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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.

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At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Challenges in solving structures from radiation-damaged tomograms of protein nanocrystals assessed by simulation

Structure-determination methods are needed to resolve the atomic details that underlie protein function. X-ray crystallography has provided most of our knowledge of protein structure, but is constrained by the need for large, well ordered crystals and the loss of phase information. The rapidly developing methods of serial femtosecond crystallography, micro-electron diffraction and single-particle reconstruction circumvent the first of these limitations by enabling data collection from nanocrystals or purified proteins. However, the first two methods also suffer from the phase problem, while many proteins fall below the molecular-weight threshold required for single-particle reconstruction. Cryo-electron tomography of protein nanocrystals has the potential to overcome these obstacles of mainstream structure-determination methods. Here, a data-processing scheme is presented that combines routines from X-ray crystallography and new algorithms that have been developed to solve structures from tomograms of nanocrystals. This pipeline handles image-processing challenges specific to tomographic sampling of periodic specimens and is validated using simulated crystals. The tolerance of this workflow to the effects of radiation damage is also assessed. The simulations indicate a trade-off between a wider tilt range to facilitate merging data from multiple tomograms and a smaller tilt increment to improve phase accuracy. Since phase errors, but not merging errors, can be overcome with additional data sets, these results recommend distributing the dose over a wide angular range rather than using a finer sampling interval to solve the protein structure.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

American Society of Composites, 32nd Technical Conference

This paper will present a general methodology by which weave draping manufacturing simulation results can be utilized to include the effects of weave draping and scissor angle in a structural multiscale simulation. While the methodology developed is general in nature, this paper will specifically demonstrate the methodology applied to a truncated pyramid, utilizing manufacturing simulation weave draping results from ESI PAM-FORM, and multiscale simulation using Altair Multiscale Designer (MDS) and OptiStruct. From a multiscale simulation perspective, the weave draping manufacturing simulation results will be used to develop a series of woven unit cells which cover the range of weave scissor angles existing within the part. For each unit cell, a multiscale material model will be developed, and applied to the corresponding spatial locations within the structural simulation mesh. In addition, the principal material orientation will be mapped from the wave draping manufacturing simulation mesh to the structural simulation mesh using Altair HyperMesh mapping technology. Results of the coupled simulation will be compared and verified against experimental data of the same available via General Motors (GM) Department of Energy (DOE) project.

42 ENGINEERING↗
DOE OSTI2019

ReaxFF molecular dynamics simulations on the structure and dynamics of electrolyte water systems at ambient temperature

Here, ReaxFF molecular dynamics simulations have been performed to study the effect of cations Li + , Na+ and K + and anion Cl - on the structural and dynamical properties of water, using the force field recently developed by Fedkin and co-workers. The structural relationship of ion and water has been analyzed from the radial distribution function and angular distribution. Comparisons of ReaxFF angle variation of ions and water within the first solvation shell were made and found to be in good agreement with literature. The disruption of hydrogen bond network of water by ions is elucidated by ion-water residence times, water-water hydrogen bond dynamics and reorientational dynamics. ReaxFF diffusion coefficient and residence times of electrolyte water system were compared with ab initio and non-reactive potentials to analyze the difference in dynamics. We gained insight into the ion interaction with water and how it can accelerate or decelerate water dynamics. ReaxFF outlines the formation and dissolution of metal hydroxides and metal chlorides over the course of simulation to explain the diffusion dynamics of water in salt solutions, allowing us to elucidate the impact of concentration on the self-diffusivity of water and ions in solutions, and to reveal that this effect always decreases the mobility and is not at all ion-specific. The obtained findings have opened new opportunities to extend the ReaxFF methodology towards systems involving electrolytes.

