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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 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

How Accurate Are Simulations and Experiments for the Lattice Energies of Molecular Crystals?

Molecular crystals play a central role in a wide range of scientific fields, including pharmaceuticals and organic semiconductor devices. However, they are challenging systems to model accurately with computational approaches because of a delicate interplay of intermolecular interactions such as hydrogen bonding and Van der Waals dispersion forces. Here, by exploiting recent algorithmic developments, we report the first set of diffusion Monte Carlo lattice energies for all 23 molecular crystals in the popular and widely used X23 dataset. Comparisons with previous state-of-the-art lattice energy predictions (on a subset of the dataset) and a careful analysis of experimental sublimation enthalpies reveals that high-accuracy computational methods are now at least as reliable as (computationally derived) experiments for the lattice energies of molecular crystals. Overall, this work demonstrates the feasibility of high-level explicitly correlated electronic structure methods for broad benchmarking studies in complex condensed phase systems, and signposts a route towards closer agreement between experiment and simulation. Published by the American Physical Society 2024

Physics↗
DOE OSTI2023

Comparison of quantum advantage experiments using random circuit sampling

Random circuit sampling, the task of sampling bit strings from a random unitary operator, has been implemented to demonstrate quantum advantage on the Sycamore quantum processor with 53 qubits and on the Zuchongzhi quantum processor with 56 and 61 qubits. Recently, it was claimed that classical computers using tensor network simulation could catch on to current noisy quantum processors for random circuit sampling. While the linear cross-entropy benchmark fidelity was used to certify all these claims, it may not capture statistical properties of outputs in detail. Here, we compare the bit strings sampled from classical computers using tensor network simulation by Pan et al. [F. Pan, K. Chen, and P. Zhang, Phys. Rev. Lett. 129, 090502 (2022)] and by Kalachev et al. [G. Kalachev, P. Panteleev, P. Zhou, and M.-H. Yung, arXiv:2112.15083] with the bit strings from the Sycamore quantum processor. It is shown that all of Kalachev et al.'s samples passed the NIST random number tests. The heat maps of bit strings show that Pan et al.'s and Kalachev et al.'s samples are quite different from the Sycamore or Zuchongzhi samples. The analysis with the Marchenko-Pastur distribution and the Wasssertein distances demonstrates that Kalachev et al.'s samples are statistically closer to the Sycamore samples than Pan et al.'s while the three datasets have similar values for the linear cross-entropy fidelity. In conclusion, our finding implies that further study is needed to certify or beat the claims of quantum advantage using random circuit sampling.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

BCSR on GPU: A Way Forward Extreme-scale Graph Processing on Accelerator-enabled Frontier Supercomputer

Handling large graphs in a distributed environment requires effective partitioning across processors and efficient management of local partitions. In 2D partitioning, local graphs often become too sparse, making memory-efficient data structures crucial. Using the Compressed Sparse Row (CSR) format wastes space, especially for > 83% of vertices with empty edges for the sparse graphs. This study explores bit-CSR (BCSR), a modified CSR representation, on GPUs to reduce memory usage in graph computations. We achieved 16.67% memory savings on a sparse rmat dataset with 268 million vertices and 357 million edges, without performance degradation, supported by both theoretical and experimental storage savings of 33%. However, we observed a 1.7× slowdown in degree lookup times due to bitwise operations on AMD CPUs. This analysis highlights the potential of BCSR on GPUs for improving Graph500 benchmark performance on GPU-accelerated systems, such as the Frontier supercomputer.

