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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 433 records · Page 24

Thermodynamic Modeling of Intrinsic Defects in MnBi₂Te₄

This repository contains the computational data supporting the manuscript titled “The critical role of intrinsic defects and many-body interactions on the stability of MnBi₂Te₄.” It includes: 1. DFT data generated using VASP, used for training and benchmarking electronic structure models. 2. Quantum Monte Carlo (QMC) data produced with QMCPACK, used to apply many-body corrections and validate the electronic and magnetic properties of MnBi₂Te₄. 3. Relevant scripts used to run, analyze, and process the calculations, enabling reproducibility and transparency of the workflows.

36 MATERIALS SCIENCE↗

Chromatin structures from integrated AI and polymer physics model

The physical organization of the genome in three-dimensional space regulates many biological processes, including gene expression and cell differentiation. Three-dimensional characterization of genome structure is critical to understanding these biological processes. Direct experimental measurements of genome structure are challenging; computational models of chromatin structure are therefore necessary. We develop an approach that combines a particle-based chromatin polymer model, molecular simulation, and machine learning to efficiently and accurately estimate chromatin structure fromindirectmeasures of genome structure. More specifically, we introduce a new approach where the interaction parameters of the polymer model are extracted from experimental Hi-C data using a graph neural network (GNN). We train the GNN on simulated data from the underlying polymer model, avoiding the need for large quantities of experimental data. The resulting approach accurately estimates chromatin structures across all chromosomes and across several experimental cell lines despite being trained almost exclusively on simulated data. The proposed approach can be viewed as a general framework for combining physical modeling with machine learning, and it could be extended to integrate additional biological data modalities. Ultimately, we achieve accurate and high-throughput estimations of chromatin structure from Hi-C data, which will be necessary as experimental methodologies, such as single-cell Hi-C, improve.

Biochemistry & Molecular Biology↗

Accelerating the Structure Exploration of Diverse Bi–Pt Nanoclusters via Physics‐Informed Machine Learning Potential and Particle Swarm Optimization

Bimetallic Bi–Pt nanoclusters exhibit diverse structural motifs, including core-shell, Janus, and mixed alloy configurations, due to the unique bonding characteristics between Bi and Pt atoms. Using density functional theory refinements from ChIMES physically machine-learned potential and CALYPSO particle swarm optimization global searches, 34 Bi20-Pt20 nanoclusters are systematically classified. The results reveal that Bi atoms predominantly occupy surface sites, driven by charge transfer effects. Cohesive energy trends alone prove insufficient for structure differentiation, necessitating a data-driven approach employing principal component analysis and K-means clustering. Furthermore, vibrational, electronic, and infrared spectral analyses provide additional insights into structure-property relationships. The findings offer an original framework for the automated classification and analysis of bimetallic nanoclusters, enhancing the understanding of their stability and functional properties.

bimetallic nanoparticles↗

Investigating Electron Conductivity Regimes in the Bacterial Cytochrome Wire OmcS

The anaerobic bacterium Geobacter sulfurreducens produces extracellular, electronically conductive cytochrome polymer wires that are conductive over micron length scales. Structure models from cryo-electron microscopy data show OmcS wires form a linear chain of hemes along the protein wire axis, which is proposed as the structural basis supporting their electronic properties. However, the mechanism by which this heme arrangement supports long-range electronic conduction remains unknown. Structure models from cryo-electron microscopy data show these wires form a linear chain of hemes along the protein wire axis, which is proposed as the structural basis supporting their electronic properties. Existing computational models using static heme redox potentials and coupling energies fail to explain experimental observations, predicting conductances 10,000 to 100,000 times lower than measured values. Here, we investigate how dynamic disorder affects site energies, interheme coupling, and long-range electronic conductivity within these cytochrome wires. We introduce an approach to extract charge carrier site information directly from Kohn–Sham density functional theory, without employing projector schemes, and show that site and coupling energies are highly sensitive to changes in interheme geometry and the surrounding electrostatic environment. Unlike models that incorporate dynamic disorder as a thermally averaged quantity, our quantum charge carrier model incorporates proxies for dynamic disorder through decoherence corrections, yielding predicted diffusion coefficient closer to what is expected from experiment and comparable with other organic-based electronic materials. Based on these simulations, we propose that the instantaneous fluctuations of the local electrostatic environment can transiently lift energy degeneracies and delocalize charge carriers. Furthermore, these studies reveal how incorporating dynamic fluctuations associated with the environment resolves the discrepancy between theory and experiment in microbial cytochrome wires and highlight design principles for bioinspired, heme-based conductive materials.

