Search NASA⌕ Search

SEARCH · Search NASA

Results for “Structural simulation”

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 829 records · Page 46
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Multiple Conformational States Contribute to the 3D Structure of a Glucan Decasaccharide: A Combined SAXS and MD Simulation Study

The inherent flexibility of carbohydrates is dependent on stereochemical arrangements, and characterization of their influence and importance will give insight into the three-dimensional structure and dynamics. In this study, a beta-(1 -> 4)/beta-(1 -> 3)-linked glucosyl decasaccharide is experimentally investigated by synchrotron small-angle X-ray scattering from which its radius of gyration (R-g) is obtained. Molecular dynamics (MD) simulations of the decasaccharide show four populated states at each glycosidic linkage, namely, syn- and anti-conformations. The calculated R-g values from the MD simulation reveal that in addition to syn-conformers the presence of anti-psi conformational states is required to reproduce experimental scattering data, unveiling inherent glycosidic linkage flexibility. The CHARMM36 force field for carbohydrates thus describes the conformational flexibility of the decasaccharide very well and captures the conceptual importance that anti-conformers are to be anticipated at glycosidic linkages of carbohydrates.

Jo, Sunhwan↗
DOE OSTI2019

Transcription preinitiation complex structure and dynamics provide insight into genetic diseases

Transcription preinitiation complexes (PICs) are vital assemblies whose function underlies the expression of protein-encoding genes. Cryo-EM advances have begun to uncover their structural organization. Nevertheless, functional analyses are hindered by incompletely modeled regions. Here we integrate all available cryo-EM data to build a practically complete human PIC structural model. This enables simulations that reveal the assembly’s global motions, define PIC partitioning into dynamic communities and delineate how structural modules function together to remodel DNA. We identify key TFIIE–p62 interactions that link core-PIC to TFIIH. p62 rigging interlaces p34, p44 and XPD while capping the DNA-binding and ATP-binding sites of XPD. PIC kinks and locks substrate DNA, creating negative supercoiling within the Pol II cleft to facilitate promoter opening. Mapping disease mutations associated with xeroderma pigmentosum, trichothiodystrophy and Cockayne syndrome onto defined communities reveals clustering into three mechanistic classes that affect TFIIH helicase functions, protein interactions and interface dynamics.

Biochemistry & Molecular Biology↗
DOE OSTI2025

Programmable exploration of magnetic states in Lieb-kagome interpolated lattices

We investigate a hybrid modeling framework in which a quantum annealer is used to simulate magnetic interactions in molecular qubit lattices inspired by experimentally realizable systems. Using phthalocyanine assemblies as a structurally constrained prototype, we model a continuous deformation from a Lieb to a kagome lattice, revealing frustration-driven disorder and magnetic field-induced reordering in the spin structure. Here, the goal is to show how a quantum annealer can operate as a physically instantiated, programmable platform to emulate experimentally relevant lattice deformations and produce observables in a manner analogous to an experimental measurement, enabling the characterization of magnetic arrangements beyond the reach of current molecular architectures. This surrogate modeling approach offers a pathway to explore and iteratively design tunable magnetic states in synthetic materials. The synthetic design, structural characterization, and quantum simulation framework established here defines a modular and scalable paradigm for probing the limits of engineered matter across chemistry, condensed matter, and quantum information science.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2020

Structure factors of the unitary gas under supernova conditions

Here, we compute with lattice field theory the vector and axial static structure factors of the unitary gas for arbitrary temperature above the superfluid transition and for fugacities 0.1 < $\mathcal{z}$ < 1.0 . Using the lattice formulation, we calculate beyond the validity of the virial expansion, a commonly used technique in many-body physics. We find qualitative differences in the behavior of the structure factors at high fugacity compared to the predictions of the virial expansion. Due to the large scattering length of neutrons, we expect the unitary gas structure factors to approximate the structure factors of hot neutron gases, and we therefore expect our calculations to be useful in supernova simulations, where neutron gas structure factors are needed to compute in-medium neutrino-neutron scattering rates.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Regional tropical rainfall shifts under global warming: an energetic perspective

