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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
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↗
NASA NTRS2000

Molecular Dynamics Simulations of Carbon Nanotubes in Water

We study the hydrophobic/hydrophilic behavior of carbon nanotubes using molecular dynamics simulations. The energetics of the carbon-water interface are mainly dispersive but in the present study augmented with a carbon quadrupole term acting on the charge sites of the water. The simulations indicate that this contribution is negligible in terms of modifying the structural properties of water at the interface. Simulations of two carbon nanotubes in water display a wetting and drying of the interface between the nanotubes depending on their initial spacing. Thus, initial tube spacings of 7 and 8 A resulted in a drying of the interface whereas spacing of > 9 A remain wet during the course of the simulation. Finally, we present a novel particle-particle-particle-mesh algorithm for long range potentials which allows for general (curvilinear) meshes and "black-box" fast solvers by adopting an influence matrix technique.

Walther, J. H.↗
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↗
DOE OSTI2015

Development of a model electronic Hamiltonian for understanding electronic relaxation dynamics of [Fe(bpy){sub 3}]{sup 2+} through molecular dynamics simulations

A model electronic Hamiltonian of [Fe(bpy){sub 3}]{sup 2+}, which was recently refined for use in molecular dynamics simulations, is reviewed with some additional results. In particular, the quality of the refined model Hamiltonian is examined in terms of the vibrational frequencies and solvation structures of the lowest singlet and quintet states.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Large-Scale Molecular Dynamics Simulation Studies on Deformation of Ni Nanowires: Surface Profile, Defects and Stacking Fault Width Analysis

We report large-scale molecular dynamics simulation deformation studies of Ni nanowire (NW) of size 100 Å (x) × 1000 Å (y) × 100 Å (z) comprising of 925,965 atoms. Surface and internal defects are introduced to study their effect on the surface profile, strength, fracture behavior and deformation mechanisms. Tensile tests have been carried out at a temperature of 10 K and at a strain rate of 10{sup 8} s{sup −1}. Periodic boundary condition is applied along the loading direction (y). Peak strength of 23 GPa is observed in the perfect NW, and the strength decreases with defects. The surface profiles of the deformed NWs show intrusion and extrusion regions corresponding to slip steps with wider valleys in the defect NWs. Several intrinsic and extrinsic parallel stacking faults (SFs) are generated after yielding by slip occurring on {111} planes. The calculated SF widths are in the range of 0.85-2.57 nm in the perfect NW. The dislocations are mainly Shockley partial dislocations of type 1/6 〈112〉, and Schmid’s factor (m) obtained is 0.471. Twinning dislocation of types 1/9 〈221〉 and 1/18 〈172〉 is also observed in the SFs. The density of Shockley partial dislocations is observed to be the maximum in all the NWs.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Effect of surface free energies on the heterogeneous nucleation of water droplet: A molecular dynamics simulation approach

Heterogeneous nucleation of water droplet on surfaces with different solid-liquid interaction intensities is investigated by molecular dynamics simulation. The interaction potentials between surface atoms and vapor molecules are adjusted to obtain various surface free energies, and the nucleation process and wetting state of nuclei on surfaces are investigated. The results indicate that near-constant contact angles are already established for nano-scale nuclei on various surfaces, with the contact angle decreasing with solid-liquid interaction intensities linearly. Meanwhile, noticeable fluctuation of vapor-liquid interfaces can be observed for the nuclei that deposited on surfaces, which is caused by the asymmetric forces from vapor molecules. The formation and growth rate of nuclei are increasing with the solid-liquid interaction intensities. For low energy surface, the attraction of surface atoms to water molecules is comparably weak, and the pre-existing clusters can depart from the surface and enter into the bulk vapor phase. The distribution of clusters within the bulk vapor phase becomes competitive as compared with that absorbed on surface. For moderate energy surfaces, heterogeneous nucleation predominates and the formation of clusters within bulk vapor phase is suppressed. The effect of high energy particles that embedded in low energy surface is also discussed under the same simulation system. The nucleation preferably initiates on the high energy particles, and the clusters that formed on the heterogeneous particles are trapped around their original positions instead of migrating around as that observed on smooth surfaces. This feature makes it possible for the heterogeneous particles to act as fixed nucleation sites, and simulation results also suggest that the number of nuclei increases monotonously with the number of high energy particles. The growth of nuclei on high energy particles can be divided into three sub-stages, beginning with the formation of a wet-spot, increase of contact angle with near-constant contact line, and finally growth with constant contact angle. The growth rate of nuclei also increases with the size of high energy particles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Parallel point defect identification in molecular dynamics simulations without post-processing: A compute and dump style for LAMMPS

Two classes for the molecular dynamics program LAMMPS – one compute style and one dump style – are presented that are designed to identify, count, and output point defects in cascade damage and related molecular dynamics simulations. The calculations are done in parallel across multiple MPI processes, and can be done at the same time as the original simulation. This drastically reduces storage requirements by eliminating the need to post-process every atom in the system. Non-cubic lattices, free surfaces, and large voids can be eliminated from the output by suitable choices of the reference lattice. The classes are derived from LAMMPS’s Dump and Compute classes, and pose no additional overhead to LAMMPS if they are not used.