Bioinorganic chemistry↗

Protein data bank: From two epidemics to the global pandemic to mRNA vaccines and Paxlovid

Structural biologists and the open-access Protein Data Bank (PDB) played decisive roles in combating the COVID-19 pandemic. Global biostructure data were turned into global knowledge, allowing scientists and engineers to understand the inner workings of coronaviruses and develop effective countermeasures. Two mRNA vaccines, initially designed with guidance from PDB structures of the SARS-CoV-1 and MERS-CoV spike proteins, prevented infections entirely or reduced the likelihood of morbidity and mortality for more than five billion individual recipients worldwide. Structure-guided drug discovery by Pfizer, Inc (facilitated by PDB structures), initiated in the 2000s in response to SARS-CoV-1 and resumed in 2020, yielded nirmatrelvir (the active ingredient of Paxlovid) -- a potent, orally-bioavailable inhibitor of the SARS-CoV-2 main protease. You've got to love the Protein Data Bank!

Burley, Stephen K.↗

FAIR Data Meets FAIR Software

Modern scientific research is increasingly defined by the interplay between data, software, and the workflows that connect them. Yet while the FAIR (Findable, Accessible, Interoperable, Reusable) principles have become foundational for scientific data stewardship, the same level of structure and expectation has only recently begun to extend to research software. This talk covers why and how FAIR principles are being applied to data and software to support data reuse. It outlines the gaps in current sharing norms, the growing federal emphasis on persistent identifiers and public access, and the opportunities created when datasets, computational workflows, code, and models are linked through rich, standardized metadata. Practical implementation pathways for the EIC and JLab communities are described, including datacards for structured dataset documentation and provenance-aware workflows. By aligning data lifecycle management with FAIR-aligned software practices, the scientific community can advance toward autonomous knowledge graphs, generative workflows, and high-quality, AI-ready scientific datasets.

McSpadden, Diana [Thomas Jefferson National Accele↗

Bifunctional Electrocatalysts with High-Entropy Alloys: Bridging Hydrogen Evolution and Oxygen Reduction

High-entropy alloys (HEAs) have emerged as a promising class of bifunctional electrocatalysts capable of simultaneously driving the hydrogen evolution reaction (HER) and the oxygen reduction reaction (ORR) with high activity and durability. Their near-equiatomic multicomponent compositions give rise to unique physicochemical characteristics, including lattice distortion, sluggish diffusion, high-entropy stabilization, and pronounced electronic heterogeneity, that collectively generate diverse and synergistic active sites inaccessible in conventional alloys. This review summarizes recent progress in HEA-based bifunctional electrocatalysis, with a focus on the fundamental mechanisms governing HER and ORR activity, stability, and selectivity. We discuss advances in synthesis strategies, ranging from confined growth and step-alloying to scalable continuous-flow methods, that enable precise control over composition, size, and surface structure. Complementary computational and data-driven approaches, including density functional theory, machine-learning-assisted screening, and descriptor development, are highlighted as essential tools for navigating the vast HEA design space and establishing structure−property relationships. Particular attention is paid to adsorption-energy distributions, multisite cooperativity, and environmental effects under realistic electrochemical conditions. Finally, we outline current challenges and future opportunities for integrating mechanistic understanding with AI-guided, closed-loop design frameworks to accelerate the discovery of next-generation HEA bifunctional electrocatalysts for sustainable energy conversion.

