SEARCH · Search NASA

Results for “dynamics 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.

SourceResearch connectionFrom yearThrough year

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

At least 325 records · Page 18

All sources NASA NTRS DOE OSTI

DOE OSTI2012

Mass Transport Properties of LiD-U Mixtures from Orbital Free Molecular Dynamics Simulations and a Pressure-Matching Mixing Rule

Mass transport properties for LiD-U mixtures were calculated using a pressure matching mixture rule for the mixing of LiD and of U properties simulated with Orbital Free Molecular Dynamics (OFMD). The mixing rule was checked against benchmark OFMD simulations for the fully interacting three-component (Li, D, U) system. To obtain transport coefficients for LiD-U mixtures of different (LiD) x U (1-x) compositions as functions of temperature and mixture density is a tedious task. Quantum molecular dynamics (MD) simulations can be employed, as in the case LiD or U. However, due to the presence of the heavy constituent U, such simulations proceed so slowly that only a limited number of numerical data points in the (x, ρ, T) phase space can be obtained. To finesse this difficulty, transport coefficients for a mixture can be obtained using a pressure-matching mixing rule discussed. For both LiD and U, the corresponding transport coefficients were obtained earlier from quantum molecular dynamics simulations. In these simulations, the quantum behavior of the electrons was represented using an orbital free (OF) version of density functional theory, and ions were advanced in time using classical molecular dynamics. The total pressure of the system, P = nk β T/V + P e , is the sum of the ideal gas pressure of the ions plus the electron pressure. The mass self-diffusion coefficient for species α, D α , the mutual diffusion coefficient for species α and β, D αβ , and the shear viscosity, η, are computed from the appropriate autocorrelation function. The details of similar QMD calculations on LiH are described in Ref. [1] for 0.5 eV < T < 3 eV, and in Ref. [2] for 2 eV < T < 6 eV.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

Hydration and reaction mechanisms on sodium silicate glass surfaces from molecular dynamics simulations with reactive force fields

Recent development of reactive force fields have enabled molecular dynamics simulations of interactions between silicate glasses and water at the atomistic scale. While multicomponent silicate glasses encompass a wide variety of compositions and properties, one common structural feature in these glasses is the combination of the network structure that is made up of silica tetrahedra linked through corner sharing interspersed with network modifiers like alkali and alkaline-earth ions that break up the Si–O–Si linkages by forming nonbridging oxygen. In reactions with water, ion exchange between alkali ions in the glass and proton or hydronium in the solution, as well as hydrolysis reaction of the Si–O–Si linkages and subsequent silanol formation, is observed and well documented. Furthermore, we have used a set of recently developed reactive force field to investigate the reactions between water and the surfaces of silica and sodium silicate glasses of different compositions for reactions up to 8 nanoseconds. Our results indicate sodium leaching into water and diffusion of water molecules up to 25 Å into the glass surface. We examined the structural and compositional changes inside the glass and around the diffused ions and use these to explain the rates of silanol formation at the surface. We also observed proton transport in the glass which has an indirect influence on the silanol formation rates. While the surface of the glass was rough to start with, it undergoes further modification into a hydrated gel-like structure in the glass for up to 5 Å in the higher alkali containing glasses. It was found that the leached sodium ions remain close to the interface and that fragments of silicate network from the surface is capable of dislodging from the bulk glass and enter the aqueous solution. These simulations thus provide insights into the formation and structure of an alteration layers commonly observed in multicomponent silicate glasses corroded in aqueous solutions.

36 MATERIALS SCIENCE↗

DOE OSTI2011

On-the-Fly Identification of Conformational Substates from Molecular Dynamics Simulations

We recently introduced a new method for discovering, characterizing, and monitoring spatiotemporal patterns in the conformational fluctuations in molecular dynamics simulation data ( J. Comput. Biol. 2010, 17 (3), 309 324). Significantly, our method, called Dynamic Tensor Analysis (DTA), can be performed as the simulation is progressing. It is therefore well-suited to analyzing long timescale simulations, which are critical for studying biologically relevant motions but may be too large for traditional analysis methods. In this paper, we demonstrate that the patterns discovered by DTA often correspond to functionally important conformational substates. In particular, we apply DTA to a 150 ns simulation of ubiquitin and discover patterns that provide unique insights into ubiquitin's ability to bind multiple substrates. Moreover, we take advantage of DTA's ability to identify patterns on different timescales and investigate how fast positional fluctuations may modulate slower, large-scale motions in functionally important regions. Our findings here suggest that DTA is well-suited to organizing, visualizing, and analyzing very large trajectories and discovering conformational substates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2012

