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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 sourcesNASA NTRSDOE OSTI
NASA NTRS2022

Advanced Statistical Methods in Spacecraft Flight Software Cost Estimation: Bayesian Regression and Nonlinear Principal Components Analysis to Support System Engineering in the Early Project Lifecycle

This paper provides an overview of the new features and model updates in the upcoming release of the NASA Analogy Software Cost Tool (ASCoT). ASCoT, hosted within the Online NASA Space Estimation Tools (ONSET) on the One NASA Cost Engineering (ONCE) Database, is a web-based tool that provides a suite of estimation tools to support early lifecycle NASA flight software cost analysis. In addition to the traditional parametric flight software costing method COCOMO II, ASCoT contains a Bayesian linear regression to predict total flight software development cost as a function of total spacecraft cost, as well as four analogic methods: k-Nearest Neighbors (kNN) and Clustering models to predict Effort (in work-months) and total source lines of code (SLOC). These methods are designed to work primarily with system-level inputs such as mission type (orbiter, lander, etc.), mission destination (Earth, Inner Planetary, etc.), and the number of instruments and deployables. Nonlinear principal components analysis (NLPCA) is performed to find the principal features of the data composed of both categorical and numerical variables and is necessary prior to defining our analogic methods. Sensitivity analyses and in- and out-of-sample model performance results are presented for the Bayesian CER and the analogic models.

Johnson, James K.↗
DOE OSTI2021

Correlated conformational dynamics of the human GluN1-GluN2A type N-methyl-D-aspartate (NMDA) receptor

N-Methyl-D-aspartate receptors (NMDARs) are glutamate-gated ion channels found in the nerve cell membranes. As a result of overexcitation of NMDARs, neuronal death occurs and may lead to diseases such as epilepsy, stroke, Alzheimer’s disease, and Parkinson’s disease. In this study, human GluN1- GluN2A type NMDAR structure is modeled based on the X-ray structure of the Xenopus laevis template and missing loops are added by ab-initio loop modeling. The final structure is chosen according to two different model assessment scores. To be able to observe the structural changes upon ligand binding, glycine and glutamate molecules are docked into the corresponding binding sites of the receptor. Subsequently, molecular dynamics simulations of 1.3 μs are performed for both apo and ligand-bound structures. Structural parameters, which have been considered to show functionally important changes in previous NMDAR studies, are monitored as conformational rulers to understand the dynamics of the conformational changes. Moreover, principal component analysis (PCA) is performed for the equilibrated part of the simulations. Additionally, from these analyses, the differences in between apo and ligand-bound simulations can be summarized as the following: The girdle right at the beginning of the pore loop, which connects M2 and M3 helices of the ion channel, partially opens. Ligands act like an adhesive for the ligand-binding domain (LBD) by keeping the bi-lobed structure together and consequently this is reflected to the overall dynamics of the protein as an increased correlation of the LBD with especially the amino-terminal domain (ATD) of the protein.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

MO-F-CAMPUS-J-02: Automatic Recognition of Patient Treatment Site in Portal Images Using Machine Learning

Purpose: To investigate the method to automatically recognize the treatment site in the X-Ray portal images. It could be useful to detect potential treatment errors, and to provide guidance to sequential tasks, e.g. automatically verify the patient daily setup. Methods: The portal images were exported from MOSAIQ as DICOM files, and were 1) processed with a threshold based intensity transformation algorithm to enhance contrast, and 2) where then down-sampled (from 1024×768 to 128×96) by using bi-cubic interpolation algorithm. An appearance-based vector space model (VSM) was used to rearrange the images into vectors. A principal component analysis (PCA) method was used to reduce the vector dimensions. A multi-class support vector machine (SVM), with radial basis function kernel, was used to build the treatment site recognition models. These models were then used to recognize the treatment sites in the portal image. Portal images of 120 patients were included in the study. The images were selected to cover six treatment sites: brain, head and neck, breast, lung, abdomen and pelvis. Each site had images of the twenty patients. Cross-validation experiments were performed to evaluate the performance. Results: MATLAB image processing Toolbox and scikit-learn (a machine learning library in python) were used to implement the proposed method. The average accuracies using the AP and RT images separately were 95% and 94% respectively. The average accuracy using AP and RT images together was 98%. Computation time was ∼0.16 seconds per patient with AP or RT image, ∼0.33 seconds per patient with both of AP and RT images. Conclusion: The proposed method of treatment site recognition is efficient and accurate. It is not sensitive to the differences of image intensity, size and positions of patients in the portal images. It could be useful for the patient safety assurance. The work was partially supported by a research grant from Varian Medical System.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Characterizing different motility-induced regimes in active matter with machine learning and noise

