Search NASA⌕ Search

SEARCH · Search NASA

Results for “Structural Modeling”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Rescattering photoelectron spectroscopy of the CO 2 molecule: Progress towards experimental discrimination between theoretical target-structure models

Photoelectron momentum distributions (PEMDs) generated in strong-field ionization of randomly oriented CO 2 molecules by intense infrared laser pulses at 1300-, 1450-, and 1650-nm wavelengths are measured experimentally and analyzed theoretically. Here, the experimental PEMDs extracted along the outermost backward rescattering caustic are well reproduced by theoretical calculations based on the recently derived factorization formula with an analytical returning photoelectron wave packet (RWP). The sensitivity of the theoretical results to the target structure models used in the calculations is investigated. It is shown that RWPs obtained in the single-active-electron (SAE) approximation and by the Hartree-Fock method have only minor differences. On the other hand, differential cross sections (DCSs) for elastic scattering of a photoelectron on the parent molecular ion calculated by ab initio , SAE, and independent-atom model methods are considerably different. This difference almost disappears after averaging over molecular orientations, so the present experiment does not enable us to discriminate between the different target structure models. However, we show that such a discrimination should become possible by measuring PEMD with aligned molecules. This will provide an access to the rich target structure information contained in the DCS.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, RCSB.org), the US Worldwide Protein Data Bank (wwPDB, wwPDB.org) data center for the global PDB archive, provides access to the PDB data via its RCSB.org research-focused web portal. We report substantial additions to the tools and visualization features available at RCSB.org, which now delivers more than 227000 experimentally determined atomic-level three-dimensional (3D) biostructures stored in the global PDB archive alongside more than 1 million Computed Structure Models (CSMs) of proteins (including models for human, model organisms, select human pathogens, crop plants and organisms important for addressing climate change). In addition to providing support for 3D structure motif searches with user-provided coordinates, new features highlighted herein include query results organized by redundancy-reduced Groups and summary pages that facilitate exploration of groups of similar proteins. Newly released programmatic tools are also described, as are enhanced training opportunities.

Burley, Stephen K.↗
DOE OSTI2021

Additively Manufactured Compliant Hybrid Gas Thrust Bearing for Supercritical Carbon Dioxide Turbomachinery: Experimental Evaluation and Fluid–Structure Model Predictions

This paper presents rotating test results and advances an analytical predictive fluid–structure model for a new type of gas-lubricated thrust bearing fabricated using direct metal laser melting. The bearing concept in this study is a compliant hybrid gas thrust bearing that uses external pressurization to increase load carrying capacity, where the testing campaign in this study was only focused on steady-state static performance. The need for the bearing concept comes from enabling highly efficient supercritical carbon dioxide (sCO2) turbomachinery by replacing oil-lubricated bearings with process gas lubrication. Leveraging the process gas of the turbomachine for bearing lubrication results in lowered bearing power loss, simplified mechanical design, and allows for novel oil-free hermetic drivetrains resulting in an efficient emission-free system. The new concept utilizes hydrostatic pressurization on individual tilting pads flexibly mounted with hermetic squeeze film dampers (HSFDs). This paper focuses on rotating tests of a 173 mm outer diameter gas thrust bearing in air up to 10 krpm and hydrostatic inlet pressures to 365 psi (2.52 MPa). The influence of thrust runner speed and bearing inlet pressure on force deflection characteristics and load carrying capability of the gas film were experimentally evaluated. This work also advances a predictive fluid–structure thrust bearing model using an isothermal ideal-gas-based compressible Reynolds flow equation directly coupled to a lumped stiffness element possessing axial and rotational degrees-of-freedom. The rotating testing demonstrated load capability of 1816 lbs (8.1 kN), which equates to a thrust bearing unit load of 67 psi (0.46 MPa). Gas film force–deflection curves reveal a nonlinear relationship between thrust load and film clearance. Comparison of film thickness values with the predictive model show good agreement under high load and inlet pressure, however deviate as load and pressure decrease. Load capability was shown to increase with increasing hydrostatic inlet pressure, while the increase in thrust runner speed revealed a small decrease in load capacity.

