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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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At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

BETO 2021 Peer Review - Advanced Catalyst Synthesis and Characterization (ACSC) Project WBS 2.5.4.304; 303; 305

The Advanced Catalyst Synthesis and Characterization (ACSC) project, in close collaboration with the Chemical Catalysis for Bioenergy (ChemCatBio) Consortium enabling projects, CatCost, and the Engineering of Catalyst Scale-Up project, (1) provides fundamental insight into working catalysts leading to actionable recommendations for all of the ChemCatBio catalysis projects, (2) addresses overarching catalysis challenges central to the ChemCatBio Consortium, and (3) adapts and applies new synthesis methodologies and in situ/operando characterization capabilities to meet the evolving needs of the catalysis projects. The outcome is a transition from empirical catalyst development to rational design through the prediction of materials with targeted properties based on advanced characterization combined with computational modeling, and the synthesis of next generation catalysts with predicted structures that yield demonstrated improvements in catalytic performance. In FY18, the ACSC helped to demonstrate the utility of the complete catalyst and process development cycle for dimethyl ether to high-octane gasoline over metal-modified zeolite catalysts for the Upgrading of C1 Building Blocks project, and in FY21 will leverage capabilities, expertise, and computational models established for this effort to target next-generation catalysts for ethanol to distillates for the Upgrading of C2 Intermediates project with enhanced performance in half the time.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2023

DIPS-Plus: The enhanced database of interacting protein structures for interface prediction

Abstract In this work, we expand on a dataset recently introduced for protein interface prediction (PIP), the Database of Interacting Protein Structures (DIPS), to present DIPS-Plus, an enhanced, feature-rich dataset of 42,112 complexes for machine learning of protein interfaces. While the original DIPS dataset contains only the Cartesian coordinates for atoms contained in the protein complex along with their types, DIPS-Plus contains multiple residue-level features including surface proximities, half-sphere amino acid compositions, and new profile hidden Markov model (HMM)-based sequence features for each amino acid, providing researchers a curated feature bank for training protein interface prediction methods. We demonstrate through rigorous benchmarks that training an existing state-of-the-art (SOTA) model for PIP on DIPS-Plus yields new SOTA results, surpassing the performance of some of the latest models trained on residue-level and atom-level encodings of protein complexes to date.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Prediction of α $IIb$ $β$ 3 integrin structures along its minimum free energy activation pathway

The adhesion protein integrin is a transmembrane heterodimer that plays a pivotal role in cellular processes such as cell signaling and cell migration. To execute its function, integrin undergoes extensive conformational changes from a bent-closed to an extended-open state. Resolving the structures across these changes remains a challenge with both experimental and computational methods, but it is crucial for understanding the activation mechanism of integrin. We address this challenge for the platelet integrin α IIb β 3 by employing finite temperature string method with structures of the images along the initial guess path generated by a multiscale data-driven framework. The full-length all-atom structures along the resulting minimum free energy path between the inactive bent-closed and active extended-open states of α IIb β 3 integrin are consistent with a variety of experimentally resolved structures. Changes in these predicted structures along the path show that the extension and separation of the α and β subunits from the bent-closed to the extended-open state require correlated movements between the subdomain pairs in α IIb β 3 . Furthermore, these results provide new insights into integrin activation mechanism, and the predicted structures have potential applications in guiding the design of integrin-targeting therapeutics.

Dasetty, Siva [University of Chicago, IL (United S↗
DOE OSTI2021

Structural- and Functional-Informed Machine Learning for Protein Function Prediction

In this project we aimed to extend methods for protein function prediction to include structural prediction data, and benchmark methods against existing tools. We proposed to apply the method to large metagenome datasets, and develop approaches to examine activity-based protein profiling results for protein function-structure patterns. Nitrogen cycle protein families were previously identified and are used here to provide a proof-of-principle for use of structure prediction in protein function classification.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Random forest prediction of crystal structure from electron diffraction patterns incorporating multiple scattering

Diffraction is the most common method to solve for unknown or partially known crystal structures. However, it remains a challenge to determine the crystal structure of a new material that may have nanoscale size or heterogeneities. Here, in this study, we train an architecture of hierarchical random forest models capable of predicting the crystal system, space group, and lattice parameters from one or more unknown two-dimensional electron diffraction patterns. Our initial model correctly identifies the crystal system of a simulated electron diffraction pattern from a 20-nm-thick specimen of arbitrary orientation 67% of the time. We achieve a topline accuracy of 79% when aggregating predictions from ten patterns of the same material but different zone axes. The space group and lattice predictions range from 70% to 90% accuracy and median errors of 0.01-0.5Å, respectively, for cubic, hexagonal, trigonal, and tetragonal crystal systems while being less reliable on orthorhombic and monoclinic systems. We apply this architecture to a four-dimensional scanning transmission electron microscopy scan of gold nanoparticles, where it accurately predicts the crystal structure and lattice constants. These random forest models can be used to significantly accelerate the analysis of electron diffraction patterns, particularly in the case of unknown crystal structures. Additionally, due to the speed of inference, these models could be integrated into live transmission electron microscopy experiments, allowing real-Time labeling of a specimen.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Improved Predictive Tools for Structural Properties of Metal–Organic Frameworks

