGN) in order to find reliable evidence for the intermediate BLR. We first check properties of the mapped AGN collected from the literature in the plane of {sigma}{sup 2}{sub H}{beta}/{sigma}H{alpha} {sup 2} versus R {sup H}{alpha}{sub BLR}/R{sub BLR} {sup H}{beta}. Commonly, virial black hole masses based on observed broad H{alpha} and H{beta} should be coincidental. However, among the mapped objects, PG 0052 and NGC 4253 are two apparent outliers in the plane of {sigma}{sup 2}{sub H}{beta}/{sigma}H{alpha} {sup 2} versus R {sup H}{alpha}{sub BLR}/R{sub BLR} {sup H}{beta}, which indicates that BLRs of PG 0052 and NGC 4253 have some special characters. Based on the 55 public spectra of PG 0052, the BLR of PG 0052 has been carefully studied in detail. We find that the line width ratio of the total observed broad H{alpha} to the total observed broad H{beta} is {approx}0.7, which is much smaller than the theoretical/observational value of {approx}0.9. Furthermore, the flux ratio of the total broad H{alpha} to the total broad H{beta} is about 6.8 (Balmer decrement), which is not a reasonable value for the blue quasar PG 0052+251. Moreover, properties of line cores based on the principal component analysis technique confirm that there is one inner broad component and one seriously obscured intermediate broad component in the BLR of PG 0052. If the seriously obscured intermediate BLR was accepted, properties of PG 0052 in the plane of {sigma}{sup 2}{sub H}{beta}/{sigma}H{alpha} {sup 2} versus R {sup H}{alpha}{sub BLR}/R{sub BLR} {sup H}{beta} could be reproduced, which indicates that the intermediate BLR actually is appropriate for the mapped quasar PG 0052+251. Finally, the large distance between the inner and the intermediate components of the BLR based on the results of the cross-correlation function rejects the possibility that the intermediate component is probably an extended part of the inner component of the BLR.

79 ASTRONOMY AND ASTROPHYSICS↗

Machine-Learned Manifold-Based Models for Large Eddy Simulation of Turbulent Combustion

Reduced-order manifold combustion models are commonly used to lower the cost of reacting Large Eddy Simulations (LES) and may be derived either from physical principles as in flamelet models or from data-driven methods like Principal Component Analysis (PCA). In either case, neural networks are increasingly used as part of these models to provide a nonlinear mapping between a small set of pre-defined variables that parameterize the manifold and outputs of interest, such as reaction rates. In this work, we propose a new manifold-based modeling approach that combines the definition of the manifold-parameterizing variables (linear combinations of species), the nonlinear mapping to the outputs, and closure of filtered quantities for LES into the structure of a single neural network. This allows the process used to train the neural network to simultaneously optimize both the functional form of the model and the identities of the inputs to the model. The new approach can flexibly incorporate thermochemical data from any combustion system; if trained on data from 1D flames it can be interpreted as an optimized flamelet model, but it can also be used to learn models from data from more complex configurations. This work presents a priori evaluations of the new approach in both contexts. Evaluation using data from 1D premixed flames demonstrates the physical interpretability of the manifold variables generated by the new approach. Evaluation using data from direct numerical simulations of turbulent flames shows improved predictions relative to either flamelet or PCA-based models in a more complex configuration.

