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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

A Mountaintop View Requires Minimal Sorting: A Faster Contour Tree Algorithm

Consider a scalar field f : M → R, where M is a triangulated simplicial mesh in R d . A level set, or contour, at value v is a connected component of f –1 (v). As v is changed, these contours change topology, merge into each other, or split. Contour trees are concise representations of f that track this contour behavior. The vertices of these trees are the critical points of f, where the gradient is zero. The edges represent changes in the topology of contours. It is a fundamental data structure in data analysis and visualization, and there is significant previous work (both theoretical and practical) on algorithms for constructing contour trees. Suppose M has n vertices, N facets, and t critical points. A classic result of Carr, Snoeyink, and Axen (2000) gives an algorithm that takes O(n log n+Nα(N)) time (where α(·) is the inverse Ackermann function). A further improvement to O(t log t + N) time was given by Chiang et al. All these algorithms involve a global sort of the critical points, a significant computational bottleneck. Unfortunately, lower bounds of Ω(t log t) also exist. We present the first algorithm that can avoid the global sort and has a refined time complexity that depends on the contour tree structure. Intuitively, if the tree is short and fat, we get significant improvements in running time. For a partition of the contour tree into a set of descending paths, P, our algorithm runs in O($\Sigma$ pϵP |p| log |p| + tα(t) + N). This is at most O(t log D + N), where D is the diameter of the contour tree. Moreover, it is O(tα(t) + N) for balanced trees, a significant improvement over the previous complexity. Our algorithm requires numerous ideas: partitioning the contour tree into join and split trees, a local growing procedure to iteratively build contour trees, and the use of heavy path decompositions for the time complexity analysis. There is a crucial use of a family of binomial heaps to maintain priorities, ensuring that any comparison made is between comparable nodes of the contour tree. We also prove lower bounds showing that the $\Sigma$ pϵP |p| log |p| complexity is inherent to computing contour trees.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Reliable and Efficient Machine Learning (Final Technical Report)

Modern scientific experiments generate massive amounts of data at a pace much faster than humans can manually analyze. While machine learning has revolutionized commercial data analysis (such as recommending movies or recognizing faces), applying these tools to complex scientific discovery is challenging because scientific answers must be precise, interpretable, and adhere to physical laws. The research under this project aims to develop new mathematical tools and computer algorithms specifically designed for scientific applications. Major progress has been made in automatically cleaning and deconstructing messy experimental data, analyzing the visual information of physical phenomena, determining the underlying physical variables, and providing rig orous mathematical analysis of interesting algorithms and concepts widely used in machine learning. This project addressed the critical gap between our ability to generate massive scientific data and our ability to extract interpretable information from it. We established mathematical foundations for Scientific Machine Learning (SciML) aimed at effective data analytics and automated discovery. Our work focused on three core objectives: (1) developing reliable feature extraction methods for dynamic high-dimensional data, (2) establishing mathematical foundations for discovering dynamics via neural networks, and (3) creating rigorous optimization techniques for these models. Key outcomes come from two fronts. On the practical side, they include the development of algorithms that significantly enhance the extraction of signals from field data, as well as the capability to handle situations that exhibit smooth variations or physical stretching due to temperature changes. They also include the creation of an automated framework for discovering fundamental state variables from raw experimental data, demonstrating the ability to identify intrinsic physical dimensions without prior knowledge of the governing laws. On the theoretical front, the research results in theoretical advances in Optimal Transport, a widely used notion in SciML, specifically regarding functions with fixed-size nodal sets, provide sharp bounds relevant to uncertainty quantification. Meanwhile, the outcomes also include the establishment of convergence theories for nonlocal gradient descent methods, enabling robust optimization with noisy data in high-dimensional settings commonly encountered in scientific modeling. The project also helps creating opportunities to train the next generation of researchers, equipping them with the necessary technical skills for today’s workplace and preparing them for future advances.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Self-learning Monte Carlo method and cumulative update in fermion systems

In this study, we develop the self-learning Monte Carlo (SLMC) method, a general-purpose numerical method recently introduced to simulate many-body systems, for studying interacting fermion systems. Our method uses a highly efficient update algorithm, which we design and dub “cumulative update”, to generate new candidate configurations in the Markov chain based on a self-learned bosonic effective model. From a general analysis and a numerical study of the double exchange model as an example, we find that the SLMC with cumulative update drastically reduces the computational cost of the simulation, while remaining statistically exact. Remarkably, its computational complexity is far less than the conventional algorithm with local updates.

