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Results for “functional Principal Component Analysis”

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DOE OSTI2019

Structural and dynamical description of the enzymatic reaction of a phosphohexomutase

Enzymes are known to adopt various conformations at different points along their catalytic cycles. Here, we present a comprehensive analysis of 15 isomorphous, high resolution crystal structures of the enzyme phosphoglucomutase from the bacterium Xanthomonas citri. The protein was captured in distinct states critical to function, including enzyme-substrate, enzyme-product, and enzyme-intermediate complexes. Key residues in ligand recognition and regions undergoing conformational change are identified and correlated with the various steps of the catalytic reaction. In addition, we use principal component analysis to examine various subsets of these structures with two goals: (1) identifying sites of conformational heterogeneity through a comparison of room temperature and cryogenic structures of the apo-enzyme and (2) a priori clustering of the enzyme-ligand complexes into functionally related groups, showing sensitivity of this method to structural features difficult to detect by traditional methods. This study captures, in a single system, the structural basis of diverse substrate recognition, the subtle impact of covalent modification, and the role of ligand-induced conformational change in this representative enzyme of the α-D-phosphohexomutase superfamily.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Identification and correction of temporal and spatial distortions in scanning transmission electron microscopy

Scanning transmission electron microscopy (STEM) has become the technique of choice for quantitative characterization of atomic structure of materials, where the minute displacements of atomic columns from high-symmetry positions can be used to map strain, polarization, octahedra tilts, and other physical and chemical order parameter fields. The latter can be used as inputs into mesoscopic and atomistic models, providing insight into the correlative relationships and generative physics of materials on the atomic level. However, these quantitative applications of STEM necessitate understanding the microscope induced image distortions and developing the pathways to compensate them both as part of a rapid calibration procedure for in situ imaging, and the post-experimental data analysis stage. Here, we explore the spatiotemporal structure of the microscopic distortions in STEM using multivariate analysis of the atomic trajectories in the image stacks. Based on the behavior of principal component analysis (PCA), we develop the Gaussian process (GP)-based regression method for quantification of the distortion function. The limitations of such an approach and possible strategies for implementation as a part of in-line data acquisition in STEM are discussed. Here, the analysis workflow is summarized in a Jupyter notebook that can be used to retrace the analysis and analyze the reader's data.

36 MATERIALS SCIENCE↗

DOE OSTI2020

XRF-MAPS

x-ray fluorescence (XRF) imaging typically involves the creation and analysis of 3D data sets, where at each scan position a full energy dispersive x-ray spectrum is recorded. This allows one to later process the data in a variety of different approaches, e.g., by spectral region of interest (ROI) summation with or without background subtraction, principal component analysis, or fitting. XRF-Maps is a C++ open source software package that implements these functions to provide a tool set for the analysis of XRF data sets.

GLOWACKI, ARTHURT↗

NASA NTRS2012

A Technique Using Principal Component Analysis to Compare Seasonal Cycles of Earth Radiation from CERES and Model Computations

A method for quantitatively comparing the seasonal cycles of two global data sets is presented. The seasonal cycles of absorbed solar radiation (ASR) and outgoing longwave radiation (OLR) have been computed from an eight-year data set from the Clouds and Earth's Radiant Energy System (CERES) scanning radiometers and from a model data set produced by the NASA Goddard Space Flight Center Global Modeling and Assimilation Office. To compare the seasonal cycles from these two data sets, principal component (PC) analysis is used, where the PCs express the time variations and the corresponding empirical orthogonal functions (EOFs) describe the geographic variations. Ocean has a long thermal response time compared to land, so land and ocean are separated for the analysis. The root-mean square values for the seasonal cycles of ASR and OLR are extremely close for the two data sets. The first three PCs are quite close, showing that the time responses and magnitudes over the globe are very similar. The agreement between the two sets of PCs is quantified by computing the matrix of inner products of the two sets. For ASR over land, the first PCs of CERES and the model agree to better than 99.9%. The EOF maps are similar for most of the globe, but differ in a few places, and the agreement of the EOF maps is likewise quantified. Maps of differences between the annual cycles show regions of agreement and disagreement.