Here we examine motility-induced phase separation (MIPS) in two-dimensional run-and-tumble disk systems using both machine learning and noise fluctuation analysis. Our measures suggest that within the MIPS state there are several distinct regimes as a function of density and run time, so that systems with MIPS transitions exhibit an active fluid, an active crystal, and a critical regime. The different regimes can be detected by combining an order parameter extracted from principal component analysis with a cluster stability measurement. The principal component-derived order parameter is maximized in the critical regime, remains low in the active fluid, and has an intermediate value in the active crystal regime. We demonstrate that machine learning can better capture dynamical properties of the MIPS regimes compared to more standard structural measures such as the maximum cluster size. The different regimes can also be characterized via changes in the noise power of the fluctuations in the average speed. In the critical regime, the noise power passes through a maximum and has a broad spectrum with a 1/f 1.6 signature, similar to the noise observed near depinning transitions or for solids undergoing plastic deformation.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Joint Bayesian Estimation of Quasar Continua and the Lyα Forest Flux Probability Distribution Function

We present a new Bayesian algorithm making use of Markov Chain Monte Carlo sampling that allows us to simultaneously estimate the unknown continuum level of each quasar in an ensemble of high-resolution spectra, as well as their common probability distribution function (PDF) for the transmitted Lyα forest flux. This fully automated PDF regulated continuum fitting method models the unknown quasar continuum with a linear principal component analysis (PCA) basis, with the PCA coefficients treated as nuisance parameters. The method allows one to estimate parameters governing the thermal state of the intergalactic medium (IGM), such as the slope of the temperature–density relation γ−1, while marginalizing out continuum uncertainties in a fully Bayesian way. Using realistic mock quasar spectra created from a simplified semi-numerical model of the IGM, we show that this method recovers the underlying quasar continua to a precision of ≃7% and ≃10% at z = 3 and z = 5, respectively. Given the number of principal component spectra, this is comparable to the underlying accuracy of the PCA model itself. Most importantly, we show that we can achieve a nearly unbiased estimate of the slope γ−1 of the IGM temperature–density relation with a precision of ±8.6% at z = 3 and ±6.1% at z = 5, for an ensemble of ten mock high-resolution quasar spectra. Applying this method to real quasar spectra and comparing to a more realistic IGM model from hydrodynamical simulations would enable precise measurements of the thermal and cosmological parameters governing the IGM, albeit with somewhat larger uncertainties, given the increased flexibility of the model.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

Balancing aggregation and smoothing errors in inverse models

Inverse models use observations of a system (observation vector) to quantify the variables driving that system (state vector) by statistical optimization. When the observation vector is large, such as with satellite data, selecting a suitable dimension for the state vector is a challenge. A state vector that is too large cannot be effectively constrained by the observations, leading to smoothing error. However, reducing the dimension of the state vector leads to aggregation error as prior relationships between state vector elements are imposed rather than optimized. Here we present a method for quantifying aggregation and smoothing errors as a function of state vector dimension, so that a suitable dimension can be selected by minimizing the combined error. Reducing the state vector within the aggregation error constraints can have the added advantage of enabling analytical solution to the inverse problem with full error characterization. We compare three methods for reducing the dimension of the state vector from its native resolution: (1) merging adjacent elements (grid coarsening), (2) clustering with principal component analysis (PCA), and (3) applying a Gaussian mixture model (GMM) with Gaussian pdfs as state vector elements on which the native-resolution state vector elements are projected using radial basis functions (RBFs). The GMM method leads to somewhat lower aggregation error than the other methods, but more importantly it retains resolution of major local features in the state vector while smoothing weak and broad features.