Alloys↗

Extracting the femtometer structure of strange baryons using the vacuum polarization effect

Abstract One of the fundamental goals of particle physics is to gain a microscopic understanding of the strong interaction. Electromagnetic form factors quantify the structure of hadrons in terms of charge and magnetization distributions. While the nucleon structure has been investigated extensively, data on hyperons are still scarce. It has recently been demonstrated that electron-positron annihilations into hyperon-antihyperon pairs provide a powerful tool to investigate their inner structure. We present a method useful for hyperon-antihyperon pairs of different types which exploits the cross section enhancement due to the effect of vacuum polarization at theJ/ψresonance. Using the 10 billionJ/ψevents collected with the BESIII detector, this allows a precise determination of the hyperon structure function. The result is essentially a precise snapshot of the$$\bar{\Lambda }{\Sigma }^{0}\,(\Lambda {\bar{\Sigma }}^{0})$$ Λ ¯ Σ 0 ( Λ Σ ¯ 0 ) transition process, encoded in the transition form factor ratio and phase. Their values are measured to beR = 0.860 ± 0.029(stat.) ± 0.015(syst.),$$\Delta {\Phi }_{\bar{\Lambda }{\Sigma }^{0}}=(1.011\pm 0.094({{\rm{stat.}}})\pm 0.010({{\rm{syst.}}}))\,{{\rm{r}}}ad$$ Δ Φ Λ ¯ Σ 0 = ( 1.011 ± 0.094 ( stat. ) ± 0.010 ( syst. ) ) r a d and$$\Delta {\Phi }_{\Lambda {\bar{\Sigma }}^{0}}=(2.128\pm 0.094({{\rm{stat.}}})\pm 0.010({{\rm{syst.}}}))\,{{\rm{r}}}ad$$ Δ Φ Λ Σ ¯ 0 = ( 2.128 ± 0.094 ( stat. ) ± 0.010 ( syst. ) ) r a d . Furthermore, charge-parity (CP) breaking is investigated in this reaction and found to be consistent with CP symmetry.

Science & Technology - Other Topics↗

MOSCATO Development and Integration in Fiscal Year 2024

MOSCATO (Molten Salt Chemistry and Transport) is a multiphysics code that provides high-fidelity, coupled simulations of fluid flow, heat transfer, mass transfer, chemistry, electrochemical phenomena, and alloy evolution for molten salt equipment. In FY24, significant developments were made to the code package, enhancing its capabilities in many aspects. The improvements and advancements can be summarized as follows: 1. Implementation of tritium transport capabilities and validation with experimental data: To enable modeling of tritium and other fission gases within MSRs, we implemented gas transport within MOSCATO via inclusion of couple mass transport equations within the salt and structural alloys. Comparisons to experimental data from literature showed good agreement with respect to tritium release rates. 2. Preliminary implementation of two-phase flow models in MOSCATO: To model tritium and other gases above their solubility limits, we implemented preliminary two-phase flow models within MOSCATO to account for bubble transport. The first model adopted was the Level-Set approach, which can handle the high void fraction regime, but with a requirement for high mesh resolution thus high computational expense. In this report, we present a verification of the Level-Set method using a simple benchmark case. We also performed a demonstration of the code as applied to an experimental case involving cover gas flow through salt in an experimental vessel. The second model adopted was the Eulerian-Eulerian dispersed flow model, which is computationally cheaper but limited to low void fraction regimes, such as bubbly flow. Validation and verification have not yet been performed for the Eulerian-Eulerian approach, but a preliminary implementation was completed. 3. Validation with static corrosion experiments: Static corrosion experimental data for stainless steel coupons within molten salts was used to further validate the corrosion model in MOSCATO. To do so, we leveraged the existing models in MOSCATO and simulated the sample mass loss and mass gain phenomena. Several ion species, including Cr 2+ , Fe 2+ and H + , were simulated in salt using the PNP solver, while Cr 0 and Fe 0 were simulated with a diffusion solver in stainless steel. The mass loss of the samples was compared with experimental data, and good agreement was achieved. These combined activities served to further expand the capabilities of MOSCATO and make it more generally applicable to the full range of phenomena that can control chemistry and corrosion in molten salt reactors.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