Sattar, Naw Safrin↗
DOE OSTI2024

A comprehensive guide to CAN IDS data and introduction of the ROAD dataset

Although ubiquitous in modern vehicles, Controller Area Networks (CANs) lack basic security properties and are easily exploitable. A rapidly growing field of CAN security research has emerged that seeks to detect intrusions or anomalies on CANs. Producing vehicular CAN data with a variety of intrusions is a difficult task for most researchers as it requires expensive assets and deep expertise. To illuminate this task, we introduce the first comprehensive guide to the existing open CAN intrusion detection system (IDS) datasets. We categorize attacks on CANs including fabrication (adding frames, e.g., flooding or targeting and ID), suspension (removing an ID’s frames), and masquerade attacks (spoofed frames sent in lieu of suspended ones). We provide a quality analysis of each dataset; an enumeration of each datasets’ attacks, benefits, and drawbacks; categorization as real vs. simulated CAN data and real vs. simulated attacks; whether the data is raw CAN data or signal-translated; number of vehicles/CANs; quantity in terms of time; and finally a suggested use case of each dataset. State-of-the-art public CAN IDS datasets are limited to real fabrication (simple message injection) attacks and simulated attacks often in synthetic data, lacking fidelity. In general, the physical effects of attacks on the vehicle are not verified in the available datasets. Only one dataset provides signal-translated data but is missing a corresponding “raw” binary version. This issue pigeon-holes CAN IDS research into testing on limited and often inappropriate data (usually with attacks that are too easily detectable to truly test the method). The scarcity of appropriate data has stymied comparability and reproducibility of results for researchers. As our primary contribution, we present the Real ORNL Automotive Dynamometer (ROAD) CAN IDS dataset, consisting of over 3.5 hours of one vehicle’s CAN data. ROAD contains ambient data recorded during a diverse set of activities, and attacks of increasing stealth with multiple variants and instances of real (i.e. non-simulated) fuzzing, fabrication, unique advanced attacks, and simulated masquerade attacks. To facilitate a benchmark for CAN IDS methods that require signal-translated inputs, we also provide the signal time series format for many of the CAN captures. Our contributions aim to facilitate appropriate benchmarking and needed comparability in the CAN IDS research field.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

SCEC/USGS Community Stress-Drop Validation Study: How Spectral Fitting Approaches Influence Measured Source Parameters

Spectral source parameters used to estimate an earthquake’s stress drop (⁠Δσ⁠) can vary significantly across measurement approaches. The Statewide California Earthquake Center/U.S. Geological Survey Community Stress‐Drop Validation Study was initiated to compare source parameter estimates, focusing initially on a dataset from the 2019 Ridgecrest earthquake sequence. As part of that validation effort, here we focus on one potential source of uncertainty: whether spectral fitting approaches alone, applied to a common set of spectra from the 2019 Ridgecrest sequence result in different source parameter estimates. By using a common set of benchmark spectra analyzed across a consistent frequency band of 1–40 Hz, we eliminate many sources of variability. A subgroup of validation study participants volunteered to estimate the low‐frequency displacement (⁠Ω 0 ⁠) and corner frequency (⁠ƒ c ⁠) by fitting a smooth function to benchmark displacement spectra. Participants used linear‐ or log‐sampled spectra, assumed a Brune or Boatwright spectral model, and applied different misfit criteria. We compare 17 approaches used to estimate ⁠Ω 0 ⁠, ƒ c ⁠, and Δσ for 54 earthquake spectra. Our results reveal that 35% of events have Δσ estimates within a factor of two, whereas others exhibit variations exceeding an order of magnitude. The variability in and can largely be attributed to whether a spectrum is consistent with the smooth function of an idealized simple crack model. The trade‐off between Ω 0 and ƒ c may be more pronounced when using linearly sampled spectra, as higher frequency spectral bumps control the fits. As expected, methods that assumed a Boatwright model tended to have lower Ω 0 and somewhat higher ƒ c compared to those assuming a Brune model, although resulting Δσ estimates are similar. Finally, when compared to the overall validation study results, the fitting approach alone may account for between 5% and 90% (25% on average) of the total variability in spectral Δσ⁠.

58 GEOSCIENCES↗
DOE OSTI2022

BUTTER - Empirical Deep Learning Dataset

The BUTTER Empirical Deep Learning Dataset represents an empirical study of the deep learning phenomena on dense fully connected networks, scanning across thirteen datasets, eight network shapes, fourteen depths, twenty-three network sizes (number of trainable parameters), four learning rates, six minibatch sizes, four levels of label noise, and fourteen levels of L1 and L2 regularization each. Multiple repetitions (typically 30, sometimes 10) of each combination of hyperparameters were preformed, and statistics including training and test loss (using a 80% / 20% shuffled train-test split) are recorded at the end of each training epoch. In total, this dataset covers 178 thousand distinct hyperparameter settings ("experiments"), 3.55 million individual training runs (an average of 20 repetitions of each experiments), and a total of 13.3 billion training epochs (three thousand epochs were covered by most runs). Accumulating this dataset consumed 5,448.4 CPU core-years, 17.8 GPU-years, and 111.2 node-years.