Turner, A. J.↗
DOE OSTI2018

Covariance of CMB anomalies

Several unexpected features are observed at large angular scales in the cosmic microwave background (CMB) temperature anisotropy measurements by both WMAP and Planck. These include the lack of both variance and correlation, alignment of the lowest multipole moments with one another, hemispherical power asymmetry, and an odd-to-even parity excess. In this work, we study the statistics of eight representative large-angle CMB features in order to evaluate their covariance in the standard Λ CDM model. We do so using two sets of simulated CMB temperature maps; an ensemble of 100 000 simple Gaussian simulations, and 1000 Full Focal Plane (FFP) simulations provided by the Planck collaboration. In measuring feature probabilities, we pay particular attention to analysis choices, making sure that we can reproduce previous results in the literature, and explain differences where appropriate. The covariance structure we find is consistent with expectations given that many of the features studied are functions of the angular power spectrum. Notably, we find significant differences in the covariance entries associated with the quadrupole-octopole alignments derived from the Gaussian and FFP simulations. We additionally perform a principal component analysis to quantitatively gauge what combinations of features capture the most information about how simulation measurements vary, and to provide an alternative assessment of the ways in which the real sky is anomalous. Here, the first four principal components explain about 90% of the simulations’ variance, with the first two roughly quantifying the lack of large-angle correlations, and the next two quantifying the phase-dependent anomalies (multipole alignments and power asymmetry). Though the results of this analysis are fairly unsurprising, its comprehensive approach serves to tie together a number of previous results, and will therefore provide context for future studies of large-angle anomalies.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS2018

In Situ Measurements of Angular-Dependent Light Scattering by Aerosols over the Contiguous United States

This work provides a synopsis of aerosol phase function (F (sub 11)) and polarized phase function (F (sub 12)) measurements made by the Polarized Imaging Nephelometer (PINeph) during the Studies of Emissions, Atmospheric Composition, Clouds and Climate Coupling by Regional Surveys (SEAC4RS) and the Deep Convection Clouds and Chemistry (DC3) field campaigns. In order to more easily explore this extensive dataset, an aerosol classification scheme is developed that identifies the different aerosol types measured during the deployments. This scheme makes use of ancillary data that include trace gases, chemical composition, aerodynamic particle size and geographic location, all independent of PI-Neph measurements. The PI-Neph measurements are then grouped according to their ancillary data classifications and the resulting scattering patterns are examined in detail. These results represent the first published airborne measurements of F (sub 11) and minus F (sub 12) divided by F (sub 11) for many common aerosol types. We then explore whether PI-Neph light-scattering measurements alone are sufficient to reconstruct the results of this ancillary data classification algorithm. Principal component analysis (PCA) is used to reduce the dimensionality of the multi-angle PI-Neph scattering data and the individual measurements are examined as a function of ancillary data classification. Clear clustering is observed in the PCA score space, corresponding to the ancillary classification results, suggesting that, indeed, a strong link exists between the angular scattering measurements and the aerosol type or composition. Two techniques are used to quantify the degree of clustering and it is found that in most cases the results of the ancillary data classification can be predicted from PI-Neph measurements alone with better than 85 percent recall. This result both emphasizes the validity of the ancillary data classification as well as the PI-Neph's ability to distinguish common aerosol types without additional information.

