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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 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Characterizing Signatures of Geothermal Exploration Data with Machine Learning Techniques: An Application to the Nevada Play Fairway Analysis

We are introducing machine learning methods to the play fairway analysis to generate geothermal potential maps to support the evaluation of geothermal resource potential and the exploration for undiscovered blind geothermal systems in the Nevada Great Basin region. Our project aims to identify new ways to combine the play fairway data and empirically organize relationships between feature weights and labels in an improved workflow. As a means of doing this, we introduce machine learning methods to evaluate the influence of certain geological and geophysical features/feature sets in predicting geothermal favorability. This report highlights promising approaches based on supervised and unsupervised learning methods. First, we demonstrate a filter method applied to supervised classification modeling. The supervised filter method is based on permutation analysis to evaluate every possible feature combination/drop out scenario and rank feature influence based on the performance variance of supervised classification models. Additionally, we present an unsupervised factor analysis based on principal component analysis coupled with a semi-supervised kmeans clustering algorithm. This analysis allows us to identify the optimal number of groups/clusters for training sites and structural settings to identify feature patterns including correlation, variance, and latent and dominant feature relationships. The results from these methods offer a promising avenue for identifying favorable sources of predictive information to identify the locations of blind geothermal systems and furthering our understanding of complex geothermal feature and label relationships in the Great Basin region and beyond.

15 GEOTHERMAL ENERGY↗
DOE OSTI2020

Structure–activity relationship-based chemical classification of highly imbalanced Tox21 datasets

Abstract The specificity of toxicant-target biomolecule interactions lends to the very imbalanced nature of many toxicity datasets, causing poor performance in Structure–Activity Relationship (SAR)-based chemical classification. Undersampling and oversampling are representative techniques for handling such an imbalance challenge. However, removing inactive chemical compound instances from the majority class using an undersampling technique can result in information loss, whereas increasing active toxicant instances in the minority class by interpolation tends to introduce artificial minority instances that often cross into the majority class space, giving rise to class overlapping and a higher false prediction rate. In this study, in order to improve the prediction accuracy of imbalanced learning, we employed SMOTEENN, a combination of Synthetic Minority Over-sampling Technique (SMOTE) and Edited Nearest Neighbor (ENN) algorithms, to oversample the minority class by creating synthetic samples, followed by cleaning the mislabeled instances. We chose the highly imbalanced Tox21 dataset, which consisted of 12 in vitro bioassays for > 10,000 chemicals that were distributed unevenly between binary classes. With Random Forest (RF) as the base classifier and bagging as the ensemble strategy, we applied four hybrid learning methods, i.e., RF without imbalance handling (RF), RF with Random Undersampling (RUS), RF with SMOTE (SMO), and RF with SMOTEENN (SMN). The performance of the four learning methods was compared using nine evaluation metrics, among which F 1 score, Matthews correlation coefficient and Brier score provided a more consistent assessment of the overall performance across the 12 datasets. The Friedman’s aligned ranks test and the subsequent Bergmann-Hommel post hoc test showed that SMN significantly outperformed the other three methods. We also found that a strong negative correlation existed between the prediction accuracy and the imbalance ratio (IR), which is defined as the number of inactive compounds divided by the number of active compounds. SMN became less effective when IR exceeded a certain threshold (e.g., > 28). The ability to separate the few active compounds from the vast amounts of inactive ones is of great importance in computational toxicology. This work demonstrates that the performance of SAR-based, imbalanced chemical toxicity classification can be significantly improved through the use of data rebalancing.

