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Results for “Dimensionality Reduction”

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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At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Physics-informed graph neural networks for predicting cetane number with systematic data quality analysis

Designing alternative fuels for advanced compression ignition engines necessitates a predictive model for cetane number (CN). In this study, the physics-informed graph neural networks are introduced for a reliable CN prediction by considering molecular features pertinent to the physical properties of molecules that affect CN. The reliability of measured data is another key factor to consider for improving the predictive model. Various experimental instruments for measuring CN exist, including standard and non-standard methods. In this regard, a systematic data quality analysis was carried out for the total 630 CNs collected from literature and new measurements in this study using Advanced Fuel Ignition Delay Analyzer (AFIDA). The results from this data curation process were reflected in the model by imposing lower sample weights on the data coming from less reliable measurement techniques. This approach effectively maximized the prediction accuracy while incorporating data from all available sources. Using the sample weights decreased the mean absolute error (MAE) up to 0.8 CN units. The accuracy was also improved by introducing the CN-related physical properties (the number of hydrogen bond donors and acceptors); the test set MAE is 5.74 and 7.01 for the model with and without such properties, respectively. Investigating molecular structural effects on CN was also carried out to gain chemical insights into factors used to design new fuel candidates. The dimensionality reduction analysis of feature vectors showed a clear clustering in terms of functional groups and CN and the structural effect derived from the model was consistent with the physicochemical insights. Finally, this physics-informed model and data curation would be helpful for accurate CN prediction and inform rational fuel design.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Online task-space motion control for positioner-coordinated multi-robot manufacturing systems

Incorporating multiple robotic manipulators into large-scale manufacturing systems enhances production efficiency and expands manufacturing capabilities beyond those of single-robot systems. Workpiece positioners in robotic manufacturing have demonstrated significant benefits for process optimization, but coordination strategies for multi-robot systems with shared positioners have received limited attention. This work presents a task-space coordinated trajectory-tracking control framework for multi-robot manufacturing systems, in which robots coordinate their motions within a shared, dynamic workpiece positioning frame. A workpiece positioner actively adjusts the pose of the manufactured component to enable greater operational concurrency and improve overall production efficiency. The proposed motion-coordination scheme employs a distributed and scalable architecture, supporting coordination across heterogeneous multi-robot systems. Two optimization methodologies are introduced to manage kinematic redundancies and maintain continuous, near-optimal operation throughout the manufacturing process. The first strategy exploits a task-space dimensionality reduction to achieve locally optimal configurations by leveraging symmetry-axis rotations of the tool. The second strategy utilizes the workpiece positioner to drive the coordinated robots toward stable and kinematically favorable configurations. For both optimization strategies, multiple objectives are defined to improve key performance metrics, including manipulability, configuration consistency, proximity to mechanical limits, and motion efficiency. Addressing a key limitation of existing coordination approaches, the framework is designed around online setpoint modification, allowing coordinated robots to respond effectively to in-situ process feedback. The proposed control framework is validated using the Robot Operating System (ROS) middleware on a combination of physical and simulated multi-robot system hardware.

Arbogast, Alex [ORNL] (ORCID:0000000154740723)↗
DOE OSTI2024

Robust Machine Learning Inference from X-ray Absorption Near Edge Spectra through Featurization

X-ray absorption spectroscopy (XAS) is a commonly employed technique for characterizing functional materials. In particular, X-ray absorption near edge spectra (XANES) encode local coordination and electronic information, and machine learning approaches to extract this information are of significant interest. To date, most ML approaches for XANES have primarily focused on using the raw spectral intensities as input, overlooking the potential benefits of incorporating spectral transformations and dimensionality reduction techniques into ML predictions. Here, in this work, we focused on systematically comparing the impact of different featurization methods on the performance of ML models for XAS analysis. We evaluated the classification and regression capabilities of these models on computed data sets and validated their performance on previously unseen experimental data sets. Our analysis revealed an intriguing discovery: the cumulative distribution function feature achieves both high prediction accuracy and exceptional transferability. This remarkably robust performance can be attributed to its tolerance to horizontal shifts in the spectra, which is crucial when validating models using experimental data. While this work exclusively focuses on XANES analysis, we anticipate that the methodology presented here will hold promise as a versatile asset to the broader spectroscopy community.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Discovery-Synthesis, Design, and Prediction of Chalcogenide Phases

