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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 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Calculating adsorption isotherms using the two-phase thermodynamic method and molecular dynamics simulations

We describe the calculation of adsorption isotherms from molecular dynamics simulations based on the two-phase thermodynamic (2PT) model. The 2PT model developed for bulk fluid phases treats the gas-like components as hard spheres (HSs), which correctly recovers the limiting behaviors of unconfined fluids. We showed that this treatment, however, does not always lead to the correct zero-loading behavior in strongly confining systems. For methane adsorption into zeolite MFI, the HS reference state underestimates entropy by up to 20% at low loadings and leads to an order-of-magnitude increase in the adsorption onset pressure. To fix these issues, we propose the use of ideal adsorbed gas (IAG) as the gas reference model, the properties of which can be computed using the Widom insertion method on an empty adsorbent. We further describe three routes to compute adsorption isotherms from the Helmholtz free energy at different loadings. Comparing against established Monte Carlo (MC) methods, we found that the adsorption isotherms obtained using the IAG reference state agrees to within 40%, which corresponds to deviations of <5% in adsorption free energy. The isotherms calculated using the HS reference state underestimate the adsorption uptake at low to medium loadings in strongly confining systems, but its accuracy improves at higher loadings and as the pore size increases relative to the sorbate diameter. The methods described here provide an alternative approach for computing adsorption isotherms when MC simulations in an open ensemble are undesirable and enable a direct comparison of computed adsorption thermodynamics with experiments.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Analytical integration of the tractions induced by non-singular dislocations on an arbitrary shaped triangular quadratic element

Here, an analytical model is proposed to evaluate the nodal force induced by a segment of dislocation upon an arbitrary shaped triangular element. This calculation is required in hybrid methods that associate dislocation dynamics to boundary or finite element to solve simultaneously the evolution of large ensembles of dislocations with complex boundary conditions. Nodal forces are defined as the triple integration of the unbalanced traction field induced by a straight dislocation upon the surface of the element. Following our previous approach (Queyreau et al 2014 Modelling Simul. Mater. Sci. Eng. 22 035004) on a simpler geometry and in the case of linear isotropic elasticity, triple integrals are solved by sequences of integration by parts that exhibit recurrence relations. The traction field is defined and finite everywhere even at the core of dislocations, thanks to the use of the non-singular stress expression formulated by Cai et al (2006 J. Mech. Phys. Solids 54 561–587). The nodal force expressions can be used when considering both a single convolution or double convolution of the Green's function with the core distribution. A solution is also proposed for the case of a semi-infinite segment through the study of the asymptotic behavior of the analytical expressions. The proposed approach is exact and very computationally efficient. The choice of an arbitrary shaped triangular element and quadratic shape functions allow the consideration of complex geometries and comply with automatic meshing procedures. These analytical expressions could also be employed to estimate dislocation interactions with interfaces.

42 ENGINEERING↗
DOE OSTI2022

Continental United States may lose 1.8 petagrams of soil organic carbon under climate change by 2100