STRUCTURAL MODELING TO SUPPORT POST-YIELD ACCEPTANCE CRITERIA FOR SPENT NUCLEAR FUEL CLADDING

Spent nuclear fuel (SNF) is evaluated for structural failure during storage and transportation scenarios. The U.S. Department of Energy’s Spent Fuel and Waste Science and Technology (SFWST) program has sponsored significant research in quantifying mechanical loads on SNF during storage and transportation scenarios using experimental and modeling methods. The SFWST program has also performed significant research on measuring the mechanical behavior of irradiated SNF as defueled cladding segments and cladding with fuel pellets to measure composite behavior. This paper considers some of the key material data from the Sibling Pin testing and uses structural modeling and analysis methods that have been informed by testing to consider post-yield acceptance criteria for SNF cladding structural analysis. Test data published by Oak Ridge National Laboratory (ORNL) and Pacific Northwest National Laboratory (PNNL) are the foundation for informing the material behavior of the models developed in this study. In particular, four-point bend (4PB) tests of fueled and defueled cladding segments provide significant information about the bending failure mode of SNF. ORNL’s 4PB test data is on fueled cladding segments, so the composite behavior of SNF is demonstrated. This paper describes PNNL’s coincident beam model that was developed to approximate the composite behavior of SNF. This paper also presents PNNL’s structural dynamic finite element models of a cask tip-over scenario, which is predicted to cause the strongest mechanical loads on SNF of all postulated storage and transportation scenarios. SNF bending loads predicted in the cask tip-over scenario and cladding acceptance criteria beyond yield are considered, with justification based on the Sibling Pin test data. ASME Boiler and Pressure Vessel code stress intensity limits are also considered. The ultimate goal of this work is to aid in the justification of structural acceptance criteria for SNF cladding beyond the cladding’s irradiated yield strength for use in structural analysis of all storage and transportation scenarios.

Klymyshyn, Nicholas A.↗

Transit Rider/Travel Behavior Inventory Survey - Minneapolis-St. Paul Metro - 2010

The Metropolitan Council administered a system-wide transit on-board survey between September and November 2010 as part of the 2010 Travel Behavior Inventory to provide detailed transit usage patterns and rider information to support modeling and planning efforts. The study’s focus was to capture only the most current and reliable data necessary to determine future public transportation needs in the Minneapolis region. The study was structured to collect detailed transit ridership data for different routes during different times of day to develop a disaggregate transit trip table that will support advanced travel demand modeling. The study was designed to leverage existing data sources, such as the 2005 on-board survey, to provide the best quality data to update the Travel Behavior Inventory in the Minneapolis-Saint Paul metropolitan area.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Dataset for "A primer on forest structure measurement with lidar for ecologists"

This repository includes data and code accompanying the case study included in the manuscript "A primer on forest structure measurement with lidar for ecologists" (submitted to Ecosphere). We compiled lidar datasets from multiple platforms in a common area to: 1. Demonstrate how differences in sensor characteristics influence density and resolution of lidar data. 2. Provide open-source, co-located datasets for users to further inspect differences in lidar data. 3. Provide example code to perform basic lidar analysis. This case study is meant to allow readers to get hands-on experience with real-world data from different platforms. This case study is not meant to be a rigorous comparison of derived ecological metrics among all sensors; such comparisons can be found throughout other publications referenced throughout the main manuscript. Code includes basic functions in R commonly used to visualize and manipulate lidar data accessible with a normal laptop computer; more sophisticated algorithms for advanced users are also referenced throughout the main manuscript. Terrestrial laser scanning (TLS), mobile laser scanning (MLS), UAS laser scanning (ULS), airborne laser scanning (ALS), and spaceborne laser scanning (SLS) data were collected within the Smithsonian Environmental Research Center (SERC) forest dynamics plot in Maryland, USA. TLS, MLS, and ALS data were collected within 1 month of the 2021 growing season; ULS data were collected in November 2020 (“leaf-off” data) and July 2022 (“leaf-on” data).