42 ENGINEERING↗
DOE OSTI2022

Molecular simulation of the structural and thermodynamic properties of n-alkane/brine interfacial systems with nonionic surfactants

All-atom molecular dynamics (MD) simulations are used to study the structural and thermodynamic properties of water + n-heptane interfacial systems in the presence of salinity (NaCl, NaI, KCl, and KI) and two different nonionic surfactants. Excellent qualitative and quantitative agreement with interfacial tension experimental data is obtained, but this requires applying a charge scaling factor to the ionic species, suggesting the likely role of polarizability effects. Tensoactive behavior is observed for the NaI and KI systems, coinciding with layering of the iodide species near the interface. Further, there are significant interaction differences between the surfactants and the different ionic species, but the structural and thermodynamic behavior of the surfactant molecules is relatively unaffected by the specific salt species. Our analysis suggest that the surfactant-surfactant interactions play a critical role in determining the interfacial behavior, with a much smaller impact associated with the composition of the brine phase.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

A transfer learning approach for acoustic emission zonal localization on steel plate-like structure using numerical simulation and unsupervised domain adaptation

The detection and localization of damage in metallic structures using acoustic emission (AE) monitoring and artificial intelligence technology such as deep learning has been widely studied. However, a current challenge of this approach is the difficulty of obtaining sufficient labeled historical AE signals for the training process of deep learning models. This problem can be approached through the implementation of transfer learning. The innovation of this paper lies in the development of a transfer learning approach for AE source localization on a stainless-steel structure when no historical labeled AE signals are available for training. A finite element model is developed to generate numerical AE signals for the training. Unsupervised domain adaptation (UDA) technology is utilized to reduce the distribution difference between the numerical and the realistic AE signals and to derive the localization results of the unlabeled realistic AE signals. Finally, the results suggest that the proposed approach is capable of localizing AE signals with high accuracy in the absence of labeled training data.

42 ENGINEERING↗
DOE OSTI2023

A methodology to generate crystal-based molecular structures for atomistic simulations

Abstract We propose a systematic method to construct crystal-based molecular structures often needed as input for computational chemistry studies. These structures include crystal ‘slabs’ with periodic boundary conditions (PBCs) and non-periodic solids such as Wulff structures. We also introduce a method to build crystal slabs with orthogonal PBC vectors. These methods are integrated into our code, Los Alamos Crystal Cut ( LCC ), which is open source and thus fully available to the community. Examples showing the use of these methods are given throughout the manuscript.

42 ENGINEERING↗
DOE OSTI2020

Molecular Dynamics Simulation of the Structures, Dynamics, and Aggregation of Dissolved Organic Matter

Dissolved organic matter (DOM) plays a significant role in the transport and transformation of pollutants in the aquatic environment. However, the experimental characterization of DOM has been limited mainly to bulk properties, and the molecular-level interactions among various components of DOM remain to be fully characterized. In this study, we use molecular dynamics (MD) simulations to probe the structural properties of model DOM systems at atomic detail. The 200 ns simulations, validated by available experimental data, reveal processes and mechanisms by which chemical species (cations, peptides, lipids, lignin, carbohydrates, and some low-molecular-weight aliphatic and aromatic compounds) aggregate to form complex DOM. The DOM aggregates are dynamic, consisting of a hydrophobic core and amphiphilic exterior. The lipid tails and other hydrophobic fragments form the core, with hydrophilic and amphiphilic groups exposed to water, making DOM accessible to both polar and nonpolar species. Thus, the lipid component acts as a nucleator, whereas cations (especially Ca 2+ ) connect the molecular fragments on the surface by coordinating with the O-containing functional groups of DOM. The structural details revealed here provide new insights including surface accessible atoms, overall assemblage, and interactions among the molecules of DOM for understanding the kinetics and mechanisms through which DOM interacts with metal and other contaminants.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Adjusting the Energy Profile for CH–O Interactions Leads to Improved Stability of RNA Stem-Loop Structures in MD Simulations

