Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “NMF”

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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Developing Reaction Chemistry Models from Reactive Molecular Dynamics: TATB

Reactive Molecular Dynamic (RMD) are used to simulate the cook-off chemistry of TATB at a variety of fixed density and fixed temperature conditions. The chemical transformations are monitored using a Coordination Geometry Analysis (CGA) approach which tracks which atom types are bonded to each specific atom. This particularly identifies oxidation state changes that occur during the transformations. Correlations between these different chemical changes are identified using a Non-negative Matrix Factorization (NMF) approach. These identify reduced order chemistry models for the TATB system which contains six components whose concentration profiles are a function of both the temperature and density/pressure. The time histories of these transformations appear to show exponential growth/decay properties that could be fit with Arrhenius rates. These components should form the basis of deflagration rate models for these materials which could then be used in mesoscale simulations to analyze accidental initiation, shock-to-detonation and detonation propagation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Phase Behavior and Domain Size in Sphingomyelin-Containing Lipid Bilayers

Membrane raft size measurements are crucial to understanding the stability and functionality of rafts in cells. The challenge of accurately measuring raft size is evidenced by the disparate reports of domain sizes, which range from nanometers to microns for the ternary model membrane system sphingomyelin (SM)/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/cholesterol (Chol). Using F rster resonance energy transfer (FRET) and differential scanning calorimetry (DSC), we established phase diagrams for porcine brain SM (bSM)/dioleoyl-sn-glycero-3-phosphocholine (DOPC)/Chol and bSM/POPC/Chol at 15 and 25 C. By combining two techniqueswith different spatial sensitivities, namely FRET and small-angle neutron scattering (SANS),we have significantly narrowed the uncertainty in domain size estimates for bSM/POPC/Chol mixtures. Compositional trends in FRET data revealed coexisting domains at 15 and 25 C for bothmixtures, while SANS measurements detected no domain formation for bSM/POPC/Chol. Together these results indicate that liquid domains in bSM/POPC/Chol are between 2 and 7 nmin radius at 25 C: that is, domains must be on the order of the 2 6 nmF rster distance of the FRET probes, but smaller than the ~7 nm minimum cluster size detectable with SANS. However, for palmitoyl SM (PSM)/POPC/Chol at a similar composition, SANS detected coexisting liquid domains. This increase in domain size upon replacing the natural SMcomponent (which consists of amixture of chain lengths) with synthetic PSM, suggests a role for SM chain length in modulating raft size in vivo.

Bio-SANS↗
DOE OSTI2017

Contaminant source identification using semi-supervised machine learning

Identification of the original groundwater types present in geochemical mixtures observed in an aquifer is a challenging but very important task. Frequently, some of the groundwater types are related to different infiltration and/or contamination sources associated with various geochemical signatures and origins. The characterization of groundwater mixing processes typically requires solving complex inverse models representing groundwater flow and geochemical transport in the aquifer, where the inverse analysis accounts for available site data. Usually, the model is calibrated against the available data characterizing the spatial and temporal distribution of the observed geochemical types. Numerous different geochemical constituents and processes may need to be simulated in these models which further complicates the analyses. In this paper, we propose a new contaminant source identification approach that performs decomposition of the observation mixtures based on Non-negative Matrix Factorization (NMF) method for Blind Source Separation (BSS), coupled with a custom semi-supervised clustering algorithm. Our methodology, called NMFk, is capable of identifying (a) the unknown number of groundwater types and (b) the original geochemical concentration of the contaminant sources from measured geochemical mixtures with unknown mixing ratios without any additional site information. NMFk is tested on synthetic and real-world site data. Finally, the NMFk algorithm works with geochemical data represented in the form of concentrations, ratios (of two constituents; for example, isotope ratios), and delta notations (standard normalized stable isotope ratios).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Speciation mapping of the oxidation layer on aged uranium dioxide using scanning transmission x-ray spectromicroscopy