Engineering↗
DOE OSTI2022

RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning

Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB PDB is also responsible for PDB data security. Annually, RCSB PDB serves >10 000 depositors of three-dimensional (3D) biostructures working on all permanently inhabited continents. RCSB PDB delivers data from its research-focused RCSB.org web portal to many millions of PDB data consumers based in virtually every United Nations-recognized country, territory, etc. This Database Issue contribution describes upgrades to the research-focused RCSB.org web portal that created a one-stop-shop for open access to ∼200 000 experimentally-determined PDB structures of biological macromolecules alongside >1 000 000 incorporated Computed Structure Models (CSMs) predicted using artificial intelligence/machine learning methods. RCSB.org is a ‘living data resource.’ Every PDB structure and CSM is integrated weekly with related functional annotations from external biodata resources, providing up-to-date information for the entire corpus of 3D biostructure data freely available from RCSB.org with no usage limitations. Within RCSB.org, PDB structures and the CSMs are clearly identified as to their provenance and reliability. Both are fully searchable, and can be analyzed and visualized using the full complement of RCSB.org web portal capabilities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

3D WHOLE-PROMINENCE FINE STRUCTURE MODELING. II. PROMINENCE EVOLUTION

We use the new three-dimensional (3D) whole-prominence fine structure model to study the evolution of prominences and their fine structures in response to changes in the underlying photospheric magnetic flux distribution. The applied model combines a detailed 3D prominence magnetic field configuration with a realistic description of the prominence plasma distributed along multiple fine structures. In addition, we utilize an approximate Hα visualization technique to study the evolution of the visible cool prominence plasma both in emission (prominence) and absorption (filament). We show that the initial magnetic field configuration of the modeled prominence is significantly disturbed by the changing position of a single polarity of a magnetic bipole as the bipole is advected toward the main body of the filament. This leads to the creation of a barb, which becomes the dominant feature visible in the synthetic Hα images of both the prominence and filament views. The evolution of the bipole also creates conditions that lead to the disappearance and reappearance of large portions of the main body. We also show that an arch-like region containing a dark void (a bubble) can be naturally produced in the synthetic prominence Hα images. While not visible in terms of the magnetic field lines, it is due to a lack of Hα emission from low-pressure, low-density plasma located in shallow magnetic dips lying along the lines of sight intersecting the dark void. In addition, a quasi-vertical small-scale feature consisting of short and deep dips, piled one above the other, is produced.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Snow Micro-Structure Model

PIKA is a MOOSE-based application for modeling micro-structure evolution of seasonal snow. The model will be useful for environmental, atmospheric, and climate scientists. Possible applications include application to energy balance models, ice sheet modeling, and avalanche forecasting. The model implements physics from published, peer-reviewed articles. The main purpose is to foster university and laboratory collaboration to build a larger multi-scale snow model using MOOSE. The main feature of the code is that it is implemented using the MOOSE framework, thus making features such as multiphysics coupling, adaptive mesh refinement, and parallel scalability native to the application. PIKA implements three equations: the phase-field equation for tracking the evolution of the ice-air interface within seasonal snow at the grain-scale; the heat equation for computing the temperature of both the ice and air within the snow; and the mass transport equation for monitoring the diffusion of water vapor in the pore space of the snow.

Micah Johnson, AndrewSlaughter↗
DOE OSTI2014

Snow Micro-Structure Model

PIKA is a MOOSE-based application for modeling micro-structure evolution of seasonal snow. The model will be useful for environmental, atmospheric, and climate scientists. Possible applications include application to energy balance models, ice sheet modeling, and avalanche forecasting. The model implements physics from published, peer-reviewed articles. The main purpose is to foster university and laboratory collaboration to build a larger multi-scale snow model using MOOSE. The main feature of the code is that it is implemented using the MOOSE framework, thus making features such as multiphysics coupling, adaptive mesh refinement, and parallel scalability native to the application. PIKA implements three equations: the phase-field equation for tracking the evolution of the ice-air interface within seasonal snow at the grain-scale; the heat equation for computing the temperature of both the ice and air within the snow; and the mass transport equation for monitoring the diffusion of water vapor in the pore space of the snow.

Micah Johnson, Andrew Slaughter↗
DOE OSTI2023

Structural models and functional annotations for the Sphagnum divinum proteome

This dataset contains the structural models for the primary transcripts of the Sphagnum divinum proteome. Additionally, for a subset of these proteins, sequence and structural alignment results are provided. This dataset represents the most thorough structural study of a Sphagnum species, also known as peat mosses, by providing three-dimensional atomic resolution structures of the majority of the encoded proteins as well as structural alignment results used in the application of annotating the proteome. References (DOI) AlphaFold v2 Monomer: https://doi.org/10.1038/s41586-021-03819-2. References (DOI) US-align2: https://doi.org/10.1038/s41592-022-01585-1