The role of ribonucleic acid (RNA) in biology continues to grow, but insight into important aspects of RNA behavior is lacking, such as dynamic structural ensembles in different environments, how flexibility is coupled to function, and how function might be modulated by small molecule binding. In the case of proteins, much progress in these areas has been made by complementing experiments with atomistic simulations, but RNA simulation methods and force fields are less mature. It remains challenging to generate stable RNA simulations, even for small systems where well-defined, thermostable structures have been established by experiments. Further many different aspects of RNA energetics have been adjusted in force fields, seeking improvements that are transferable across a variety of RNA structural motifs. In this work, the role of weak CH···O interactions is explored, which are ubiquitous in RNA structure but have received less attention in RNA force field development. By comparing data extracted from high-resolution RNA crystal structures to energy profiles from quantum mechanics and force field calculations, it is shown that CH···O interactions are overly repulsive in the widely used Amber RNA force fields. A simple, targeted adjustment of CH···O repulsion that leaves the remainder of the force field unchanged was developed. Then, the standard and modified force fields were tested using molecular dynamics (MD) simulations with explicit water and salt, amassing over 300 μs of data for multiple RNA systems containing important features such as the presence of loops, base stacking interactions as well as canonical and noncanonical base pairing. In this work and others, standard force fields lead to reproducible unfolding of the NMR-based structures. Including a targeted CH···O adjustment in an otherwise identical protocol dramatically improves the outcome, leading to stable simulations for all RNA systems tested.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Enzyme kinetics by GH7 cellobiohydrolases on chromogenic substrates is dictated by non‐productive binding: insights from crystal structures and MD simulation

Cellobiohydrolases (CBHs) in the glycoside hydrolase family 7 (GH7) ( EC3.2.1.176 ) are the major cellulose degrading enzymes both in industrial settings and in the context of carbon cycling in nature. Small carbohydrate conjugates such as p‐ nitrophenyl‐β‐ d ‐cellobioside (pNPC), p‐ nitrophenyl‐β‐ d ‐lactoside (pNPL) and methylumbelliferyl‐β‐ d ‐cellobioside have commonly been used in colorimetric and fluorometric assays for analysing activity of these enzymes. Despite the similar nature of these compounds the kinetics of their enzymatic hydrolysis vary greatly between the different compounds as well as among different enzymes within the GH7 family. Through enzyme kinetics, crystallographic structure determination, molecular dynamics simulations, and fluorometric binding studies using the closely related compound o‐nitrophenyl‐β‐ d ‐cellobioside (oNPC), in this work we examine the different hydrolysis characteristics of these compounds on two model enzymes of this class, TrCel7A from Trichoderma reesei and PcCel7D from Phanerochaete chrysosporium . Protein crystal structures of the E212Q mutant of TrCel7A with pNPC and pNPL, and the wildtype TrCel7A with oNPC, reveal that non‐productive binding at the product site is the dominating binding mode for these compounds. Enzyme kinetics results suggest the strength of non‐productive binding is a key determinant for the activity characteristics on these substrates, with PcCel7D consistently showing higher turnover rates ( k cat ) than TrCel7A, but higher Michaelis–Menten ( K M ) constants as well. Furthermore, oNPC turned out to be useful as an active‐site probe for fluorometric determination of the dissociation constant for cellobiose on TrCel7A but could not be utilized for the same purpose on PcCel7D, likely due to strong binding to an unknown site outside the active site.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Molecular Dynamics Simulations of Water Structure and Diffusion in a 1 nm Diameter Silica Nanopore as a Function of Surface Charge and Alkali Metal Counterion Identity

Water confined in nanopores-particularly in pores narrower than 2 nm-displays distinct physicochemical properties that remain incompletely examined despite their importance in nanofluidics, molecular biology, geology, and materials sciences. In this study, we use molecular dynamics simulations to investigate the coordination structure and mobility of water and alkali metals (Li, Na, K, Cs) inside a 1 nm diameter cylindrical silica nanopore as a function of surface charge density, a model system particularly relevant to the alteration kinetics of silicate glasses and minerals in geologic formations. We find that the presence of a negative surface charge and adsorbed counterions within the pore strongly impacts water structure and dynamics. In particular, it significantly orients water O-H bonds toward the surface and slows water diffusion by almost 1 order of magnitude. Ion crowding in the charged nanopore enhances the tendency of counterions to coordinate closely with the silica surface, which moderates the impact of ions on water dynamics. Co-ions are strongly excluded from the nanopore at all surface charges, suggesting that the 1 nm diameter cylindrical silica nanopores likely exhibit nearly ideal semipermeable membrane transport properties.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2019

Molecular Dynamics Simulation of the Structure and Properties of CaO-SiO{sub 2}-CaF{sub 2} Slag Systems