In this study, UO 2 was aged in humid air and prepared as a thin section using a focused ion beam (FIB) instrument. The specimen was measured using synchrotron radiation spectromicroscopy techniques at the Beamline 11.0.2 STXM end station of the Advanced Light Source (ALS). Non-negative matrix factorization (NMF) methods were used to identify and map three component x-ray absorption near-edge structure (XANES) spectra in the oxygen K-edge data, revealing a surface layer of U 4 O 9 with a thickness of 206 ± 21 nm, and the bulk of the sample remaining as UO 2 . Uranium N 4,5 -edge XANES spectromicroscopy supports these results. The diffusion-controlled parabolic rate constant for UO 2 oxidation to U 4 O 9 was calculated from the observed layer thickness and compared to literature values. Complementary transmission electron microscopy (TEM) was used to image the sample and identify the phases present in various regions, confirming the STXM results.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2022

Correlated mechanochemical maps of Arabidopsis thaliana primary cell walls using atomic force microscope infrared spectroscopy

Spatial heterogeneity in composition and organisation of the primary cell wall affects the mechanics of cellular morphogenesis. However, directly correlating cell wall composition, organisation and mechanics has been challenging. To overcome this barrier, we applied atomic force microscopy coupled with infrared (AFM-IR) spectroscopy to generate spatially correlated maps of chemical and mechanical properties for paraformaldehyde-fixed, intact Arabidopsis thaliana epidermal cell walls. AFM-IR spectra were deconvoluted by non-negative matrix factorisation (NMF) into a linear combination of IR spectral factors representing sets of chemical groups comprising different cell wall components. This approach enables quantification of chemical composition from IR spectral signatures and visualisation of chemical heterogeneity at nanometer resolution. Cross-correlation analysis of the spatial distribution of NMFs and mechanical properties suggests that the carbohydrate composition of cell wall junctions correlates with increased local stiffness. Together, our work establishes new methodology to use AFM-IR for the mechanochemical analysis of intact plant primary cell walls.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Multimodal Chemical Imaging for Linking Adhesion with Local Chemistry in Agrochemical Multicomponent Polymeric Coatings

Seed coatings improve germination and offer higher crop yields through a blend of active ingredients (such as insecticides and fungicides), polymers, waxes, fillers, and pigments. To reach their full potential, fundamental formulation challenges bridging structure and function need to be addressed. In some instances, during industrial-volume packing and transportation, coated seeds do not flow well through elevators, conveyers, and applicators, which may reduce yield and add cost. In this work, we illustrate a combinatorial chemical imaging approach to study seed coatings at the microscale to link chemical and physical properties responsible for low seed flowability. The local chemical composition was examined using time-of-flight secondary ion mass spectrometry (ToF-SIMS) and at comparable length scales, the local adhesive properties were examined using atomic force microscopy (AFM) force volume mapping. The link between the chemical and the adhesive properties was established by non-negative matrix factorization (NMF). The correlative multimodal imaging approach developed here utilizing AFM force volume mapping, ToF-SIMS chemical mapping, and data analytics offers a path for linking function with localized chemistry when investigating multicomponent soft material systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Node Distortion as a Tunable Mechanism for Negative Thermal Expansion in Metal–Organic Frameworks

Chemically functionalized series of metal–organic frameworks (MOFs), with subtle differences in local structure but divergent properties, provide a valuable opportunity to explore how local chemistry can be coupled to long-range structure and functionality. Using in situ synchrotron X-ray total scattering, with powder diffraction and pair distribution function (PDF) analysis, we investigate the temperature dependence of the local- and long-range structure of MOFs based on NU-1000, in which Zr 6 O 8 nodes are coordinated by different capping ligands (H 2 O/OH, Cl – ions, formate, acetylacetonate, and hexafluoroacetylacetonate). We show that the local distortion of the Zr 6 nodes depends on the lability of the ligand and contributes to a negative thermal expansion (NTE) of the extended framework. Using multivariate data analyses, involving non-negative matrix factorization (NMF), we demonstrate a new mechanism for NTE: progressive increase in the population of a smaller, distorted node state with increasing temperature leads to global contraction of the framework. The transformation between discrete node states is noncooperative and not ordered within the lattice, i.e., a solid solution of regular and distorted nodes. Density functional theory calculations show that removal of ligands from the node can lead to distortions consistent with the Zr···Zr distances observed in the experiment PDF data. Control of the node distortion imparted by the nonlinker ligand in turn controls the NTE behavior. Furthermore, these results reveal a mechanism to control the dynamic structure of MOFs based on local chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Robust design of semi-automated clustering models for 4D-STEM datasets