Smith, G. Louis↗

DOE OSTI2024

Operando pair distribution function analysis of nanocrystalline functional materials: the case of TiO 2 -bronze nanocrystals in Li-ion battery electrodes

Structural modelling of operando pair distribution function (PDF) data of complex functional materials can be highly challenging. To aid the understanding of complex operando PDF data, this article demonstrates a toolbox for PDF analysis. The tools include denoising using principal component analysis together with the structureMining , similarityMapping and nmfMapping apps available through the online service `PDF in the cloud' ( PDFitc , https://pdfitc.org/). The toolbox is used for both ex situ and operando PDF data for 3 nm TiO 2 -bronze nanocrystals, which function as the active electrode material in a Li-ion battery. The tools enable structural modelling of the ex situ and operando PDF data, revealing two pristine TiO 2 phases (bronze and anatase) and two lithiated Li x TiO 2 phases (lithiated versions of bronze and anatase), and the phase evolution during galvanostatic cycling is characterized.

Chemistry↗

DOE OSTI2021

A physics-informed and hierarchically regularized data-driven model for predicting fluid flow through porous media

This paper presents a new deep learning data-driven model for predicting structure dependent pore-fluid velocity fields in rock. The model is based on a Convolutional Auto-Encoder (CAE) artificial neural network capable of learning from image data generated by direct numerical simulations of fluid flow through pore-structures, such as by Lattice Boltzmann or molecular dynamics methods. The main novelty of the model in comparison to previous CAE-based data-driven approaches consists of three parts. The first is a methodology for decomposing the full-domain of the porous media into sub-regions, or “sub-domains”, in order to reduce the overall size of the CAE, batch process the sub-domains in parallel, and enable the CAE to learn local and generalizable nonlinear mappings of pore-fluid velocities. The second consists of embedding the finite difference solutions of the incompressible Navier-Stokes and continuity equations into convolutional layers prior to the CAE in order to provide the CAE with knowledge of fluid dynamics physics (PhyFlow). The third main novelty is that the training of the CAE is regularized with a hierarchical loss function that encourages the learning of fluid flow patterns (in a way similar to ranked modes in principal component analysis), ranking from most to least important. This is shown to increase the stability in learning, reduce over-fitting, and promote interpretability of the CAE neural network layers (HierCAE). The comprehensive new data-driven model, which we call the PhyFlow-HierCAE model, is shown to exhibit improved accuracy and generalizability of flow field predictions over conventional CAE models, attributable to the embedded physical knowledge and the hierarchical regularization, as well as realize orders of magnitude speed-ups in computation times as a surrogate for the direct numerical simulations. Examples of training and forward predictions on unseen pore-structures are provided and evaluated for data from Lattice Boltzmann and molecular dynamics simulations of pore-fluid flow. The model is shown to be a fast and accurate emulator (or “surrogate”) for predicting effective permeability of unseen pore-structures based on learning from relatively small direct numerical simulation datasets.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Reinforcement learning for real-time process control in high-temperature superconductor manufacturing

With high efficiency and low energy loss, high-temperature superconductors (HTS) have demonstrated their profound applications in various fields, such as medical imaging, transportation, accelerators, microwave devices, and power systems. The high-field applications of HTS tapes have raised the demand for producing cost-effective tapes with long lengths in superconductor manufacturing. However, achieving the uniform and enhanced performance of a long HTS tape is challenging due to the unstable growth conditions in the manufacturing process. Although it is confirmed that the process parameters during the advanced metal organic chemical vapor deposition (A-MOCVD) process influence the uniformity of the produced HTS tapes, the high-dimensional process parameter signals and their complicated interactions make it difficult to develop an effective control policy. In this paper, we propose a local measure for the uniformity of HTS tapes to provide instant feedback for our control policy. Then, we model the manufacturing of HTS tapes as a Markov decision process (MDP) with continuous state and action spaces to assess the instant reward in real time in our feedback control model. As our MDP involves continuous and high-dimensional state and action spaces, a neural fitted Q-iteration (NFQ) algorithm is adopted to solve the MDP with artificial neural network (ANN) function approximation. The collinearity of process parameters can restrict our capability of adjusting the process parameters, which is addressed by the principal component analysis (PCA) in our method. The control policy adjusts the PCA of process parameters using the NFQ algorithm. In conclusion, based on our case studies on real A-MOCVD dataset, the obtained control policy increases the average uniformity of tapes by 5.6% and performs especially well on sample HTS tapes with a low uniformity.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2015