36 MATERIALS SCIENCE↗
DOE OSTI2025

G2PDeep-v2: A Web-Based Deep-Learning Framework for Phenotype Prediction and Biomarker Discovery for All Organisms Using Multi-Omics Data

Multi-omics data offers rich insights into complex traits across organisms, yet integrating and analyzing these datasets for phenotype prediction and marker discovery remains challenging. Researchers need accessible tools that combine deep learning, hyperparameter optimization, visualization, and downstream analysis in a unified web platform. To address this, we developed G2PDeep-v2, a web-based platform powered by deep learning for phenotype prediction and marker discovery from multi-omics data across a wide range of organisms, including humans and plants. The server provides multiple services for researchers to create deep-learning models through an interactive interface and train these models using an automated hyperparameter tuning algorithm on high-performance computing resources. Users can visualize the results of phenotype and markers predictions and perform Gene Set Enrichment Analysis for the significant markers to provide insights into the molecular mechanisms underlying complex diseases, conditions and other biological phenotypes being studied.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers

ABSTRACT Accurate biomolecular structure prediction enables the prediction of mutational effects, the speculation of function based on predicted structural homology, the analysis of ligand binding modes, experimental model building, and many other applications. Such algorithms to predict essential functional and structural features remain out of reach for biomolecular complexes containing nucleic acids. Here, we report a quantitative and qualitative evaluation of nucleic acid structures for the CASP16 blind prediction challenge by 12 of the experimental groups who provided nucleic acid targets. Blind predictions accurately model secondary structure and some aspects of tertiary structure, including reasonable global folds for some complex RNAs; however, predictions often lack accuracy in the regions of highest functional importance. All models have inaccuracies in non‐canonical regions where, for example, the nucleic‐acid backbone bends, deviating from an A‐form helix geometry, or a base forms a non‐standard hydrogen bond (not a Watson‐Crick base pair). These bends and non‐canonical interactions are integral to forming functionally important regions such as RNA enzymatic active sites. Additionally, the modeling of conserved and functional interfaces between nucleic acids and ligands, proteins, or other nucleic acids remains poor. For some targets, the experimental structures may not represent the only structure the biomolecular complex occupies in solution or in its functional life cycle, posing a future challenge for the community.

Biochemistry & Molecular Biology↗
DOE OSTI2019

Computing the small-scale galaxy power spectrum and bispectrum in configuration space

ABSTRACT We present a new class of estimators for computing small-scale power spectra and bispectra in configuration space via weighted pair and triple counts, with no explicit use of Fourier transforms. Particle counts are truncated at $R_0\sim 100\, h^{-1}\, \mathrm{Mpc}$ via a continuous window function, which has negligible effect on the measured power spectrum multipoles at small scales. This gives a power spectrum algorithm with complexity $\mathcal {O}(NnR_0^3)$ (or $\mathcal {O}(Nn^2R_0^6)$ for the bispectrum), measuring N galaxies with number density n. Our estimators are corrected for the survey geometry and have neither self-count contributions nor discretization artefacts, making them ideal for high-k analysis. Unlike conventional Fourier-transform-based approaches, our algorithm becomes more efficient on small scales (since a smaller R0 may be used), thus we may efficiently estimate spectra across k-space by coupling this method with standard techniques. We demonstrate the utility of the publicly available power spectrum algorithm by applying it to BOSS DR12 simulations to compute the high-k power spectrum and its covariance. In addition, we derive a theoretical rescaled-Gaussian covariance matrix, which incorporates the survey geometry and is found to be in good agreement with that from mocks. Computing configuration- and Fourier-space statistics in the same manner allows us to consider joint analyses, which can place stronger bounds on cosmological parameters; to this end we also discuss the cross-covariance between the two-point correlation function and the small-scale power spectrum.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Large Scale Tensor Factorization via Parallel Sketches

Tensor factorization methods have recently gained increased popularity. A key feature that renders tensors attractive is the ability to directly model multi-relational data. In this work, we propose ParaSketch, a parallel tensor factorization algorithm that enables massive parallelism, to deal with large tensors. The idea is to compress the large tensor into multiple small tensors, decompose each small tensor in parallel, and combine the results to reconstruct the desired latent factors. Prior art in this direction entails potentially very high complexity in the (Gaussian) compression and final combining stages. Adopting sketching matrices for compression, the proposed method enjoys a dramatic reduction in compression complexity, and features a much lighter combining step. Moreover, theoretical analysis shows that the compressed tensors inherit latent identifiability under mild conditions, hence establishing correctness of the overall approach. Numerical experiments corroborate the theory and demonstrate the effectiveness of the proposed algorithm.