The discovery of new materials and their efficient syntheses is a fundamental goal of chemistry. A related objective is to identify foundational and rational approaches to enhance the art of synthesis by combining the exquisite predictability of organic synthesis with the high yields of solid-state chemistry. In contrast to so-called solid-state methods, inorganic syntheses in liquid fluxes permit bond formation, framework assembly, and crystallization at lower temperatures because of facile diffusion and chemical reactions with and within the flux itself. The fluxes are bona fide solvents similar to conventional organic or aqueous solvents. Such reactions can produce a wide range of materials, often metastable, from oxides to intermetallics, but typically the formation mechanisms are poorly understood. This article discusses how one can design, perform, observe, understand, and engineer the formation of compounds from inorganic melts. The focus is also design concepts such as "dimensional reduction", "phase homologies", and "panoramic synthesis", and their broad applicability. When well-defined building blocks are present and stable in the reaction, prospects for increased structural diversity and product control increase substantially. Common structural motifs within these materials systems may be related to structural precursors in the melt that may be controlled by tuning reaction conditions and composition. Stabilization of a particular building block is often accomplished with tuning of the flux composition, which controls the Lewis basicity and redox potential. In such tunable and dynamic fluxes, the synthesis can be directed toward new materials. Using complementary techniques of in situ X-ray diffraction, we can create time-dependent maps of reaction space and probe the mobile species present in melts. Lastly, certain thoughts toward the ultimate goal of targeted materials synthesis by controlling inorganic melt chemistry are discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Navigating Large Chemical Spaces Using Graph Theory and Integer Programming

Navigating and analyzing large chemical spaces are necessary to accelerate the design and discovery of new molecules and chemical processes. In this work, we introduce a computational framework that integrates graph theory and integer programming to enable the efficient navigation of large chemical spaces. Our framework represents the chemical space as a graph, wherein nodes represent molecules and edges represent the degree of similarity or connectivity based on domain-specific information. Using the graph representation, we identify representative molecules by computing the so-called minimum dominating set (MDS), which in our context is the minimum set of molecules that is connected to all other molecules. We present a suite of solution strategies for the MDS problem including heuristic and rigorous integer programming (IP) approaches. We show that these approaches allow us to capture physicochemical properties and domain-specific logic and constraints, facilitating the identification of molecules with the target properties. We demonstrate the effectiveness of the proposed approach by navigating the chemical space of per- and polyfluoroalkyl substances (PFAS); this comprises approximately 15,000 molecular structures. We compare our framework against traditional dimensionality reduction and clustering methods such as t-SNE and K-means clustering.

Chemical structure↗
DOE OSTI2022

Multitask Machine Learning of Collective Variables for Enhanced Sampling of Rare Events

Computing accurate reaction rates is a central challenge in computational chemistry and biology because of the high cost of free energy estimation with unbiased molecular dynamics. In this work, a data-driven machine learning algorithm is devised to learn collective variables with a multitask neural network, where a common upstream part reduces the high dimensionality of atomic configurations to a low dimensional latent space and separate downstream parts map the latent space to predictions of basin class labels and potential energies. Here, the resulting latent space is shown to be an effective low-dimensional representation, capturing the reaction progress and guiding effective umbrella sampling to obtain accurate free energy landscapes. This approach is successfully applied to model systems including a 5D Müller Brown model, a 5D three-well model, the alanine dipeptide in vacuum, and an Au(110) surface reconstruction unit reaction. It enables automated dimensionality reduction for energy controlled reactions in complex systems, offers a unified and data-efficient framework that can be trained with limited data, and outperforms single-task learning approaches, including autoencoders.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

First-Principles Characterization of Surface Phonons of Halide Perovskite CsPbI 3 and Their Role in Stabilization

The stability of halide perovskites has been a long-standing issue for their real-world application. Approaches to improve stability include nanostructuring, dimensionality reduction, and strain engineering, where surfaces play an important role in the formation of a stable structure. To understand the mechanism we compute the lattice dynamics of the surface of CsPbI 3 using density functional theory. We demonstrate, for the first time, that CsPbI 3 crystals exhibit surface phonons that are localized on the outermost layers of the slabs, and we perform a complete symmetry characterization including an identification of the Raman/IR active modes. These surface phonons are present in the optically active cubic phase but are absent in the optically inactive "yellow" phase. Furthermore, we show that the surface suppresses bulk instabilities by hardening soft modes of the bulk cubic phase, resulting in phase stabilization and quenching of dynamical disorder. Finally, this study is fundamental for understanding the structural behavior of halide perovskite materials with high surface area-to-volume ratios, and for guiding stabilization strategies.