Array↗
DOE OSTI2026

Transplatformer: translating toxicogenomic profiles between generations of platforms

Background Transcriptomic profiling technologies have advanced the analysis of biological and toxicological responses. However, substantial differences in probe design, dynamic range, gene coverage, and preprocessing pipelines across platforms introduce artifacts that limit cross-study integration and hinder the reuse of historical datasets. We aim to develop computational methods for accurate cross-platform translation to maximize the value of legacy resources. Results We present TransPlatformer a deep learning framework for translating gene expression profiles across heterogeneous toxicogenomics platforms. TransPlatformer employs a novel attention-based architecture to map high-dimensional fold-change vectors from legacy microarray technologies to current platforms. Models are trained and evaluated using DrugMatrix, spanning three technological generations. We investigate mixed-tissue, single-tissue, and cross-tissue training paradigms and benchmark performance against multilayer perceptron and matrix-completion baselines. In mixed-tissue training, TransPlatformer achieves a greater than 50% reduction in mean absolute error (0.043 vs. 0.09) and nearly doubles Pearson correlation ( ≈ 0.71 vs. 0.37) relative to baseline methods. Importantly, TransPlatformer preserves rare but biologically meaningful over- and under-expressed signals, with mean absolute error below 0.22. Single-tissue models yield further improvements for well-represented organs, such as a 10% reduction in liver mean absolute error, while underscoring the need for data augmentation strategies in low-sample tissues.ra Conclusions TransPlatformer provides an effective and scalable computational solution for cross-platform transcriptomic translation. By enabling biologically faithful harmonization of gene expression data, the proposed approach facilitates the reuse of legacy toxicogenomics datasets, enhances downstream biomarker discovery, and supports more reproducible predictive modeling in toxicology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

ℤ2 × ℤ2 Equivariant Quantum Neural Networks: Benchmarking against Classical Neural Networks

This paper presents a comparative analysis of the performance of Equivariant Quantum Neural Networks (EQNNs) and Quantum Neural Networks (QNNs), juxtaposed against their classical counterparts: Equivariant Neural Networks (ENNs) and Deep Neural Networks (DNNs). We evaluate the performance of each network with three two-dimensional toy examples for a binary classification task, focusing on model complexity (measured by the number of parameters) and the size of the training dataset. Our results show that the Z2×Z2 EQNN and the QNN provide superior performance for smaller parameter sets and modest training data samples.

Dong, Zhongtian (ORCID:0000000210003454)↗
DOE OSTI2025

Computational investigation of the impact of metal–organic framework topology on hydrogen storage capacity

Metal–organic frameworks (MOFs) are promising, tunable materials for hydrogen storage. For application under cryogenic operating conditions, past work has run into a ceiling on performance due to a trade-off in the volumetric deliverable capacity (VDC) versus the gravimetric deliverable capacity (GDC). In this study, we computationally constructed and screened 105 230 MOF structures based on 529 nets to explore the effect of underlying topology on the hydrogen storage performance of the resulting materials. A machine learning model was developed based on simulated hydrogen uptake to facilitate screening of the entire dataset, and it successfully identified the top 10% of materials with a root-mean-square error of approximately 1 g L −1 as validated by subsequent grand canonical Monte Carlo simulations. We identified a promising structure based on the tsx topology that exhibits both VDC and GDC higher than the current benchmark material, MOF-5. Our data-driven analysis indicates that nets with higher net density yield MOFs with enhanced volumetric and gravimetric surface areas, thereby improving maximum VDC while shifting the capacity trade-off toward higher GDC.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Parameter Sensitivity Analysis of the SparTen High Performance Sparse Tensor Decomposition Software (Extended Analysis)

Tensor decomposition models play an increasingly important role in modern data science applications. One problem of particular interest is fitting a low-rank Canonical Polyadic (CP) tensor decomposition model when the tensor has sparse structure and the tensor elements are nonnegative count data. SparTen is a high-performance C++ library which computes a low-rank decomposition using different solvers: a first-order quasi-Newton or a second-order damped Newton method, along with the appropriate choice of runtime parameters. Since default parameters in SparTen are tuned to experimental results in prior published work on a single real-world dataset conducted using MATLAB implementations of these methods, it remains unclear if the parameter defaults in SparTen are appropriate for general tensor data. Furthermore, it is unknown how sensitive algorithm convergence is to changes in the input parameter values. This report addresses these unresolved issues with large-scale experimentation on three benchmark tensor data sets. Experiments were conducted on several different CPU architectures and replicated with many initial states to establish generalized profiles of algorithm convergence behavior.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Best Practices for Nuclear Experiment Data Preservation at Idaho National Laboratory: A Guide for Researchers and Reactor Operators