As a fundamental slag system in metallurgical processes, the CaO-SiO{sub 2}-CaF{sub 2} system, its properties, and related microstructures are of critical importance. The effect of the binary basicity and addition of CaF{sub 2} on the structure and viscosity of CaO-SiO{sub 2}-CaF{sub 2} slag were investigated using molecular dynamics simulations and Fourier transform infrared spectrometry. The average bond lengths of Si-O, Ca-O, and O-O were 1.61, 2.31, and 2.61 Å, respectively, and the coordinate number of Si remained constant. O-Si-O maintained an angle of 109.2, which was considered to be unaffected by the basicity changes. With increasing basicity, the network connectivity degrees Q{sup 3} and Q{sup 4} decreased, and the microstructure of the melt was significantly simpler. The effect of CaF{sub 2} on the depolymerization of the network structure was not obvious, and CaF{sub 2} acted mainly as a diluent. The calculations showed that the viscosity decreased upon setting up a ratio of nonbridging oxygen over tetrahedrally coordinated atoms (NBO/T). A good linear relationship was confirmed between the viscosity of the molten slag and the NBO/T.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Ferromagnetic Nanoparticles of Ising Spin-1 with a Rubik’s Cube Structure: Monte Carlo Simulations

Using Monte Carlo simulations, magnetic properties of the ferromagnetic nanoparticles of Ising spin-1 are investigated in the framework of the Ising model. The system is considered to have a Rubik’s cube structure composed of nanocubes having an equivalent exchange coupling, while, between adjacent nanocubes, the exchange coupling is assumed to vary. Both size effects and system parameters’ influence on phase diagrams of the nanosystem are studied. Thus, the magnetic properties of the system such as the critical temperature, the magnetization, and the coercive field are computed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer

Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here, we present a general optimization procedure for finding the most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated LC-18 (LC-18t) aptamer LC-18t was developed. A three-dimensional (3D) shape of LC-18t was reported based on small-angle X-ray scattering (SAXS) experiments and molecular modeling by fragment molecular orbital or molecular dynamic methods. Molecular simulations revealed an ensemble of possible aptamer conformations in solution that were in close agreement with measured SAXS data. The aptamer LC-18t had stronger binding to cancerous cells in lung tumor tissues and shared the binding site with the original larger aptamer. The suggested approach reveals 3D shapes of aptamers and helps in designing better affinity probes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Capturing thin structures in VOF simulations with two-plane reconstruction

A novel interface reconstruction strategy for volume of fluid (VOF) methods is introduced that represents the liquid-gas interface as two planes that co-exist within a single computational cell. In comparison to the piecewise linear interface calculation (PLIC), this new algorithm greatly improves the accuracy of the reconstruction, in particular when dealing with thin structures such as films. The placement of the two planes requires the solution of a non-linear optimization problem in six dimensions, which has the potential to be overly expensive. Further, an efficient solution to this optimization problem is presented here that exploits two key ideas: an algorithm for extracting multiple plane orientations from transported surface data, and an efficient and mass-conserving distance-finding algorithm that accounts for two planes with arbitrary orientation. Additionally, a simple and robust strategy is presented to accurately represent the surface tension forces produced at the interface of subgrid-thickness films. The performance of this new VOF reconstruction is demonstrated on several test cases that illustrate the capability to handle arbitrarily thin films.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Numerical Simulation of the Structure and Mechanical Properties of Silicene Layers on Graphite during the Lithium Ion Motion

The molecular dynamics method is applied to study structural and mechanical effects appearing during the lithium ion motion in a dc electric field along a planar channel formed by perfect silicene sheets and sheets containing vacancy-type defects. Mono-, di-, tri-, and hexavacancies of rather densely and uniformly filled silicene sheets are arranged one above the other on a graphite substrate. The times of Li{sup +} ion passage through silicene channels with various gaps are determined. The construction of Voronoi polyhedra and truncated polyhedrons, whose centers coincide with the moving ion position allowed revealing the structural features inherent to the two-dimensional layered structure. The nature of stresses appearing in silicene sheets most critical to ion motion over the channel is determined.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