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

Effect of Co/SiO 2 Single-Site Heterogeneity on Small Alkane Dehydrogenation Kinetics

Atomically dispersed, high-spin Co(II) atoms in distorted tetrahedral coordination to an amorphous silica (am-SiO 2 ) support, and more recently in zeolite frameworks, are active and selective for light alkane dehydrogenation. This paper investigates how variations in the geometry of the active sites affect the ethane dehydrogenation activity of atomically dispersed Co(II) on an am-SiO 2 support. We generate a distribution of sites and determine the geometric parameters that exhibit the strongest correlation with the coordination geometry and activity of the metal atom by means of linear dimensionality reduction techniques. We perform electronic structure calculations and microkinetic modeling and deduce the mechanism and kinetics for a representative sample of sites. Irrespective of the active site geometry, the rate of ethane dehydrogenation is governed by the β-hydride elimination, which involves quartet-doublet spin-crossing and proceeds adiabatically due to strong spin-orbit coupling. Informed by the complete microkinetic analysis of the sites, we derive the reduced rate expression as a function of three site-dependent quantities. We show that these site-dependent quantities correlate with the energy of formation of the ethyl intermediate that forms via C-H bond activation. This correlation allows us to derive the site-averaged rate for the entire distribution of sites. Among various sites, the tri-coordinate and planar tetra-coordinate Co sites exhibit higher Lewis acidity than the tetrahedral sites, and consequently, higher initial rates. Finally, we discuss the implications for more active catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Data Analytics for Catalysis Predictions: Are We Ready Yet?

Catalysis informatics has received tremendous attention in recent years as a tool to design catalysts and discover unique descriptors that capture the relationships between chemical properties and catalytic performance. One of the stop-gaps in understanding catalytic effects, which is often ignored and limits the deployment of data science tools, relates to the lack of uniform data. The catalytic cleavage of C–X (X= H, C, N, and O) bonds is relevant to many fundamental catalytic processes. In this Perspective, we performed data analytics on four groups of C–X cleavage reactions that are common in production, upcycling, or reactive separation: the C–C cleavage in cyclopropyl alcohol, the C–H cleavage in hydroacylation reactions, the C–O cleavage in β-O-4 linkages, and the C–N cleavage in amides, using experimental data collected from the literature to understand their underlying correlations. Experimental variables of high impact are identified for each reaction by dimensionality reduction methods. We highlight the urgent need for experimental data sets that include full details on the reaction conditions, such as reagent concentration, reaction temperature, or time in machine-readable forms. We discuss the potential improvement of the data of these reactions and promising approaches such as autonomous experiments to fill the gaps in unbiased experimental data. Finally, we also address the early stage consideration of separation aspects in the experimental design of efficient catalytic systems for these fundamental examples of chemical reactivity.

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

Conjugated Metal–Organic Macrocycles: Synthesis, Characterization, and Electrical Conductivity

The dimensional reduction of solids into smaller fragments provides a route to achieve new physical properties and gain deeper insight into the extended parent structures. Here, we report the synthesis of CuTOTP-OR (TOTP n – = 2,3,6,7-tetraoxidotriphenylene), a family of copper-based macrocycles that resemble truncated fragments of the conductive 2D metal–organic framework Cu 3 (HHTP) 2 (HHTP = 2,3,6,7,10,11-hexahydroxytriphenylene). The planar metal–organic macrocycles self-assemble into ordered nanotubes with internal diameters of ~2 nm and short interlayer distances of ~3.20 Å. Strong π–π stacking interactions between macrocycles facilitate out-of-plane charge transport, and pressed pellet conductivities as high as 2(1)×10 -3 S cm -1 are observed. Peripheral alkyl functionalization enhances solution processability and enables the fabrication of thin-film field-effect transistor devices. Ambipolar charge transport is observed, suggesting similar behavior may be operative in Cu 3 (HHTP) 2 . By coupling the attractive features of metal–organic frameworks with greater processability, these macrocycles enable facile device integration and a more nuanced understanding of out-of-plane charge transport in 2D conductive metal–organic frameworks.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Robust Predictive Design of Field Measurements for Evapotranspiration Barriers Using Universal Multiple linear Regression

Surface barriers are normally installed to reduce downward water movement into contaminated zones. Specifically, evapotranspiration (ET) barriers are used to store water and release it, via ET, before it can percolate into an underlying waste zone. To assess the effectiveness of a surface barrier, we used an existing data set, model-simulated data, and a dimensionality reduction approach called universal multiple linear regression (uMLR) to optimize the required number of sensors in a 2-m thick surface barrier. To understand the usefulness of implementing predictive uMLR to accommodate multiple monitoring objectives, we compare several network designs, selected based on down-sampling of existing data, with a recommended sensor design based on model simulations performed without consideration of existing data. We further added consideration of “fuzzy” design, which allows more practical guidelines for field implementation of uMLR. We discovered that uMLR, combined with robust decision-making, provides a simple, flexible, and high-quality network design for monitoring the total water stored in a surface barrier across multiple uncertain conditions.