Idakwo, Gabriel↗
NASA NTRS2013

Probabilistic Analysis for Comparing Fatigue Data Based on Johnson-Weibull Parameters

Leonard Johnson published a methodology for establishing the confidence that two populations of data are different. Johnson's methodology is dependent on limited combinations of test parameters (Weibull slope, mean life ratio, and degrees of freedom) and a set of complex mathematical equations. In this report, a simplified algebraic equation for confidence numbers is derived based on the original work of Johnson. The confidence numbers calculated with this equation are compared to those obtained graphically by Johnson. Using the ratios of mean life, the resultant values of confidence numbers at the 99 percent level deviate less than 1 percent from those of Johnson. At a 90 percent confidence level, the calculated values differ between +2 and 4 percent. The simplified equation is used to rank the experimental lives of three aluminum alloys (AL 2024, AL 6061, and AL 7075), each tested at three stress levels in rotating beam fatigue, analyzed using the Johnson- Weibull method, and compared to the ASTM Standard (E739 91) method of comparison. The ASTM Standard did not statistically distinguish between AL 6061 and AL 7075. However, it is possible to rank the fatigue lives of different materials with a reasonable degree of statistical certainty based on combined confidence numbers using the Johnson- Weibull analysis. AL 2024 was found to have the longest fatigue life, followed by AL 7075, and then AL 6061. The ASTM Standard and the Johnson-Weibull analysis result in the same stress-life exponent p for each of the three aluminum alloys at the median, or L(sub 50), lives

Vlcek, Brian L.↗
DOE OSTI2023

Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15

To enhance the AlphaFold-Multimer-based protein complex structure prediction, we developed a quaternary structure prediction system (MULTICOM) to improve the input fed to AlphaFold-Multimer and evaluate and refine its outputs. MULTICOM samples diverse multiple sequence alignments (MSAs) and templates for AlphaFold-Multimer to generate structural predictions by using both traditional sequence alignments and Foldseek-based structure alignments, ranks structural predictions through multiple complementary metrics, and refines the structural predictions via a Foldseek structure alignment-based refinement method. The MULTICOM system with different implementations was blindly tested in the assembly structure prediction in the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) in 2022 as both server and human predictors. MULTICOM_qa ranked 3 rd among 26 CASP15 server predictors and MULTICOM_human ranked 7 th among 87 CASP15 server and human predictors. The average TM-score of the first predictions submitted by MULTICOM_qa for CASP15 assembly targets is ~0.76, 5.3% higher than ~0.72 of the standard AlphaFold-Multimer. The average TM-score of the best of top 5 predictions submitted by MULTICOM_qa is ~0.80, about 8% higher than ~0.74 of the standard AlphaFold-Multimer. Moreover, the Foldseek Structure Alignment-based Multimer structure Generation (FSAMG) method outperforms the widely used sequence alignment-based multimer structure generation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Bayesian High-Rank Hankel Matrix Completion for Nonlinear Synchrophasor Data Recovery

Phasor measurement units (PMUs) provide high temporal-resolution synchrophasor measurements for power system monitoring and control. The frequent data quality issues, such as missing and bad data, prevent the incorporation of synchrophasor data in real-time operations. Most existing data-driven data recovery methods assume the power system dynamics can be approximated by a linear dynamical system, and the recovery performance degrades significantly when the power system is experiencing nonlinear dynamics during significant events. Here, this paper proposes a data-driven Bayesian nonlinear synchrophasor data recovery method (Ba-NSDR) that can recover a consecutive time period of simultaneous data losses or errors across all channels, even when the underlying system is highly nonlinear. The idea is to lift the Hankel matrix of the spatial-temporal synchrophasor data to a higher dimension such that the lifted Hankel matrix is low-rank in that space and can be processed with the kernel trick. Our proposed Bayesian method then infers the probabilistic distributions of synchrophasor from the partial observations. Some distinctive features of Ba-NSDR include an uncertainty index to measure the accuracy of the recovery result and the robustness to parameter selections. Our method is verified on both synthetic and recorded event datasets.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2020

Risk Importance Ranking of Fire Data Parameters to Enhance Fire PRA Model Realism