Abstract Aims High‐resolution information on soils’ vulnerability to climate‐induced soil organic carbon (SOC) loss can enable environmental scientists, land managers, and policy makers to develop targeted mitigation strategies. This study aims to estimate baseline and decadal changes in continental US surface SOC stocks under future emission scenarios. Location Continental United States. Time period 2014–2100. Methods We used recent SOC field observations ( n = 6,213 sites), environmental factors ( n = 32), and an ensemble machine learning (ML) approach to estimate baseline SOC stocks in surface soils across the continental United States at 100‐m spatial resolution, and decadal changes under the projected climate scenarios of Coupled Model Intercomparison Project Phase Six (CMIP6) earth system models (ESMs). Results Baseline SOC projections from ML approaches captured more than 50% of variability in SOC observations, whereas ESMs represented only 6–16% of observed SOC variability. ML estimates showed a mean total loss of 1.8 Pg C from US surface soils under the high‐emission scenario by 2100, whereas ESMs showed no significant change in SOC stocks with wide variation among ESMs. Both ML and ESM predictions agree on the direction of SOC change (net emissions or sequestration) across 46–51% of continental US land area. These differences are attributable to the high‐resolution site‐specific data used in the ML models compared to the relatively coarse grid represented in CMIP6 ESMs. Main conclusions Our high‐resolution estimates of baseline SOC stocks, identification of key environmental controllers, and projection of SOC changes from US land cover types under future climate scenarios suggest the need for high‐resolution simulations of SOC in ESMs to represent the heterogeneity of SOC. We found that the SOC change is sensitive to key soil related factors (e.g. soil drainage and soil order) that have not been historically considered as input parameters in ESMs, because currently more than 95% variability in the SOC of CMIP6 ESMs is controlled by net primary productivity, temperature, and precipitation. Using additional environmental factors to estimate the baseline SOC stocks and predict the future trajectory of SOC change can provide more accurate results.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Unleashing the Power of Industrial Big Data through Scalable Manual Labeling

Big Data plays a central role in the remarkable results achieved by Machine Learning (ML) and especially Deep Learning (DL) in the recent years. However, the difficulty in obtaining a reasonable amount of labeled samples limits ML/DL application in various domains, including industrial equipment and system monitoring. In this paper the need for methods that turn manual labeling into a scalable process is highlighted. A real world problem is analyzed for which weak supervision methods, successfully employed in other domains, did not produce acceptable results. An alternative approach based on clustering ensembles is described and tested, achieving good performance.

Paes Leao, Bruno↗
DOE OSTI2022

QRF4P-NRT: Probabilistic Post-Processing of Near-Real-Time Satellite Precipitation Estimates Using Quantile Regression Forests

Accurate and reliable near-real-time satellite precipitation estimation is of great importance for operational large-scale flood forecasting and drought monitoring. The state-of-the-art precipitation post-processing model is based on a deterministic approach to construct relationships between satellites estimates and ground observations. We propose a probabilistic postprocessor, the Probabilistic Post-Processing of Near-Real-Time Satellite Precipitation Estimates using Quantile Regression Forests (QRF4P-NRT), based on quantile modeling, yielding both deterministic and probabilistic predictions. The experimental design incorporates different solutions of near-real-time predictors to further improve the model performance. Using the Integrated Multi-satellitE Retrievals Early Run for Global Precipitation Measurement Mission (IMERG-E) product as an example, we illustrate that the proposed method significantly improves the overall quality of the raw IMERG-E and is also superior to the bias-corrected product (IMERG Final Run, IMERG-F) at daily scale in a complex mountain basin. Evaluations of the corrected IMERG-E, raw IMERG-E, and IMERG-F using ground observation show that the corrected IMERG-E improves correlation coefficients (0.7), mean error (-0.14 mm/day) and root mean square error (3.3 mm/day) relative to the raw IMERG-E (0.31, -0.72 and 5.5 mm/day) and IMERG-F (0.34, -0.09 and 6.0 mm/day). The error decomposition further confirms that the QRF4P-NRT improves on the various deficiencies of the raw IMERG-E product. The ensemble assessment also demonstrates that the quantile outputs provide reliable prediction spread and sharp prediction intervals. The promising results indicate the great potential of the proposed method for probabilistic post-processing for near-real-time satellite precipitation estimates, and for further applications such as hydrological ensemble forecasting.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Operator learning for energy-efficient building ventilation control with computational fluid dynamics simulation of a real-world classroom