block term decomposition↗
DOE OSTI2021

Reaction paths of methane activation and oxidation of surface intermediates over NiO on Ceria-Zirconia catalysts studied by In-situ FTIR spectroscopy

Methane activation over NiO/Ce 0.82 Zr 0.18 O 2 catalysts synthesized by combustion synthesis is studied by in-situ IR spectroscopy and correlated to the properties and oxygen speciation of the catalyst. Through XRD, H 2 -TPR, and pyridine adsorption followed by FTIR spectroscopy, the reducibility and Lewis acidity of the catalysts are assessed. In-situ FTIR spectroscopy is used to monitor the methane activation on catalyst surfaces. Complex IR features of methane-derived surface species are observed and are attributed to the formation of surface alkyl/alkoxy, aldehyde, formate/carbonate, and aromatic species. A data analysis algorithm is developed to evaluate the evolution of different surface species over time. The formation of formate and carbonate species is driven by adsorbed surface oxygen, while less reactive oxygen species associated with NiO allow for the production of aromatics and alkoxy intermediates. Finally, by tuning the reducibility and Lewis acidity of the catalyst, the selectivity to alkoxy intermediates can be improved.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Theoretical simulation of a signal for a scheme of an atomic spin gyroscope with optical detection

An operation scheme of an atomic spin gyroscope with optical detection is described, in which two noble gas isotopes, {sup 129} Xe and {sup 131} Xe, are used as carriers of the spin of an atomic nucleus. Based on this scheme, we construct a theoretical model of the dynamics of the spin polarisation of an alkali metal and the magnetisation of a noble gas under conditions of spin-exchange interaction and optical pumping. This model allows one to simulate the pumping and signal readout in the gyroscope scheme. The time dependences of this signal are plotted, the analysis of which shows that the signal has a sophisticated complex structure. Thus, the problem arises of demodulating this signal based on the improvement of demodulation methods and algorithms. (paper)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

MEASURING RISK IMPORTANCE IN A DYNAMIC PRA FRAMEWORK

Risk importance measures are indexes that are used to rank systems, structures and components (SSCs) using risk-informed methods. The most used/known measures are: Risk Reduction Worth (RRW), Risk Achievement Worth (RAW), Birnbaum (B) and Fussell-Vesely (FV). Once obtained from classical Probabilistic Risk Analysis (PRA) analyses, these risk measures can be effectively employed to optimize component testing and maintenance. In contrast to classical PRA methods, Dynamic PRA methods couple stochastic methods with safety analysis codes to determine risk associate to complex systems such as nuclear plants. Compared to classical PRA methods, they can evaluate with higher resolution the safety impact of timing and sequencing of events on the accident progression. The objective of this paper is to present a series of algorithms that can be used to determine classical risk importance measures (RRW, RAW, B and FV) along with newly developed ones from a Dynamic PRA analysis.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Three-dimensional imaging of grain boundaries via quantitative fluorescence X-ray tomography analysis

Abstract Three-dimensional visualization of material composition within multiple grains and across complex networks of grain boundaries at nanoscales can provide new insight into the structure evolution and emerging functional properties of the material for diverse applications. Here, using nanoscale scanning X-ray fluorescence tomography, coupled with an advanced self-absorption correction algorithm developed in this work, we analyze the three-dimensional gain distributions and compositions in a Ce 0.8 Gd 0.2 O 2-δ -CoFe 2 O 4 mixed ionic-electronic conductor system with high accuracy and statistical significance. Our systematic investigation reveals an additional emergent phase and uncovers highly intriguing composition stability ranges for the multiple material phases within this system. The presented visualization of composition variations across complex interfaces, supported by our quantitative composition analysis, discloses mechanistic pathways of the diverse phase transformations occurring in the material synthesis, providing insights for the optimization of transport properties in the mixed ionic-electronic conductor system.

36 MATERIALS SCIENCE↗
DOE OSTI2019

DiaMonD: An Integrated Multifaceted Approach to Mathematics at the Interfaces of Data, Models, and Decisions

DiaMonD is a multi-institutional DOE MMICC effort that aims to address the challenges of end-to-end, data-to-decisions modeling and simulation for complex computational science and engineering problems in a unified, systematic, and integrated fashion. Institutions involved are Colorado State, Florida State, Los Alamos, MIT, Oak Ridge, Stanford, and UT-Austin. The goals of DiaMonD are (1) to develop advanced mathematical methods and analysis for multimodel, multiphysics, multiscale model problems driven by frontier DOE applications, including those in subsurface energy and environmental flows, materials for energy storage and conversion, and ice sheet dynamics; (2) to create theory and algorithms for integrated inversion, optimization, and uncertainty quantification for these complex problems; and (3) to disseminate the philosophy of an integrated end-to-end, data-to-decisions approach to modeling and simulation of complex problems to the broader applied math and computational science communities through workshops and other outreach.