54 ENVIRONMENTAL SCIENCES↗

Multifrequency radar observations of marine clouds during the EPCAPE campaign

The Eastern Pacific Cloud Aerosol Precipitation Experiment (EPCAPE) was a year-round campaign conducted by the US Department of Energy at the Scripps Institution of Oceanography in La Jolla, CA, USA, with a focus on characterizing atmospheric processes at a coastal location. The ground-based prototype of a new Ka-, W-, and G-band (35.75, 94.88, and 238.8 GHz) profiling atmospheric radar, named CloudCube, which was developed at the Jet Propulsion Laboratory, took part in the experiment during 6 weeks in March and April 2023. This article describes the unique data sets that were obtained during the field campaign from a variety of marine clouds and light precipitation. These are, to the best of the authors' knowledge, the first observations of atmospheric clouds using simultaneous multifrequency measurements including 238.8 GHz. These data sets therefore provide an exceptional opportunity to study and analyze hydrometeors with diameters in the millimeter- and submillimeter size range that can be used to better understand cloud and precipitation structure, formation, and evolution. The data sets referenced in this article are intended to provide a complete, extensive, and high-quality collection of G-band data in the form of Doppler spectra and Doppler moments. In addition, Ka-band and W-band reflectivity and Ka-, W-, and G-band reflectivity ratio profiles are included for several cases of interest on 6 different days.

54 ENVIRONMENTAL SCIENCES↗

Native Architecture of Wheat Straw Cell Walls: A Unified Model from X-ray Scattering and Solid-State NMR

Plant secondary cell walls constitute the dominant reservoir of renewable biomass, comprising tightly packed cellulose, hemicellulose, and lignin at the nanoscale. Recent advances in solid-state NMR spectroscopy and the availability of small-angle X-ray scattering for biomass characterization have led to an accumulation of experimental data on cell wall organization, yet no explicit structure model has simultaneously satisfied both Xray and NMR observations. Using wheat straw as a model system, we propose a structural framework consistent with current knowledge of cellulose biosynthesis, X-ray scattering data, and one- and two-dimensional 13 C solid-state NMR spectra. In this model, 18-chain elementary fibrils align in parallel and populate the cross-section at random. Arabinose-substituted xylan shows no conformational dependence for cellulose-binding in wheat, and only a minor fraction of 2-fold xylan appears in close proximity to cellulose, unlike in Arabidopsis, where xylan is more tightly attached to the cellulose surface. While NMR data cannot unambiguously resolve the internal arrangement of the 18 glucan chains, X-ray scattering profiles uniquely constrain the fibril size and exclude the possibility of tight bundling in the intact walls. The specific interaction between the matrix polymers and the cellulose elementary fibrils must be reconsidered in light of the small interfibril spaces, which bring the matrix components into spatial proximity with cellulose even in the absence of attractive interactions. These findings provide fundamental molecular-level insight into cellulose fibril architecture and matrix−polymer interactions, resolving longstanding discrepancies between spectroscopic and scattering data and advancing our understanding of biopolymer assembly into structurally and functionally versatile lignocellulosic biomaterials.

Carbohydrates↗

Compressive Response and Energy Absorption of Additively Manufactured Elastomers with Varied Simple Cubic Architectures

Additive manufacturing, and particularly the vat photopolymerization process, enables the fabrication of complex geometries at high resolution and small length scales, making it well-suited for fabricating cellular structures (e.g., foams and lattices). Among these, elastomeric cellular structures are of growing interest due to their tunable compliance and energy dissipation. However, comprehensive data on the compressive behavior of these structures remains limited, especially for investigating the structure-property effects from changing the density and distribution of material within the cellular structure. This study explores how the mechanical response of polyurethane-based simple cubic structures changes when varying volume fraction, unit cell length, and unit cell patterning, which have not been systematically investigated previously in additively manufactured elastomers. Increasing volume fraction from 10% to 50% yielded significant changes in compressive stress–strain performance (decreasing strain at 0.5 MPa by 41.6% and increasing energy absorption density by 3962.5%). Although changing the unit cell length between 2.5 and 7 mm in ~30 mm parts did not result in statistically different stress–strain responses, modifying the configuration of struts of different thicknesses across designs with 30% volume fraction altered the stress–strain behavior (differences of 12.5% in strain at 0.5 MPa and 109.4% for energy absorption density). Power law relationships were developed to understand the interactions between volume fraction, unit cell length, and elastic modulus, and experimental data showed strong fits (R 2 > 0.91). These findings enhance the understanding of how multiple structural design aspects influence the performance of elastomeric cellular materials, providing a foundation for informing strategic design of tailorable materials for diverse mechanical applications.