Energy-efficient ventilation control plays an important role in reducing building energy consumption while ensuring occupant health and comfort. While Computational Fluid Dynamics (CFD) simulations provide detailed and physically accurate representations of indoor airflow, their high computational cost limits their use in real-time building control. In this work, we present a neural operator learning framework that combines the physical accuracy of CFD with the computational efficiency of machine learning to enable building ventilation control with the high-fidelity fluid dynamics models. Our method jointly optimizes the airflow supply rates and vent angles to reduce energy use and adhere to air quality constraints. We train an ensemble of neural operator transformer models to learn the mapping from building control actions to airflow fields using high-resolution CFD data. This learned neural operator is then embedded in an optimization-based control framework for building ventilation control. Experimental results show that our approach achieves significant energy savings compared to maximum airflow rate control, rule-based control, as well as data-driven control methods using spatially averaged CO 2 prediction and deep learning–based reduced-order models, while consistently maintaining safe indoor air quality. These results highlight the practicality and scalability of our method in maintaining energy efficiency and indoor air quality in real-world buildings.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2026

Crystal Orientation and Defect Mapping in Electron-Beam-Sensitive Zeolites with Near-Axis Transmission Kikuchi Diffraction

Porous materials are vital in catalysis, energy conversion, and environmental remediation. Understanding structural heterogeneity in zeolites is key to linking synthesis, framework intergrowths, and catalytic performance, yet current methods for phase identification and spatial mapping lack sufficient resolution or throughput. We present a high-throughput approach using near-axis transmission Kikuchi diffraction in a scanning electron microscope, achieving high phase and spatial resolution for electron-beam-sensitive zeolites, including ZSM-5 and, for the first time, Zeolite A. Here, this method enables direct visualization of intergrowth features that critically affect catalytic and adsorption behavior, bridging the gap between ensemble-averaged X-ray diffraction and high-resolution but low-throughput transmission electron microscopy. Combining nanoscale mapping with statistical sampling is highly suited for machine-learning pipelines guiding new structure function understanding and could be extended to other beam-sensitive porous materials such as metal–organic or covalent–organic frameworks.

crystallography↗
DOE OSTI2021

A consensus-based ensemble approach to improve transcriptome assembly

Systems-level analyses, such as differential gene expression analysis, co-expression analysis, and metabolic pathway reconstruction, depend on the accuracy of the transcriptome. Multiple tools exist to perform transcriptome assembly from RNAseq data. However, assembling high quality transcriptomes is still not a trivial problem. This is especially the case for non-model organisms where adequate reference genomes are often not available. Different methods produce different transcriptome models and there is no easy way to determine which are more accurate. Furthermore, having alternative-splicing events exacerbates such difficult assembly problems. While benchmarking transcriptome assemblies is critical, this is also not trivial due to the general lack of true reference transcriptomes. In this study, we first provide a pipeline to generate a set of the simulated benchmark transcriptome and corresponding RNAseq data. Using the simulated benchmarking datasets, we compared the performance of various transcriptome assembly approaches including both de novo and genome-guided methods. The results showed that the assembly performance deteriorates significantly when alternative transcripts (isoforms) exist or for genome-guided methods when the reference is not available from the same genome. To improve the transcriptome assembly performance, leveraging the overlapping predictions between different assemblies, we present a new consensus-based ensemble transcriptome assembly approach, ConSemble. Without using a reference genome, ConSemble using four de novo assemblers achieved an accuracy up to twice as high as any de novo assemblers we compared. When a reference genome is available, ConSemble using four genome-guided assemblies removed many incorrectly assembled contigs with minimal impact on correctly assembled contigs, achieving higher precision and accuracy than individual genome-guided methods. Furthermore, ConSemble using de novo assemblers matched or exceeded the best performing genome-guided assemblers even when the transcriptomes included isoforms. We thus demonstrated that the ConSemble consensus strategy both for de novo and genome-guided assemblers can improve transcriptome assembly. The RNAseq simulation pipeline, the benchmark transcriptome datasets, and the script to perform the ConSemble assembly are all freely available from: http://bioinfolab.unl.edu/emlab/consemble/.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

An extensible perturbed parameter ensemble for the Community Atmosphere Model version 6