47 OTHER INSTRUMENTATION↗

Bayesian estimation of Karhunen–Loève expansions; A random subspace approach

One of the most widely-used statistical procedures for dimensionality reduction of high dimensional random fields is Principal Component Analysis (PCA), which is based on the Karhunen-Lo eve expansion (KLE) of a stochastic process with finite variance. The KLE is analogous to a Fourier series expansion for a random process, where the goal is to find an orthogonal transformation for the data such that the projection of the data onto this orthogonal subspace is optimal in the L 2 sense, i.e, which minimizes the mean square error. In practice, this orthogonal transformation is determined by performing an SVD (Singular Value Decomposition) on the sample covariance matrix or on the data matrix itself. Sampling error is typically ignored when quantifying the principal components, or, equivalently, basis functions of the KLE. Furthermore, it is exacerbated when the sample size is much smaller than the dimension of the random field. In this paper, we introduce a Bayesian KLE procedure, allowing one to obtain a probabilistic model on the principal components, which can account for inaccuracies due to limited sample size. The probabilistic model is built via Bayesian inference, from which the posterior becomes the matrix Bingham density over the space of orthonormal matrices. We use a modified Gibbs sampling procedure to sample on this space and then build a probabilistic Karhunen-Lo eve expansions over random subspaces to obtain a set of low-dimensional surrogates of the stochastic process. We illustrate this probabilistic procedure with a finite dimensional stochastic process inspired by Brownian motion.

97 MATHEMATICS AND COMPUTING↗

Representation of Probability Density Functions from Orbit Determination using the Particle Filter

Statistical orbit determination enables us to obtain estimates of the state and the statistical information of its region of uncertainty. In order to obtain an accurate representation of the probability density function (PDF) that incorporates higher order statistical information, we propose the use of nonlinear estimation methods such as the Particle Filter. The Particle Filter (PF) is capable of providing a PDF representation of the state estimates whose accuracy is dependent on the number of particles or samples used. For this method to be applicable to real case scenarios, we need a way of accurately representing the PDF in a compressed manner with little information loss. Hence we propose using the Independent Component Analysis (ICA) as a non-Gaussian dimensional reduction method that is capable of maintaining higher order statistical information obtained using the PF. Methods such as the Principal Component Analysis (PCA) are based on utilizing up to second order statistics, hence will not suffice in maintaining maximum information content. Both the PCA and the ICA are applied to two scenarios that involve a highly eccentric orbit with a lower apriori uncertainty covariance and a less eccentric orbit with a higher a priori uncertainty covariance, to illustrate the capability of the ICA in relation to the PCA.

Mashiku, Alinda K.↗

Short-term time variability of Cygnus X-1. II

A complete theory for shot-noise analysis is presented. The theory takes into account the effects of counting statistics, time resolution, and finite observing times on the autocorrelation function and on the moments of data assumed to consist of shot noise plus a steady component. When applied to X-ray observations of Cyg X-1 in the high and low states, the results provide evidence that both the typical correlation time (about 0.5 s) and the fraction of flux in shots (about 30%) are constant, independent of the state. The rate of occurrence of the shots may also be constant at approximately one shot per second, a possibility which, if verified, would imply that the principal difference in time variability in the two states is the amplitude of the shots. We also suggest that the occasionally observed large flares may possibly be just the rare superposition of several shots.

Sutherland, P. G.↗

A cluster analysis method for identification of subpopulations of cells in flow cytometric list-mode arrays

A specialized program was developed for flow cytometric list-mode data using an heirarchical tree method for identifying and enumerating individual subpopulations, the method of principal components for a two-dimensional display of 6-parameter data array, and a standard sorting algorithm for characterizing subpopulations. The program was tested against a published data set subjected to cluster analysis and experimental data sets from controlled flow cytometry experiments using a Coulter Electronics EPICS V Cell Sorter. A version of the program in compiled BASIC is usable on a 16-bit microcomputer with the MS-DOS operating system. It is specialized for 6 parameters and up to 20,000 cells. Its two-dimensional display of Euclidean distances reveals clusters clearly, as does its 1-dimensional display. The identified subpopulations can, in suitable experiments, be related to functional subpopulations of cells.