Materials discovery and design require characterizing material structures at the nanometer and sub-nanometer scale. Four-Dimensional Scanning Transmission Electron Microscopy (4D-STEM) resolves the crystal structure of materials, but many 4D-STEM data analysis pipelines are not suited for the identification of anomalous and unexpected structures. This work introduces improvements to the iterative Non-Negative Matrix Factorization (NMF) method by implementing consensus clustering for ensemble learning. We evaluate the performance of models during parameter tuning and find that consensus clustering improves performance in all cases and is able to recover specific grains missed by the best performing model in the ensemble. The methods introduced in this work can be applied broadly to materials characterization datasets to aid in the design of new materials.

Bruefach, Alexandra (ORCID:0000000209323477)↗
DOE OSTI2016

Stability-driven nonnegative matrix factorization to interpret spatial gene expression and build local gene networks

Spatial gene expression patterns enable the detection of local covariability and are extremely useful for identifying local gene interactions during normal development. The abundance of spatial expression data in recent years has led to the modeling and analysis of regulatory networks. The inherent complexity of such data makes it a challenge to extract biological information. We developed staNMF, a method that combines a scalable implementation of nonnegative matrix factorization (NMF) with a new stability-driven model selection criterion. When applied to a set of Drosophila early embryonic spatial gene expression images, one of the largest datasets of its kind, staNMF identified 21 principal patterns (PP). Providing a compact yet biologically interpretable representation of Drosophila expression patterns, PP are comparable to a fate map generated experimentally by laser ablation and show exceptional promise as a data-driven alternative to manual annotations. Our analysis mapped genes to cell-fate programs and assigned putative biological roles to uncharacterized genes. Finally, we used the PP to generate local transcription factor regulatory networks. Spatially local correlation networks were constructed for six PP that span along the embryonic anterior-posterior axis. Using a two-tail 5% cutoff on correlation, we reproduced 10 of the 11 links in the well-studied gap gene network. In conclusion, the performance of PP with the Drosophila data suggests that staNMF provides informative decompositions and constitutes a useful computational lens through which to extract biological insight from complex and often noisy gene expression data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Distributed-Memory Parallel Symmetric Nonnegative Matrix Factorization

We develop the first distributed-memory parallel implementation of Symmetric Nonnegative Matrix Factorization (SymNMF), a key data analytics kernel for clustering and dimensionality reduction. Our implementation includes two different algorithms for SymNMF, which give comparable results in terms of time and accuracy. The first algorithm is a parallelization of an existing sequential approach that uses solvers for non symmetric NMF. The second algorithm is a novel approach based on the Gauss-Newton method. It exploits second-order information without incurring large computational and memory costs. We evaluate the scalability of our algorithms on the Summit system at Oak Ridge National Laboratory, scaling up to 128 nodes (4,096 cores) with 70% efficiency. Additionally, we demonstrate our software on an image segmentation task.

Eswar, Srinivas↗
DOE OSTI2026

Data-Driven Optimization of Pixelated CdZnTe Spectrometers for Uranium Enrichment Assay

Here, in recent work [Vavrek et al. (2025)], we developed the performance optimization framework spectre-ml for gamma spectrometers with variable performance across many readout channels. The framework uses non-negative matrix factorization (NMF) and clustering to learn groups of similarly-performing channels and sweep through various learned channel combinations to optimize the performance tradeoff of including worse-performing channels for better total efficiency. In this work, we integrate the pyGEM uranium enrichment assay code with our spectre-ml framework, and show that the U-235 enrichment relative uncertainty can be directly used as an optimization target. We find that this optimization reduces relative uncertainties after a 30 -minute measurement by an average of 20%, as tested on six different H3D M400 CdZnTe spectrometers, which can significantly improve uranium non-destructive assay measurement times in nuclear safeguards contexts. Additionally, this work demonstrates that the spect re-ml optimization framework can accommodate arbitrary end-user spectroscopic analysis code and performance metrics, enabling future optimizations for complex Pu spectra.

