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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 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
NASA NTRS1997

Molecular Dynamics Simulations of Laser Powered Carbon Nanotube Gears

Dynamics of laser powered carbon nanotube gears is investigated by molecular dynamics simulations with Brenner's hydrocarbon potential. We find that when the frequency of the laser electric field is much less than the intrinsic frequency of the carbon nanotube, the tube exhibits an oscillatory pendulam behavior. However, a unidirectional rotation of the gear with oscillating frequency is observed under conditions of resonance between the laser field and intrinsic gear frequencies. The operating conditions for stable rotations of the nanotube gears, powered by laser electric fields are explored, in these simulations.

Srivastava, Deepak↗
DOE OSTI2015

Dynamic Simulation over Long Time Periods with 100% Solar Generation.

This project aimed to identify the path forward for dynamic simulation tools to accommodate these needs by characterizing the properties of power systems (with high PV penetration), analyzing how these properties affect dynamic simulation software, and offering solutions for potential problems.

14 SOLAR ENERGY↗
DOE OSTI2018

ReaxFF molecular dynamics simulation of intermolecular structure formation in acetic acid-water mixtures at elevated temperatures and pressures

The intermolecular structure formation in liquid and supercritical acetic acid-water mixtures was explored using ReaxFF-based molecular dynamics simulations. The microscopic structures of acetic acid-water mixtures with different acetic acid mole fractions (1.0 ≥ x HAc ≥ 0.2) at ambient and critical conditions were examined. The potential energy surface associated with the dissociation of acetic acid molecules was calculated using a metadynamics procedure to optimize the dissociation energy of ReaxFF potential. At ambient conditions, depending on the acetic acid concentration, either acetic acid clusters or water clusters are dominant in the liquid mixture. When acetic acid is dominant (0.4 ≤ x HAc ), cyclic dimers and chain structures between acetic acid molecules are present in the mixture. Both structures disappear at increased water content of the mixture. It was found by simulations that the acetic acid molecules released from these dimer and chain structures tend to stay in a dipole-dipole interaction. These structural changes are in agreement with the experimental findings. When switched to critical conditions, the long-range interactions (e.g., second or fourth neighbor) disappear and the water-water and acetic acid-acetic acid structural formations become disordered. The simulated radial distribution function for water-water interactions is in agreement with experimental and computational studies. The first neighbor interactions between acetic acid and water molecules are preserved at relatively lower temperatures of the critical region. As higher temperatures are reached in the critical region, these interactions were observed to weaken. These simulations suggest that ReaxFF molecular dynamics simulations are an appropriate tool for studying supercritical water/organic acid mixtures.

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

Characterization of three phases of liquid carbon by tight-binding molecular dynamics simulations

In this work, we have performed systematic molecular dynamics simulations to study the structures of liquid carbon at 5000 K with the weight density ranging from 1.4 to 3.5 g cm –3 , using a three-center tight-binding potential of carbon. The simulation results show that the bonding characteristics of the liquid changes predominately from twofold to threefold, and then to fourfold coordination as the density increases. Signals of two structural changes at the densities of about 1.9 and 3.0 g cm –3 respectively are revealed by the slope changes in the density dependence of structural, electronic and dynamical properties. Our simulation results suggest that there are three distinct liquid carbon phases in this density range. However, further thermodynamics calculations, e.g. , free energy calculations, would be required to clarify the possible liquid–liquid transitions.

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

Equilibration and analysis of first-principles molecular dynamics simulations of water