Li, Z. K.↗

Global Monitoring of Terrestrial Chlorophyll Fluorescence from Moderate-Spectral-Resolution Near-Infrared Satellite Measurements: Methodology, Simulations, and Application to GOME-2

Globally mapped terrestrial chlorophyll fluorescence retrievals are of high interest because they can provide information on the functional status of vegetation including light-use efficiency and global primary productivity that can be used for global carbon cycle modeling and agricultural applications. Previous satellite retrievals of fluorescence have relied solely upon the filling-in of solar Fraunhofer lines that are not significantly affected by atmospheric absorption. Although these measurements provide near-global coverage on a monthly basis, they suffer from relatively low precision and sparse spatial sampling. Here, we describe a new methodology to retrieve global far-red fluorescence information; we use hyperspectral data with a simplified radiative transfer model to disentangle the spectral signatures of three basic components: atmospheric absorption, surface reflectance, and fluorescence radiance. An empirically based principal component analysis approach is employed, primarily using cloudy data over ocean, to model and solve for the atmospheric absorption. Through detailed simulations, we demonstrate the feasibility of the approach and show that moderate-spectral-resolution measurements with a relatively high signal-to-noise ratio can be used to retrieve far-red fluorescence information with good precision and accuracy. The method is then applied to data from the Global Ozone Monitoring Instrument 2 (GOME-2). The GOME-2 fluorescence retrievals display similar spatial structure as compared with those from a simpler technique applied to the Greenhouse gases Observing SATellite (GOSAT). GOME-2 enables global mapping of far-red fluorescence with higher precision over smaller spatial and temporal scales than is possible with GOSAT. Near-global coverage is provided within a few days. We are able to show clearly for the first time physically plausible variations in fluorescence over the course of a single month at a spatial resolution of 0.5 0.5. We also show some significant differences between fluorescence and coincident normalized difference vegetation indices (NDVI) retrievals.

Fluorescence↗

Global Monitoring of Terrestrial Chlorophyll Fluorescence from Moderate-spectral-resolution Near-infrared Satellite Measurements: Methodology, Simulations, and Application to GOME-2

Globally mapped terrestrial chlorophyll fluorescence retrievals are of high interest because they can provide information on the functional status of vegetation including light-use efficiency and global primary productivity that can be used for global carbon cycle modeling and agricultural applications. Previous satellite retrievals of fluorescence have relied solely upon the filling-in of solar Fraunhofer lines that are not significantly affected by atmospheric absorption. Although these measurements provide near-global coverage on a monthly basis, they suffer from relatively low precision and sparse spatial sampling. Here, we describe a new methodology to retrieve global far-red fluorescence information; we use hyperspectral data with a simplified radiative transfer model to disentangle the spectral signatures of three basic components: atmospheric absorption, surface reflectance, and fluorescence radiance. An empirically based principal component analysis approach is employed, primarily using cloudy data over ocean, to model and solve for the atmospheric absorption. Through detailed simulations, we demonstrate the feasibility of the approach and show that moderate-spectral-resolution measurements with a relatively high signal-to-noise ratio can be used to retrieve far-red fluorescence information with good precision and accuracy. The method is then applied to data from the Global Ozone Monitoring Instrument 2 (GOME-2). The GOME-2 fluorescence retrievals display similar spatial structure as compared with those from a simpler technique applied to the Greenhouse gases Observing SATellite (GOSAT). GOME-2 enables global mapping of far-red fluorescence with higher precision over smaller spatial and temporal scales than is possible with GOSAT. Near-global coverage is provided within a few days. We are able to show clearly for the first time physically plausible variations in fluorescence over the course of a single month at a spatial resolution of 0.5 deg × 0.5 deg. We also show some significant differences between fluorescence and coincident normalized difference vegetation indices (NDVI) retrievals.

remote sensing↗

Reducing the matrix effect in mass spectral imaging of biofilms using flow-cell culture