Preserving experimental data is essential for supporting advancements in nuclear science and ensuring the longevity of Idaho National Laboratory's contributions to reactor technology and safety. This report provides a comprehensive guide to best practices for experimental data management and preservation, focusing on standardized data formats, redundancy in storage, metadata documentation, and alignment with international standards. By following these recommendations, experimentalists and reactor operators can enhance the accessibility, reproducibility, and utility of critical datasets for regulatory review, validation computational methods, and future research.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2024

KETCHUP: Parameterizing of large-scale kinetic models using multiple datasets with different reference states

Large-scale kinetic models provide the computational means to dynamically link metabolic reaction fluxes to metabolite concentrations and enzyme levels while also conforming to substrate level regulation. However, the development of broadly applicable frameworks for efficiently and robustly parameterizing models remains a challenge. Challenges arise due to both the heterogeneity, paucity, and difficulty in obtaining flux and/or concentration data but also due to the computational difficulties of the underlying parameter identification problem. Both the computational demands for parameterization, degeneracy of obtained parameter solutions and interpretability of results has so far limited widespread adoption of large-scale kinetic models despite their potential. Herein, we introduce the Kinetic Estimation Tool Capturing Heterogeneous Datasets Using Pyomo (KETCHUP), a flexible parameter estimation tool that leverages a primal-dual interior-point algorithm to solve a nonlinear programming (NLP) problem that identifies a set of parameters capable of recapitulating the (non)steady-state fluxes and concentrations in wild-type and perturbed metabolic networks. KETCHUP is benchmarked against previously parameterized large-scale kinetic models demonstrating an at least an order of magnitude faster convergence than the tool K-FIT while at the same time attaining better data fits. Finally, this versatile toolbox accepts different kinetic descriptions, metabolic fluxes, enzyme levels and metabolite concentrations, under either steady-state or instationary conditions to enable robust kinetic model construction and parameterization. KETCHUP supports the SBML format and can be accessed at https://github.com/maranasgroup/KETCHUP.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Fast and deep phosphoproteome analysis with the Orbitrap Astral mass spectrometer

Owing to its roles in cellular signal transduction, protein phosphorylation plays critical roles in myriad cell processes. That said, detecting and quantifying protein phosphorylation has remained a challenge. We describe the use of a novel mass spectrometer (Orbitrap Astral) coupled with data-independent acquisition (DIA) to achieve rapid and deep analysis of human and mouse phosphoproteomes. With this method, we map approximately 30,000 unique human phosphorylation sites within a half-hour of data collection. The technology is benchmarked to other state-of-the-art MS platforms using both synthetic peptide standards and with EGF-stimulated HeLa cells. We apply this approach to generate a phosphoproteome multi-tissue atlas of the mouse. Altogether, we detect 81,120 unique phosphorylation sites within 12 hours of measurement. With this unique dataset, we examine the sequence, structural, and kinase specificity context of protein phosphorylation. Finally, we highlight the discovery potential of this resource with multiple examples of phosphorylation events relevant to mitochondrial and brain biology.

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

VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses

Abstract Background Viruses are a significant player in many biosphere and human ecosystems, but most signals remain “hidden” in metagenomic/metatranscriptomic sequence datasets due to the lack of universal gene markers, database representatives, and insufficiently advanced identification tools. Results Here, we introduce VirSorter2, a DNA and RNA virus identification tool that leverages genome-informed database advances across a collection of customized automatic classifiers to improve the accuracy and range of virus sequence detection. When benchmarked against genomes from both isolated and uncultivated viruses, VirSorter2 uniquely performed consistently with high accuracy (F1-score > 0.8) across viral diversity, while all other tools under-detected viruses outside of the group most represented in reference databases (i.e., those in the order Caudovirales ). Among the tools evaluated, VirSorter2 was also uniquely able to minimize errors associated with atypical cellular sequences including eukaryotic genomes and plasmids. Finally, as the virosphere exploration unravels novel viral sequences, VirSorter2’s modular design makes it inherently able to expand to new types of viruses via the design of new classifiers to maintain maximal sensitivity and specificity. Conclusion With multi-classifier and modular design, VirSorter2 demonstrates higher overall accuracy across major viral groups and will advance our knowledge of virus evolution, diversity, and virus-microbe interaction in various ecosystems. Source code of VirSorter2 is freely available ( https://bitbucket.org/MAVERICLab/virsorter2 ), and VirSorter2 is also available both on bioconda and as an iVirus app on CyVerse ( https://de.cyverse.org/de ).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

gdess: A framework for evaluating simulated atmospheric CO 2 in Earth System Models

