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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
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 OSTI2018

A close look onto structural models and primary ligands of metallo-β-lactamases

β-Lactamases are hydrolytic enzymes capable of opening the β-lactam ring of antibiotics such as penicillin, thus endowing the bacteria that produce them with antibiotic resistance. Of particular medical concern are metallo-β-lactamases (MBLs), with an active site built around coordinated Zn cations. MBLs are pan-reactive enzymes that can break down almost all classes of β-lactams, including such last-resort antibiotics as carbapenems. They are not only broad-spectrum-reactive but are often plasmid-borne (e.g., the New Delhi enzyme, NDM), and can spread horizontally even among unrelated bacteria. Acquired MBLs are encoded by mobile genetic elements, which often include other resistance genes, making the microbiological situation particularly alarming. There is an urgent need to develop MBL inhibitors in order to rescue our antibiotic armory. A number of such efforts have been undertaken, most notably using the 3D structures of various MBLs as drug-design targets. Structure-guided drug discovery depends on the quality of the structures that are collected in the Protein Data Bank (PDB) and on the consistency of the information in dedicated β-lactamase databases. Here, we conducted a careful review of the crystal structures of class B β-lactamases, concluding that the quality of these structures varies widely, especially in the regions where small molecules interact with the macromolecules. In a number of examples the interpretation of the bound ligands (e.g., inhibitors, substrate/product analogs) is doubtful or even incorrect, and it appears that in some cases the modeling of ligands was not supported by electron density. For ten MBL structures, alternative interpretations of the original diffraction data could be proposed and the new models have been deposited in the PDB. In four cases, these models, prepared jointly with the authors of the original depositions, superseded the previous deposits. This review emphasizes the importance of critical assessment of structural models describing key drug design targets at the level of the raw experimental data. Since the structures reviewed here are the basis for ongoing design of new MBL inhibitors, it is important to identify and correct the problems with ambiguous crystallographic interpretations, thus enhancing reproducibility in this highly medically relevant area.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

MO-DE-BRA-05: Developing Effective Medical Physics Knowledge Structures: Models and Methods

Purpose: Develop a method and supporting online resources to be used by medical physics educators for teaching medical imaging professionals and trainees so they develop highly-effective physics knowledge structures that can contribute to improved diagnostic image quality on a global basis. Methods: The different types of mental knowledge structures were analyzed and modeled with respect to both the learning and teaching process for their development and the functions or tasks that can be performed with the knowledge. While symbolic verbal and mathematical knowledge structures are very important in medical physics for many purposes, the tasks of applying physics in clinical imaging--especially to optimize image quality and diagnostic accuracy--requires a sensory conceptual knowledge structure, specifically, an interconnected network of visually based concepts. This type of knowledge supports tasks such as analysis, evaluation, problem solving, interacting, and creating solutions. Traditional educational methods including lectures, online modules, and many texts are serial procedures and limited with respect to developing interconnected conceptual networks. A method consisting of the synergistic combination of on-site medical physics teachers and the online resource, CONET (Concept network developer), has been developed and made available for the topic Radiographic Image Quality. This was selected as the inaugural topic, others to follow, because it can be used by medical physicists teaching the large population of medical imaging professionals, such as radiology residents, who can apply the knowledge. Results: Tutorials for medical physics educators on developing effective knowledge structures are being presented and published and CONET is available with open access for all to use. Conclusion: An adjunct to traditional medical physics educational methods with the added focus on sensory concept development provides opportunities for medical physics teachers to share their knowledge and experience at a higher cognitive level and produce medical professionals with the enhanced ability to apply physics to clinical procedures.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Coupling the Modeled Structural Transmissibility of a Used Nuclear Fuel Conveyance to Over the Road Data - 16215