36 MATERIALS SCIENCE↗

Protein-ligand binding affinity prediction using multi-instance learning with docking structures

Recent advances in 3D structure-based deep learning approaches demonstrate improved accuracy in predicting protein-ligand binding affinity in drug discovery. These methods complement physics-based computational modeling such as molecular docking for virtual high-throughput screening. Despite recent advances and improved predictive performance, most methods in this category primarily rely on utilizing co-crystal complex structures and experimentally measured binding affinities as both input and output data for model training. Nevertheless, co-crystal complex structures are not readily available and the inaccurate predicted structures from molecular docking can degrade the accuracy of the machine learning methods. We introduce a novel structure-based inference method utilizing multiple molecular docking poses for each complex entity. Our proposed method employs multi-instance learning with an attention network to predict binding affinity from a collection of docking poses. We validate our method using multiple datasets, including PDBbind and compounds targeting the main protease of SARS-CoV-2. The results demonstrate that our method leveraging docking poses is competitive with other state-of-the-art inference models that depend on co-crystal structures. This method offers binding affinity prediction without requiring co-crystal structures, thereby increasing its applicability to protein targets lacking such data.

97 MATHEMATICS AND COMPUTING↗

Integrating chromosome conformation and DNA repair in a computational framework to assess cell radiosensitivity

Objective. The arrangement of chromosomes in the cell nucleus has implications for cell radiosensitivity. The development of new tools to utilize Hi-C chromosome conformation data in nanoscale radiation track structure simulations allows for in silico investigation of this phenomenon. We have developed a framework employing Hi-C-based cell nucleus models in Monte Carlo radiation simulations, in conjunction with mechanistic models of DNA repair, to predict not only the initial radiation-induced DNA damage, but also the repair outcomes resulting from this damage, allowing us to investigate the role chromosome conformation plays in the biological outcome of radiation exposure. Approach. In this study, we used this framework to generate cell nucleus models based on Hi-C data from fibroblast and lymphoblastoid cells and explore the effects of cell type-specific chromosome structure on radiation response. The models were used to simulate external beam irradiation including DNA damage and subsequent DNA repair. The kinetics of the simulated DNA repair were compared with previous results. Main results. We found that the fibroblast models resulted in a higher rate of inter-chromosome misrepair than the lymphoblastoid model, despite having similar amounts of initial DNA damage and total misrepairs for each irradiation scenario. Significance. This framework represents a step forward in radiobiological modeling and simulation allowing for more realistic investigation of radiosensitivity in different types of cells.

59 BASIC BIOLOGICAL SCIENCES↗

SO(3)-invariant PCA with application to molecular data

Principal component analysis (PCA) is a fundamental technique for dimensionality reduction and denoising; however, its application to three-dimensional data with arbitrary orientations -- common in structural biology -- presents significant challenges. A naive approach requires augmenting the dataset with many rotated copies of each sample, incurring prohibitive computational costs. In this paper, we extend PCA to 3D volumetric datasets with unknown orientations by developing an efficient and principled framework for SO(3)-invariant PCA that implicitly accounts for all rotations without explicit data augmentation. By exploiting underlying algebraic structure, we demonstrate that the computation involves only the square root of the total number of covariance entries, resulting in a substantial reduction in complexity. We validate the method on real-world molecular datasets, demonstrating its effectiveness and opening up new possibilities for large-scale, high-dimensional reconstruction problems.

Fraiman, Michael [Tel Aviv Univ., Tel Aviv (Israel↗