Abstract Future climate simulations feature pronounced spatial shifts in the structure of tropical rainfall. We apply a novel atmospheric energy flux analysis to diagnose late 21st century tropical rainfall shifts in a large ensemble of simulations of 21st century climate. The method reconstructs 2D spatial changes in rainfall based on horizontal shifts in the lines of zero meridional and zonal divergent energy flux, called the energy flux equator (EFE) and energy flux prime meridian (EFPM), respectively. Two main sources of future atmospheric energy flux changes, and hence rainfall shifts, are identified by the analysis: the high-latitude North Atlantic due to a weakened Atlantic Meridional Overturning Circulation that shifts tropical rainfall southwards over the greater Tropical Atlantic sector and eastern Pacific; and the eastern tropical Pacific due to a permanent El-Niño-like response that produces zonal shifts over the Maritime Continent and South America. To first order, the shifts in the EFE and EFPM mirror gross distributional changes in tropical precipitation, with a southward shift in rainfall over the tropical Atlantic, West Africa, and eastern tropical Pacific and an eastward shift over the Maritime Continent and western Pacific. When used to reconstruct future rainfall shifts in the tropical Atlantic and Sahel, the method reasonably represents the simulated meridional structure of rainfall shifts but does not do so for the zonal structures.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

The Borg Cube Simulation: Cosmological Hydrodynamics with CRK-SPH

A challenging requirement posed by next-generation observations is a firm theoretical grasp of the impact of baryons on structure formation. Cosmological hydrodynamic simulations modeling gas physics are vital in this regard. A high degree of modeling flexibility exists in this space, making it important to explore a range of methods in order to gauge the accuracy of simulation predictions. We present results from the first cosmological simulation using Conservative Reproducing Kernel Smoothed Particle Hydrodynamics (CRK-SPH). We employ two simulations: one evolved purely under gravity, and the other with nonradiative hydrodynamics. Each contains 2 × 2304 3 cold dark matter plus baryon particles in an 800 h -1 Mpc box. We compare statistics to previous nonradiative simulations including power spectra, mass functions, baryon fractions, and concentration. We find self-similar radial profiles of gas temperature, entropy, and pressure and show that a simple analytic model recovers these results to better than 40% over two orders of magnitude in mass. We quantify the level of nonthermal pressure support in halos and demonstrate that hydrostatic mass estimates are biased low by 24% (10%) for halos of mass 10 15 (10 13 ) h -1 M⊙. Here, we compute angular power spectra for the thermal and kinematic Sunyaev–Zel’dovich effects and find good agreement with the low-ℓ Planck measurements. Finally, artificial scattering between particles of unequal mass is shown to have a large impact on the gravity-only run, and we highlight the importance of better understanding this issue in hydrodynamic applications. This is the first in a simulation campaign using CRK-SPH, with future work including subresolution gas treatments.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Building Toward the Future in Chemical and Materials Simulation with Accessible and Intelligently Designed Web Applications

Over the last few decades, significant progress has been made in the development and use of electronic structure and other molecular simulation methods. As these methods become more mature and are able to simulate larger and more complex chemical simulations, the need for improvement in scientific visualization, molecular builders, simplified input to simulation methods, and the development of new approaches and languages to describe simulations, along with workflows to carry them out, becomes more apparent. In this chapter, we describe our recent efforts in developing a prototype open-source computational tool called Arrows that combines NWChem, SQL and NoSQL databases, email, web APIs, and web applications in a way that make molecular and materials modeling accessible to all scientists and engineers. At the same time, because of its simplified input, it provides a framework for expert users to carry out large numbers of calculations and run complex workflows.