This paper documents the methodology and preliminary results from a perturbed parameter ensemble (PPE) technique, where multiple parameters are varied simultaneously and the parameter values are determined with Latin hypercube sampling. This is done with the Community Atmosphere Model version 6 (CAM6), the atmospheric component of the Community Earth System Model version 2 (CESM2). We apply the PPE method to CESM2–CAM6 to understand climate sensitivity to atmospheric physics parameters. The initial simulations vary 45 parameters in the microphysics, convection, turbulence and aerosol schemes with 263 ensemble members. These atmospheric parameters are typically the most uncertain in many climate models. Control simulations and targeted simulations to understand climate forcing due to aerosols and fast climate feedbacks are analyzed. The use of various emulators is explored in the multi-dimensional space mapping input parameters to output metrics. Parameter impacts on various model outputs, such as radiation, cloud and aerosol properties, are evaluated. Machine learning is also used to probe optimal parameter values against observations. Our findings show that PPE is a valuable tool for climate uncertainty analysis. Furthermore, by varying many parameters simultaneously, we find that many different combinations of parameter values can produce results consistent with observations, and thus careful analysis of tuning is important. The CESM2–CAM6 PPE is publicly available and extensible to other configurations to address questions of other model processes in the atmosphere and other model components (e.g., coupling to the land surface).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting

Recent advances in cryo-electron microscopy (cryo-EM) have enabled modeling macromolecular complexes that are essential components of the cellular machinery. The density maps derived from cryo-EM experiments are often integrated with manual, knowledge or artificial intelligence driven, and physics-guided computational methods to build, fit, and refine molecular structures. Going beyond a single stationary- structure determination scheme, it is becoming more common to interpret the experimental data with an ensemble of models, which contributes to an average observation. Hence, there is a need to decide on the quality of an ensemble of protein structures on-the-fly, while refining them against the density maps. Here, we introduce such an adaptive decision making scheme during the molecular dynamics flexible fitting (MDFF) of biomolecules. Using RADICAL-Cybertools, and the new RADICAL augmented MDFF implementation (R-MDFF) is examined in high-performance computing environments for refinement of two protein systems, Adenylate Kinase and Carbon Monoxide Dehydrogenase. For the test cases, use of multiple replicas in flexible fitting with adaptive decision making in R-MDFF improves the overall correlation to the density by 40% relative to the refinements of the brute-force MDFF. The improvements are particularly significant at high, 2 - 3 Å, map resolutions. More importantly, the ensemble model captures key features of biologically relevant molecular dynamics that is inaccessible to a single-model interpretation. Finally, the pipeline is applicable to systems of growing sizes, which is demonstrated using ensemble refinement of capsid proteins from Chimpanzee adenovirus. The overhead for decision making remaining low and robust to computing environments. The software is publicly available on GitHub and includes a short user guide to install the R-MDFF on different computing environments, from local Linux based workstations to High Performance Computing (HPC) environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Fast calculation of diffraction patterns from an ensemble of aligned molecules

We report an algorithm to calculate electron diffraction patterns for molecules with anisotropic angular distribution, which is significantly faster than existing methods. The algorithm uses a transform to convert the molecular orientation distribution, which is a function of three Euler angles, to the atom-pair distribution functions which depend on the polar and azimuthal angles. The diffraction signal can then be calculated from the atom-pair distributions. We demonstrate the computation method numerically by calculating electron diffraction patterns for a symmetric top molecule (trifluoroiodomethane) and an asymmetric top molecule (formaldehyde) and show that it reduces the calculation time by approximately two orders of magnitude compared to the standard brute-force method. Here, the method can also be applied to the calculation of x-ray diffraction patterns.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Evidential Deep Learning for Probabilistic Modelling of Extreme Storm Events