Gamma-ray detection↗
DOE OSTI2017

ShiftNMFk 1.2

The ShiftNMFk1.2 code, or as we call it, GreenNMFk, represents a hybrid algorithm combining unsupervised adaptive machine learning and Green's function inverse method. GreenNMFk allows an efficient and high performance de-mixing and feature extraction of a multitude of nonnegative signals that change their shape propagating through the medium. The signals are mixed and recorded by a network of uncorrelated sensors. The code couples Non-negative Matrix Factorization (NMF) and inverse-analysis Green's functions method. GreenNMF synergistically performs decomposition of the recorded mixtures, finds the number of the unknown sources and uses the Green's function of the governing partial differential equation to identify the unknown sources and their charecteristics. GreenNMF can be applied directly to any problem controlled by a known partial-differential parabolic equation where mixtures of an unknown number of sources are measured at multiple locations. Full GreenNMFk method is a subject LANL U.S. Patent application S133364.000 August, 2017. The ShiftNMFk 1.2 version here is a toy version of this method that can work with a limited number of unknown sources (4 or less).

Alexandrov, BoianS.↗
DOE OSTI2021

Machine learning to identify geologic factors associated with production in geothermal fields: a case-study using 3D geologic data, Brady geothermal field, Nevada

Abstract In this paper, we present an analysis using unsupervised machine learning (ML) to identify the key geologic factors that contribute to the geothermal production in Brady geothermal field. Brady is a hydrothermal system in northwestern Nevada that supports both electricity production and direct use of hydrothermal fluids. Transmissive fluid-flow pathways are relatively rare in the subsurface, but are critical components of hydrothermal systems like Brady and many other types of fluid-flow systems in fractured rock. Here, we analyze geologic data with ML methods to unravel the local geologic controls on these pathways. The ML method, non-negative matrix factorization with k -means clustering (NMF k ), is applied to a library of 14 3D geologic characteristics hypothesized to control hydrothermal circulation in the Brady geothermal field. Our results indicate that macro-scale faults and a local step-over in the fault system preferentially occur along production wells when compared to injection wells and non-productive wells. We infer that these are the key geologic characteristics that control the through-going hydrothermal transmission pathways at Brady. Our results demonstrate: (1) the specific geologic controls on the Brady hydrothermal system and (2) the efficacy of pairing ML techniques with 3D geologic characterization to enhance the understanding of subsurface processes.