Big Data in Reciprocal Space: Sliding Fast Fourier Transforms for Determining Periodicity

Significant advances in atomically resolved imaging of crystals and surfaces have occurred in the last decade allowing unprecedented insight into local crystal structures and periodicity. Yet, the analysis of the long-range periodicity from the local imaging data, critical to correlation of functional properties and chemistry to the local crystallography, remains a challenge. Here, we introduce a Sliding Fast Fourier Transform (FFT) filter to analyze atomically resolved images of in-situ grown La5/8Ca3/8MnO3 films. We demonstrate the ability of sliding FFT algorithm to differentiate two sub-lattices, resulting from a mixed-terminated surface. Principal Component Analysis (PCA) and Independent Component Analysis (ICA) of the Sliding FFT dataset reveal the distinct changes in crystallography, step edges and boundaries between the multiple sub-lattices. The method is universal for images with any periodicity, and is especially amenable to atomically resolved probe and electron-microscopy data for rapid identification of the sub-lattices present.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2022

Decomposition of Irganox 1010 in plastic bonded explosives

Abstract Degradation pathways of Irganox 1010 in aged plastic bonded explosive (PBX) 9501 were investigated using ultrahigh performance liquid chromatography coupled to quadrupole time of flight mass spectrometry (UHPLC‐QTOF). Using a targeted approach, a total of 44 Irganox 1010 decomposition products were discovered. These decomposition products were formed through hydrolysis, scission, and/or oxidation of Irganox 1010. The hydrolytic decomposition of Irganox is a straightforward process resulting in the cleavage of the ester group(s) while oxidation and scission are more complicated and can happen at multiple locations on the Irganox 1010 molecule. Moreover, due to the symmetric nature of Irganox 1010, multiple decomposition reactions can occur. Indeed some decomposition products exhibited hydrolysis, oxidation, and scission. In order to probe any trends in the aged PBX 9501 samples, principal component analysis (PCA) was implemented. The greatest chemical differences between the aged PBX samples was hydrolysis of the ester functional groups on Irganox 1010. Despite the negative connotations of hydrolysis, the Irganox 1010 decomposition products are still able to function as a radical scavenger in PBX 9501 as intended.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Evaluation of CMIP6 GCMs Over the CONUS for Downscaling Studies

Despite the necessity of Global Climate Models (GCMs) sub-selection in downscaling studies, an objective approach for their selection is currently lacking. Building on the previously established concepts in GCMs evaluation frameworks, we develop a weighted averaging technique to remove the redundancy in the evaluation criteria and rank 37 GCMs from the sixth phase of the Coupled Models Intercomparison Project over the contiguous United States. GCMs are rated based on their average performance across 66 evaluation measures in the historical period (1981–2014) after each metric is weighted between zero and one, depending on its uniqueness. The robustness of the outcome is tested by repeating the process with the empirical orthogonal function analysis in which each GCM is ranked based on its sum of distances from the reference in the principal component space. The two methodologies work in contrasting ways to remove the metrics redundancy but eventually develop similar GCMs rankings. A disparity in GCMs' behavior related to their sensitivity to the size of the evaluation suite is observed, highlighting the need for comprehensive multi-variable GCMs evaluation at varying timescales for determining their skillfulness over a region. The sub-selection goal is to use a representative set of skillful models over the region of interest without substantial overlap in their future climate responses and modeling errors in representing historical climate. Additional analyses of GCMs' independence and spread in their future projections provide the necessary information to objectively select GCMs while keeping all aspects of necessity in view.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Validation of non-negative matrix factorization for rapid assessment of large sets of atomic pair distribution function data