The interactions between soil microorganisms and soil minerals play a crucial role in the formation and evolution of minerals and the stability of soil aggregates. Due to the heterogeneity and diversity of the soil environment, the under-standing of the functions of bacterial biofilms in soil minerals at the microscale is limited. A soil mineral-bacterial biofilm system was used as a model in this study, and it was analyzed by time-of-flight secondary ion mass spectrometry (ToF-SIMS) to acquire molecular level information. Static culture in multi-wells and dynamic flow-cell culture in microfluidics of biofilms were investigated. Our results show that more characteristic molecules of biofilms can be observed in SIMS spectra of the flow-cell culture. In contrast, biofilm signature peaks are buried under the mineral components in SIMS spectra in the static culture case. Spectral overlay was used in peak selection prior to performing Principal component analysis (PCA). Comparisons of the PCA results between the static and flow-cell culture show more pronounced molecular features and higher loadings of organic peaks of the dynamic cultured specimens. For example, fatty acids secreted from bacterial biofilm extracellular polymeric substance are likely to be responsible for biofilm dispersal due to mineral treatment up to 48 h. Such findings suggest that the use of microfluidic cells to dynamically culture biofilms be a more suitable method for reducing the matrix effect arisen from the growth medium and minerals as a perturbation fac-tor for improved spectral and multivariate analysis of complex mass spectral data in ToF-SIMS. These results show that the interaction mechanism between biofilms and soil minerals at the molecular level can be better studied using the flow-cell culture and advanced mass spectral imaging techniques like ToF-SIMS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

POINT-SPREAD FUNCTIONS FOR THE EXTREME-ULTRAVIOLET CHANNELS OF SDO/AIA TELESCOPES

We present the stray-light point-spread functions (PSFs) and their inverses we characterized for the Atmospheric Imaging Assembly (AIA) EUV telescopes on board the Solar Dynamics Observatory (SDO) spacecraft. The inverse kernels are approximate inverses under convolution. Convolving the original Level 1 images with them produces images with improved stray-light characteristics. We demonstrate the usefulness of these PSFs by applying them to two specific cases: photometry and differential emission measure (DEM) analysis. The PSFs consist of a narrow Gaussian core, a diffraction component, and a diffuse component represented by the sum of a Gaussian-truncated Lorentzian and a shoulder Gaussian. We determined the diffraction term using the measured geometry of the diffraction pattern identified in flare images and the theoretically computed intensities of the principal maxima of the first few diffraction orders. To determine the diffuse component, we fitted its parameterized model using iterative forward-modeling of the lunar interior in the SDO/AIA images from the 2011 March 4 lunar transit. We find that deconvolution significantly improves the contrast in dark features such as miniature coronal holes, though the effect was marginal in bright features. On a percentage-scattering basis, the PSFs for SDO/AIA are better by a factor of two than that of the EUV telescope on board the Transition Region And Coronal Explorer mission. A preliminary analysis suggests that deconvolution alone does not affect DEM analysis of small coronal loop segments with suitable background subtraction. We include the derived PSFs and their inverses as supplementary digital materials.

79 ASTRONOMY AND ASTROPHYSICS↗

Secondary structure determines electron transport in peptides

Proteins play a key role in biological electron transport, but the structure–function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, nonequilibrium Green’s function-density functional theory (NEGF-DFT), and unsupervised machine learning to understand the role of secondary structure on electron transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn or 3 10 helices) and a low-conductance state occurring for extended peptide structures. These results highlight the importance of helical conformations on electron transport in peptides. Conformer selection for the peptide structures is rationalized using principal component analysis of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonable qualitative agreement with experiments. Projected density of states calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides broad avenues for understanding the electronic properties of proteins.

Science & Technology - Other Topics↗

Lower molar shape and size in prosimian and platyrrhine primates

Abstract The goal of this research is to evaluate the relative strength of the influences of diet, size, and phylogenetic signal on dental geometric shape. Accurate comprehension of these factors and their interaction is important for reconstructing diet and deriving characters for a cladistic analysis in fossil primates. Geometric morphometric analysis is used to identify axes of shape variation in the lower second molars of (a) prosimian primates and (b) platyrrhines. Landmarks were placed on µCT‐generated surface renderings. Landmark configurations were aligned using generalized Procrustes analysis. Principal components analysis and phylogenetic principal components analysis (pPCA) were performed on species average landmark co‐ordinates. pPCs were examined with phylogenetic generalized least squares analysis for association with size and with diet. PCs from both phylogenetic and non‐phylogenetic analyses were sufficient to separate species by broad dietary categories, including insectivores and folivores. In neither analysis was pPC1 correlated with tooth size, but some other pPCs were significantly correlated with size. The pattern of association between pPCs and size altered when centroid size and dietary variables were combined in the model; effects of diet factors typically exceeded effects of size. These results indicate a dominant phylogenetic and dietary signal in molar shape but also show some shape change correlated with size in the absence of obvious dietary associations. Geometric morphometric analysis appears to be useful for tracking functional traits in molars, particularly in tracking differences between folivorous and insectivorous species.