Molecular dynamics simulations of solid state recrystallization I: Observation of grain growth in annealed iron nanoparticles

Molecular dynamics simulations of solid state recrystallization and grain growth in iron nanoparticles containing 1436 atoms were carried out. During the period of relaxation of supercooled liquid drops and during thermal annealing of the solids they froze to, changes in disorder were followed by monitoring changes in energy and the migration of grain boundaries. All 27 polycrystalline nanoparticles, which were generated with different grain boundaries, were observed to recystallize into single crystals during annealing. Larger grains consumed the smaller ones. In particular, two sets of solid particles, designated as A and B, each with two grains, were treated to generate 18 members of each set with different thermal histories. This provided small ensembles (of 18 members each) from which rates at which the larger grain engulfed the smaller one, could be determined. The rate was higher, the smaller the degree of misorientation between the grains, a result contrary to the general rule based on published experiments, but the reason was clear. Crystal A, which happened to have a somewhat lower angle of misorientation, also had a higher population of defects, as confirmed by its higher energy. Accordingly, its driving force to recrystallize was greater. Although the mechanism of recrystallization is commonly called nucleation, our results, which probe the system on an atomic scale, were not able to identify nuclei unequivocally. By contrast, our technique can and does reveal nuclei in the freezing of liquids and in transformations from one solid phase to another. An alternative rationale for a nucleation-like process in our results is proposed. - Graphical Abstract: Time dependence of energy per atom in the quenching of liquid nanoparticles A-C of iron. Nanoparticle C freezes directly into a single crystal but A and B freeze to solids with two grains. A and B eventually recrystallize into single crystals. Highlights: Black-Right-Pointing-Pointer Solid state material synthesis. Black-Right-Pointing-Pointer Experimental study of nucleation in condensed materials. Black-Right-Pointing-Pointer Computation Study of nucleation in condensed materials. Black-Right-Pointing-Pointer Observation of recrystallization in atomic detail.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Molecular dynamical simulations of melting behaviors of metal clusters

The melting behaviors of metal clusters are studied in a wide range by molecular dynamics simulations. The calculated results show that there are fluctuations in the heat capacity curves of some metal clusters due to the strong structural competition; For the 13-, 55- and 147-atom clusters, variations of the melting points with atomic number are almost the same; It is found that for different metal clusters the dynamical stabilities of the octahedral structures can be inferred in general by a criterion proposed earlier by F. Baletto et al. [J. Chem. Phys. 116 3856 (2002)] for the statically stable structures.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Code modernization strategies for short-range non-bonded molecular dynamics simulations

Modern HPC systems are increasingly relying on greater core counts and wider vector registers. Thus, applications need to be adapted to fully utilize these hardware capabilities. One class of applications that can benefit from this increase in parallelism are molecular dynamics simulations. In this paper, we describe our efforts at modernizing the ESPResSo++ simulation package for molecular dynamics by restructuring its particle data layout for efficient memory accesses and applying vectorization techniques to benefit the calculation of short-range non-bonded forces, which results in an overall three times speedup and serves as a baseline for further optimizations. We also implement fine-grained parallelism for multi-core CPUs through HPX, a C++ runtime system which uses lightweight threads and an asynchronous many-task approach to maximize concurrency. Our goal is to evaluate the performance of an HPX-based approach compared to the bulk-synchronous MPI-based implementation. This requires the introduction of an additional layer to the domain decomposition scheme that defines the task granularity. On spatially inhomogeneous systems, which impose a corresponding load-imbalance in traditional MPI-based approaches, we demonstrate that by choosing an optimal task size, the efficient work-stealing mechanisms of HPX can overcome the overhead of communication resulting in an overall 1.4 times speedup compared to the baseline MPI version.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2013

Generic solar photovoltaic system dynamic simulation model specification

This document is intended to serve as a specification for generic solar photovoltaic (PV) system positive-sequence dynamic models to be implemented by software developers and approved by the WECC MVWG for use in bulk system dynamic simulations in accordance with NERC MOD standards. Two specific dynamic models are included in the scope of this document. The first, a Central Station PV System model, is intended to capture the most important dynamic characteristics of large scale (> 10 MW) PV systems with a central Point of Interconnection (POI) at the transmission level. The second, a Distributed PV System model, is intended to represent an aggregation of smaller, distribution-connected systems that comprise a portion of a composite load that might be modeled at a transmission load bus.