42 ENGINEERING↗
DOE OSTI2022

Peak Rain Rate Sensitivity to Observed Cloud Condensation Nuclei and Turbulence in Continental Warm Shallow Clouds During CACTI

Abstract Warm clouds strongly affect Earth's energy budget but remain imperfectly represented in climate models, partly due to the complexity and covariability of relevant processes influencing warm rain. This work presents a detailed analysis of different factors affecting rain rate peak intensity (RR) in continental warm clouds. Clouds were identified with vertically pointing radar and lidar observations and categorized via a temperature‐based cloud type classification algorithm from which warm clouds were isolated. Observations and retrievals of liquid water path (LWP), cloud condensation nuclei concentration (N CCN ), cloud depth, and cloud duration of more than 3,000 separate warm clouds sampled during the Cloud, Aerosol, and Complex Terrain Interactions (CACTI) field campaign are analyzed in this work. Multiple linear regression (MLR) and random forest (RF) models are applied to assess the relative impact of these variables on RR. Overall, RR tends to increase as cloud depth, LWP, and cloud duration increase, or N CCN decreases. Cloud depth affects RR the most while N CCN impacts it the least. When considering over 170 warm clouds observed at least 1 hr in which in‐cloud turbulence is retrieved, the effect of N CCN on RR remains most likely suppressive, but it is not significant at a 75% level for MLR and is highly uncertain for RF. The impact of in‐cloud turbulence depends on the moment and location it is sampled. Cloud base turbulence around the time of RR suppresses RR, while cloud top turbulence effects are inconclusive. Possible difficulties in isolating robust CCN and turbulence effects on RR are discussed.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

K-space algorithmic reconstruction (KAREN): a robust statistical methodology to separate Bragg and diffuse scattering

Diffuse scattering occurring in the Bragg diffraction pattern of a long-range-ordered structure represents local deviation from the governing regular lattice. However, interpreting the real-space structure from the diffraction pattern presents a significant challenge because of the dramatic difference in intensity between the Bragg and diffuse components of the total scattering function. In contrast to the sharp Bragg diffraction, the diffuse signal has generally been considered to be a weak expansive or continuous background signal. In this paper, using 1D and 2D models, it is demonstrated that diffuse scattering in fact consists of a complex array of high-frequency features that must not be averaged into a low-frequency background signal. To evaluate the actual diffuse scattering effectively, an algorithm has been developed that uses robust statistics and traditional signal processing techniques to identify Bragg peaks as signal outliers which can be removed from the overall scattering data and then replaced by statistically valid fill values. This method, described as a 'K-space algorithmic reconstruction' (KAREN), can identify Bragg reflections independent of prior knowledge of a system's unit cell. KAREN does not alter any data other than that in the immediate vicinity of the Bragg reflections, and reconstructs the diffuse component surrounding the Bragg peaks without introducing discontinuities which induce Fourier ripples or artifacts from underfilling `punched' voids. The KAREN algorithm for reconstructing diffuse scattering provides demonstrably better resolution than can be obtained from previously described punch-and-fill methods. The superior structural resolution obtained using the KAREN method is demonstrated by evaluating the complex ordered diffuse scattering observed from the neutron diffraction of a single plastic crystal of CBr 4 using pair distribution function analysis.

36 MATERIALS SCIENCE↗
DOE OSTI2019

CDR3α drives selection of the immunodominant Epstein Barr virus (EBV) BRLF1-specific CD8 T cell receptor repertoire in primary infection