2↗
DOE OSTI2021

Fast Emulation of Expensive Simulations using Approximate Gaussian Processes [Slides]

Nuclear Computational Low-Energy Initiative (NUCLEI) collaboration uses Density Functional Theory (DFT) simulations to predict the structure and binding energies of nuclei over a wide range of proton (Z) and neutron (N) numbers. The DFT simulations utilize a particular parameterization of a Skyrme energy density functional called UNEDF1 which depends on 12 free parameters that must be fit to data (M Kortelainen et al 2014). Fitting involves comparing (e.g.) predicted binding energies of nuclei to experimentally measured values. We use only binding energies as observables, but DFT with UNEDF1 will predict structure (shape) observables as well. In this work, assessing the capability of approximate GP emulators to balance emulator accuracy with computational speed to facilitate improved UNEDF1 calibration. Sparse GPs are straightforward to train and accurate. Calibration is not straightforward with MCMC (using MH or HMC/NUTS). We produced reusable software for continuing and building on this work as well as accessing and using Darwin cluster compute resources

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Understanding the U 3 Si 2 crystal structure evolution as a function of temperature by neutron diffraction and simulation

U 3 Si 2 is actively researched as an accident tolerant fuel. Detailed knowledge of the crystal structure evolution, including knowledge of the anisotropic tetragonal lattice parameters, as a function of temperature and chemical composition is of paramount importance for predictions ranging from thermo-mechanical stresses to phase transformations to crystal lattice sites of fission products. Knowledge of the stability range of U 3 Si 2 is of great importance to understand whether changes of the stoichiometry, either from burn-up or due to synthesis variations, will lead to undesirable phase decomposition. To investigate these topics, stoichiometric U3Si2.00 and hyper-stoichiometric U 3 Si 2.01 were synthesized and characterized at ambient conditions and up to 1150°C using time-of-flight neutron diffraction on the HIPPO instrument at the Los Alamos Neutron Science Center (LANSCE) at LANL.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

Ab initio study of the structure and properties of amorphous silicon hydride from accelerated molecular dynamics simulations

This paper presents a large-scale ab initio simulation study of amorphous silicon hydride (a-Si 1-x H x ) with an emphasis on the structure and properties of the material across a range of hydrogen concentration by combining accelerated molecular dynamics (MD) simulations with first-principles density-functional calculations. The accelerated MD scheme relied on classical metadynamics, which enabled the development of 2500+ high-quality structural models of a-Si 1-x H x , with system sizes ranging from 150 to 6000 atoms and hydrogen concentrations vary from 6 to 20 at. %. The resulting amorphous networks were found to be completely free from any coordination defects and that they all exhibited a pristine band-gap in their electronic spectrum. The microstructural properties of hydrogen distributions were examined with an emphasis on the presence of isolated and clustered environments of hydrogen atoms. The results were compared with experimental data obtained from X-ray diffraction, infrared spectroscopy and nuclear magnetic resonance studies.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Ab initio study of the structure and properties of amorphous silicon hydride from accelerated molecular dynamics simulations

This paper presents a large-scale ab initio simulation study of amorphous silicon hydride (a-Si 1-x H x ) with an emphasis on the structure and properties of the material across a range of hydrogen concentration by combining accelerated molecular dynamics (MD) simulations with first-principles density-functional calculations. The accelerated MD scheme relied on classical metadynamics, which enabled the development of 2600+ high-quality structural models of a-Si 1-x H x , with system sizes ranging from 150 to 6,000 atoms and hydrogen concentrations vary from 6 to 20 at. %. The resulting amorphous networks were found to be completely free from any coordination defects and that they all exhibited a pristine band-gap in their electronic spectrum. The microstructural properties of hydrogen distributions were examined with great emphasis on the presence of isolated and clustered environments of hydrogen atoms. The results were compared with a suite of experimental data obtained from x-ray diffraction, infrared spectroscopy, spectroscopic ellipsometry and nuclear magnetic resonance studies.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Modeling adsorption properties of structurally deformed metal–organic frameworks using structure–property map