58 GEOSCIENCES↗
DOE OSTI2024

Reduced‐Order Probabilistic Emulation of Physics‐Based Ring Current Models: Application to RAM‐SCB Particle Flux

Abstract In this work, we address the computational challenge of large‐scale physics‐based simulation models for the ring current. Reduced computational cost allows for significantly faster than real‐time forecasting, enhancing our ability to predict and respond to dynamic changes in the ring current, valuable for space weather monitoring and mitigation efforts. Additionally, it can also be used for a comprehensive investigation of the system. Thus, we aim to create an emulator for the Ring current‐Atmosphere interactions Model with Self‐Consistent magnetic field (RAM‐SCB) particle flux that not only improves efficiency but also facilitates forecasting with reliable estimates of prediction uncertainties. The probabilistic emulator is built upon the methodology developed by Licata and Mehta (2023), https://doi.org/10.1029/2022sw003345 . A novel discrete sampling is used to identify 30 simulation periods over 20 years of solar and geomagnetic activity. Focusing on a subset of particle flux, we use Principal Component Analysis for dimensionality reduction and Long Short‐Term Memory (LSTM) neural networks to perform dynamic modeling. Hyperparameter space was explored extensively resulting in about 5% median symmetric accuracy across all data sets for one‐step dynamic prediction. Using a hierarchical ensemble of LSTMs, we have developed a reduced‐order probabilistic emulator (ROPE) tailored for time‐series forecasting of particle flux in the ring current. This ROPE offers accurate predictions of omnidirectional flux at a single energy with no pitch angle information, providing robust predictions on the test set with an error score below 11% and calibration scores under 8% with bias under 2% providing a significant speed up as compared to the full RAM‐SCB run.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Performance efficient macromolecular mechanics via sub-nanometer shape based coarse graining

Dimensionality reduction via coarse grain modeling is a valuable tool in biomolecular research. For large assemblies, ultra coarse models are often knowledge-based, relying on a priori information to parameterize models thus hindering general predictive capability. Here, we present substantial advances to the shape based coarse graining (SBCG) method, which we refer to as SBCG2. SBCG2 utilizes a revitalized formulation of the topology representing network which makes high-granularity modeling possible, preserving atomistic details that maintain assembly characteristics. Further, we present a method of granularity selection based on charge density Fourier Shell Correlation and have additionally developed a refinement method to optimize, adjust and validate high-granularity models. We demonstrate our approach with the conical HIV-1 capsid and heteromultimeric cofilin-2 bound actin filaments. Our approach is available in the Visual Molecular Dynamics (VMD) software suite, and employs a CHARMM-compatible Hamiltonian that enables high-performance simulation in the GPU-resident NAMD3 molecular dynamics engine.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Active learning of ternary alloy structures and energies

Abstract Machine learning models with uncertainty quantification have recently emerged as attractive tools to accelerate the navigation of catalyst design spaces in a data-efficient manner. Here, we combine active learning with a dropout graph convolutional network (dGCN) as a surrogate model to explore the complex materials space of high-entropy alloys (HEAs). We train the dGCN on the formation energies of disordered binary alloy structures in the Pd-Pt-Sn ternary alloy system and improve predictions on ternary structures by performing reduced optimization of the formation free energy, the target property that determines HEA stability, over ensembles of ternary structures constructed based on two coordinate systems: (a) a physics-informed ternary composition space, and (b) data-driven coordinates discovered by the Diffusion Maps manifold learning scheme. Both reduced optimization techniques improve predictions of the formation free energy in the ternary alloy space with a significantly reduced number of DFT calculations compared to a high-fidelity model. The physics-based scheme converges to the target property in a manner akin to a depth-first strategy, whereas the data-driven scheme appears more akin to a breadth-first approach. Both sampling schemes, coupled with our acquisition function, successfully exploit a database of DFT-calculated binary alloy structures and energies, augmented with a relatively small number of ternary alloy calculations, to identify stable ternary HEA compositions and structures. This generalized framework can be extended to incorporate more complex bulk and surface structural motifs, and the results demonstrate that significant dimensionality reduction is possible in thermodynamic sampling problems when suitable active learning schemes are employed.

