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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
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 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↗
DOE OSTI2021

Structural color from a coupled nanowire pair beyond the bonding and antibonding model

Optical resonances in nanostructures can be harnessed to produce a wide range of structural colors. Conversely, the analysis of structural colors has been used to clarify the nature of optical resonances. Here, we show that silicon nanowire (NW) pairs can display a wide range of structural colors by controlling their radiative coupling. This is accomplished by exciting a series of Fabry–Pérot-like modes where light is repeatedly scattered between two NWs. These modes are beyond the expectation from the conventional chemical bonding model under a quasi-electrostatic approximation, in which only bonding and antibonding modes can be formed in a pair system through modal hybridization. The additional eigenmodes found in a two-resonator system originate from the nonlinear, frequency-dependent coupling strength derived from the radiative nature of low- Q resonators. The Fabry–Pérot modes can be tuned across the entire visible frequency range by varying the distance between two NWs, leading to what we believe is a new type of universal building blocks that can provide structural color within a subwavelength footprint. The presented results pave the way toward the design and usage of highly tunable resonances that exploit the radiative coupling of high-index nanostructures.

Li, Qitong↗
DOE OSTI2025

Integrated structural model of the palladin–actin complex using XL ‐ MS , docking, NMR , and SAXS

Abstract Palladin is an actin‐binding protein that accelerates actin polymerization and is linked to the metastasis of several types of cancer. Previously, three lysine residues in an immunoglobulin‐like domain of palladin have been identified as essential for actin binding. However, it is still unknown where palladin binds to F‐actin. Evidence that palladin binds to the sides of actin filaments to facilitate branching is supported by our previous study showing that palladin was able to compensate for Arp2/3 in the formation of Listeria actin comet tails. Here, we used chemical crosslinking to covalently link palladin and F‐actin residues based on spatial proximity. Samples were then enzymatically digested, separated by liquid chromatography, and analyzed by tandem mass spectrometry. Peptides containing the crosslinks and specific residues involved were then identified for input to the HADDOCK docking server to model the most likely binding conformation. Small‐angle x‐ray scattering was used to provide further insight into palladin flexibility and the binding interface, and NMR spectra identified potential interactions between palladin's Ig domains. Our final structural model of the F‐actin:palladin complex revealed how palladin interacts with and stabilizes F‐actin at the interface between two actin monomers. Three actin residues that were identified in this study also appear commonly in the actin‐binding interface with other proteins such as myotilin, myosin, and tropomodulin. An accurate structural representation of the complex between palladin and actin extends our understanding of palladin's role in promoting cancer metastasis through the regulation of actin dynamics.

Sargent, Rachel [Department of Chemistry and Bioch↗
DOE OSTI2023

Multilevel atomic structural model for interstratified opal materials

The structure of opal has long fascinated scientists. It occurs in a number of structural states, ranging from amorphous to exhibiting features of stacking disorder. Opal-CT, where C and T signify cristobalite- and tridymite-like interstratification, represents an important link in the length scales between amorphous and crystalline states. However, details about local atomic (dis)order and arrangements extending to long-range stacking faults in opal polymorphs remain incompletely understood. Here, a multilevel modeling approach is reported that considers stacking states in correlation with the abundance of C and T segments as a high-level structural parameter (i.e. not each atom). Optimization accounting for inter-tetrahedral bond lengths and angles and the regularity of the silicate tetrahedra is included as lower levels of structural parameters. Together, a set of parameters with both coarse-grained and atomistic features for different levels of structural details is refined. Structural disorder at the ~10–100 Å distance scale is evaluated using experimental pair distribution function and diffraction datasets, comparing peak intensities, widths and asymmetry. Here this work presents a complete multilevel structural description of natural opal-CT and explains many of the unusual features observed in X-ray powder diffraction patterns. This modeling approach can be adopted generally for analyzing layered materials and their assembly into 3D structures.

36 MATERIALS SCIENCE↗
DOE OSTI2024

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.↗
DOE OSTI2020

BISON High Burnup Structure Modeling Capabilities Validated with a Selection of the Halden IFA-650 Rods

The U.S. Department of Energy (DOE)’s Nuclear Energy Advanced Modeling and Simulation (NEAMS)program aims to develop predictive capabilities using computational methods for the analysis and design of advanced reactor and fuel cycle systems. This program has been supporting the development of BISON, a high-fidelity and high-resolution fuel performance tool at the engineering scale. This document continues analysis and refinement of capabilities added to BISON early this calendar year in regards to the incorporation of capabilities applicable to extended burnups in response to industry interest. Details are provided on high burnup thermal conductivity models, a refitting of the high-burnup structure (HBS) porosity formation model to include additional data, the coupling of the HBS volume fraction model to thermal conductivity and fine fragmentation models, and validation activities. The IFA-650.4 and IFA-650.9 loss of coolant accident (LOCA) analyses are revisited with the latest developments in this report. A new validation case, IFA-650.14 has also been added to the BISON test suite.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2021

Transforming a Simple Structure Model to Represent a Complex Dynamic System with Unknown Boundary Restraints

Imposing a boundary condition on a structure can significantly alter its dynamic properties. However, sometimes the specifics of the new boundary conditions are not known. When the effects of a boundary condition are uncertain or there is not enough information, engineers need to excite the complex structure to obtain these modified properties. In order to experimentally obtain the new properties, engineers need multiple experiments and many outputs for interpolation in order to sufficiently represent the entire structure. In this study, the researchers attached a stinger to a cantilever beam, acting as a new transverse restraint of unknown properties. This paper presents a conversion expression that predicts the dynamic behavior of any point in the system with the new boundary condition. This expression relies only on one impact hammer experiment with one output and the model of the stinger-free cantilever beam, referred to as the simple structure. Researchers estimated the Transfer Function (TRF) of the beam and compared it with an experimentally measured TRF to validate the method. The mean absolute error of the estimated TRF compared to the experimental TRF is 1.99 dB. This demonstrates the use of the proposed method for estimating unmeasured TRFs in a system with an uncertain boundary condition using a single input, single output (SISO) test and a model of the simple structure.