Fire is historically and analytically a significant contributor to nuclear power plant risk. The level of fire risk and the methods, tools and data for modeling this risk is highly debated by experts. One area of debate is the input data used in fire modeling and how to deal with this data’s high uncertainty. This report outlines initial work performed for determining the key parameters causing this uncertainty and how it propagates into nuclear power plant models. This research paves the way for the development of methods to reduce fire data uncertainty used in modeling. The Nuclear Regulatory Commission has mandated that nuclear power plants perform fire risk modeling. However, there are several issues with the current risk modeling implementation that affect the results. Approved modeling methods can be overly conservative and often do not match plant experience. Also, the data used in the modeling can have high uncertainties and is influenced by expert judgement. To evaluate input data uncertainty, researchers performed an initial review of several fire experiments done at Sandia National Laboratories. Uncertainties for fire data can come from many sources, such as experiment design constraints, environmental conditions, or other plant-specific aspects. There are many different significant and insignificant parameters driving the uncertainty. Additionally, the uncertainty of the different input data used in the fire modeling could have a significant or insignificant effect on the entire plant risk. A four-step methodology was developed to perform Integrated Probabilistic Risk Assessment Importance Ranking. A demonstration case using these steps was set up and three of the four steps were completed in fiscal year (FY) 2019 and the fourth step done FY 2020. These steps are: 1. The qualitative analysis of potential sources was conducted with the following items identified for the demonstration. • Maximum heat release rate • Time to maximum heat release rate • Duration of max heat release rate • Time to decay • Thermal conductivity of concrete • Specific heat of concrete • Density of concrete • Cable jacket thickness 2. A quantitative characterization of dominant sources of uncertainty was performed. A list of distributions and determined values of the dominant sources is shown in Appendix A. 3. A quantitative screening of the potential sources of uncertainty using Morris Elementary Effects Analysis was completed. An experimental model using the physics-based fire modeling tool Fire Dynamics Simulator was developed and coupled with the Risk Analysis Virtual Environment. The Morris analysis identified at least two parameters that can be eliminated as significant contributors (specific heat of concrete and cable jacket thickness). 4. Global importance measure (Global IM) analysis to generate a comprehensive ranking based on their influence on the plant risk. In this research, a moment-independent Global IM is used since it can address (a) uncertainty in the input parameters of the fire model, (b) uncertainty in the risk outputs, and (c) non-linearity and interactions among input parameters in the fire model, more accurately than the correlation-based and variance-based global methods. The observations from the research showed that, depending on the initial and boundary conditions of the fire scenarios, fire-induced damage could have a very small probability and could be dominated by the tail of the uncertainty distribution; hence, the accuracy of the correlation-based and variance-based methods is questionable. The moment-independent Global IM analysis in this research provides a better understanding of how experimental uncertainty data affects industry’s plant models and where improvements in that data will have the largest benefit for improving fire modeling accuracy in causing core damage. Among the five unscreened parameters obtained from the Morris EE analysis, the Global IM analysis results for the case study indicated that max heat release rate and fire location are the most important parameters. The report also outlines benefits of using a unified computational platform that integrates the underlying simulations (e.g., a fire progression model), quantitative screening (using the Morris EE method), and the Global IM analysis. A unified platform can (i) facilitate the ranking of input parameters considering multiple key fire scenarios simultaneously, rather than considering one scenario at a time, (ii) contribute to more explicit and accurate treatment of dependencies at multiple levels of Fire PRA, (iii) facilitate the sampling-based uncertainty quantification for Fire PRA, and (iv) help generating both “industry-wide” and "plant-specific" ranking of uncertainty sources in Fire PRA. Future research should be done to include additional parameters such as detection/suppression or cable fire spread. Adding a PRA software such as SAPHIRE to the RAVEN platform would help with plant model integration and improve treatment of fire-induced dependency. The I-PRA risk importance ranking methodology offered in this report can provide valuable information for efficiently (a) enhancing the realism of Fire PRA for existing plants and (b) supporting the development of Dynamic Fire PRA for advanced reactors and new plants.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Improving protein tertiary structure prediction by deep learning and distance prediction in CASP14