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

RCSB protein data Bank: Next‐generation advanced search for exploration of experimental structures and computed structure models

Abstract The Protein Data Bank (PDB), established in 1971, is the primary global, open‐access archive for experimentally determined 3D macromolecular structures (proteins, RNA, DNA). The research‐focused RCSB.org web‐portal provides access to these data alongside more than one million machine‐learning‐predicted structure models, greatly expanding the available structural landscape. Rapid growth of both experimental and computational structures has increased the need for powerful yet accessible search tools that serve a broad and diverse scientific community. Herein, we describe a redesigned RCSB Protein Data Bank RCSB.org Advanced Search capability that supports intuitive discovery of 3D structures through a unified interface. This interface integrates annotation‐, sequence‐, and 3D structure‐based searches, embeds an interactive 3D viewer, and incorporates curated biological knowledge, such as catalytic site definitions from Mechanism and Catalytic Site Atlas and ligand‐guided structural motifs, for constructing geometry‐driven queries. A new Chemical Search tool allows definition of chemical queries via an integrated drawing tool or standard identifiers, seamlessly combining them with annotation filters. By allowing query definition directly within spatial and chemical contexts, these search interfaces reduce the need for detailed knowledge of residue numbering, chain identifiers, or external cheminformatics software. This capability enables efficient exploration of structures, chemical diversity, and structure–function relationships across all life domains. The redesigned interfaces can be accessed directly at rcsb.org/search/advanced for Advanced Search and rcsb.org/search/chemical for Chemical Search.

Rose, Yana [Research Collaboratory for Structural ↗
DOE OSTI2015

Implications of Model Structure and Detail for Utility Planning. Scenario Case Studies using the Resource Planning Model

We examine how model investment decisions change under different model configurations and assumptions related to renewable capacity credit, the inclusion or exclusion of operating reserves, dispatch period sampling, transmission power flow modeling, renewable spur line costs, and the ability of a planning region to import and export power. For all modeled scenarios, we find that under market conditions where new renewable deployment is predominantly driven by renewable portfolio standards, model representations of wind and solar capacity credit and interactions between balancing areas are most influential in avoiding model investments in excess thermal capacity. We also compare computation time between configurations to evaluate tradeoffs between computational burden and model accuracy. From this analysis, we find that certain advanced dispatch representations (e.g., DC optimal power flow) can have dramatic adverse effects on computation time but can be largely inconsequential to model investment outcomes, at least at the renewable penetration levels modeled. Finally, we find that certain underappreciated aspects of new capacity investment decisions and model representations thereof, such as spur lines for new renewable capacity, can influence model outcomes particularly in the renewable technology and location chosen by the model. Though this analysis is not comprehensive and results are specific to the model region, input assumptions, and optimization-modeling framework employed, the findings are intended to provide a guide for model improvement opportunities.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2023

RootSlice —A novel functional-structural model for root anatomical phenotypes

Root anatomy is an important determinant of root metabolic costs, soil exploration, and soil resource capture. Root anatomy varies substantially within and among plant species. RootSlice is a multicellular functional-structural model of root anatomy developed to facilitate the analysis and understanding of root anatomical phenotypes. RootSlice can capture phenotypically accurate root anatomy in three dimensions of different root classes and developmental zones, of both monocotyledonous and dicotyledonous species. Several case studies are presented illustrating the capabilities of the model. For maize nodal roots, the model illustrated the role of vacuole expansion in cell elongation; and confirmed the individual and synergistic role of increasing root cortical aerenchyma and reducing the number of cortical cell files in reducing root metabolic costs. Integration of RootSlice for different root zones as the temporal properties of the nodal roots in the whole-plant and soil model OpenSimRoot/maize enabled the multiscale evaluation of root anatomical phenotypes, highlighting the role of aerenchyma formation in enhancing the utility of cortical cell files for improving plant performance over varying soil nitrogen supply. Such integrative in silico approaches present avenues for exploring the fitness landscape of root anatomical phenotypes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Practical considerations for atomistic structure modeling with Cryo-EM maps

We present our experiences and opinions with selected software with respect to atomistic structure modeling with single particle analysis derived maps. These are atomistic model building and fitting method selection criteria and implementation procedures. Since we explain common concepts and caveats that we have explained to our collaborators, we hope that this short perspective will help facilitate active discussion between scientists at different levels and backgrounds.