Aerosol phase function↗
DOE OSTI2025

MODE: A Web Application for Interactive Visualization and Exploration of Omics Data

Studies generating transcriptomics, proteomics, lipidomics, and metabolomics (colloquially referred to as “omics”) data allow researchers to find biomarkers or molecular targets, or understand complex biological structures and functions by identifying changes in biomolecule abundance and expression between experimental conditions. Omics data is multi-dimensional and oftentimes summarization techniques such as principal component analysis (PCA) are used to identify high-level patterns in data. Though useful, these summaries don’t allow exploration of detailed patterns in omics data that may have biological relevance. The use of interactive HTML displays with plots allows researchers to interact with omics data at a detailed level, but building these displays requires significant coding expertise. To overcome this barrier, the software MODE was built to empower users to build their own interactive HTML displays to support scientific discovery. These displays are easily shareable, do not depend on a specific operating system, and allow users to effortlessly sort and filter plots by categorical or numerical variables. MODE allows users to build and share these displays with several options for plot design and meta selection. In conclusion, the MODE web application and its capabilities are presented and then demonstrated on lipidomics data from a leaf wounding study.

lipidomics↗
NASA NTRS1991

Characterization of exopolymers of aquatic bacteria by pyrolysis-mass spectrometry

Exopolymers from a diverse collection of marine and freshwater bacteria were characterized by pyrolysis-mass spectrometry (Py-MS). Py-MS provides spectra of pyrolysis fragments that are characteristic of the original material. Analysis of the spectra by multivariate statistical techniques (principal component and canonical variate analysis) separated these exopolymers into distinct groups. Py-MS clearly distinguished characteristic fragments, which may be derived from components responsible for functional differences between polymers. The importance of these distinctions and the relevance of pyrolysis information to exopolysaccharide function in aquatic bacteria is discussed.

NASA Program CELSS↗
DOE OSTI2026

Novel Cell-Type-Specific Drought-Responsive Proteins in Root Tips of Field-Grown Perennial Switchgrass

The root-tip region of plants, including the root cap, forms the most basal terminal of the root and exhibits a high degree of cellular complexity in terms of morphology, cytological function, and interaction with environmental cues in the soil. Cells in this region follow a developmental trajectory, transitioning from stem cells to meristematic cells, and ultimately to fully differentiated cell types. However, our understanding of root-tip cell-type specific proteomic responses to abiotic stresses, such as drought, particularly under field conditions, remains limited. This study aimed to identify spatially resolved, cell type-specific proteomes in switchgrass (Panicum virgatum) root tips under drought stress. Root tips were collected from seven-year-old, field-grown switchgrass ‘Alamo’ plants excavated under both well-watered and long-term drought conditions. Cell type-specific proteins were identified using laser capture microdissection (LCM) coupled with nanoPOTS (Nanodroplet Processing in One Pot for Trace Samples) and nano-LC-MS proteomics analysis. Five distinct cell types were targeted: (1) cells in the quiescent center and stem cell niche (QuC), (2) protodermal epidermal cells (PEC) in the meristematic zone, (3) epidermal cells in the transition and elongation zones above the root cap (Epi), (4) peripheral root cap cells (PRC), forming 2–3 layers below the PEC and 1–2 layers above the root border cells, and (5) columella root cap cells (Col) comprising of the columella initials and a single underlying layer of cells undergoing active growth. Principal component analysis (PCA) revealed clear separation among the five targeted cell types, confirming distinct proteomic profiles. Proteins predominantly enriched in each cell type were linked to distinct cellular functions, with QuC cells showing involvement in chromosomal behavior, DNA replication, and mitosis—key processes for stem cell niche regulation. Drought stress resulted in alterations of proteostasis, as evidenced by significant decreases in ribosomal proteins and increases in protein synthesis inhibitors. Moreover, drought stress induced unique cell-type–specific proteins involved in phytohormone biosynthesis and signaling pathways, including auxin, cytokinin, and jasmonic acid. In particular, QuC cells were more highly enriched in proteins associated with DNA repair and mitotic processes. Metabolic pathways related to amino acids, carbohydrates, and lipids were differentially affected in a cell-type–dependent manner, whereas general stress-responsive proteins exhibited consistent changes across all five cell types. Overall, this study provides unique spatially resolved, cell-type-specific proteomic profiles in root tips, representing a significant advancement in our understanding of the cellular mechanisms underlying plant responses to drought stress in natural field conditions.