The accurate determination of structural parameters is necessary to understand the electronic and magnetic properties of metal–organic frameworks (MOFs) and is a first step toward accurate calculations of electronic structure and function for separations and catalysis. Theoretical structural determination of metal-organic frameworks is particularly challenging because they involve ionic, covalent, and noncovalent interactions, which must be treated in a balanced fashion. Here, we apply a diverse group of local exchange-correlation functionals (PBE, PBEsol, PBE-D2, PBE-D3, vdW-DF2, SOGGA, MN15-L, revM06-L, SCAN, and revTPSS) to a broad test set of MOFs to seek the most accurate functionals to study various structural aspects of porous solids, in particular to study lattice constants, unit cell volume, two types of pore size characteristics, bond lengths, bond angles, and torsional angles). The recently developed meta functionals revM06-L and SCAN, without adding any molecular mechanics terms, are able to predict more accurate structures than previously recommended functionals, both those without molecular mechanics terms (PBE, PBEsol, vdW-DF2, and revTPSS) and those with them (PBE-D2 and PBE-D3). To provide a broader test, these two functionals are also tested for lattice constants and band gaps of unary, binary, and ternary semiconductors.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Development and Validation of a Simulation Tool to Predict the Combined Structural, Electrical, Electrochemical and Thermal Responses of Automotive Batteries

Battery safety is one of the most important design factors of electrified vehicles (EVs) since battery failure may lead to a catastrophic consequence. To improve the safety of battery systems in EVs, battery behaviors under various abuse conditions should be well understood. One way to examine battery response under extreme conditions is to conduct abuse tests in different scenarios. They can provide first-hand pass/fail information on battery safety, but they are usually expensive and time-consuming, which is inconvenient during design iterations and optimization. On the other hand, computational modeling can predict the battery behaviors in a more efficient and cost-effective way, which becomes an important tool to evaluate battery safety. Modeling battery responses and failure is challenging since it involves multiple coupled physical processes, needs to consider complex material properties and is computationally intensive. This project aims to develop a practical simulation tool to predict the combined structural, electrical, electrochemical, and thermal responses of automotive batteries to crash-induced crush and short circuit and validate it for conditions relevant to automotive crash. Advanced material constitutive models will be utilized to capture the mechanical response of cell components. Moreover, methods will be developed to reduce computational complexity of the model and allow battery safety simulations to extend from cell-level to module/pack level with affordable computational resources.

25 ENERGY STORAGE↗
DOE OSTI2023

TwoFold: Highly accurate structure and affinity prediction for protein-ligand complexes from sequences

We describe our development of ab initio protein-ligand binding pose prediction models based on transformers and binding affinity prediction models based on the neural tangent kernel (NTK). Folding both protein and ligand, the TwoFold models achieve efficient and quality predictions matching state-of-the-art implementations while additionally reconstructing protein structures. In conclusion, solving NTK models points to a new use case for highly optimized linear solver benchmarking codes on HPC.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

High-Performance Deep Learning Toolbox for Genome-Scale Prediction of Protein Structure and Function

Computational biology is one of many scientific disciplines ripe for innovation and acceleration with the advent of high-performance computing (HPC). In recent years, the field of machine learning has also seen significant benefits from adopting HPC practices. In this work, we present a novel HPC pipeline that incorporates various machine-learning approaches for structure-based functional annotation of proteins on the scale of whole genomes. Our pipeline makes extensive use of deep learning and provides computational insights into best practices for training advanced deep-learning models for high-throughput data such as proteomics data. We showcase methodologies our pipeline currently supports and detail future tasks for our pipeline to envelop, including large-scale sequence comparison using SAdLSA and prediction of protein tertiary structures using AlphaFold2.

Gao, Mu↗
DOE OSTI2024

Deep Learning Prediction of Protein Complex Structures

Proteins interact to form protein complex to carry out biological functions such as catalytic chemical reaction. Therefore, it is important to develop computational methods to predict protein-protein interaction and the structures of protein complexes to study and enhance protein function. In this project, we successfully developed several deep learning methods to predict inter-protein contacts and the reinforcement learning and optimization methods to reconstruct protein complex structures from predicted inter-chain contacts. The methods were integrated with the MULTICOM protein complex structure prediction system and applied to predict the complex structures of biomass production-related proteins of green algae. During the two and a half years of research and development, all the specific milestones of the project were achieved successfully. 16 publications/manuscripts were produced. 10 software tools were developed. A patent application was submitted. Our MULTICOM predictors leveraging some tools developed in this project were ranked among the top predictors in the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) in 2022.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Short-term traffic state prediction from latent structures: Accuracy vs. efficiency

Recently, deep learning models have shown promising performances in many research areas, including traffic states prediction, due to their ability to model complex nonlinear relationships. However, deep learning models also have drawbacks that make them less preferable for certain short-term traffic prediction applications. For example, they require a large amount of data for model training, which is also computationally expensive. Moreover, deep learning models lack interpretability of the results. This paper develops a short-term traffic states forecasting algorithm based on partial least square (PLS) to help enhance real-time decision-making and build better insights into traffic data. The proposed model is capable of predicting short-term traffic states accurately and efficiently by capturing dominant spatiotemporal features and day-to-day variations from collinear and correlated traffic data. Three case studies are developed to demonstrate the proposed model in short-term traffic prediction applications.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2026