14 SOLAR ENERGY↗

DOE OSTI2020

Dynamic Simulation Technoeconomic Model for Power Generation

Sandia National Laboratories has built and successfully tested a dynamic simulation technoeconomic model of the Palo Verde Generating Station that is now being updated to help other US power plants improve operations. Palo Verde, located west of Phoenix, Arizona, is the largest electricity generator in the US at 4 GW. Palo Verde uses — 60 million gallons per day of treated wastewater from Phoenix to cool reactors, and disposes of blowdown in evaporation ponds. The model built for Palo Verde numerically evaluates the economic impact of changing, for example, alternative cooling technologies, water usage and treatment, and influent water chemistry, and is based on detailed accounting of mass, energy, and cash flows.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2014

Molecular Dynamics Simulations of Tri-n-butyl-phosphate/n-Dodecane Mixture: Thermophysical Properties and Molecular Structure

Molecular dynamics simulations of tri-n-butyl-phosphate (TBP)/n-dodecane mixture in the liquid phase have been carried out using two recently developed TBP force field models (J. Phys. Chem. B 2012, 116, 305) in combination with the all-atom optimized potentials for liquid simulations (OPLS-AA) force field model for n-dodecane. Specifically, the electric dipole moment of TBP, mass density of the mixture, and the excess volume of mixing were computed with TBP mole fraction ranging from 0 to 1. It is found that the aforementioned force field models accurately predict the mass density of the mixture in the entire mole fraction range. Commensurate with experimental measurements, the electric dipole moment of the TBP was found to slightly increase with the mole fraction of TBP in the mixture. Also, in accord with experimental data, the excess volume of mixing is positive in the entire mole fraction range, peaking at TBP mole fraction range 0.3 0.5. Finally, a close examination of the spatial pair correlation functions between TBP molecules, and between TBP and n-dodecane molecules, revealed formation of TBP dimers through self-association at close distance, a phenomenon with ample experimental evidence.

de Almeida, Valmor F↗

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 OSTI2022

Propagating Parameter Uncertainty in Power System Nonlinear Dynamic Simulations Using a Koopman Operator-Based Surrogate Model

In this work, we propose a Koopman operator-based surrogate model for propagating parameter uncertainties in power system nonlinear dynamic simulations. First, we augment a priori known state-space model by reformulating parameters deemed uncertain as pseudo-state variables. Then, we apply the Koopman operator theory to the resulting state-space model and obtain a linear dynamical system model. This transformation allows us to analyze the evolution of the system dynamics through its Koopman eigenfunctions, eigenvalues, and modes. Of particular importance for this letter, the obtained linear dynamical system is a surrogate that enables the evaluation of parameter uncertainties by simply perturbing the initial conditions of the Koopman eigenfunctions associated with the pseudo-state variables. Simulations carried out on the New England test system reveal the excellent performance of the proposed method in terms of accuracy and computational efficiency.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2016

Coarse-Grained Reactive Molecular Dynamics Simulations of Heterogeneities in Shocked Energetic Materials (LDRD Final Report)

This report summarizes the result of LDRD project 16-0161, titled "Coarse-Grained Re- active Molecular Dynamics Simulations of Heterogeneities in Shocked Energetic Materials." The purpose of the project was to develop a coarse-grained reactive molecular dynamics capability in LAMMPS enabling simulations of initiation in energetic materials comparable in accuracy to what is currently possible using large-scale reactive molecular dynamics, but with greatly reduced computational cost. The starting point for this work was the reactive dissipative particle dynamics (DPD) approach, which has been implemented as the new USER-DPD package in LAMMPS by researchers at Army Research Laboratory. Using modified versions of the examples provided with the new package, we examined the computational efficiency of the method, as well as its ability to model energy release in energetic materials. We observed that the Shardlow splitting method provides a great speed and accuracy advantage over conventional velocity Verlet time integration. We observed that the generic model of an energetic material provided with the USER-DPD package exhibited incomplete reaction under constant volume conditions. This was caused by quenching of the internal temperature of the molecules due to a rapid build-up of repulsive interactions between product gas components under constant volume conditions. Under constant pressure conditions, complete reaction was observed, as volume expansion prevented the buildup of strong repulsive interactions. Finally, a more realistic model calibrated to reproduce the equation of state of the RDX molecular crystal was examined. This model exhibited much less quenching of the internal temperature under constant volume conditions and reacted very rapidly under constant pressure conditions.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2023

Near-surface damage and mixing in Si-Cl 2 -Ar atomic layer etching processes: Insights from molecular dynamics simulations