42 ENGINEERING↗
DOE OSTI2020

Structural modeling and validation of laminated stacks in magnetic gearing applications

Laminated structures are commonly employed in magnetic gears based on their ability to direct magnetic flux, while inhibiting eddy currents. Unfortunately, the stiffness of the laminated structure is much lower than a solid part, which can lead to unacceptable deflections, given the large magnetic forces and small air gaps in magnetic gears. Finite element analysis of laminations to accurately predict these deflections can be computationally expensive due to the small elements needed to model the thin lamination dimensions. These analyses also have some uncertainty due to the assignment of bonding stiffness. This paper presents a means of accurately modelling the deflection of a laminated stack with reduced complexity and computational time, which is compared to experimental results. Here, the resulting methods are then used to assess the magnetic and mechanical advantages of different designs for the modulating pieces of a magnetic gear.

42 ENGINEERING↗
DOE OSTI2023

A structural model of the long-term degradation of the concrete biological shield

The concrete biological shield (CBS) of light water reactors is exposed to high neutron radiation dose in the long term, which may lead to the degradation of the concrete’s mechanical properties. Given the important shielding role of the CBS, it is necessary to investigate the irradiation effects at the structural scale and provide estimates of the damage extent from the wall’s inner surface to study potential license renewals. For this purpose, we developed a mechanical model accounting for radiation-induced expansion, creep, and damage in concrete using the Grizzly finite element code, informed by ex-core neutron flux calculations using the VERA tool. The model was applied to a 3D CBS structure represented by the CBS wall, a steel liner, reinforcement bars, and a concrete base mat and evaluated damage at 40, 60, and 80 years of operation. The VERA model predicted a maximum fluence of approximately 2 x 10 19 ncm -2 at 80 years of operation. The results showed that damage is highest at the inner surface of the CBS wall and gradually decreases with depth. It extends beyond the rebar after 60 years and reaches a depth of approximately 12 cm at 80 years.

42 ENGINEERING↗
DOE OSTI2023

RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure models of proteins

Recent advances in Artificial Intelligence and Machine Learning (e.g., AlphaFold, RosettaFold, and ESMFold) enable prediction of three-dimensional (3D) protein structures from amino acid sequences alone at accuracies comparable to lower-resolution experimental methods. These tools have been employed to predict structures across entire proteomes and the results of large-scale metagenomic sequence studies, yielding an exponential increase in available biomolecular 3D structural information. Given the enormous volume of this newly computed biostructure data, there is an urgent need for robust tools to manage, search, cluster, and visualize large collections of structures. Equally important is the capability to efficiently summarize and visualize metadata, biological/biochemical annotations, and structural features, particularly when working with vast numbers of protein structures of both experimental origin from the Protein Data Bank (PDB) and computationally-predicted models. Moreover, researchers require advanced visualization techniques that support interactive exploration of multiple sequences and structural alignments. This paper introduces a suite of tools provided on the RCSB PDB research-focused web portal RCSB. org, tailor-made for efficient management, search, organization, and visualization of this burgeoning corpus of 3D macromolecular structure data.

3D visualization↗
DOE OSTI2022

Nonconventional NMR Spin-Coupling Constants in Oligosaccharide Conformational Modeling: Structural Dependencies Determined from Density Functional Theory Calculations

Nonconventional NMR spin-coupling constants were investigated to determine their potential as conformational constraints in MA’AT modeling of the O-glycosidic linkages of oligosaccharides. Four ( 1 J C1',H1' , 1 J C1',C2' , 2 J C1',H2' , and 2 J C2',H1' ) and eight ( 1 J C4,H4 , 1 J C3,C4 , 1 J C4,C5 , 2 J C3,H4 , 2 J C4,H3 , 2 J C5,H4 , 2 J C4,H5 , and 2 J C3,C5 ) spin-couplings in methyl β-d-galactopyranosyl-(1→4)-β-d-glucopyranoside (methyl β-lactoside) were calculated using density functional theory (DFT) to determine their dependencies on O-glycosidic linkage C–O torsion angles, $\phi$ and ψ, respectively. Long-range 4 J H1',H4 was also examined as a potential conformational constraint of either $\phi$ or ψ. Secondary effects of exocyclic (hydroxyl) C–O bond rotation within or proximal to these coupling pathways were investigated. Based on the findings of methyl β-lactoside, analogous J-couplings were studied in five additional two-bond O-glycosidic linkages [βGlcNAc-(1→4)-βMan, 2-deoxy-βGlc-(1→4)-βGlc, αMan-(1→3)-βMan, αMan-(1→2)-αMan, and βGlcNAc(1→2)-αMan] to determine whether the coupling behaviors observed in methyl β-lactoside were more broadly observed. Of the 13 nonconventional J-couplings studied, 7 exhibit properties that may be useful in future MA’AT modeling of O-glycosidic linkages, none of which involve coupling pathways that include the linkage C–O bonds. The findings also provide new insights into the general effects of exocyclic C–O bond conformation on the magnitude of experimental spin-couplings in saccharides and other hydroxyl-containing molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