The U.S. Department of Energy Office of Nuclear Energy (DOE-NE), Office of Fuel Cycle Technology, has established the Used Fuel Disposition Campaign (UFDC) to conduct research and development activities related to storage, transportation, and disposal of used nuclear fuel (UNF) and high-level radioactive waste (HLW). The mission of the UFDC is to identify alternatives and conduct scientific research and technology development to enable storage, transportation and disposal of used nuclear fuel and HLW generated by existing and future nuclear fuel cycles. The Storage and Transportation staff within the UFDC is responsible for addressing issues regarding the long-term or extended storage (ES) of UNF and its subsequent transportation. Current information is insufficient to determine the ability of UNF, including high-burnup fuel, to withstand shock and vibration loads that could occur when UNF is shipped by rail from nuclear power plant sites to a storage or disposal facility after extended storage. In order to make this determination, the magnitude of the transportation loads transmitted to the UNF must be quantified. Previous preliminary modeling work has shown how the structural transmissibility of the transport system can affect the magnitude of these loads and the importance of modeling all aspects of the transport system (i.e. rail car, transport cradle, cask, canister, and fuel). The work presented herein proposes a methodology for determining the structural transmissibility of a hypothetical transport system, and conditions existing over the road test (OTR) data to predict the performance of the hypothetical system. This method utilizes the modeled frequency response of the hypothetical system to scale the existing OTR acceleration data. This work will be relevant in creating models of a UNF conveyance during transport. As such, preliminary work in coupling the rail vehicle dynamics code NUCARS{sup C}, a general purpose multi-body rail vehicle dynamics simulation package developed by Transportation Technology Center Inc. (TTCI), to existing models of UNF during transport are also discussed herein. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
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 OSTI2016

Charge distribution and hydrogen bonding of a collagen α 2 ‐chain in vacuum, hydrated, neutral, and charged structural models

A challenging task in computational biophysics is to ascertain the solvent effect on the electronic structure and interatomic bonding at the atomistic level. Simulations must be carried out on reasonably large biomolecules for accurate calculations to yield valid results. We report the results of a calculation on collagen model in the form of a peptide under three different environments: vacuum, solvated and with neutral and charged sites. Quantitative results and analysis of the partial charge (PC) distribution on each amino acid are discussed. A significant charge transfer of more than 1 electron from protein to water molecules is found with similar results when the model contains charged sites. The main contributions to the interatomic bonding are from hydrogen bonds (HBs) between water‐water and water‐protein pairs. A connection between PC and HBs can be established since the nonpolar amino acids form no HBs and have the smallest PC and vice versa. The ab initio PC obtained are used in the NAMD simulation showing significant improvement over the default values as reflected in the root mean square deviation of atomic positions in the MD steps and the total free energy in energy minimization. These results could facilitate the interpretation of data on interaction of various ligands in charged proteins in relation to isoelectric points. © 2016 Wiley Periodicals, Inc.

Eifler, Jay↗
DOE OSTI2015

Defining a Two-pronged Structural Model for PB1 (Phox/Bem1p) Domain Interaction in Plant Auxin Responses

Phox/Bem1p (PB1) domains are universal structural modules that use surfaces of different charge for protein-protein association. In plants, PB1-mediated interactions of auxin response factors (ARF) and auxin/indole 3-acetic acid inducible proteins regulate transcriptional events modulated by the phytohormone auxin. Here we investigate the thermodynamic and structural basis for Arabidopsis thaliana ARF7 PB1 domain self-interaction. Isothermal titration calorimetry and NMR experiments indicate that key residues on both the basic and acidic faces of the PB1 domain contribute to and organize coordinately to stabilize protein-protein interactions. Calorimetric analysis of ARF7PB1 site-directed mutants defines a two-pronged electrostatic interaction. Furthermore, the canonical PB1 interaction between a lysine and a cluster of acidic residues provides one prong with an arginine and a second cluster of acidic residues defining the other prong. Evolutionary conservation of this core recognition feature and other co-varying interface sequences allows for versatile PB1-mediated interactions in auxin signaling.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2016

Landau-Zener extension of the Tavis-Cummings model: Structure of the solution

We explore the recently discovered solution of the driven Tavis-Cummings model (DTCM). It describes interaction of an arbitrary number of two-level systems with a bosonic mode that has linearly time-dependent frequency. We derive compact and tractable expressions for transition probabilities in terms of the well-known special functions. In this form, our formulas are suitable for fast numerical calculations and analytical approximations. As an application, we obtain the semiclassical limit of the exact solution and compare it to prior approximations. Furthermore, we also reveal connection between DTCM and q -deformed binomial statistics.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2017

Detailed assessment of global transport-energy models’ structures and projections