The T cell receptor (TCR) repertoire is an essential component of the CD8 T-cell immune response. Here, we seek to investigate factors that drive selection of TCR repertoires specific to the HLA-A2-restricted immunodominant epitope BRLF1 109-117 (YVLDHLIVV) over the course of primary Epstein Barr virus (EBV) infection. Using single-cell paired TCRαβ sequencing of tetramer sorted CD8 T cells ex vivo , we show at the clonal level that recognition of the HLA-A2-restricted BRLF1 (YVL-BR, BRLF-1109) epitope is mainly driven by the TCRα chain. For the first time, we identify a CDR3α (complementarity determining region 3 α) motif, KDTDKL, resulting from an obligate AV8.1-AJ34 pairing that was shared by all four individuals studied. This observation coupled with the fact that this public AV8.1-KDTDKL-AJ34 TCR pairs with multiple different TCRβ chains within the same donor (median 4; range: 1–9), suggests that there are some unique structural features of the interaction between the YVL-BR/MHC and the AV8.1-KDTDKL-AJ34 TCR that leads to this high level of selection. Newly developed TCR motif algorithms identified a lysine at position 1 of the CDR3α motif that is highly conserved and likely important for antigen recognition. Crystal structure analysis of the YVL-BR/HLA-A2 complex revealed that the MHC-bound peptide bulges at position 4, exposing a negatively charged aspartic acid that may interact with the positively charged lysine of CDR3α. TCR cloning and site-directed mutagenesis of the CDR3α lysine ablated YVL-BR-tetramer staining and substantially reduced CD69 upregulation on TCR mutant-transduced cells following antigen-specific stimulation. Reduced activation of T cells expressing this CDR3 motif was also observed following exposure to mutated (D4A) peptide. In summary, we show that a highly public TCR repertoire to an immunodominant epitope of a common human virus is almost completely selected on the basis of CDR3α and provide a likely structural basis for the selection. These studies emphasize the importance of examining TCRα, as well as TCRβ, in understanding the CD8 T cell receptor repertoire.

Microbiology↗
DOE OSTI2019

Energy Efficient Mobility Systems 2018 Annual Progress Report

Energy Efficient Mobility Systems (EEMS) Program activities during FY 2018 focused on analytical research to understand the impacts that new mobility technologies and services will have at the vehicle, traveler, and overall transportation system-level. This research included the development of vehicle and transportation system simulation models and tools to evaluate the complex interactions among the various actors within the mobility landscape, analysis of empirical data to characterize which solutions may provide the largest benefits, and development of new control systems and algorithms that use vehicle connectivity and automation to improve the performance and efficiency of individual vehicles as well as the overall traffic system This document presents a brief overview of the EEMS Program and documents progress and results for projects within four of the five EEMS activity areas: (1) the SMART (Systems and Modeling for Accelerated Research in Transportation) Mobility Lab Consortium, (2) High Performance Computing and Big Data Solutions for Mobility Data, (3) Advanced R&D Projects conducted by industry and academia, and (4) Core Modeling, Simulation, and Evaluation, Similarly, the remaining EEMS activity area – (5) Living Labs (managed under VTO’s Technology Integration Program). Each of the individual progress reports provide a project overview and highlights of the technical results.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2020

FY2019 Energy Efficient Mobility Systems Annual Progress Report

EEMS Program activities during FY 2019 focused on analytical research to understand the impacts that new mobility technologies and services will have at the vehicle, traveler, and overall transportation system-level. This research included the development of vehicle and transportation system simulation models and tools to evaluate the complex interactions among the various actors within the mobility landscape, analysis of empirical data to characterize which solutions may provide the largest benefits, and development of new control systems and algorithms that use vehicle connectivity and automation to improve the performance and efficiency of individual vehicles as well as the overall traffic system. This document presents a brief overview of the EEMS Program and documents progress and results for projects within four of the five EEMS activity areas: (1) the SMART (Systems and Modeling for Accelerated Research in Transportation) Mobility Lab Consortium, (2) High Performance Computing and Big Data Solutions for Mobility Data, (3) Advanced R&D Projects conducted by industry and academia, and (4) Core Modeling, Simulation, and Evaluation, Similarly, the remaining EEMS activity area – (5) Living Labs (managed under VTO’s Technology Integration Program). Each of the individual progress reports provide a project overview and highlights of the technical results.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2021

FY2020 Energy Efficient Mobility Systems Annual Progress Report

EEMS Program activities during FY 2020 focused on analytical research and large-scale modeling and simulation to understand the impacts that new mobility technologies and services will have at the vehicle-, traveler-, and overall transportation system-level. This research included the development of a multi-fidelity, end-to-end transportation system models and tools to evaluate the complex interactions among the various actors within the mobility landscape, analysis of empirical data to characterize which solutions may provide the largest benefits, and development of new control systems and algorithms that use vehicle connectivity and automation to improve the performance and efficiency of individual vehicles as well as the overall traffic system. This document presents a brief overview of the EEMS Program and documents progress and results from projects within each of the EEMS activity areas. The Computational Modeling and Simulation key activity area summarizes work within the sub-areas of (1) the SMART (Systems and Modeling for Accelerated Research in Transportation) Mobility Lab Consortium, (2) Artificial Intelligence, High-Performance Computing, and Data Analytics, and (3) Core Simulation and Evaluation Tools. Additionally, the program’s advanced R&D projects are summarized within (4) the Connectivity and Automation Technology key activity area. Each of the individual progress reports provide a project overview and highlights of the technical results.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