Chemistry↗
DOE OSTI2020

The ANI-1ccx and ANI-1x data sets, coupled-cluster and density functional theory properties for molecules

Abstract Maximum diversification of data is a central theme in building generalized and accurate machine learning (ML) models. In chemistry, ML has been used to develop models for predicting molecular properties, for example quantum mechanics (QM) calculated potential energy surfaces and atomic charge models. The ANI-1x and ANI-1ccx ML-based general-purpose potentials for organic molecules were developed through active learning; an automated data diversification process. Here, we describe the ANI-1x and ANI-1ccx data sets. To demonstrate data diversity, we visualize it with a dimensionality reduction scheme, and contrast against existing data sets. The ANI-1x data set contains multiple QM properties from 5 M density functional theory calculations, while the ANI-1ccx data set contains 500 k data points obtained with an accurate CCSD(T)/CBS extrapolation. Approximately 14 million CPU core-hours were expended to generate this data. Multiple QM calculated properties for the chemical elements C, H, N, and O are provided: energies, atomic forces, multipole moments, atomic charges, etc. We provide this data to the community to aid research and development of ML models for chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Neural network-based order parameter for phase transitions and its applications in high-entropy alloys

Phase transition is one of the most important phenomena in nature and plays a central role in materials design. All phase transitions are characterized by suitable order parameters, including the order–disorder phase transition. However, finding a representative order parameter for complex systems is non-trivial, such as for high-entropy alloys. Given the strength of dimensionality reduction of a variational autoencoder (VAE), we introduce a VAE-based order parameter. Here, we propose that the Manhattan distance in the VAE latent space can serve as a generic order parameter for order–disorder phase transitions. The physical properties of our order parameter are quantitatively interpreted and demonstrated by multiple refractory high-entropy alloys. Using this order parameter, a generally applicable alloy design concept is proposed by mimicking the natural mixing process of elements. Our physically interpretable VAE-based order parameter provides a computational technique for understanding chemical ordering in alloys, which can facilitate the development of rational alloy design strategies.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Seeking regularity from irregularity: unveiling the synthesis–nanomorphology relationships of heterogeneous nanomaterials using unsupervised machine learning

Nanoscale morphology of functional materials determines their chemical and physical properties. However, despite increasing use of transmission electron microscopy (TEM) to directly image nanomorphology, it remains challenging to quantify the information embedded in TEM data sets, and to use nanomorphology to link synthesis and processing conditions to properties. We develop an automated, descriptor-free analysis workflow for TEM data that utilizes convolutional neural networks and unsupervised learning to quantify and classify nanomorphology, and thereby reveal synthesis–nanomorphology relationships in three different systems. While TEM records nanomorphology readily in two-dimensional (2D) images or three-dimensional (3D) tomograms, we advance the analysis of these images by identifying and applying a universal shape fingerprint function to characterize nanomorphology. After dimensionality reduction through principal component analysis, this function then serves as the input for morphology grouping through unsupervised learning. We demonstrate the wide applicability of our workflow to both 2D and 3D TEM data sets, and to both inorganic and organic nanomaterials, including tetrahedral gold nanoparticles mixed with irregularly shaped impurities, hybrid polymer-patched gold nanoprisms, and polyamide membranes with irregular and heterogeneous 3D crumple structures. In each of these systems, unsupervised nanomorphology grouping identifies both the diversity and the similarity of the nanomaterial across different synthesis conditions, revealing how synthetic parameters guide nanomorphology development. Our work opens possibilities for enhancing synthesis of nanomaterials through artificial intelligence and for understanding and controlling complex nanomorphology, both for 2D systems and in the far less explored case of 3D structures, such as those with embedded voids or hidden interfaces.

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

Unsupervised learning of representative local atomic arrangements in molecular dynamics data

Molecular dynamics (MD) simulations present a data-mining challenge, given that they can generate a considerable amount of data but often rely on limited or biased human interpretation to examine their information content. By not asking the right questions of MD data we may miss critical information hidden within it. Here we combine dimensionality reduction (UMAP) and unsupervised hierarchical clustering (HDBSCAN) to quantitatively characterize prevalent coordination environments of chemical species within MD data. By focusing on local coordination, we significantly reduce the amount of data to be analyzed by extracting all distinct molecular formulas within a given coordination sphere. We then efficiently combine UMAP and HDBSCAN with alignment or shape-matching algorithms to partition these formulas into structural isomer families indicating their relative populations. The method was employed to reveal details of cation coordination in electrolytes based on molecular liquids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