42 ENGINEERING↗
DOE OSTI2013

Parallel implementation of three-dimensional molecular dynamic simulation for laser-cluster interaction

The objective of this article is to report the parallel implementation of the 3D molecular dynamic simulation code for laser-cluster interactions. The benchmarking of the code has been done by comparing the simulation results with some of the experiments reported in the literature. Scaling laws for the computational time is established by varying the number of processor cores and number of macroparticles used. The capabilities of the code are highlighted by implementing various diagnostic tools. To study the dynamics of the laser-cluster interactions, the executable version of the code is available from the author.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2019

Understanding the release of helium atoms from nanochannel tungsten: a molecular dynamics simulation

The design of highly radiation-tolerant plasma-facing materials (PFMs) is of great importance for fusion reactors. Our recent experiments have shown that nanochannel tungsten (W) films have clearly superior radiation tolerance properties. In the present work, helium clustering and release from nanochannel tungsten were studied by molecular dynamics simulations. The effects of temperature and vacancy concentration on the helium release from a tungsten cylinder were investigated. Our results show that nanochannel W that consists of thin W cylinders releases He atoms more quickly than bulk W with flat surfaces, thus greatly reducing the He concentration and suppressing the formation and growth of He bubbles, which leads to increased radiation tolerance. Moreover, the micro-structural changes due to increasing He fluence are smaller in nanochannel W than those in bulk W. Although vacancies in nanochannel W will trap He atoms, the nanochannel W also has a stronger tendency to stabilize helium retention than bulk W. The mechanism of helium release from nanochannel W was also examined. The results reported here are beneficial for guiding future work in the design of radiation resistant PFMs.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2019

Variational control forces for enhanced sampling of nonequilibrium molecular dynamics simulations

We introduce a variational algorithm to estimate the likelihood of a rare event within a nonequilibrium molecular dynamics simulation through the evaluation of an optimal control force. Optimization of a control force within a chosen basis is made possible by explicit forms for the gradients of a cost function in terms of the susceptibility of driven trajectories to changes in variational parameters. We consider probabilities of time-integrated dynamical observables as characterized by their large deviation functions and find that in many cases, the variational estimate is quantitatively accurate. Additionally, we provide expressions to exactly correct the variational estimate that can be evaluated directly. We benchmark this algorithm against the numerically exact solution of a model of a driven particle in a periodic potential, where the control force can be represented with a complete basis. Additionally, we then demonstrate the utility of the algorithm in a model of repulsive particles on a line, which undergo a dynamical phase transition, resulting in singular changes to the form of the optimal control force. In both systems, we find fast convergence and are able to evaluate large deviation functions with significant increases in statistical efficiency over alternative Monte Carlo approaches.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Molecular dynamics simulations of concentration-dependent defect production in Fe-Cr and Fe-Cu alloys

Molecular dynamics simulations are conducted to study the effects of alloying elements on the primary damage behaviors in three Fe-based ferritic alloy systems: (1) a Fe-Cr system in which the heat of mixing changes its sign with the Cr concentration; (2) a Fe-Cu system that has a positive heat of mixing; and (3) an ideal but artificial Fe-Cr system that has a zero heat of mixing, which is used as a reference system to investigate solute interstitial formation based on probability. It is found that in these alloys, the solute type and concentration do not have a significant effect on the total number of surviving Frenkel pairs. However, the fraction of solute interstitials has distinct behaviors. In Fe-Cr, the Cr interstitial fraction is much higher than the Cr solute concentration and the Cr interstitial production efficiency decreases with the increasing Cr concentration. By contrast, in Fe-Cu, Cu interstitials are barely produced. In the ideal alloy, the solute interstitial fraction is close to the solute concentration. The defect formation energies in both dilute and concentrated alloys, interstitial binding energies, liquid diffusivities of Fe and solute atoms, and heat of mixing have been calculated for both Fe-Cr and Fe-Cu alloys. Among them, we find that the relative thermodynamic stability between Fe self-interstitials and solute interstitials plays the most important role in the solute interstitial production behaviors. The decrease of Cr interstitial production efficiency with increasing Cr concentration can be explained by the probability distribution functions of solute interstitial formation energy in concentrated alloys.