Structural deformation and collapse in metal-organic frameworks (MOFs) can lead to loss of long-range order, making it a challenge to model these amorphous materials using conventional computational methods. In this work, we show that a structure–property map consisting of simulated data for crystalline MOFs can be used to indirectly obtain adsorption properties of structurally deformed MOFs. The structure–property map (with dimensions such as Henry coefficient, heat of adsorption, and pore volume) was constructed using a large data set of over 12000 crystalline MOFs from molecular simulations. By mapping the experimental data points of deformed SNU-200, MOF-5, and Ni-MOF-74 onto this structure–property map, we show that the experimentally deformed MOFs share similar adsorption properties with their nearest neighbor crystalline structures. Furthermore, once the nearest neighbor crystalline MOFs for a deformed MOF are selected from a structure–property map at a specific condition, then the adsorption properties of these MOFs can be successfully transformed onto the degraded MOFs, leading to a new way to obtain properties of materials whose structural information is lost.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

NWChem: Past, present, and future

Specialized computational chemistry packages have permanently reshaped the landscape of chemical sciences by providing tools to support and guide the experimental effort and for prediction of chemical and materials properties. In this regard, a special role has been played by electronic structure packages where complex chemical and materials processes can be modeled using first-principle-driven methodologies. Over the last few decades, the rapid development of computing technologies and a tremendous increase in computational power has offered a unique chance to study complex chemical transformations using sophisticated and predictive many-body techniques to describe correlated behavior of electrons in molecular and condensed phase systems at different levels of theory. In enabling these simulations, a critical role has been played by novel parallel algorithms capable of taking advantage of computational resources to address polynomial scaling of electronic structure methods. NWChem was among the first electronic structure codes that focused on delivering scalable performance for electronic structure simulations. Herein, we briefly review the NWChem suite of computational codes including its history, design principles, parallel tools, current capabilities, outreach and outlook.

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

Early age volume changes in metakaolin geopolymers: Insights from molecular simulations and experiments

The early age volume changes occurring during the geopolymerisation reaction are not sufficiently understood yet, due to shortage of experimental data and theoretical models. This work presents new results on chemical and autogenous deformation of sodium-activated geopolymers from metakaolin, focussing on the first 72 h of reaction. The results show that the geopolymers undergo early-age chemical expansion, not shrinkage. A model is proposed to explain the experimental result, leveraging recent advances from molecular simulations. The model predicts how the extent of chemical expansion is controlled by confined water in the molecular structure of the geopolymer. However, despite this underlying chemical expansion, geopolymer samples undergo autogenous shrinkage at the macroscale, which excludes self-desiccation as the origin of autogenous deformation. A better insight is gained by monitoring the kinetics of geopolymerisation using isothermal and differential calorimetry. Two kinetic regimes are identified, with apparent activation energies of approximately 90 kJ/mol and 70 kJ/mol. This suggests that two microscopic mechanisms concur to determine the early-age volume changes of geopolymer pastes.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Thermal tomography 3D imaging of additively manufactured metallic structures

Thermal tomography is a computational method for heat diffusion-based imaging of solids, which provides 3D visualization of data from flash thermography measurements. We investigate thermal tomography imaging and nondestructive evaluation of stainless steel and nickel super alloy metallic structures produced with the laser powder bed fusion (LPBF) additive manufacturing (AM) process. Metallic structures produced with LPBF contain defects, and there are limited capabilities to evaluate these structures non-destructively. Thermal tomography reconstruction of 3D apparent spatial effusivity provides information about AM structure geometry and internal material flaws. We study performance of thermal tomography in imaging of metallic structures through COMSOL computer simulations of transient heat transfer and through reconstruction of data obtained from experimental measurements. Thermal tomography reconstructions of structure shape and dimensions are shown for the Inconel 718 AM structure which has variations in the horizontal plane but is uniform along the depth dimension. Reconstruction of internal defects is investigated using a stainless steel 316L specimen with flat bottom hole (FBH) indentations, and the Inconel 718 plate is produced with the LPBF method, which contains imprinted hemispherical shape low density regions containing non-sintered metallic powder. The FBHs have the same sizes as the imprinted defects in the LPBF specimens but offer better imaging contrast. Thermal tomography reconstructions provide visualizations of internal defects and allow for estimation of their sizes and locations. Results of this study demonstrate that thermal tomography can be used for visualization and quality control in AM.