Silicon-chlorine-argon (Si-Cl 2 -Ar) atomic layer etching (ALE) is simulated using classical molecular dynamics (MD). The simulations provide a detailed view into the near-surface region during ALE processing. Bombardment of Ar + ions creates a mixed amorphous region that significantly differs from the picture of ideal ALE. There is also a significant change in the Si etch yield and the etch product distribution as a function of Ar + ion fluence. The Si etch yield is the highest at the beginning of the bombardment step but eventually decays to the physical sputtering yield. Atomic Cl and silicon chlorides are major etch products at the start of an ion bombardment step, but quickly decay. Atomic Si yields remain relatively constant as a function of Ar + ion fluence. As a result, a new schematic of Si-Cl 2 -Ar ALE is presented in order to emphasize the complex behavior observed in MD simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

Rupture Dynamics Simulations for Shallow Crustal Earthquakes

In this study we perform simulations of rupture dynamics for shallow crustal earthquakes. The objective is to investigate the implication of multi-scale and depth-dependent stress drop variations on rupture dynamics, and creation of strong motion generation areas (SMGAs) and long period ground motion generation areas (LMGAs) for a M6.7crustal earthquake on a strike slip vertical fault. In our fault rupture simulation we used heterogenous stress drop models with correlated stochastic perturbations, following the work of Pitarka et al. (2009). The stress model with multiscale variability is designed to accommodate high-stress drop asperity areas and small-scale spatial stress variations. The stress drop and size of asperities are based on the IM2011 (Irikura and Miyake, 2011) recipe.

58 GEOSCIENCES↗

DOE OSTI2012

Molecular dynamics simulations studies of laser ablation in metals

An overview of several aspects of our recent molecular dynamics simulations of femtosecond laser ablation is presented. This includes the study of phase diagrams for suitable interactions, analysis of ablated material and bubble formation below threshold, study of two-pulse ablation and the classification of materials with respect to electron properties and electron-phonon coupling in the two-temperature model. A treatment of boundary conditions and of an extended twotemperature model is also included. Most of the results apply to aluminum, others also to copper and iron, and to metals in general.

36 MATERIALS SCIENCE↗

DOE OSTI2020

RAS Protein Molecular Dynamics Simulations

This dataset contains 6401 files that describe parameters and other inputs for running molecular dynamics computer simulations of Ras proteins associated with a lipid-based cell membrane model in water, as well as resulting time-trajectories of atomic motion in these simulations. Specifically, the content includes: (a) 21 files containing generalized force field parameters, and (b) 22 files of similar format and content for each of 290 separate molecular dynamics simulations (22 ´ 290 = 6,380). The total size of this data set is 1.0 TB.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Ab initio molecular dynamics simulations of ion-solid interactions in zirconate pyrochlores

In this paper, an ab initio molecular dynamics method is employed to study low energy recoil events in zirconate pyrochlores (A 2 Zr 2 O 7 , A = La, Nd and Sm). It shows that both cations and anions in Nd 2 Zr 2 O 7 and Sm 2 Zr 2 O 7 are generally more likely to be displaced than those in La 2 Zr 2 O 7 . The damage end states mainly consist of Frenkel pair defects, and the Frenkel pair formation energies in Nd 2 Zr 2 O 7 and Sm 2 Zr 2 O 7 are lower than those in La 2 Zr 2 O 7 . These results suggest that the order–disorder structural transition more easily occurs in Nd 2 Zr 2 O 7 and Sm 2 Zr 2 O 7 resulting in a defect-fluorite structure, which agrees well with experimental observations. Our calculations indicate that oxygen migration from 48f and 8b to 8a sites is dominant under low energy irradiation. A number of new defects, including four types of cation Frenkel pairs and six types of anion Frenkel pairs, are revealed by ab initio molecular dynamics simulations. The present findings may help to advance the fundamental understanding of the irradiation response behavior of zirconate pyrochlores.

36 MATERIALS SCIENCE↗

DOE OSTI2019

Adaptive Dynamic Simulations for Distribution Systems Using Multistate Load Models

Running electromechanical simulations with a small time-step for a long period of time is computationally challenging, especially when large system models are used. Typically, simulations with a small time-step, 1 millisecond or less, are only run for a few seconds or a couple of minutes. While this trade-off has allowed for short duration simulations of large systems, it has prevented the complete analysis of power system phenomena that span minutes to hours, such as fault induced delayed voltage recovery. As power system operations become more complex with the deployment of new technologies, it will become more important to model dynamic behavior over greater time scales. This will include the ability to model system dynamics at the distribution level, including the end-use loads. This paper will present a computationally efficient method of adaptive dynamic simulations that enable transitions between time-series and dynamic modes, as necessary to capture system dynamics, while also being able to run for extended periods of time. This capability can support the direct analysis of dynamic events, co-simulation of transmission and distribution systems, and the development of reduced-order models.

24 POWER TRANSMISSION AND DISTRIBUTION↗