Zhang, Yaxuan↗
DOE OSTI2017

Thermal Hydraulic Computational Fluid Dynamics Simulations and Experimental Investigation of Deformed Fuel Assemblies

The project, Toward a Longer Life Core: Thermal Hydraulic CFD Simulations and Experimental Investigation of Deformed Fuel Assemblies, DOE Project code DE-NE0008321, was a verification and validation project for flow and heat transfer through wire wrapped simulated liquid metal fuel assemblies that included both experiments and computational fluid dynamics simulations of those experiments. This project was a two year collaboration between AREVA, TerraPower, Argonne National Laboratory and Texas A&M University. Experiments were performed by AREVA and Texas A&M University. Numerical simulations of these experiments were performed by TerraPower and Argonne National Lab. Project management was performed by AREVA Federal Services. The first of a kind project resulted in the production of both local point temperature measurements and local flow mixing experiment data paired with numerical simulation benchmarking of the experiments. The project experiments included the largest wire-wrapped pin assembly Mass Index of Refraction (MIR) experiment in the world, the first known wire-wrapped assembly experiment with deformed duct geometries and the largest numerical simulations ever produced for wire-wrapped bundles.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
NASA NTRS1996

Applying Parallel Processing Techniques to Tether Dynamics Simulation

The focus of this research has been to determine the effectiveness of applying parallel processing techniques to a sizable real-world problem, the simulation of the dynamics associated with a tether which connects two objects in low earth orbit, and to explore the degree to which the parallelization process can be automated through the creation of new software tools. The goal has been to utilize this specific application problem as a base to develop more generally applicable techniques.

Wells, B. Earl↗
DOE OSTI2025

Combining Reactive Quantum-Mechanical Molecular-Dynamics Simulations with Mutagenesis, Crystallography, and Enzyme Kinetics to Reveal Plausible Steps of Isocyanide Hydratase Catalysis

A complete understanding of enzyme mechanisms requires atomistic details of chemical reactions. Quantum-based molecular dynamics simulations (QMD) are a potential source of this information, but trade-offs between accuracy and computational cost have limited their use. We previously developed extended Lagrangian Born–Oppenheimer molecular dynamics (XL-BOMD) methods that leverage a negligible compromise in accuracy to substantially decrease the cost of QMD simulations. Here, we develop a reactive QMD approach using the latest XL-BOMD formulation, which enables efficient simulations of highly reactive systems, and use it to investigate mechanisms of intermediate formation in isocyanide hydratase (ICH) catalysis. In QMD simulations, molecular analogs of ICH active site residues reacted with para-nitrophenyl isocyanide, forming a thioimidate. Analysis of simulated atomic configurational and charge dynamics revealed a pathway where protonation of the isocyanide carbon occurs prior to thioimidate formation and suggested a possible role of Asp17 as a proton donor in the early phase of ICH catalysis. To test whether the pathway seen using the reactive QMD approach might be relevant to ICH catalysis, we performed X-ray crystallography and pre-steady-state enzyme kinetics studies of wild-type and D17N mutant ICH. Both the structure and kinetics are sensitive to the D17N mutation in a manner that is consistent with the order of the reaction steps seen in the simulations. Mobile protons play essential roles in many enzymes, yet they are difficult to observe experimentally, making the ordering of proton-dependent steps ambiguous in many enzyme mechanisms. The ability to directly simulate model reactions for the design of experiments that provide information about enzyme mechanisms involving mobile protons demonstrates the significance of our reactive QMD approach and motivates further biological applications.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering

Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structure to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Molecular Dynamics Simulations of Complexation of Am(III) with a Preorganized Dicationic Ligand in an Ionic Liquid

Preorganized ligands with imidazolium arms have been found to be highly selective in extracting Am(III) into ionic liquids (ILs), but the detailed structure and mechanism of the complexation process in the ionic solvation environment are unclear. Here, we carry out molecular dynamics simulation of the complexation of Am(III) with a preorganized 1,10-phenanthroline-2,9-dicarboxamide complexant (L) functionalized with alkyl chains and imidazolium cations in the butylmethylimidazolium bistriflimide ([BMIM][NTf 2 ]) IL. Both Am:L (1:1) and Am:L 2 (1:2) complexes are examined. In the absence of the ligand, Am(III) is found to be coordinated by six NTf 2 anions via nine O donors in the first solvation shell. In the Am:L complex, Am(III) is coordinated to the ligand via two O donors and four NTf 2 anions via seven O donors in the first coordination shell. In the Am:L 2 complex, Am(III) is coordinated to the two ligands via four O donors and four NTf 2 anions via five O donors. The imidazolium arms of the ligands play an important role in the secondary solvation environment by attracting NTf 2 anions closer to the metal center. As a result, we find that the binding free energy for the second L 2+ ligand is twice that for the first L 2+ ligand, making the Am:L 2 complex significantly more stable than the Am:L complex. This study highlights the multiple factors and tunability in using preorganized ligands with charged functional groups in an ionic solvation environment, which could hold the key to achieving desired selectivity in ion extraction efficiency.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