Abstract Substantial progresses in protein structure prediction have been made by utilizing deep‐learning and residue‐residue distance prediction since CASP13. Inspired by the advances, we improve our CASP14 MULTICOM protein structure prediction system by incorporating three new components: (a) a new deep learning‐based protein inter‐residue distance predictor to improve template‐free (ab initio) tertiary structure prediction, (b) an enhanced template‐based tertiary structure prediction method, and (c) distance‐based model quality assessment methods empowered by deep learning. In the 2020 CASP14 experiment, MULTICOM predictor was ranked seventh out of 146 predictors in tertiary structure prediction and ranked third out of 136 predictors in inter‐domain structure prediction. The results demonstrate that the template‐free modeling based on deep learning and residue‐residue distance prediction can predict the correct topology for almost all template‐based modeling targets and a majority of hard targets (template‐free targets or targets whose templates cannot be recognized), which is a significant improvement over the CASP13 MULTICOM predictor. Moreover, the template‐free modeling performs better than the template‐based modeling on not only hard targets but also the targets that have homologous templates. The performance of the template‐free modeling largely depends on the accuracy of distance prediction closely related to the quality of multiple sequence alignments. The structural model quality assessment works well on targets for which enough good models can be predicted, but it may perform poorly when only a few good models are predicted for a hard target and the distribution of model quality scores is highly skewed. MULTICOM is available at https://github.com/jianlin-cheng/MULTICOM_Human_CASP14/tree/CASP14_DeepRank3 and https://github.com/multicom-toolbox/multicom/tree/multicom_v2.0 .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Automated AI-driven Molecular Design for Therapeutic Discovery

In recent years, artificial intelligence and machine learning (AI/ML) approaches have revolutionized the process of designing new therapeutics, enabling scientists to rapidly respond to emerging threats from various pathogens. A prime example is the SARS-CoV-2 main protease, a key target for the development of antiviral inhibitors. In this study, we employed a novel, integrated approach that combines AI-driven iterative design of inhibitor candidates, screening based on physio-chemical properties and toxicity, physics-based computational modeling of protein-inhibitor interactions, and AI-assisted analysis of Native MS biophysical assay and characterization of designed candidates. Our deep learning 3D-scaffold model, which uses an input scaffold as a starting point, generated tens of thousands of compounds while preserving the key scaffold. To optimize these candidates, we calculated a comprehensive set of 136 descriptors, including both 2D and 3D molecular features, for compounds targeting the SARS-CoV-2 Main protease (Mpro) and a neurodegenerative disease-associated protein, cyclophilin (Cyp). The generated compounds were initially filtered based on their properties and then ranked according to their predicted binding affinity using our automated modeling and ML methods. Experimental validation of the Mpro candidates showing inhibitory activity demonstrates that our workflow can expedite the therapeutic discovery.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Hourglass control in staggered-grid hydrodynamics using virtual element stabilization techniques

Numerical simulations using the staggered-grid hydrodynamics (SGH) discretization suffer from hourglass instabilities. In this work, we develop a stabilization method to suppress the hourglass instabilities using techniques from the virtual element method (VEM). The stiffness matrix of the VEM consists of two terms: the consistency matrix which is rank deficient and the stability matrix. Here, we first show that in two dimensions and on general polygons, the stiffness matrix of the SGH is identical to the consistency matrix of the linear VEM for both the diffusion equation and the linear elasticity equation. These analyses explain the origin of the hourglass instabilities of the SGH discretization method, and establish a theoretical foundation for our proposed stabilization method by augmenting the stiffness matrix of the SGH discretization using the VEM stability matrix. Then, we present numerical examples using Lagrangian SGH simulations. The numerical experiments demonstrate that the proposed VEM stabilization method is effective at eliminating hourglass modes in the SGH discretization.