First-principles molecular dynamics (FPMD) simulations based on density functional theory are becoming increasingly popular for the description of liquids. In view of the high computational cost of these simulations, the choice of an appropriate equilibration protocol is critical. In this study, we assess two methods of estimation of equilibration times using a large dataset of first-principles molecular dynamics simulations of water. The Gelman-Rubin potential scale reduction factor [A. Gelman and D. B. Rubin, Stat. Sci. 7, 457 (1992)] and the marginal standard error rule heuristic proposed by White [Simulation 69, 323 (1997)] are evaluated on a set of 32 independent 64-molecule simulations of 58 ps each, amounting to a combined cumulative time of 1.85 ns. The availability of multiple independent simulations also allows for an estimation of the variance of averaged quantities, both within MD runs and between runs. We analyze atomic trajectories, focusing on correlations of the Kohn-Sham energy, pair correlation functions, number of hydrogen bonds, and diffusion coefficient. The observed variability across samples provides a measure of the uncertainty associated with these quantities, thus facilitating meaningful comparisons of different approximations used in the simulations. We find that the computed diffusion coefficient and average number of hydrogen bonds are affected by a significant uncertainty in spite of the large size of the dataset used. Lastly, a comparison with classical simulations using the TIP4P/2005 model confirms that the variability of the diffusivity is also observed after long equilibration times. Complete atomic trajectories and simulation output files are available online for further analysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Hypercrosslinked polystyrene networks: An atomistic molecular dynamics simulation combined with a mapping/reverse mapping procedure

An algorithm involving classical molecular dynamics simulations with mapping and reverse mapping procedure is here suggested to simulate the crosslinking of the polystyrene dissolved in dichloroethane by monochlorodimethyl ether. The algorithm comprises consecutive stages: molecular dynamics atomistic simulation of a polystyrene solution, the mapping of atomistic structure onto coarse-grained model, the crosslink formation, the reverse mapping, and finally relaxation of the structure dissolved in dichloroethane and in dry state. The calculated values of the specific volume and the elastic modulus are in reasonable quantitative correspondence with experimental data.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1995

Determination of Quantum Chemistry Based Force Fields for Molecular Dynamics Simulations of Aromatic Polymers

Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).

Jaffe, Richard↗
DOE OSTI2016

Molecular dynamics simulation of the structural, elastic, and thermal properties of pyrochlores

We present a comprehensive simulation study of the effect of composition on the structural, elastic and thermal properties of 25 different compounds from the pyrochlore family. We joined a repulsive potential to an existing interatomic potential to enable molecular dynamics simulations of conditions away from equilibrium. We systematically varied the chemistry of the pyrochlore by substituting different cations in the A and B sites of the A2B2O7 formula unit. The A cations varied from Lu3+ to La3+, and the B cations from Ti4+ to Ce4+. The lattice parameter increased steadily with increasing the radius of A or B cations, but the bulk modulus showed a decreasing trend with increasing cation radius. However, the specific heat capacity and thermal expansion coefficient remained almost unchanged with increasing the radii of A and B cations. It is of interest to note that Ce on the B site significantly reduces the specific heat capacity and thermal expansion coefficient, which could have implications for annealing of radiation damage in cerate pyrochlores. The present results are consistent with the experimental measurements, which validates these potentials for simulation of dynamical processes, such as radiation damage, in pyrochlores.

computer simulation↗
DOE OSTI2015

Molecular dynamic simulation of Ar-Kr mixture across a rough walled nanochannel: Velocity and temperature profiles

This paper presents the results from a molecular dynamics simulation of mixture of argon and krypton in the Poiseuille flow across a rough walled nanochannel. The roughness effect on liquid nanoflows has recently drawn attention The computational software used for carrying out the molecular dynamics simulations is LAMMPS. The fluid flow takes place between two parallel plates and is bounded by horizontal rough walls in one direction and periodic boundary conditions are imposed in the other two directions. Each fluid atom interacts with other fluid atoms and wall atoms through Leenard-Jones (LJ) potential with a cut off distance of 5.0. To derive the flow a constant force is applied whose value is varied from 0.1 to 0.3 and velocity profiles and temperature profiles are noted for these values of forces. The velocity profile and temperature profiles are also looked at different channel widths of nanochannel and at different densities of mixture. The velocity profile and temperature profile of rough walled nanochannel are compared with that of smooth walled nanochannel and it is concluded that mean velocity increases with increase in channel width, force applied and decrease in density also with introduction of roughness in the walls of nanochannel mean velocity again increases and results also agree with the analytical solution of a Poiseuille flow.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

Optimizing the performance of reactive molecular dynamics simulations for many-core architectures