Virtual Growth of SRF Materials: A Machine Learning Approach to Predict the Crystalline Structural Ordering in Nb Surface Oxides

Niobium's native surface oxide affects SRF cavity and superconducting qubit performance, motivating interest in controlling its crystalline structure. We combine a literature-derived machine-learning analysis with temperature-dependent XRD to study crystalline ordering in Nb2O5. Random Forest models, trained on 74 processing conditions from 17 papers and validated by leave-one-group-out cross-validation, predicted broad crystallinity outcomes well (balanced accuracy 0.809), but struggled with specific polymorph identity (0.577). Annealing temperature was the dominant predictor across all targets; oxygen partial pressure showed negligible importance, reflecting narrow literature coverage rather than physical irrelevance. Temperature-dependent XRD on anodized and H2O2-treated Niobium showed structural evolution consistent with the machine learning predictions. Our model and overall approach provide a data-driven framework for identifying and optimizing conditions that promote crystallization in initially amorphous oxides. This framework can guide the selection of growth and post-annealing conditions for Nb surfaces by narrowing the experimental parameter space, thereby reducing trial-and-error efforts in developing oxide structures relevant to SRF applications.

Tilkin, Anthony [Unlisted, US, IL; Fermilab]↗
DOE OSTI2025

A structured framework for predicting sustainable aviation fuel properties using liquid-phase FTIR and machine learning

Sustainable aviation fuels have the potential to improve efficiency, reduce emissions, and enhance energy security. To help identify viable sustainable aviation fuels and accelerate research, machine learning models have been developed to predict relevant physicochemical properties. However, many models have limited applicability, leverage data from complex analytical techniques with confined spectral ranges, or use feature decomposition methods that offer limited interpretability. Using liquid-phase Fourier Transform Infrared (FTIR) spectra, this study presents a structured method for creating accurate and interpretable property prediction models for neat molecules, aviation fuels, and blends. Liquid FTIR spectra can be collected quickly and consistently, offering high reliability, sensitivity, and component specificity using less than 2 ml of sample. The method first decomposes FTIR spectra into fundamental building blocks using non-negative matrix factorization (NMF) to enable scientific analysis of FTIR spectra attributes and fuel properties. The NMF features are then used to create five ensemble models for predicting final boiling point, flash point, freezing point, density at 15°C, and kinematic viscosity at -20°C. All models were trained using experimental property data from neat molecules, aviation fuels, and blends. The models accurately predict key properties across a broad range of neat molecules and representative fuels and blends, while enabling interpretation of relationships between compositional elements, such as functional groups or chemical classes, and their resulting properties. This demonstrates strong potential to support sustainable aviation fuel research and development. The models and data are available on an interactive web tool.

Fourier transform infrared spectroscopy↗
DOE OSTI2022

Deep learning-based quasi-continuum theory for structure of confined fluids

Predicting the structural properties of water and simple fluids confined in nanometer scale pores and channels is essential in, for example, energy storage and biomolecular systems. Classical continuum theories fail to accurately capture the interfacial structure of fluids. In this work, we develop a deep learning-based quasi-continuum theory (DL-QT) to predict the concentration and potential profiles of a Lennard-Jones (LJ) fluid and water confined in a nanochannel. The deep learning model is built based on a convolutional encoder–decoder network (CED) and is applied for high-dimensional surrogate modeling to relate the fluid properties to the fluid–fluid potential. The CED model is then combined with the interatomic potential-based continuum theory to determine the concentration profiles of a confined LJ fluid and confined water. Further, we show that the DL-QT model exhibits robust predictive performance for a confined LJ fluid under various thermodynamic states and for water confined in a nanochannel of different widths. The DL-QT model seamlessly connects molecular physics at the nanoscale with continuum theory by using a deep learning model.

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

Topological structure of complex predictions

Abstract Current complex prediction models are the result of fitting deep neural networks, graph convolutional networks or transducers to a set of training data. A key challenge with these models is that they are highly parameterized, which makes describing and interpreting the prediction strategies difficult. We use topological data analysis to transform these complex prediction models into a simplified topological view of the prediction landscape. The result is a map of the predictions that enables inspection of the model results with more specificity than dimensionality-reduction methods such as tSNE and UMAP. The methods scale up to large datasets across different domains. We present a case study of a transformer-based model previously designed to predict expression levels of a piece of DNA in thousands of genomic tracks. When the model is used to study mutations in the BRCA1 gene, our topological analysis shows that it is sensitive to the location of a mutation and the exon structure of BRCA1 in ways that cannot be found with tools based on dimensionality reduction. Moreover, the topological framework offers multiple ways to inspect results, including an error estimate that is more accurate than model uncertainty. Further studies show how these ideas produce useful results in graph-based learning and image classification.

Computer Science↗