97 MATHEMATICS AND COMPUTING↗
NASA NTRSDate not supplied

Comparative Analysis of Thermal Conversion Technologies for Deep Space Missions

Radioisotope power systems (RPS) utilizing Plutonium-238 as a heat source for thermal-to-electric energy conversion have been used as a reliable power source for NASA’s deep space missions for sixty years. Recent innovations and improvements to thermal energy technologies show potential increases to radioisotope system efficiencies from current measurements of ~5-7% to efficiencies upwards of 20%. This report surveys and ranks recent, innovative thermal-to-electric energy conversion research technologies. Technologies being developed at universities and industry are compared with respect to thermal conversion method and relevant key performance parameters. Key performance parameters are identified as system specific power per kg, efficiency, power output, technology readiness level, and system mass. Analytical Hierarchy Process (AHP) was utilized to create weighted values for each evaluation criterion. The AHP tables combined with decision matrices create table scores for past, present, and potential future systems. The table score was combined with a conversion method score in an adjustable system to add value to flight-proven or well-tested thermal conversion technologies such as thermoelectrics. While the three highest-ranking systems reviewed are currently being developed by NASA’s RPS Program, the additional highest-ranking systems not under-development by RPS could warrant further research.

Radioisotope Power System↗
DOE OSTI2021

OzDES reverberation mapping program: Lag recovery reliability for 6-yr C iv analysis

ABSTRACT We present the statistical methods that have been developed to analyse the OzDES reverberation mapping sample. To perform this statistical analysis we have created a suite of customizable simulations that mimic the characteristics of each source in the OzDES sample. These characteristics include: the variability in the photometric and spectroscopic light curves, the measurement uncertainties, and the observational cadence. By simulating the sources in the OzDES sample that contain the C iv emission line, we developed a set of criteria that rank the reliability of a recovered time-lag depending on the agreement between different recovery methods, the magnitude of the uncertainties, and the rate at which false positives were found in the simulations. These criteria were applied to simulated light curves and these results used to estimate the quality of the resulting Radius–Luminosity relation. We grade the results using three quality levels (gold, silver, and bronze). The input slope of the R–L relation was recovered within 1σ for each of the three quality samples, with the gold standard having the lowest dispersion with a recovered a R–L relation slope of 0.454 ± 0.016 with an input slope of 0.47. Future work will apply these methods to the entire OzDES sample of 771 AGN.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Randomized Algorithms for Low-Rank Matrix and Tensor Decompositions

This paper surveys randomized algorithms in numerical linear algebra for low-rank decompositions of matrices and tensors. The survey begins with a review of classical matrix algorithms that can be accelerated by randomized dimensionality reduction, such as the singular value decomposition (SVD) or interpolative (ID) and CUR decompositions. Recent advances in randomized dimensionality reduction are discussed, including new methods of fast matrix sketching and sampling techniques, which are incorporated into classical matrix algorithms for fast low-rank matrix approximations. The extension of randomized matrix algorithms to tensors is then explored for several low-rank tensor decompositions in the CP and Tucker formats, including the higher-order SVD, ID, and CUR decomposition.

Pearce, Katherine J. [The University of Texas at A↗
DOE OSTI2024

Ligand-Based Compound Activity Prediction via Few-Shot Learning

Predicting the activities of new compounds against biophysical or phenotypic assays based on the known activities of one or a few existing compounds is a common goal in early stage drug discovery. This problem can be cast as a “few-shot learning” challenge, and prior studies have developed few-shot learning methods to classify compounds as active versus inactive. However, the ability to go beyond classification and rank compounds by expected affinity is more valuable. We describe Few-Shot Compound Activity Prediction (FS-CAP), a novel neural architecture trained on a large bioactivity data set to predict compound activities against an assay outside the training set, based on only the activities of a few known compounds against the same assay. Our model aggregates encodings generated from the known compounds and their activities to capture assay information and uses a separate encoder for the new compound whose activity is to be predicted. The new method provides encouraging results relative to traditional chemical-similarity-based techniques as well as other state-of-the-art few-shot learning methods in tests on a variety of ligand-based drug discovery settings and data sets.