Kim, Doo Nam↗
DOE OSTI2016

Empirically testing vaterite structural models using neutron diffraction and thermal analysis

Otoliths, calcium carbonate (CaCO 3 ) ear bones, are among the most commonly used age and growth structures of fishes. Most fish otoliths are comprised of the most dense CaCO 3 polymorph, aragonite. Sturgeon otoliths, in contrast, have been characterized as the rare and structurally enigmatic polymorph, vaterite a metastable polymorph of CaCO 3 . Vaterite is an important material ranging from biomedical to personal care applications although its crystal structure is highly debated. We characterized the structure of sturgeon otoliths using thermal analysis and neutron powder diffraction, which is used non-destructively. We confirmed that while sturgeon otoliths are primarily composed of vaterite, they also contain the denser CaCO 3 polymorph, calcite. For the vaterite fraction, neutron diffraction data provide enhanced discrimination of the carbonate group compared to x-ray diffraction data, owing to the different relative neutron scattering lengths, and thus offer the opportunity to uniquely test the more than one dozen crystal structural models that have been proposed for vaterite. Of those, space group P6 5 22 model, a = 7.1443(4)Å , c = 25.350(4)Å , V = 1121.5(2)Å 3 provides the best fit to the neutron powder diffraction data, and allows for a structure refinement using rigid carbonate groups.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

A local structure model for network analysis

The statistical analysis of networks is a popular research topic with ever widening applications. Exponential random graph models (ERGMs), which specify a model through interpretable, global network features, are common for this purpose. In this study we introduce a new class of models for network analysis, called local structure graph models (LSGMs). In contrast to an ERGM, a LSGM specifies a network model through local features and allows for an interpretable and controllable local dependence structure. In particular, LSGMs are formulated by a set of full conditional distributions for each network edge, e.g., the probability of edge presence/absence, depending on neighborhoods of other edges. Additional model features are introduced to aid in specification and to help alleviate a common issue (occurring also with ERGMs) of model degeneracy. Finally, the proposed models are demonstrated on a network of tornadoes in Arkansas where a LSGM is shown to perform significantly better than a model without local dependence.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Structural modeling and dynamic analysis of condensate storage tanks in nuclear power plants

Condensate storage tanks (CSTs) in nuclear power plants (NPPs) are classified as critical equipment capable of surviving strong shaking in a design basis earthquake to assure the ability to subsequently provide cooling water. Structural modeling and dynamic analysis of CSTs are complicated due to fluid-structure interaction (FSI) and coupling issues, which could have significant effects on seismic response. The capability of a number of approximate models to capture seismic response is investigated using dynamic analysis results from detailed finite element models. Modal analyses and time history analyses are carried out using both 2D and 3D models to predict the dynamic behavior of CSTs as a function of ground motion intensity. Although 2D simplified models can be used to quickly evaluate the dynamic response of CSTs when there is substantial margin to failure, a detailed 3D model is required when it is necessary to examine a limit state associated with the failure mode of the tank. The findings show good agreement between the natural frequencies of convective modes determined from the 2D and 3D CST models. The difference between the frequencies of impulsive modes were found to be equal to or less than 25%.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Molecular structure models of amorphous bismuth and cerium carboxylate catalyst precursors

As our societal need for materials and energy has grown, so has our need for catalyst processes in hydrogen production. A major function in these applications, for both homogenous and heterogeneous catalysis processes, is the synthesis of an active metal catalyst. It must first be soluble to control the physical properties of the metal being used. Recent work in metal precursors has begun to turn toward these metal carboxylate types of material. Here, structural models are proposed for bismuth 2-ethylhexanoate and 2,2-dimethyloctanoate and cerium 2-ethylhexanoate. The bismuth compounds have been characterized at different ratios of bismuth to carboxylate as solutions of the free acids. Their structures are most consistent with a Bi 4 (RCO 2 ) 12 motif where the Bi ions are arranged in a flattened tetrahedron with Bi – Bi distances of about 4.3 Å. There is evidence for Bi – O – Bi linkages at low free acid concentrations. The cerium compound is most consistent with a linear tetracerium molecule where the Ce – Ce distances repeat at about 4.3 Å out to 16.4 Å. The models were generated by analogy with known crystal structures and compared to high-energy x-ray scattering data. To further evaluate the models, DFT calculations were made, and the equilibrium geometries were compared. The vibrational spectra calculated from those geometries are presented and compared to the experimental results. Magnetization vs. temperature data was collected on the cerium compound, and its behavior was consistent with the proposed model. A geometrical approach to determining the dimensionality and relative positions of the metal ions in these structures is presented.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