Reactive molecular dynamics simulations are computationally demanding. Reaching spatial and temporal scales where interesting scientific phenomena can be observed requires efficient and scalable implementations on modern hardware. In this article, we focus on optimizing the performance of the widely used LAMMPS/ReaxC package for many-core architectures. As hybrid parallelism allows better leverage of the increasing on-node parallelism, we adopt thread parallelism in the construction of bonded and nonbonded lists and in the computation of complex ReaxFF interactions. To mitigate the I/O overheads due to large volumes of trajectory data produced and to save users the burden of post-processing, we also develop a novel in situ tool for molecular species analysis. We analyze the performance of the resulting ReaxC-OMP package on two different architectures: (i) Mira, an IBM Blue Gene/Q system and (ii) Cori-II, a Cray XC-40 sytem with Knights Landing processors. For Pentaerythritol tetranitrate (PETN) systems of sizes ranging from 32 thousand to 16.6 million particles, we observe speedups in the range of 1.5-4.5x. We observe sustained performance improvements for up to 262,144 cores (1,048,576 processes) of Mira and a weak scaling efficiency of 91.5% in large simulations containing 16.6 million particles. Finally, the in situ molecular species analysis tool incurs only insignificant overheads across various system sizes and runs configurations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Photodynamics of oxybenzone sunscreen: Nonadiabatic dynamics simulations

Herein we have used combined static electronic structure calculations and “on-the-fly” global-switching trajectory surface-hopping dynamics simulations to explore the photochemical mechanism of oxybenzone sunscreen. We have first employed the multi-configurational CASSCF method to optimize minima, conical intersections, and minimum-energy reaction paths related to excited-state intramolecular proton transfer (ESIPT) and excited-state decays in the {sup 1}ππ{sup ∗}, {sup 1}nπ{sup ∗}, and S{sub 0} states (energies are refined at the higher MS-CASPT2 level). According to the mapped potential energy profiles, we have identified two ultrafast excited-state deactivation pathways for the initially populated {sup 1}ππ{sup ∗} system. The first is the diabatic ESIPT process along the {sup 1}ππ{sup ∗} potential energy profile. The generated {sup 1}ππ{sup ∗} keto species then decays to the S{sub 0} state via the keto {sup 1}ππ{sup ∗}/gs conical intersection. The second is internal conversion to the dark {sup 1}nπ{sup ∗} state near the {sup 1}ππ{sup ∗} /{sup 1}nπ{sup ∗} crossing point in the course of the diabatic {sup 1}ππ{sup ∗} ESIPT process. Our following dynamics simulations have shown that the ESIPT and {sup 1}ππ{sup ∗} → S{sub 0} internal conversion times are 104 and 286 fs, respectively. Finally, our present work demonstrates that in addition to the ESIPT process and the {sup 1}ππ{sup ∗} → S{sub 0} internal conversion in the keto region, the {sup 1}ππ{sup ∗} → {sup 1}nπ{sup ∗} internal conversion in the enol region plays as well an important role for the excited-state relaxation dynamics of oxybenzone.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Integration of Dynamic Simulation for Infrastructure and Full Hardware Testing Capability into SCEPTRE

Sandia National Laboratories has an existing capability for hybrid control systems testing called SCEPTRE. This article proposes an architecture to add dynamic simulation capability for the underlying physical process (e.g. the power grid). Dynamic simulation for SCEPTRE will enable very accurate simulation, and allow the full integration of analog control systems hardware.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2026

Molecular dynamics simulation of hydrodynamic transport coefficients in plasmas

Molecular dynamics simulations are used to calculate transport coefficients in a two-component plasma interacting through a repulsive Coulomb potential. The thermal conductivity, electrical conductivity, electrothermal coefficient, thermoelectric coefficient, and shear viscosity are computed using the Green–Kubo formalism over a broad range of Coulomb coupling strength, 0.01 ≤ Γ ≤ 140. Emphasis is placed on testing standard results of the Chapman–Enskog solution in the weakly coupled regime (Γ ≪ 1) using these first-principles simulations. As expected, the results show good agreement for Γ ≲ 0.1. However, this agreement is only possible if careful attention is paid to the definitions of linear constitutive relations in each of the theoretical models, a point that is often overlooked. For example, the standard Green–Kubo expression for thermal conductivity is a linear combination of thermal conductivity, electrothermal, and thermoelectric coefficients computed in the Chapman–Enskog formalism. Meaningful results for electrical conductivity are obtained over the full range of coupling strengths explored, but it is shown that potential and virial components of the other transport coefficients diverge in the strongly coupled regime (Γ ≫ 1). In this regime, only the kinetic components of the transport coefficients are meaningful for a classical plasma.