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

Challenging the Curse of Dimensionality in Multidimensional Numerical Integration by Using a Low-Rank Tensor-Train Format

Numerical integration is a basic step in the implementation of more complex numerical algorithms suitable, for example, to solve ordinary and partial differential equations. The straightforward extension of a one-dimensional integration rule to a multidimensional grid by the tensor product of the spatial directions is deemed to be practically infeasible beyond a relatively small number of dimensions, e.g., three or four. In fact, the computational burden in terms of storage and floating point operations scales exponentially with the number of dimensions. This phenomenon is known as the curse of dimensionality and motivated the development of alternative methods such as the Monte Carlo method. The tensor product approach can be very effective for high-dimensional numerical integration if we can resort to an accurate low-rank tensor-train representation of the integrand function. In this work, we discuss this approach and present numerical evidence showing that it is very competitive with the Monte Carlo method in terms of accuracy and computational costs up to several hundredths of dimensions if the integrand function is regular enough and a sufficiently accurate low-rank approximation is available.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Collective mode Brownian dynamics: A method for fast relaxation of statistical ensembles

Sampling equilibrium configurations of correlated systems of particles with long relaxation times (e.g., polymeric solutions) using conventional molecular dynamics and Monte Carlo methods can be challenging. This is especially true for systems with complicated, extended bond network topologies and other interactions that make the use and design of specialized relaxation protocols infeasible. We introduce a method based on Brownian dynamics simulations that can reduce the computational time it takes to reach equilibrium and draw decorrelated samples. Importantly, the method is completely agnostic to the particle configuration and the specifics of interparticle forces. In particular, we develop a mobility matrix that excites non-local, collective motion of N particles and can be computed efficiently in $\mathcal{O}(N)$ time. Particle motion in this scheme is computed by integrating the overdamped Langevin equation with an Euler–Maruyama scheme, in which Brownian displacements are drawn efficiently using a low-rank representation of the mobility matrix in position and wave space. We demonstrate the efficacy of the method with various examples from the realm of soft condensed matter and release a massively parallel implementation of the code as a plugin for the open-source package HOOMD-blue [J. A. Anderson et al., J. Comput. Phys. 227, 5342 (2008) and J. Glaser et al., Comput. Phys. Commun. 192, 97 (2015)] which runs on graphics processing units

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

Dark Energy Survey Year 3 results: marginalization over redshift distribution uncertainties using ranking of discrete realizations

ABSTRACT Cosmological information from weak lensing surveys is maximized by sorting source galaxies into tomographic redshift subsamples. Any uncertainties on these redshift distributions must be correctly propagated into the cosmological results. We present hyperrank, a new method for marginalizing over redshift distribution uncertainties, using discrete samples from the space of all possible redshift distributions, improving over simple parametrized models. In hyperrank, the set of proposed redshift distributions is ranked according to a small (between one and four) number of summary values, which are then sampled, along with other nuisance parameters and cosmological parameters in the Monte Carlo chain used for inference. This approach can be regarded as a general method for marginalizing over discrete realizations of data vector variation with nuisance parameters, which can consequently be sampled separately from the main parameters of interest, allowing for increased computational efficiency. We focus on the case of weak lensing cosmic shear analyses and demonstrate our method using simulations made for the Dark Energy Survey (DES). We show that the method can correctly and efficiently marginalize over a wide range of models for the redshift distribution uncertainty. Finally, we compare hyperrank to the common mean-shifting method of marginalizing over redshift uncertainty, validating that this simpler model is sufficient for use in the DES Year 3 cosmology results presented in companion papers.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Lattice phase shifts and mixing angles for an arbitrary number of coupled channels

We present a lattice method for determining scattering phase shifts and mixing angles for the case of an arbitrary number of coupled channels. The proposed method combines a spherical wall boundary condition and a channel-mixing auxiliary potential to extract the full-rank S-matrix from the radial wave functions. We consider the scattering problem of two spin-1 bosons interacting with a test potential involving up to four coupled channels. For this benchmark system, the phase shifts and mixing angles are shown to agree on the lattice and in the continuum. Our method should allow to extend previous two-channel nuclear lattice EFT simulations to mixing of more than two partial waves.

Bovermann, Lukas↗