This paper focuses on comparing the frameworks and projections from four major global transportation models with considerable transportation technology and behavioral detail. We analyze and compare the modeling frameworks, underlying data, assumptions, intermediate parameters, and projections to identify the sources of divergence or consistency, as well as key knowledge gaps. We find that there are significant differences in the base-year data and key parameters for future projections, especially for developing countries. These include passenger and freight activity, mode shares, vehicle ownership rates, and even energy consumption by mode, particularly for shipping, aviation and trucking. This may be due in part to a lack of previous efforts to do such consistency-checking and “bench-marking.” We find that the four models differ in terms of the relative roles of various mitigation strategies to achieve a 2°C / 450 ppm CO2e target: the economics-based integrated assessment models favor the use of low carbon fuels as the primary mitigation option followed by efficiency improvements, whereas transport-only and expert-based models favor efficiency improvements of vehicles followed by mode shifts. We offer recommendations for future modeling improvements focusing on (1) reducing data gaps; (2) translating the findings from this study into relevant policy implications such as feasibility of current policy goals, additional policy targets needed, regional vs. global reductions, etc.; (3) modeling strata of demographic groups to improve understanding of vehicle ownership levels, travel behavior, and urban vs. rural considerations; and (4) conducting coordinated efforts in aligning input assumptions and historical data, policy analysis, and modeling insights.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2014

A Structural Model for Binding of the Serine-Rich Repeat Adhesin GspB to Host Carbohydrate Receptors

GspB is a serine-rich repeat (SRR) adhesin of Streptococcus gordonii that mediates binding of this organism to human platelets via its interaction with sialyl-T antigen on the receptor GPIb{alpha}. This interaction appears to be a major virulence determinant in the pathogenesis of infective endocarditis. To address the mechanism by which GspB recognizes its carbohydrate ligand, we determined the high-resolution x-ray crystal structure of the GspB binding region (GspB{sub BR}), both alone and in complex with a disaccharide precursor to sialyl-T antigen. Analysis of the GspB{sub BR} structure revealed that it is comprised of three independently folded subdomains or modules: (1) an Ig-fold resembling a CnaA domain from prokaryotic pathogens; (2) a second Ig-fold resembling the binding region of mammalian Siglecs; (3) a subdomain of unique fold. The disaccharide was found to bind in a pocket within the Siglec subdomain, but at a site distinct from that observed in mammalian Siglecs. Confirming the biological relevance of this binding pocket, we produced three isogenic variants of S. gordonii, each containing a single point mutation of a residue lining this binding pocket. These variants have reduced binding to carbohydrates of GPIb{alpha}. Further examination of purified GspB{sub BR}-R484E showed reduced binding to sialyl-T antigen while S. gordonii harboring this mutation did not efficiently bind platelets and showed a significant reduction in virulence, as measured by an animal model of endocarditis. Analysis of other SRR proteins revealed that the predicted binding regions of these adhesins also had a modular organization, with those known to bind carbohydrate receptors having modules homologous to the Siglec and Unique subdomains of GspBBR. This suggests that the binding specificity of the SRR family of adhesins is determined by the type and organization of discrete modules within the binding domains, which may affect the tropism of organisms for different tissues.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Tuning Optical Properties of Conjugated Molecules by Lewis Acids: Insights from Electronic Structure Modeling

Understanding and controlling the optoelectronic properties of organic semiconductors at the molecular level remains a challenge due to the complexity of chemical structures and intermolecular interactions. A common strategy to address this challenge is to utilize both experimental and computational approaches. In this contribution, we show that density functional theory (DFT) calculation is a useful tool to provide insights into the bonding, electron population distribution, and optical transitions of adducts between conjugated molecules and Lewis acids (CM-LA). Adduct formation leads to relevant modifications of key properties, including a red shift in optical transitions and an increase in charge carrier density and charge mobility, compared to the parent conjugated molecules. We show that electron density transfer from the CM to the LA, which was hypothesized to cause the experimental red shift in absorption spectra upon LA binding, can be quantified and interpreted by population analysis. Experimental red shifts in optical transitions for all molecular families can also be predicted by time dependent DFT calculations with different density functionals. Finally, these detailed insights help to optimize a priori design guidelines for future applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Polymorphous band structure model of gapping in the antiferromagnetic and paramagnetic phases of the Mott insulators MnO, FeO, CoO, and NiO