The use of the non-negative matrix factorization (NMF) technique is validated for automatically extracting physically relevant components from atomic pair distribution function (PDF) data from time-series data such as in situ experiments. The use of two matrix-factorization techniques, principal component analysis and NMF, on PDF data is compared in the context of a chemical synthesis reaction taking place in a synchrotron beam, applying the approach to synthetic data where the correct composition is known and on measured PDFs from previously published experimental data. The NMF approach yields mathematical components that are very close to the PDFs of the chemical components of the system and a time evolution of the weights that closely follows the ground truth. Lastly, it is discussed how this would appear in a streaming context if the analysis were being carried out at the beamline as the experiment progressed.

36 MATERIALS SCIENCE↗

DOE OSTI2014

Interactive XCMS Online: Simplifying Advanced Metabolomic Data Processing and Subsequent Statistical Analyses

XCMS Online (xcmsonline.scripps.edu) is a cloud-based informatic platform designed to process and visualize mass-spectrometry-based, untargeted metabolomic data. Initially, the platform was developed for two-group comparisons to match the independent, “control” versus “disease” experimental design. Here, we introduce an enhanced XCMS Online interface that enables users to perform dependent (paired) two-group comparisons, meta-analysis, and multigroup comparisons, with comprehensive statistical output and interactive visualization tools. Newly incorporated statistical tests cover a wide array of univariate analyses. Multigroup comparison allows for the identification of differentially expressed metabolite features across multiple classes of data while higher order meta-analysis facilitates the identification of shared metabolic patterns across multiple two-group comparisons. Given the complexity of these data sets, we have developed an interactive platform where users can monitor the statistical output of univariate (cloud plots) and multivariate (PCA plots) data analysis in real time by adjusting the threshold and range of various parameters. On the interactive cloud plot, metabolite features can be filtered out by their significance level (p-value), fold change, mass-to-charge ratio, retention time, and intensity. The variation pattern of each feature can be visualized on both extracted-ion chromatograms and box plots. The interactive principal component analysis includes scores, loadings, and scree plots that can be adjusted depending on scaling criteria. The utility of XCMS functionalities is demonstrated through the metabolomic analysis of bacterial stress response and the comparison of lymphoblastic leukemia cell lines.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2001

Non-seasonal Gravitational Effects of Interannual Meteorological Oscillations in Atmosphere and Ocean

Via mass transport, the interannual meteorological oscillations (ENSO, NAO, etc.) produce slight variations in the global gravitational field, which can be observed by satellite laser ranging (SLR) and anticipated space missions such as GRACE. The meteorological oscillation modes are identified using empirical orthogonal function and principal component decomposition using de-seasoned surface fields produced from the 40-years of NCEP reanalysis. This decompositional analysis requires an accounting for issues associated with area-weighting and non-zero mean. The atmospheric contributions to gravitational variation, mode by mode and in combinations, are then computed via regional integration. To address the corresponding oceanic contributions, we examine the output of the numerical POCM ocean circulation model (1992-1998) in two ways: ocean bottom pressure field and ocean surface topography minus steric effect. The resulting lowest-degree Stokes coefficients for both NCEP reanalysis and POCM are then compared with space geodetic SLR observations, to identify the importance of each meteorological oscillations in gravitational variation signals.

Chao, Benjamin F.↗

DOE OSTI2025

Accelerating the Structure Exploration of Diverse Bi–Pt Nanoclusters via Physics‐Informed Machine Learning Potential and Particle Swarm Optimization

Bimetallic Bi–Pt nanoclusters exhibit diverse structural motifs, including core-shell, Janus, and mixed alloy configurations, due to the unique bonding characteristics between Bi and Pt atoms. Using density functional theory refinements from ChIMES physically machine-learned potential and CALYPSO particle swarm optimization global searches, 34 Bi20-Pt20 nanoclusters are systematically classified. The results reveal that Bi atoms predominantly occupy surface sites, driven by charge transfer effects. Cohesive energy trends alone prove insufficient for structure differentiation, necessitating a data-driven approach employing principal component analysis and K-means clustering. Furthermore, vibrational, electronic, and infrared spectral analyses provide additional insights into structure-property relationships. The findings offer an original framework for the automated classification and analysis of bimetallic nanoclusters, enhancing the understanding of their stability and functional properties.