58 GEOSCIENCES↗
DOE OSTI2022

GeoThermalCloud: Machine Learning for Geothermal Resource Exploration

Geothermal is a renewable energy source that can provide reliable and flexible electricity generation for the world. In the past decade, the U.S. Geological Survey's resource assessments, Play Fairway Analyses (PFA), and GeoVision report by the U.S. Department of Energy's Geothermal Technologies Office provided insights on enormous untapped potential for geothermal energy to contribute to the U.S. domestic energy needs. The past studies identified that geothermal resources without surface expression (e.g., blind/hidden hydrothermal systems) comprise a huge potential. These blind systems can significantly increase power generation. But a primary challenge is locating and quantifying these hidden resources, which do not have any thermal manifestations on the surface. PFA has successfully identified some blind systems in the western USA (e.g., specific locations in the Great Basin region within Nevada). However, a comprehensive search for these blind systems can be time-consuming, expensive, and resource-intensive with a low probability of success. Accelerated discovery of these blind resources is needed with growing energy needs and higher chances of exploration success. Recent advances in machine learning (ML) have shown promise in shortening the timeline for this discovery. This paper presents a novel ML-based methodology for geothermal exploration towards PFA applications. Our methodology is provided through our open-source ML framework called GeoThermalCloud \url{https://github.com/SmartTensors/GeoThermalCloud.jl}. GeoThermalCloud uses a series of unsupervised, supervised, and physics-informed ML methods available in SmartTensors AI platform \url{https://github.com/SmartTensors}. Here, the presented analyses are performed using our unsupervised ML algorithm called NMF$k$, which is available in the SmartTensors AI platform. Our ML algorithm facilitates the discovery of new phenomena, hidden patterns, and mechanisms that helps us to make informed decisions. Moreover, the GeoThermalCloud enhances the collected PFA data and discovers signatures representative of geothermal resources. Through GeoThermalCloud, we were able to identify hidden patterns in the geothermal field data needed for the efficient discovery of blind systems. Crucial geothermal signatures often overlooked in traditional PFA are extracted using GeoThermalCloud and analyzed by the subject matter experts to provide ML-enhanced PFA, which is informative for efficient exploration. We applied our ML methodology on various open-source geothermal datasets within the U.S. (some of these are collected by past PFA work), and the results provide valuable insights on resource types within those explored regions. This ML-enhanced workflow makes GeoThermalCloud attractive for the geothermal community to improve existing datasets and extract valuable information often unnoticed during geothermal exploration.

machine learning (ML), geothermal energy↗
DOE OSTI2020

Updates on LANL AM Data Analysis

The NMF k algorithm results in strong classification scores and informative basis functions to describe the spectra associated with pore formation.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
NASA NTRS1994

A comparative survey of current and proposed tropospheric refraction-delay models for DSN radio metric data calibration

The standard tropospheric calibration model implemented in the operational Orbit Determination Program is the seasonal model developed by C. C. Chao in the early 1970's. The seasonal model has seen only slight modification since its release, particularly in the format and content of the zenith delay calibrations. Chao's most recent standard mapping tables, which are used to project the zenith delay calibrations along the station-to-spacecraft line of sight, have not been modified since they were first published in late 1972. This report focuses principally on proposed upgrades to the zenith delay mapping process, although modeling improvements to the zenith delay calibration process are also discussed. A number of candidate approximation models for the tropospheric mapping are evaluated, including the semi-analytic mapping function of Lanyi, and the semi-empirical mapping functions of Davis, et. al.('CfA-2.2'), of Ifadis (global solution model), of Herring ('MTT'), and of Niell ('NMF'). All of the candidate mapping functions are superior to the Chao standard mapping tables and approximation formulas when evaluated against the current Deep Space Network Mark 3 intercontinental very long baselines interferometry database.

Estefan, J. A.↗
NASA NTRS2004

MIT Haystack Observatory Analysis Center Report

The data from twenty years of the NCEP numerical weather model have been used to calculate the IMF hydrostatic mapping function for several sites distributed in latitude from -66 degrees to +78 degrees. Comparison of heights estimated with the NMF hydrostatic mapping function demonstrates that using NMFh results in height errors at annual and semi-annual periods with amplitudes as large as approximately 8 mm and 4 mm, respectively, when data down to 5 degrees are included. The errors are smallest at the equator and increase towards the poles.

Niell, Arthur↗
DOE OSTI2016

Matrix Factorizations at Scale: a Comparison of Scientific Data Analytics in Spark and C+MPI Using Three Case Studies

We explore the trade-offs of performing linear algebra using Apache Spark, compared to traditional C and MPI implementations on HPC platforms. Spark is designed for data analytics on cluster computing platforms with access to local disks and is optimized for data-parallel tasks. We examine three widely-used and important matrix factorizations: NMF (for physical plausibility), PCA (for its ubiquity) and CX (for data interpretability). We apply these methods to 1.6TB particle physics, 2.2TB and 16TB climate modeling and 1.1TB bioimaging data. The data matrices are tall-and-skinny which enable the algorithms to map conveniently into Spark’s data parallel model. We perform scaling experiments on up to 1600 Cray XC40 nodes, describe the sources of slowdowns, and provide tuning guidance to obtain high performance.

Gittens, Alex↗