perennial grass↗
NASA NTRS2009

Use of UV Sources for Detection and Identification of Explosives

Measurement of Raman and native fluorescence emission using ultraviolet (UV) sources (<400 nm) on targeted materials is suitable for both sensitive detection and accurate identification of explosive materials. When the UV emission data are analyzed using a combination of Principal Component Analysis (PCA) and cluster analysis, chemicals and biological samples can be differentiated based on the geometric arrangement of molecules, the number of repeating aromatic rings, associated functional groups (nitrogen, sulfur, hydroxyl, and methyl), microbial life cycles (spores vs. vegetative cells), and the number of conjugated bonds. Explosive materials can be separated from one another as well as from a range of possible background materials, which includes microbes, car doors, motor oil, and fingerprints on car doors, etc. Many explosives are comprised of similar atomic constituents found in potential background samples such as fingerprint oils/skin, motor oil, and soil. This technique is sensitive to chemical bonds between the elements that lead to the discriminating separability between backgrounds and explosive materials.

Hug, William↗
DOE OSTI2019

Function Preserving Projection

With function preserving projection (FPP), we aim to address high-dimensional data exploration challenges common in many scientific applications. Instead of preserving the global or local geometric structure of a dataset like traditional dimensionality reduction methods (e.g., principal component analysis, t-stochastic neighborhood embedding), the proposed approach finds a linear projection that reveal interpretable (yet potentially nonlinear) pattern of the properties of interests defined on a highdimensional domain (e.g., simulation yield defined on the input parameter space). The key insight driving FPP is the fact that while non-linear embeddings are difficult to interpret, humans are highly skilled in understanding complex visual patterns. FPP lets users select the complexity of a pattern they consider interpretable, allows to find a joint projection that explains multiple functions, and provides a confidence statistic (akin to a p-value) indicating how salient the resulting pattern is. We demonstrate the efficacy of the proposed method on several synthetic and scientific datasets for both continuous (regression) and discrete (classification) problems of interests and illustrate the scalability of FPP by finding an optimal projection for close to 40 gigabytes in around 10 minutes.

Liu, SHUSEN↗
DOE OSTI2022

Training and projecting: A reduced basis method emulator for many-body physics

Here, we present the reduced basis method as a tool for developing emulators for equations with tun able parameters within the context of the nuclear many-body problem. The method uses a basis expansion informed by a set of solutions for a few values of the model parameters and then projects the equations over a well-chosen low-dimensional subspace. We connect some of the results in the eigenvector continuation literature to the formalism of reduced basis methods and show how these methods can be applied to a broad set of problems. As we illustrate, the possible success of the formalism on such problems can be diagnosed beforehand by a principal component analysis. We apply the reduced basis method to the one-dimensional Gross-Pitaevskii equation with a harmonic trap ping potential and to nuclear density functional theory for 48 Ca, achieving speed-ups of more than x150 and x250, respectively, when compared to traditional solvers. The outstanding performance of the approach, together with its straightforward implementation, show promise for its application to the emulation of computationally demanding calculations, including uncertainty quantification.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Material Identification Using Dual Energy X-ray Absorptiometry