Electrical conductivity↗
DOE OSTI2016

Modeling of Protection in Dynamic Simulation Using Generic Relay Models and Settings

This paper shows how generic protection relay models available in planning tools can be augmented with settings that are based on NERC standards or best engineering practice. Selected generic relay models in Siemens PSS®E have been used in dynamic simulations in the proposed approach. Undervoltage, overvoltage, underfrequency, and overfrequency relays have been modeled for each generating unit. Distance-relay protection was modeled for transmission system protection. Two types of load-shedding schemes were modeled: underfrequency (frequency-responsive non-firm load shedding) and underfrequency and undervoltage firm load shedding. Several case studies are given to show the impact of protection devices on dynamic simulations. This is useful for simulating cascading outages.

cascading failures↗
DOE OSTI2015

Characterizing Dynamics of Anion/Pi Interactions through Molecular Dynamics Simulations

Proteins are not static structures, but undergo dynamical variations at room temperature that can lead to changes in the number and strength of different non-covalent interactions. The negatively charged (Asp/Glu) and aromatic (Phe/Trp/Tyr) amino acid groups in proteins can form anion/pi interactions, that have been shown to have a distance and angle dependency. This study characterizes the dynamic stability of these interactions in RmlC (PDB-1EP0), a homodimeric epimerase showing a cluster of six anion/pi pairs in crystal structure, as a function of time using Molecular Dynamics (MD) simulations. The dynamic variations found in these interactions correspond to a potential of mean force (PMF) that exhibits a relatively wide range of distances (~4.5 to~8.5Å) and angles (0 to~45deg) sampled by these anion/pi pairs. The corresponding PMF indicates an associated free energy change that can be more stabilizing (up to -5kcal/mol) than the ab initio-calculated interaction energy for the pairs in the crystal structure (-2.2kcal/mol). Possible anion/pi pairs and triplets (anion/anion/pi or anion/pi/pi) not seen in the crystal structure are also observed in other conformations sampled by the protein- both at the dimer interface and active site of the protein, forming an extensive network of anion/pi interactions covering most of the protein structure. Initial site-directed mutagenesis (SDM) experiments targeting one of these pairs, Asp84-Phe112, show that the single Phe/Met mutation decreases the stability of the protein compared to the wild type. Together these results suggest that anion-pi interactions can play an important role in maintaining both the structural stability and function of the proteins.

Kapoor, Karan↗
DOE OSTI2014

Interplay between the structure and dynamics in liquid and undercooled boron: An ab initio molecular dynamics simulation study

In the present work, the structural and dynamic properties of liquid and undercooled boron are investigated by means of ab initio molecular dynamics simulation. Our results show that both liquid and undercooled states present a well pronounced short-range order (SRO) mainly due to the formation of inverted umbrella structural units. Moreover, we observe the development of a medium-range order (MRO) in the undercooling regime related to the increase of inverted umbrella structural units and of their interconnection as the temperature decreases. We also evidence that this MRO leads to a partial crystallization in the β-rhombohedral crystal below T = 1900 K. Finally, we discuss the role played by the SRO and MRO in the nearly Arrhenius evolution of the diffusion and the non-Arrhenius temperature dependence of the shear viscosity, in agreement with the experiment.

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

Bringing Molecular Dynamics Simulation Data into View

Molecular Dynamics (MD) simulations monitor time-resolved motions of macromolecules. While visualization of MD trajectories allows an instant and intuitive understanding of dynamics and function, so far mainly static representations are provided in published literature. Recent advances in browser technology may allow for the sharing of trajectories through interactive visualization on the web. We believe that by providing intuitive and interactive visualization along with related protocols and analysis data promotes understanding, reliability, and re-usability of MD simulations. Existing barriers for sharing MD simulations are discussed and emerging solutions are highlighted. We predict that interactive visualization of MD trajectories will quickly be adopted by researchers, research consortiums, journals, and funding agencies to gather and distribute results from MD simulations via the web.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