The existence of band gaps in both the antiferromagnetic (AFM) and paramagnetic (PM) phases of the classic NaCl-structure Mott insulators MnO, FeO, CoO, and NiO is traditionally viewed and taught as a manifestation of strong correlation whereby insulation results from electrons moving across the lattice forming states with doubly occupied d orbitals on certain atomic sites and empty d orbitals on other sites. Within such theories, the gap of the AFM and PM phases of these oxides emerges even in the absence of spatial symmetry breaking. The need for such a correlated picture is partially based on the known failure of the commonly used band models for the PM phase that assume for such a spin disordered state the macroscopically averaged NaCl structure, where all transition metal (TM) sites are symmetry-equivalent (a monomorphous description), producing a gapless PM state with zero magnetic moments, in sharp conflict with experiment. Here, we seek to understand the minimum theoretical description needed to capture the leading descriptors of ground state Mott insulation in the classic, 3d monoxide Mott systems—gapping and moment formation in the AFM and PM phase. As noted by previous authors, the spin-ordered AFM phase in these materials already shows in band theory a significant band gap when one doubles the NaCl unit cell by permitting different potentials for transition-metal atoms with different spins. For the spin-disordered PM phase, we allow analogously larger NaCl-type supercells where each TM site can have different spin direction and local bonding environments (i.e., disordered), yet the total spin is zero. Such a polymorphous description has the flexibility to acquire symmetry-breaking energy-lowering patterns that can lift the degeneracy of the d orbitals and develop large on-site magnetic moments without violating the global, averaged NaCl symmetry. Electrons are exchanged between spin-up and spin-down bands to create closed-shell insulating configurations that lend themselves to a single determinental description. It turns out that such a polymorphous description of the structure within the single-determinant, mean-field, Bloch periodic band structure approach (based on DFT+U) allows large on-site magnetic moments to develop spontaneously, leading to significant (1–3 eV) band gaps and large local moments in the AFM and PM phases of the classic NaCl-structure Mott insulators MnO, FeO, CoO, and NiO in agreement with experiment. We adapt to the spin disordered polymorphous configurations the “special quasirandom structure” (SQS) construct known from the theory of disordered substitutional alloys whereby supercell approximants which represent the best random configuration average (not individual snapshots) for finite (64, 216 atoms, or larger) supercells of a given lattice symmetry are constructed. We conclude that the basic features of these paradigmatic Mott insulators can be approximated by the physics included in energy-lowering symmetry broken DFT.

36 MATERIALS SCIENCE↗
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↗
DOE OSTI2022

Gauge symmetry breaking with fluxes and natural Standard Model structure from exceptional GUTs in F-theory

We give a general description of gauge symmetry breaking using vertical and remainder fluxes in 4D F-theory models. The fluxes can break a geometric gauge group to a smaller group and induce chiral matter, even when the larger group admits no chiral matter representations. We focus specifically on applications to realizations of the Standard Model gauge group and chiral matter spectrum through breaking of rigid exceptional gauge groups E 7 , E 6 , which are ubiquitous in the 4D F-theory landscape. Supplemented by an intermediate SU(5) group, these large classes of models give natural constructions of Standard Model-like theories with small numbers of generations of matter in F-theory.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2015

Light Water Reactor Sustainability Program Advanced Seismic Soil Structure Modeling

Risk calculations should focus on providing best estimate results, and associated insights, for evaluation and decision-making. Specifically, seismic probabilistic risk assessments (SPRAs) are intended to provide best estimates of the various combinations of structural and equipment failures that can lead to a seismic induced core damage event. However, in some instances the current SPRA approach has large uncertainties, and potentially masks other important events (for instance, it was not the seismic motions that caused the Fukushima core melt events, but the tsunami ingress into the facility). SPRA’s are performed by convolving the seismic hazard (this is the estimate of all likely damaging earthquakes at the site of interest) with the seismic fragility (the conditional probability of failure of a structure, system, or component given the occurrence of earthquake ground motion). In this calculation, there are three main pieces to seismic risk quantification, 1) seismic hazard and nuclear power plants (NPPs) response to the hazard, 2) fragility or capacity of structures, systems and components (SSC), and 3) systems analysis. Two areas where NLSSI effects may be important in SPRA calculations are, 1) when calculating in-structure response at the area of interest, and 2) calculation of seismic fragilities (current fragility calculations assume a lognormal distribution for probability of failure of components). Some important effects when using NLSSI in the SPRA calculation process include, 1) gapping and sliding, 2) inclined seismic waves coupled with gapping and sliding of foundations atop soil, 3) inclined seismic waves coupled with gapping and sliding of deeply embedded structures, 4) soil dilatancy, 5) soil liquefaction, 6) surface waves, 7) buoyancy, 8) concrete cracking and 9) seismic isolation The focus of the research task presented here-in is on implementation of NLSSI into the SPRA calculation process when calculating in-structure response at the area of interest. The specific nonlinear soil behavior included in the NLSSI calculation presented in this report is gapping and sliding. Other NLSSI effects are not included in the calculation. The results presented in this report document initial model runs in the linear and nonlinear analysis process. Final comparisons between traditional and advanced SPRA will be presented in the September 30th deliverable.

54 ENVIRONMENTAL SCIENCES↗