Uncertainty quantification (UQ) methods play an important role in reducing errors in weather forecasting. Conventional approaches in UQ for weather forecasting rely on generating an ensemble of forecasts from physics-based simulations to estimate the uncertainty. However, it is computationally expensive to generate many forecasts to predict real-time extreme weather events. Evidential Deep Learning (EDL) is an uncertainty-aware deep learning approach designed to provide confidence about its predictions using only one forecast. It treats learning as an evidence acquisition process where more evidence is interpreted as increased predictive confidence. We apply EDL to storm forecasting using real-world weather datasets and compare its performance with traditional methods. Our findings indicate that EDL not only reduces computational overhead but also enhances predictive uncertainty. This method opens up novel opportunities in research areas such as climate risk assessment, where quantifying the uncertainty about future climate is crucial.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Physics-Based Machine Learning Methods for U-235 Forensics Signatures

Signatures of low-intensity U-235 sources have been recently studied by utilizing a variety of machine learning (ML) classifiers using features derived from gamma spectral measurements collectedunder structured campaigns. Several ML classifiers, such as ensemble of tress and classification trees, revealed misleadingly-optimistic training error due to over-fitting, and furthermore,their performance is not directly relatable to the physical properties due to their data-driven, opaque designs. We present a regression-based ML method that first estimates the inverse distanceto the source and then utilizes a threshold to infer its presence, by representing the background as a source located at an infinite distance. For the inverse distance estimation, we study the ensembleof trees and Gaussian process regression methods, and a hyper parameter auto-tuning and selection method that employs five regression estimators. These methods avoid the over-fittingobserved in several ML classifiers, while providing the classification error nearly comparable to them based on independent test data. Their error is directly related to estimates of the inversephysical distance to source, and the precision of error determines the seperability property that determines the false alarm and missed detection rates. The property of monotonic decrease of thesource strength with increasing detector distance combined with Poisson distribution of measurements is utilized to analytically validate these methods by deriving the generalization equations ofunderlying regression methods.

Rao, Nageswara↗
DOE OSTI2020

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

In this work, we present a supercomputer-driven pipeline for in silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. Ensemble docking makes use of MD results by docking compound databases into representative protein binding-site conformations, thus taking into account the dynamic properties of the binding sites. We also describe preliminary results obtained for 24 systems involving eight proteins of the proteome of SARS-CoV-2. The MD involves temperature replica exchange enhanced sampling, making use of massively parallel supercomputing to quickly sample the configurational space of protein drug targets. Using the Summit supercomputer at the Oak Ridge National Laboratory, more than 1 ms of enhanced sampling MD can be generated per day. We have ensemble docked repurposing databases to 10 configurations of each of the 24 SARS-CoV-2 systems using AutoDock Vina. Comparison to experiment demonstrates remarkably high hit rates for the top scoring tranches of compounds identified by our ensemble approach. We also demonstrate that, using Autodock-GPU on Summit, it is possible to perform exhaustive docking of one billion compounds in under 24 h. Finally, we discuss preliminary results and planned improvements to the pipeline, including the use of quantum mechanical (QM), machine learning, and artificial intelligence (AI) methods to cluster MD trajectories and rescore docking poses.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

High-Energy Coherent X-Ray Dffraction Microscopy of Polycrystal Grains: First Steps Towards a Multi-Scale Approach