St. Clair, Elizabeth M.↗

Orientational Pair Correlations and Local Structure of Benzonitrile from Molecular Dynamics Simulations with Comparisons to Experiments [plus supplemental information]

Here, we present an experimentally parametrized molecular dynamics study of single-molecule and collective orientational relaxation in neat benzonitrile through the analysis of the reorientational anisotropy and polarizability anisotropy time-correlation function (PA-TCF). The simulations show that the PA-TCF is dominated by collective reorientation after 20 ps. Collective reorientation is found to be slower than single-molecule reorientation by a factor of 1.67, consistent with recent experiments. The simulations provide direct evidence of local antiparallel benzonitrile configurations. These structures, which have been the center of some debate, are responsible for the slower rate of collective vs. single-molecule reorientation in the liquid. Further structural analysis indicates that significant Coulombic interactions between the nitrile group and hydrogen atoms on adjacent molecules play a role in the formation of the antiparallel structures. The single-molecule dynamics reflected in the anisotropy are complex and consist of a ballistic regime, restricted angular diffusion, and spatially anisotropic free diffusion. The principal components of the rotational diffusion tensor are independently obtained and shown to reproduce the free diffusion regime of the anisotropy for each principal axis according to the predictions of a previous theory.

14 SOLAR ENERGY↗

Galactic plane gamma-radiation

Analysis of the SAS 2 data together with the COS B results shows that the distribution of galactic gamma-radiation has several similarities to that of other large-scale tracers of galactic structure. The radiation is primarily confined to a thin disc which exhibits offsets from b = 0 degrees similar to warping at radio frequencies. The principal distinction of the gamma-radiation is a stronger contrast in intensity between the region from 310 to 45 degrees in longitude and the regions away from the center that can be attributed to a variation in cosmic-ray density as a function of position in Galaxy. The diffuse galactic gamma-ray energy spectrum shows no significant variation in direction, and the spectrum seen along the plane is the same as that for the galactic component of the gamma-radiation at high altitudes. The uniformity of the galactic gamma-ray spectrum, the smooth decrease in intensity as a function of altitude, and the absence of any galactic gamma-ray sources at high altitudes indicate a diffuse origin for bulk of the galactic gamma-radiation rather than a collection of localized sources.

Hartman, R. C.↗

Identification of blood protein biomarkers associated with prostate cancer risk using genetic prediction models: analysis of over 140,000 subjects

Prostate cancer (PCa) brings huge public health burden in men. A growing number of conventional observational studies report associations of multiple circulating proteins with PCa risk. However, the existing findings may be subject to incoherent biases of conventional epidemiologic studies. To better characterize their associations, herein, we evaluated associations of genetically predicted concentrations of plasma proteins with PCa risk. In this study, we developed comprehensive genetic prediction models for protein levels in plasma. After testing 1308 proteins in 79 194 cases and 61 112 controls of European ancestry included in the consortia of BPC3, CAPS, CRUK, PEGASUS, and PRACTICAL, 24 proteins showed significant associations with PCa risk, including 16 previously reported proteins and eight novel proteins. Of them, 14 proteins showed negative associations and 10 showed positive associations with PCa risk. For 18 of the identified proteins, potential functional somatic changes of encoding genes were detected in PCa patients in The Cancer Genome Atlas (TCGA). Genes encoding these proteins were significantly involved in cancer-related pathways. We further identified drugs targeting the identified proteins, which may serve as candidates for drug repurposing for treating PCa. In conclusion, this study identifies novel protein biomarker candidates for PCa risk, which may provide new perspectives on the etiology of PCa and improve its therapeutic strategies.