Two implementations of dual energy X-ray absorptiometry were studied to identify materials using X-ray attenuation data taken with the Digital Radiography and Computed Tomography (DRCT) systems that were developed for the Recovered Chemical Materiel Directorate (RCMD). Maitrejean et al.’s approach utilizes eigen effects through Principal Component Analysis, while Osipov et al.’s approach proposed a physics-based method. Both approaches approximate mass attenuation coefficients of materials as a linear combination of basis functions (eigen effects) or physics-based equations. A set of coefficients {a 1 , a 2 , a 3 } or {B, D} were found by parameter optimization in EXCEL Solver. The identification parameters, {$\frac{a_{2}}{a_{1}}$, $\frac{a_{3}}{a_{1}}$} or estimated effective atomic number $\hat{Z}$ from {B, D}, were calculated to identify material of an aluminum 8 step wedge and a steel 8 step wedge in X-ray radiography images taken by a DRCT system. Maitrejean et al.’s approach was unable to provide reliable $\frac{a_{3}}{a_{1}}$ ratio values for identification of materials. Osipov et al.’s approach was found to be more robust in identify materials with a semi-empirical formula derived from test results in this study.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Dimensional Reduction for Sampled Priors and Application to Photometric Redshift Distributions

A typical Bayesian inference on the values of some parameters of interest q from some data D involves running a Markov Chain (MC) to sample from the posterior $p$($q$,$n$|$D$) $\propto$ $\mathcal{L}$($D$|$q$,$n$)$p$(q)$p$($n$), where n are some nuisance parameters with a separable prior. In some cases, the nuisance parameters are high-dimensional, and their prior p(n) is itself defined only by a set of samples that have been drawn from some other MC. The MC for the posterior will typically require evaluation of p(n) at arbitrary values of n, i.e., one needs to provide a density estimator over the full n space from the provided samples. But the high dimensionality of n hinders both the density estimation and the efficiency of the MC for the posterior. We describe a solution to this problem: a linear compression of the n space into a much lower-dimensional space u, which projects away directions in n space that cannot appreciably alter $\mathcal{L}$. The algorithm for doing so is a slight modification to principal components analysis, and is less restrictive on p(n) than other proposed solutions to this issue. We demonstrate this “mode projection” technique using the analysis of 2-point correlation functions of weak lensing fields and galaxy density in the Dark Energy Survey, where n is a binned representation of the redshift distribution n(z) of the galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1985

Materials requirements for optical processing and computing devices

Devices for optical processing and computing systems are discussed, with emphasis on the materials requirements imposed by functional constraints. Generalized optical processing and computing systems are described in order to identify principal categories of requisite components for complete system implementation. Three principal device categories are selected for analysis in some detail: spatial light modulators, volume holographic optical elements, and bistable optical devices. The implications for optical processing and computing systems of the materials requirements identified for these device categories are described, and directions for future research are proposed.

Tanguay, A. R., Jr.↗
DOE OSTI2023

Exploring the dependence of gas cooling and heating functions on the incident radiation field with machine learning

ABSTRACT Gas cooling and heating functions play a crucial role in galaxy formation. But, it is computationally expensive to exactly compute these functions in the presence of an incident radiation field. These computations can be greatly sped up by using interpolation tables of pre-computed values, at the expense of making significant and sometimes even unjustified approximations. Here, we explore the capacity of machine learning to approximate cooling and heating functions with a generalized radiation field. Specifically, we use the machine learning algorithm XGBoost to predict cooling and heating functions calculated with the photoionization code cloudy at fixed metallicity, using different combinations of photoionization rates as features. We perform a constrained quadratic fit in metallicity to enable a fair comparison with traditional interpolation methods at arbitrary metallicity. We consider the relative importance of various photoionization rates through both a principal component analysis (PCA) and calculation of SHapley Additive exPlanation (shap) values for our XGBoost models. We use feature importance information to select different subsets of rates to use in model training. Our XGBoost models outperform a traditional interpolation approach at each fixed metallicity, regardless of feature selection. At arbitrary metallicity, we are able to reduce the frequency of the largest cooling and heating function errors compared to an interpolation table. We find that the primary bottleneck to increasing accuracy lies in accurately capturing the metallicity dependence. This study demonstrates the potential of machine learning methods such as XGBoost to capture the non-linear behaviour of cooling and heating functions.

79 ASTRONOMY AND ASTROPHYSICS↗