Here, we present proof-of-concept imaging measurements of a polycrystalline material that integrate the elements of conventional high-energy x-ray diffraction microscopy with coherent diffraction-imaging techniques, and that can enable in situ strain-sensitive imaging of lattice structure in ensembles of deeply embedded crystals over five decades of length scale upon full realization. We demonstrate that the combination of these two characterization methods enables a more complete picture of the crystal-lattice strain than either method is capable of providing individually. Such complementary imaging capabilities are critical to addressing questions in a variety of research areas such as materials science and engineering, chemistry, and solid-state physics. Towards this eventual goal, the following key aspects are demonstrated: (1) high-energy Bragg coherent diffraction imaging (HE BCDI) of submicron-scale crystallites at 52 keV at current third-generation synchrotron light sources, (2) HE BCDI performed in conjunction with far-field high-energy diffraction microscopy (FF HEDM) on the grains of a polycrystalline sample in a smoothly integrated manner, and (3) the orientation information of an ensemble of grains obtained via FF HEDM used to perform complementary HE BCDI on multiple Bragg reflections of a single targeted grain. The imaged structures are seen to be 477 ± 50 nm or smaller in size, with an estimated strain resolution of 2.5 x 10 -4 . These steps lay the foundation for integration of HE BCDI, which typically provides a spatial resolution tens of nanometers, into a broad suite of well-established HEDM methods, extending HEDM beyond the few-micrometer resolution bound and into the nanoscale, and positioning the approach to take full advantage of the orders-of-magnitude improvement of x-ray coherence expected at fourth-generation light sources presently being built and commissioned worldwide.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Structural basis of differential gene expression at eQTLs loci from high-resolution ensemble models of 3D single-cell chromatin conformations

Abstract Motivation Techniques such as high-throughput chromosome conformation capture (Hi-C) have provided a wealth of information on nucleus organization and genome important for understanding gene expression regulation. Genome-Wide Association Studies have identified numerous loci associated with complex traits. Expression quantitative trait loci (eQTL) studies have further linked the genetic variants to alteration in expression levels of associated target genes across individuals. However, the functional roles of many eQTLs in noncoding regions remain unclear. Current joint analyses of Hi-C and eQTLs data lack advanced computational tools, limiting what can be learned from these data. Results We developed a computational method for simultaneous analysis of Hi-C and eQTL data, capable of identifying a small set of nonrandom interactions from all Hi-C interactions. Using these nonrandom interactions, we reconstructed large ensembles (×105) of high-resolution single-cell 3D chromatin conformations with thorough sampling, accurately replicating Hi-C measurements. Our results revealed many-body interactions in chromatin conformation at the single-cell level within eQTL loci, providing a detailed view of how 3D chromatin structures form the physical foundation for gene regulation, including how genetic variants of eQTLs affect the expression of associated eGenes. Furthermore, our method can deconvolve chromatin heterogeneity and investigate the spatial associations of eQTLs and eGenes at subpopulation level, revealing their regulatory impacts on gene expression. Together, ensemble modeling of thoroughly sampled single-cell chromatin conformations combined with eQTL data, helps decipher how 3D chromatin structures provide the physical basis for gene regulation, expression control, and aid in understanding the overall structure-function relationships of genome organization. Availability and implementation It is available at https://github.com/uic-liang-lab/3DChromFolding-eQTL-Loci.

Du, Lin (ORCID:0009000289869812)↗
DOE OSTI2024

Distribution of centrality measures on undirected random networks via the cavity method

The Katz centrality of a node in a complex network is a measure of the node’s importance as far as the flow of information across the network is concerned. For ensembles of locally tree-like undirected random graphs, this observable is a random variable. Its full probability distribution is of interest but difficult to handle analytically because of its “global” character and its definition in terms of a matrix inverse. Leveraging a fast Gaussian Belief Propagation-Cavity algorithm to solve linear systems on tree-like structures, we show that i) the Katz centrality of a single instance can be computed recursively in a very fast way, and ii) the probability P ( K ) that a random node in the ensemble of undirected random graphs has centrality K satisfies a set of recursive distributional equations, which can be analytically characterized and efficiently solved using a population dynamics algorithm. We test our solution on ensembles of Erdős-Rényi and Scale Free networks in the locally tree-like regime, with excellent agreement. The analytical distribution of centrality for the configuration model conditioned on the degree of each node can be employed as a benchmark to identify nodes of empirical networks with over- and underexpressed centrality relative to a null baseline. We also provide an approximate formula based on a rank- 1 projection that works well if the network is not too sparse, and we argue that an extension of our method could be efficiently extended to tackle analytical distributions of other centrality measures such as PageRank for directed networks in a transparent and user-friendly way.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