59 BASIC BIOLOGICAL SCIENCES↗

Manifold projection image segmentation for nano-XANES imaging

As spectral imaging techniques are becoming more prominent in science, advanced image segmentation algorithms are required to identify appropriate domains in these images. We present a version of image segmentation called manifold projection image segmentation (MPIS) that is generally applicable to a broad range of systems without the need for training because MPIS uses unsupervised machine learning with a few physically motivated hyperparameters. We apply MPIS to nanoscale x-ray absorption near edge structure (XANES) imaging, where XANES spectra are collected with nanometer spatial resolution. We show the superiority of manifold projection over linear transformations, such as the commonly used principal component analysis (PCA). Moreover, MPIS maintains accuracy while reducing computation time and sensitivity to noise compared to the standard nano-XANES imaging analysis procedure. Finally, we demonstrate how multimodal information, such as x-ray fluorescence data and spatial location of pixels, can be incorporated into the MPIS framework. We propose that MPIS is adaptable for any spectral imaging technique, including scanning transmission x-ray microscopy, where the length scale of domains is larger than the resolution of the experiment.

36 MATERIALS SCIENCE↗

PySFD: comprehensive molecular insights from significant feature differences detected among many simulated ensembles

Motivation Many modeling analyses of molecular dynamics (MD) simulations are based on a definition of states that can be (groups of) clusters of simulation frames in a feature space composed of molecular coordinates. With increasing dimension of this feature space (due to the increasing size or complexity of a simulated molecule), it becomes very difficult to cluster the underlying MD data and estimate a statistically robust model. To mitigate this “curse of dimensionality”, one can reduce the feature space, e.g., with principal component or time-lagged independent component analysis transformations, focusing the analysis on the most important modes of transitions. In practice, however, all these reduction strategies may neglect important molecular details that are susceptible to experimental verification. Results To recover such molecular details, I have developed PySFD (Significant Feature Differences analyzer for Python), a multi-processing software package that efficiently selects significantly different features of any user-defined feature type among potentially many different simulated state ensembles, such as meta-stable states of a Markov State Model (MSM). Applying PySFD on MSMs of an aggregate of 300 microseconds MD simulations recently performed on the major histocompatibility complex class II (MHCII) protein, I demonstrate how this toolkit can extract and visualize valuable mechanistic information from big MD simulation data, e.g., in form of networks of dynamic interaction changes connecting functionally relevant sites of a protein complex.

Biochemistry & Molecular Biology↗

Plasmonics-based detection of H 2 and CO: discrimination between reducing gases facilitated by material control

Monitoring emissions in high-temperature-combustion applications is very important for regulating the discharge of gases such as NO 2 and CO as well as unburnt fuel into the environment. This work reports the detection of H 2 and CO gases by employing a metal–metal oxide nanocomposite (gold–yttria stabilized zirconia (Au–YSZ)) film fabricated through layer-by-layer physical vapor deposition (PVD). The change in the peak position of the localized surface plasmon resonance (LSPR) was monitored as a function of time and gas concentration. The responses of the films were preferential towards H 2 , as observed from the results of exposing the films to the gases at temperatures of 500 °C in a background of dry air. Characterization of the samples by XRD and SEM enabled the correlation of material properties with the differences in the CO- and H 2 -induced LSPR peak shifts, including the relative desensitization towards NO 2 . Sensing characteristics of films with varying support thicknesses and metal-particle diameters have been studied, and the results are presented. A comparison has been made to films fabricated through co-sputtered PVD, and the calibration curves of the sensing response show a preferential response towards H 2 . The distinction between H 2 and CO responses is also seen through the use of principal-component analysis (PCA). Such material arrangements, which can be tuned for their selectivity by changing certain parameters such as particle size, support thickness, etc., have direct applications within optical chemical sensors for turbine engines, solid-oxide fuel cells, and other high-temperature applications.

36 MATERIALS SCIENCE↗