36 MATERIALS SCIENCE↗
DOE OSTI2020

PETSc DMNetwork: A Library for Scalable Network PDE-Based Multiphysics Simulations

We present DMNetwork, a high-level package included in the PETSc library for the simulation of multiphysics phenomena over large-scale networked systems. The library aims at applications that have networked structures such as those in electrical, gas, and water distribution systems. DMNetwork provides data and topology management, parallelization for multiphysics systems over a network, and hierarchical and composable solvers to exploit the problem structure. DMNetwork eases the simulation development cycle by providing the necessary infrastructure through simple abstractions to define and query the network components. This article presents the design of DMNetwork, illustrates its user interface, and demonstrates its ability to solve multiphysics systems, such as an electric circuit, a network of power grid and water subnetworks, and transient hydraulic systems over large networks with more than 2 billion variables on extreme-scale computers using up to 30,000 processors.

extreme-scale computing↗
DOE OSTI2022

Molecular Dynamics Simulation and Cryo-Electron Microscopy Investigation of AOT Surfactant Structure at the Hydrated Mica Surface

Structural properties of the anionic surfactant dioctyl sodium sulfosuccinate (AOT or Aerosol-OT) adsorbed on the mica surface were investigated by molecular dynamics simulation, including the effect of surface loading in the presence of monovalent and divalent cations. The simulations confirmed recent neutron reflectivity experiments that revealed the binding of anionic surfactant to the negatively charged surface via adsorbed cations. At low loading, cylindrical micelles formed on the surface, with sulfate head groups bound to the surface by water molecules or adsorbed cations. Cation bridging was observed in the presence of weakly hydrating monovalent cations, while sulfate groups interacted with strongly hydrating divalent cations through water bridges. The adsorbed micelle structure was confirmed experimentally with cryogenic electronic microscopy, which revealed micelles approximately 2 nm in diameter at the basal surface. At higher AOT loading, the simulations reveal adsorbed bilayers with similar surface binding mechanisms. Adsorbed micelles were slightly thicker (2.2–3.0 nm) than the corresponding bilayers (2.0–2.4 nm). Upon heating the low loading systems from 300 K to 350 K, the adsorbed micelles transformed to a more planar configuration resembling bilayers. The driving force for this transition is an increase in the number of sulfate head groups interacting directly with adsorbed cations.

58 GEOSCIENCES↗
DOE OSTI2017

Structural Evaluation of Complex Subcomponents Manufactured by Large Scale Extrusion Deposition of Carbon Fiber Reinforced ABS

The large scale extrusion deposition process has recently been commercialized in the form of additive manufacturing machines such as the BAAM from Cincinnati Inc., which enables layered production of chopped fiber reinforced thermoplastic polymer systems. The application of this process to the automotive market is being pursued by Local Motors to enable rapid design to market cycles and build on-demand capability for a wide range of vehicle styles from a distributed network of micro-factories. This endeavor will require an understanding of the structural performance of components with complex geometries, where the properties are known to vary as a function of printing conditions, as well as orientation and shape. In order to rapidly build a database of structural performance, a beam specimen with outer dimensions of 914 x 305 x 64 mm3 was selected to be subjected to bending, torsion, and shear loading with full field displacement measurement by digital image correlation (DIC). A total of 25 different specimen configurations were designed including variation of print geometry, reinforcement by foam filling, and overwrapping with advanced composites. This work documents the results of the study and presents the relative performance of the structures in addition to the approach to simulation that is being initiated to serve as a framework for efficient design of structures manufactured in this way. The results are presented as a table of structural efficiency including stiffness and strength as functions of mass for each design. Additional results will also be provided in the form of surface displacements from DIC; future work will utilize this data to better optimize simulations for predicting structural performance of articles manufactured by this process.

Bedsole, Robert↗