Atmospheric carbon dioxide (CO 2 ) plays a key role in the global carbon cycle and global warming. Climate-carbon feedbacks are often studied and estimated using Earth System Models (ESMs), which couple together multiple model components—including the atmosphere, ocean, terrestrial biosphere, and cryosphere—to jointly simulate mass and energy exchanges within and between these components. Despite tremendous advances, model intercomparisons and benchmarking are aspects of ESMs that warrant further improvement (Fer et al., 2021; Smith et al., 2014). Such benchmarking is critical because comparing the value of state variables in these simulations against observed values provides evidence for appropriately refining model components; moreover, researchers can learn much about Earth system dynamics in the process (Randall et al., 2019). We introduce `gdess` (a.k.a., Greenhouse gas Diagnostics for Earth System Simulations), which parses observational datasets and ESM simulation output, combines them to be in a consistent structure, computes statistical metrics, and generates diagnostic visualizations. In its current incarnation, `gdess` facilitates evaluating a model's ability to reproduce observed temporal and spatial variations of atmospheric CO 2 . The diagnostics implemented modularly in `gdess` support more rapid assessment and improvement of model-simulated global CO 2 sources and sinks associated with land and ocean ecosystem processes. We intend for this set of automated diagnostics to form an extensible, open source framework for future comparisons of simulated and observed concentrations of various greenhouse gases across Earth system models.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Scaling laws in jet classification

We demonstrate the emergence of scaling laws in the benchmark top versus QCD jet classification problem in collider physics. Six distinct physically-motivated classifiers exhibit power-law scaling of the binary cross-entropy test loss as a function of training set size, with distinct power law indices. This result highlights the importance of comparing classifiers as a function of dataset size rather than for a fixed training set, as the optimal classifier may change considerably as the dataset is scaled up. We speculate on the interpretation of our results in terms of previous models of scaling laws observed in natural language and image datasets.

Batson, Joshua↗
DOE OSTI2025

High-Fidelity, Large-Scale, Realistic Dataset Development

The final report summarizes the work performed for supporting the ARPA-E Grid Optimization Competition (Challenge 2 and Challenge 3) within the stated period. Challenge 2 For the challenge period, the main responsibility of the team is to investigate, gen- erate, and deliver parts of the data sets for the competition, based on the competition model for Challenge 2, existing data sets from Challenge 1, and data source supplied by other data set teams. Challenge 3 For the challenge period, the main responsibility of the team is to propose, create, deliver, and maintain the data format during the competition period. The data format will specify how the benchmark data will be represented and communicated to competitors. It will also specify how competitors should report back the solutions. The data format will be closely aligned with the problem formulation (maintained by the formulation team) and the solution validation process (maintained by the validation team). Our team is also responsible in investigating, generating, and delivering parts of the data sets for the competition. The data sets will be created based on the competition model for Challenge 3, existing data sets from Challenge 1 and Challenge 2, and data source supplied by other data set teams.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2024

Predicting metabolic modules in incomplete bacterial genomes with MetaPathPredict

The reconstruction of complete microbial metabolic pathways using ‘omics data from environmental samples remains challenging. Computational pipelines for pathway reconstruction that utilize machine learning methods to predict the presence or absence of KEGG modules in incomplete genomes are lacking. Here, we present MetaPathPredict, a software tool that incorporates machine learning models to predict the presence of complete KEGG modules within bacterial genomic datasets. Using gene annotation data and information from the KEGG module database, MetaPathPredict employs deep learning models to predict the presence of KEGG modules in a genome. MetaPathPredict can be used as a command line tool or as a Python module, and both options are designed to be run locally or on a compute cluster. Benchmarks show that MetaPathPredict makes robust predictions of KEGG module presence within highly incomplete genomes.

59 BASIC BIOLOGICAL SCIENCES↗