bimetallic nanoparticles↗

DOE OSTI2023

Mallat Scattering Transformation based surrogate for Magnetohydrodynamics

Abstract A Machine and Deep Learning (MLDL) methodology is developed and applied to give a high fidelity, fast surrogate for 2D resistive MagnetoHydroDynamic (MHD) simulations of Magnetic Liner Inertial Fusion (MagLIF) implosions. The resistive MHD code is used to generate an ensemble of implosions with different liner aspect ratios, initial gas preheat temperatures (that is, different adiabats), and different liner perturbations. The liner density and magnetic field as functions of x , y , and z were generated. The Mallat Scattering Transformation (MST) is taken of the logarithm of both fields and a Principal Components Analysis (PCA) is done on the logarithm of the MST of both fields. The fields are projected onto the PCA vectors and a small number of these PCA vector components are kept. Singular Value Decompositions of the cross correlation of the input parameters to the output logarithm of the MST of the fields, and of the cross correlation of the SVD vector components to the PCA vector components are done. This allows the identification of the PCA vectors vis-a-vis the input parameters. Finally, a Multi Layer Perceptron (MLP) neural network with ReLU activation and a simple three layer encoder/decoder architecture is trained on this dataset to predict the PCA vector components of the fields as a function of time. Details of the implosion, stagnation, and the disassembly are well captured. Examination of the PCA vectors and a permutation importance analysis of the MLP show definitive evidence of an inverse turbulent cascade into a dipole emergent behavior. The orientation of the dipole is set by the initial liner perturbation. The analysis is repeated with a version of the MST which includes phase, called Wavelet Phase Harmonics (WPH). While WPH do not give the physical insight of the MST, they can and are inverted to give field configurations as a function of time, including field-to-field correlations.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2015

Couplings between hierarchical conformational dynamics from multi-time correlation functions and two-dimensional lifetime spectra: Application to adenylate kinase

An analytical method based on a three-time correlation function and the corresponding two-dimensional (2D) lifetime spectrum is developed to elucidate the time-dependent couplings between the multi-timescale (i.e., hierarchical) conformational dynamics in heterogeneous systems such as proteins. In analogy with 2D NMR, IR, electronic, and fluorescence spectroscopies, the waiting-time dependence of the off-diagonal peaks in the 2D lifetime spectra can provide a quantitative description of the dynamical correlations between the conformational motions with different lifetimes. The present method is applied to intrinsic conformational changes of substrate-free adenylate kinase (AKE) using long-time coarse-grained molecular dynamics simulations. It is found that the hierarchical conformational dynamics arise from the intra-domain structural transitions among conformational substates of AKE by analyzing the one-time correlation functions and one-dimensional lifetime spectra for the donor-acceptor distances corresponding to single-molecule Förster resonance energy transfer experiments with the use of the principal component analysis. In addition, the complicated waiting-time dependence of the off-diagonal peaks in the 2D lifetime spectra for the donor-acceptor distances is attributed to the fact that the time evolution of the couplings between the conformational dynamics depends upon both the spatial and temporal characters of the system. The present method is expected to shed light on the biological relationship among the structure, dynamics, and function.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Extreme_SeaState_Contour_v1

This software generates environmental contours of extreme sea states using buoy observations of significant wave height and energy period or peak period. The code transforms these observations using principal component analysis (PCA) to create an uncorrelated representation of the data. The subsequent components are modeled using probability distributions and parameter fitting functions. The inverse first-order reliability method (I-FORM) is then applied to these models in order to generate an extreme event contour based on a given return period (i.e., 100 years).The subsequent contour is then transformed back into the original input space defined by the variables of interest in order to create an environmental contour of extreme sea states.

Eckert, Aubrey↗

DOE OSTI2015

Extreme_SeaState_Contour_v1

Source record↗